Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7445011.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=3 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_7445011.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7445011.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" } 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 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: 1.96, per 1000 atoms: 0.58 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: 0.42 Conformation dependent library (CDL) restraints added in 137.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 565 0.92 - 1.17: 1086 1.17 - 1.43: 689 1.43 - 1.69: 779 1.69 - 1.95: 34 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.448 1.633 -0.185 9.00e-03 1.23e+04 4.22e+02 bond pdb=" C THR A 125 " pdb=" O THR A 125 " ideal model delta sigma weight residual 1.234 1.453 -0.218 1.20e-02 6.94e+03 3.31e+02 bond pdb=" N VAL A 8 " pdb=" CA VAL A 8 " ideal model delta sigma weight residual 1.459 1.673 -0.214 1.24e-02 6.50e+03 2.97e+02 bond pdb=" CA GLU A 147 " pdb=" C GLU A 147 " ideal model delta sigma weight residual 1.522 1.315 0.206 1.21e-02 6.83e+03 2.91e+02 bond pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 1.459 1.661 -0.202 1.20e-02 6.94e+03 2.82e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 3178 4.72 - 9.43: 1878 9.43 - 14.15: 614 14.15 - 18.86: 95 18.86 - 23.58: 12 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 107.20 121.65 -14.45 1.00e+00 1.00e+00 2.09e+02 angle pdb=" ND1 HIS A 138 " pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 106.10 92.21 13.89 1.00e+00 1.00e+00 1.93e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.45 121.18 -10.73 7.80e-01 1.64e+00 1.89e+02 angle pdb=" O BLYS A 175 " pdb=" C BLYS A 175 " pdb=" N GLU A 176 " ideal model delta sigma weight residual 122.09 136.56 -14.47 1.08e+00 8.57e-01 1.79e+02 angle pdb=" CA AGLY A 65 " pdb=" C AGLY A 65 " pdb=" O AGLY A 65 " ideal model delta sigma weight residual 121.62 108.23 13.39 1.05e+00 9.07e-01 1.63e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 1290 16.90 - 33.81: 133 33.81 - 50.71: 36 50.71 - 67.62: 21 67.62 - 84.52: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 144.63 -21.83 0 2.50e+00 1.60e-01 7.62e+01 dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -143.56 20.96 0 2.50e+00 1.60e-01 7.03e+01 dihedral pdb=" C BGLU A 64 " pdb=" N BGLU A 64 " pdb=" CA BGLU A 64 " pdb=" CB BGLU A 64 " ideal model delta harmonic sigma weight residual -122.60 -101.66 -20.94 0 2.50e+00 1.60e-01 7.01e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 130 0.246 - 0.491: 67 0.491 - 0.737: 31 0.737 - 0.982: 11 0.982 - 1.228: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 42 " pdb=" N ASP A 42 " pdb=" C ASP A 42 " pdb=" CB ASP A 42 " both_signs ideal model delta sigma weight residual False 2.51 3.74 -1.23 2.00e-01 2.50e+01 3.77e+01 chirality pdb=" CA BGLU A 64 " pdb=" N BGLU A 64 " pdb=" C BGLU A 64 " pdb=" CB BGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" CA VAL A 8 " pdb=" N VAL A 8 " pdb=" C VAL A 8 " pdb=" CB VAL A 8 " both_signs ideal model delta sigma weight residual False 2.44 3.45 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.052 2.00e-02 2.50e+03 6.31e-02 1.19e+02 pdb=" CG PHE A 164 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.102 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.067 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.097 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.002 2.00e-02 2.50e+03 5.52e-02 9.14e+01 pdb=" CG TYR A 139 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.115 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.085 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.065 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.050 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.011 2.00e-02 2.50e+03 5.32e-02 8.49e+01 pdb=" CG PHE A 119 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.134 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.012 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 801 2.28 - 2.86: 7823 2.86 - 3.44: 10644 3.44 - 4.02: 15320 4.02 - 4.60: 22098 Nonbonded interactions: 56686 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.701 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.791 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.823 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.826 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O LEU A 185 " pdb=" H GLY A 159 " model vdw sym.op. 1.826 2.450 x-y,-y,-z-4/3 ... (remaining 56681 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 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 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_7445011_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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3619 r_free= 0.2062 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469961 | | target function (ml) not normalized (work): 22036.906887 | | target function (ml) not normalized (free): 1149.457873 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3804 0.2251 4.8565 4.8929| | 2: 3.78 - 3.00 1.00 2430 110 0.3394 0.1742 4.0723 4.1334| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2500 142 0.50 48.94 0.83 0.13 6620.70| | 2: 3.78 - 3.00 2430 110 0.94 11.33 1.48 0.26 446.33| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 373.55 max = 12074.18 mean = 3577.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.40| |phase err.(test): min = 0.00 max = 89.96 mean = 33.48| |-----------------------------------------------------------------------------| ----------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 0.280 1557 Z= 5.469 Angle : 5.315 16.752 2118 Z= 3.778 Chirality : 0.375 1.228 243 Planarity : 0.032 0.101 284 Dihedral : 13.984 84.523 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 23.24 % 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: -1.66 (0.48), residues: 224 helix: -1.85 (0.42), residues: 103 sheet: 0.01 (0.93), residues: 28 loop : -0.27 (0.54), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.078 0.024 ARG A 48 TYR 0.104 0.035 TYR A 139 PHE 0.107 0.042 PHE A 164 HIS 0.084 0.038 HIS A 138 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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3619 r_free= 0.2062 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469961 | | target function (ml) not normalized (work): 22036.906887 | | target function (ml) not normalized (free): 1149.457873 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3576 0.3652 0.2174 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3576 0.3652 0.2174 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2548 0.2174 n_refl.: 5178 overall B=-2.84 to atoms: r(all,work,free)=0.2417 0.2436 0.2124 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1552 0.1547 0.1643 n_refl.: 5178 remove outliers: r(all,work,free)=0.1548 0.1542 0.1643 n_refl.: 5176 ======================== 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 0.3879 449.739 407.734 0.647 1.081 0.404 11.894-9.307 99.02 97 4 0.1859 714.446 693.496 0.922 1.078 0.392 9.237-7.194 100.00 213 7 0.2116 584.275 576.500 0.962 1.069 0.374 7.162-5.571 100.00 427 22 0.2283 438.427 422.470 0.931 1.054 0.336 5.546-4.326 100.00 867 58 0.1383 601.899 593.206 0.976 1.029 0.247 4.315-3.360 100.00 1859 96 0.1298 572.412 567.224 1.056 0.988 0.200 3.356-3.002 100.00 1373 60 0.1570 440.896 432.943 1.077 0.946 0.097 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6249 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1542 r_free=0.1643 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 3 r_work=0.1543 r_free=0.1648 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.698944 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.145735 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1161 0.1767 0.0606 0.010 1.0 3.2 0.5 0.0 0 9.849 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 17.67 6.06 3.013 16.022 2.146 0.018 10.19 17.67 7.49 5.128 16.220 2.146 0.014 Individual atomic B min max mean iso aniso Overall: 1.88 111.46 17.42 5.48 1785 0 Protein: 1.88 110.66 14.73 5.48 1519 0 Water: 4.42 111.46 33.08 N/A 258 0 Other: 15.62 37.02 23.70 N/A 8 0 Chain A: 1.88 111.46 17.42 N/A 1785 0 Histogram: Values Number of atoms 1.88 - 12.84 906 12.84 - 23.80 489 23.80 - 34.76 190 34.76 - 45.71 110 45.71 - 56.67 57 56.67 - 67.63 16 67.63 - 78.59 8 78.59 - 89.55 5 89.55 - 100.50 1 100.50 - 111.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.1019 r_free=0.1767 r_work=0.1014 r_free=0.1776 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1014 r_free = 0.1776 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1018 r_free = 0.1785 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1018 r_free= 0.1785 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014089 | | target function (ls_wunit_k1) not normalized (work): 69.374427 | | target function (ls_wunit_k1) not normalized (free): 10.320568 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1058 0.1018 0.1785 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2111 0.2111 0.2215 n_refl.: 5176 remove outliers: r(all,work,free)=0.2111 0.2111 0.2215 n_refl.: 5176 overall B=-0.94 to atoms: r(all,work,free)=0.2072 0.2070 0.2205 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1058 0.1019 0.1780 n_refl.: 5176 remove outliers: r(all,work,free)=0.1058 0.1019 0.1780 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3315 330.285 313.041 0.675 1.018 0.387 11.894-9.307 99.02 97 4 0.1531 524.684 516.139 0.973 1.019 0.371 9.237-7.194 100.00 213 7 0.1683 429.088 428.532 1.015 1.017 0.331 7.162-5.571 100.00 427 22 0.1628 321.978 319.150 0.972 1.013 0.312 5.546-4.326 100.00 867 58 0.0914 442.030 438.872 0.993 1.007 0.232 4.315-3.360 100.00 1859 96 0.0776 420.376 420.366 1.043 0.997 0.201 3.356-3.002 100.00 1373 60 0.1001 323.791 321.964 1.020 0.987 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3558 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1019 r_free=0.1780 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1021 r_free=0.1781 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1021 r_free=0.1781 | n_water=258 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.1047 r_free=0.1771 | n_water=249 | time (s): 19.080 (total time: 19.620) Filter (q & B) r_work=0.1047 r_free=0.1775 | n_water=246 | time (s): 1.430 (total time: 21.050) Compute maps r_work=0.1047 r_free=0.1775 | n_water=246 | time (s): 0.650 (total time: 21.700) Filter (map) r_work=0.1332 r_free=0.1810 | n_water=143 | time (s): 1.300 (total time: 23.000) Find peaks r_work=0.1332 r_free=0.1810 | n_water=143 | time (s): 0.510 (total time: 23.510) Add new water r_work=0.1682 r_free=0.2075 | n_water=222 | time (s): 1.540 (total time: 25.050) Refine new water occ: r_work=0.1174 r_free=0.1678 adp: r_work=0.1155 r_free=0.1679 occ: r_work=0.1153 r_free=0.1660 adp: r_work=0.1144 r_free=0.1657 occ: r_work=0.1144 r_free=0.1647 adp: r_work=0.1142 r_free=0.1649 ADP+occupancy (water only), MIN, final r_work=0.1142 r_free=0.1649 r_work=0.1142 r_free=0.1649 | n_water=222 | time (s): 7.730 (total time: 32.780) Filter (q & B) r_work=0.1142 r_free=0.1651 | n_water=221 | time (s): 1.240 (total time: 34.020) Filter (dist only) r_work=0.1147 r_free=0.1650 | n_water=217 | time (s): 16.560 (total time: 50.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.511957 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.983641 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1031 0.1776 0.0745 0.009 1.0 4.2 0.5 0.6 0 11.256 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.31 17.76 7.45 4.781 16.775 2.984 0.014 9.60 18.17 8.57 5.696 17.209 2.984 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 108.17 16.57 6.71 1744 0 Protein: 0.00 108.17 15.12 6.70 1519 0 Water: 0.00 62.81 26.48 N/A 217 0 Other: 9.69 38.97 22.60 N/A 8 0 Chain A: 0.00 108.17 15.85 N/A 1668 0 Chain S: 5.69 58.70 32.34 N/A 76 0 Histogram: Values Number of atoms 0.00 - 10.82 681 10.82 - 21.63 665 21.63 - 32.45 206 32.45 - 43.27 113 43.27 - 54.08 42 54.08 - 64.90 24 64.90 - 75.72 6 75.72 - 86.53 3 86.53 - 97.35 3 97.35 - 108.17 1 =========================== Idealize ADP of riding H ========================== r_work=0.0960 r_free=0.1817 r_work=0.0957 r_free=0.1822 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0957 r_free = 0.1822 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0956 r_free = 0.1804 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0956 r_free= 0.1804 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012483 | | target function (ls_wunit_k1) not normalized (work): 61.468009 | | target function (ls_wunit_k1) not normalized (free): 9.819304 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0999 0.0956 0.1804 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2174 0.2181 0.2209 n_refl.: 5176 remove outliers: r(all,work,free)=0.2174 0.2181 0.2209 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2174 0.2181 0.2209 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1002 0.0959 0.1795 n_refl.: 5176 remove outliers: r(all,work,free)=0.1000 0.0957 0.1795 n_refl.: 5175 ======================== 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 0.3300 327.503 313.034 0.659 1.026 0.358 11.894-9.307 99.02 97 4 0.1477 524.684 517.974 0.966 1.028 0.340 9.237-7.194 100.00 213 7 0.1476 429.088 428.623 1.007 1.026 0.320 7.162-5.571 100.00 427 22 0.1420 321.978 319.980 0.976 1.020 0.310 5.546-4.326 100.00 867 58 0.0804 442.030 439.791 1.000 1.011 0.240 4.315-3.360 100.00 1859 96 0.0746 420.376 420.060 1.064 0.996 0.211 3.356-3.002 100.00 1373 60 0.0997 323.791 322.209 1.049 0.980 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.2780 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0957 r_free=0.1795 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.0957 r_free=0.1798 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0957 r_free=0.1798 | n_water=217 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0965 r_free=0.1799 | n_water=215 | time (s): 16.660 (total time: 17.190) Filter (q & B) r_work=0.1053 r_free=0.1782 | n_water=212 | time (s): 1.700 (total time: 18.890) Compute maps r_work=0.1053 r_free=0.1782 | n_water=212 | time (s): 0.410 (total time: 19.300) Filter (map) r_work=0.1283 r_free=0.1875 | n_water=146 | time (s): 1.460 (total time: 20.760) Find peaks r_work=0.1283 r_free=0.1875 | n_water=146 | time (s): 0.580 (total time: 21.340) Add new water r_work=0.1651 r_free=0.2213 | n_water=227 | time (s): 1.410 (total time: 22.750) Refine new water occ: r_work=0.1054 r_free=0.1755 adp: r_work=0.1045 r_free=0.1780 occ: r_work=0.1035 r_free=0.1759 adp: r_work=0.1034 r_free=0.1768 occ: r_work=0.1027 r_free=0.1751 adp: r_work=0.1026 r_free=0.1763 ADP+occupancy (water only), MIN, final r_work=0.1026 r_free=0.1763 r_work=0.1026 r_free=0.1763 | n_water=227 | time (s): 13.290 (total time: 36.040) Filter (q & B) r_work=0.1027 r_free=0.1762 | n_water=226 | time (s): 1.910 (total time: 37.950) Filter (dist only) r_work=0.1029 r_free=0.1765 | n_water=223 | time (s): 17.680 (total time: 55.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.104466 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.227801 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0946 0.1785 0.0839 0.011 1.1 4.8 0.5 0.0 0 0.552 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.46 17.85 8.39 5.572 17.943 0.228 5.163 9.08 17.60 8.52 7.375 17.953 0.228 5.076 Individual atomic B min max mean iso aniso Overall: 0.00 106.47 16.43 9.14 1750 0 Protein: 0.00 106.47 15.25 9.14 1519 0 Water: 0.00 57.81 24.21 N/A 223 0 Other: 10.92 41.38 23.20 N/A 8 0 Chain A: 0.00 106.47 15.94 N/A 1655 0 Chain S: 0.00 56.28 24.97 N/A 95 0 Histogram: Values Number of atoms 0.00 - 10.65 665 10.65 - 21.29 650 21.29 - 31.94 240 31.94 - 42.59 123 42.59 - 53.23 34 53.23 - 63.88 20 63.88 - 74.53 7 74.53 - 85.17 6 85.17 - 95.82 4 95.82 - 106.47 1 =========================== Idealize ADP of riding H ========================== r_work=0.0908 r_free=0.1760 r_work=0.0912 r_free=0.1765 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0912 r_free = 0.1765 target_work(ml) = 5.081 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0899 r_free = 0.1751 target_work(ml) = 5.072 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0899 r_free= 0.1751 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.072144 | | target function (ml) not normalized (work): 24970.165643 | | target function (ml) not normalized (free): 1765.009101 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0943 0.0899 0.1751 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2175 0.2185 0.2146 n_refl.: 5175 remove outliers: r(all,work,free)=0.2175 0.2185 0.2146 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2175 0.2185 0.2146 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0937 0.0895 0.1748 n_refl.: 5175 remove outliers: r(all,work,free)=0.0935 0.0893 0.1748 n_refl.: 5174 ======================== 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 0.3596 329.682 301.065 0.626 0.998 0.354 11.894-9.307 99.02 97 4 0.1722 524.684 511.408 0.949 1.002 0.330 9.237-7.194 100.00 213 7 0.1860 429.088 421.892 1.003 1.003 0.310 7.162-5.571 100.00 427 22 0.1806 321.978 314.104 0.964 1.003 0.290 5.546-4.326 100.00 867 58 0.0941 442.030 437.426 0.990 1.003 0.250 4.315-3.360 100.00 1859 96 0.0593 420.376 419.659 1.051 1.001 0.210 3.356-3.002 100.00 1373 60 0.0628 323.791 322.627 1.028 1.000 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.0508 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0893 r_free=0.1748 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0901 r_free=0.1737 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0901 r_free=0.1737 | n_water=223 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0926 r_free=0.1769 | n_water=217 | time (s): 17.590 (total time: 18.180) Filter (q & B) r_work=0.0958 r_free=0.1788 | n_water=216 | time (s): 1.440 (total time: 19.620) Compute maps r_work=0.0958 r_free=0.1788 | n_water=216 | time (s): 0.540 (total time: 20.160) Filter (map) r_work=0.1205 r_free=0.1858 | n_water=154 | time (s): 1.220 (total time: 21.380) Find peaks r_work=0.1205 r_free=0.1858 | n_water=154 | time (s): 0.390 (total time: 21.770) Add new water r_work=0.1527 r_free=0.2148 | n_water=225 | time (s): 1.430 (total time: 23.200) Refine new water occ: r_work=0.1011 r_free=0.1777 adp: r_work=0.1008 r_free=0.1784 occ: r_work=0.1000 r_free=0.1769 adp: r_work=0.1000 r_free=0.1775 occ: r_work=0.0993 r_free=0.1762 adp: r_work=0.0992 r_free=0.1768 ADP+occupancy (water only), MIN, final r_work=0.0992 r_free=0.1768 r_work=0.0992 r_free=0.1768 | n_water=225 | time (s): 9.420 (total time: 32.620) Filter (q & B) r_work=0.0992 r_free=0.1768 | n_water=224 | time (s): 1.910 (total time: 34.530) Filter (dist only) r_work=0.0988 r_free=0.1772 | n_water=222 | time (s): 16.810 (total time: 51.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.995940 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.232475 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0906 0.1819 0.0913 0.011 1.1 5.4 0.5 0.0 0 0.498 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.06 18.19 9.13 7.114 18.044 0.232 5.039 8.84 18.47 9.63 8.325 18.155 0.232 4.977 Individual atomic B min max mean iso aniso Overall: 0.00 104.30 16.66 10.83 1749 0 Protein: 0.00 104.30 15.63 10.83 1519 0 Water: 0.00 58.86 23.41 N/A 222 0 Other: 12.99 44.73 24.73 N/A 8 0 Chain A: 0.00 104.30 16.20 N/A 1644 0 Chain S: 0.00 52.20 23.90 N/A 105 0 Histogram: Values Number of atoms 0.00 - 10.43 639 10.43 - 20.86 637 20.86 - 31.29 262 31.29 - 41.72 119 41.72 - 52.15 54 52.15 - 62.58 15 62.58 - 73.01 11 73.01 - 83.44 7 83.44 - 93.87 3 93.87 - 104.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.0884 r_free=0.1847 r_work=0.0888 r_free=0.1857 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0888 r_free = 0.1857 target_work(ml) = 4.981 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0879 r_free = 0.1843 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0879 r_free= 0.1843 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.974452 | | target function (ml) not normalized (work): 24484.253676 | | target function (ml) not normalized (free): 2086.084352 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0928 0.0879 0.1843 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2122 0.2124 0.2222 n_refl.: 5174 remove outliers: r(all,work,free)=0.2122 0.2124 0.2222 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2122 0.2124 0.2222 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0924 0.0876 0.1839 n_refl.: 5174 remove outliers: r(all,work,free)=0.0924 0.0876 0.1839 n_refl.: 5174 ======================== 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 0.3617 329.682 304.757 0.616 0.987 0.336 11.894-9.307 99.02 97 4 0.1980 524.684 508.552 0.961 0.993 0.333 9.237-7.194 100.00 213 7 0.2067 429.088 418.272 1.002 0.996 0.288 7.162-5.571 100.00 427 22 0.1971 321.978 312.282 0.977 0.998 0.265 5.546-4.326 100.00 867 58 0.0993 442.030 436.694 1.006 1.000 0.260 4.315-3.360 100.00 1859 96 0.0555 420.376 420.135 1.072 1.003 0.220 3.356-3.002 100.00 1373 60 0.0455 323.791 323.611 1.047 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0682 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0876 r_free=0.1839 After: r_work=0.0879 r_free=0.1838 ================================== NQH flips ================================== r_work=0.0879 r_free=0.1838 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.0879 r_free=0.1839 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0879 r_free=0.1839 | n_water=222 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0879 r_free=0.1839 | n_water=222 | time (s): 16.570 (total time: 17.080) Filter (q & B) r_work=0.0976 r_free=0.1880 | n_water=218 | time (s): 1.920 (total time: 19.000) Compute maps r_work=0.0976 r_free=0.1880 | n_water=218 | time (s): 0.580 (total time: 19.580) Filter (map) r_work=0.1209 r_free=0.1925 | n_water=160 | time (s): 1.550 (total time: 21.130) Find peaks r_work=0.1209 r_free=0.1925 | n_water=160 | time (s): 0.590 (total time: 21.720) Add new water r_work=0.1492 r_free=0.2265 | n_water=228 | time (s): 1.840 (total time: 23.560) Refine new water occ: r_work=0.0987 r_free=0.1822 adp: r_work=0.0983 r_free=0.1830 occ: r_work=0.0976 r_free=0.1808 adp: r_work=0.0975 r_free=0.1820 occ: r_work=0.0967 r_free=0.1794 adp: r_work=0.0967 r_free=0.1807 ADP+occupancy (water only), MIN, final r_work=0.0967 r_free=0.1807 r_work=0.0967 r_free=0.1807 | n_water=228 | time (s): 15.200 (total time: 38.760) Filter (q & B) r_work=0.0968 r_free=0.1802 | n_water=225 | time (s): 1.530 (total time: 40.290) Filter (dist only) r_work=0.0976 r_free=0.1790 | n_water=222 | time (s): 17.300 (total time: 57.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.992037 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.211146 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0924 0.1819 0.0895 0.011 1.1 8.0 0.5 0.0 0 0.496 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.24 18.19 8.95 8.238 18.486 0.211 5.018 9.05 18.42 9.37 9.009 18.605 0.211 4.963 Individual atomic B min max mean iso aniso Overall: 0.00 102.99 17.08 11.96 1749 0 Protein: 0.00 102.99 16.04 11.95 1519 0 Water: 0.36 63.15 23.88 N/A 222 0 Other: 15.20 48.73 24.88 N/A 8 0 Chain A: 0.00 102.99 16.51 N/A 1638 0 Chain S: 0.36 63.15 25.36 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.30 610 10.30 - 20.60 635 20.60 - 30.90 285 30.90 - 41.19 114 41.19 - 51.49 58 51.49 - 61.79 19 61.79 - 72.09 14 72.09 - 82.39 8 82.39 - 92.69 3 92.69 - 102.99 3 =========================== Idealize ADP of riding H ========================== r_work=0.0905 r_free=0.1842 r_work=0.0907 r_free=0.1845 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0907 r_free = 0.1845 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0900 r_free = 0.1842 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0900 r_free= 0.1842 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.961929 | | target function (ml) not normalized (work): 24422.615358 | | target function (ml) not normalized (free): 2166.388808 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1289 0.1828 5.5512 6.2342| | 2: 3.78 - 3.00 1.00 2430 110 0.0426 0.1865 4.3576 11.647| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2492 142 0.91 12.49 1.00 0.98 13520.82| | 2: 3.78 - 3.00 2430 110 0.99 1.87 1.00 1.01 910.74| |alpha: min = 0.97 max = 1.01 mean = 1.00| |beta: min = 576.68 max = 22622.11 mean = 7295.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.99 mean = 7.25| |phase err.(test): min = 0.00 max = 79.60 mean = 7.25| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0949 0.0900 0.1842 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2157 0.2160 0.2228 n_refl.: 5174 remove outliers: r(all,work,free)=0.2157 0.2160 0.2228 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2157 0.2160 0.2228 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0948 0.0900 0.1841 n_refl.: 5174 remove outliers: r(all,work,free)=0.0948 0.0900 0.1841 n_refl.: 5174 ======================== 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 0.3702 329.682 299.771 0.622 0.989 0.344 11.894-9.307 99.02 97 4 0.1940 524.684 513.037 0.966 0.994 0.340 9.237-7.194 100.00 213 7 0.2200 429.088 415.994 1.000 0.998 0.284 7.162-5.571 100.00 427 22 0.2083 321.978 311.972 0.981 0.999 0.270 5.546-4.326 100.00 867 58 0.1061 442.030 436.172 1.012 1.001 0.230 4.315-3.360 100.00 1859 96 0.0572 420.376 420.515 1.094 1.003 0.210 3.356-3.002 100.00 1373 60 0.0410 323.791 323.886 1.072 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.0313 ================= 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 : 0.3619 0.2062 0.083 5.315 8.8 119.3 19.9 258 0.000 1_bss: 0.1542 0.1643 0.083 5.315 6.0 116.5 17.0 258 0.000 1_settarget: 0.1542 0.1643 0.083 5.315 6.0 116.5 17.0 258 0.000 1_nqh: 0.1543 0.1648 0.083 5.315 6.0 116.5 17.0 258 0.010 1_weight: 0.1543 0.1648 0.083 5.315 6.0 116.5 17.0 258 0.010 1_xyzrec: 0.1161 0.1767 0.010 0.972 6.0 116.5 17.0 258 0.206 1_adp: 0.1019 0.1767 0.010 0.972 1.9 111.5 17.4 258 0.206 1_regHadp: 0.1014 0.1776 0.010 0.972 1.9 111.5 17.4 258 0.206 1_occ: 0.1018 0.1785 0.010 0.972 1.9 111.5 17.4 258 0.206 2_bss: 0.1019 0.1780 0.010 0.972 0.9 110.5 16.5 258 0.206 2_settarget: 0.1019 0.1780 0.010 0.972 0.9 110.5 16.5 258 0.206 2_updatecdl: 0.1019 0.1780 0.010 1.004 0.9 110.5 16.5 258 0.206 2_nqh: 0.1021 0.1781 0.010 1.004 0.9 110.5 16.5 258 0.206 2_sol: 0.1147 0.1650 0.010 1.004 0.9 109.7 15.7 217 n/a 2_weight: 0.1147 0.1650 0.010 1.004 0.9 109.7 15.7 217 n/a 2_xyzrec: 0.1031 0.1776 0.009 0.974 0.9 109.7 15.7 217 n/a 2_adp: 0.0960 0.1817 0.009 0.974 0.0 108.2 16.6 217 n/a 2_regHadp: 0.0957 0.1822 0.009 0.974 0.0 108.2 16.6 217 n/a 2_occ: 0.0956 0.1804 0.009 0.974 0.0 108.2 16.6 217 n/a 3_bss: 0.0957 0.1795 0.009 0.974 0.0 108.2 16.6 217 n/a 3_settarget: 0.0957 0.1795 0.009 0.974 0.0 108.2 16.6 217 n/a 3_updatecdl: 0.0957 0.1795 0.009 0.980 0.0 108.2 16.6 217 n/a 3_nqh: 0.0957 0.1798 0.009 0.980 0.0 108.2 16.6 217 n/a 3_sol: 0.1029 0.1765 0.009 0.980 0.0 108.2 16.4 223 n/a 3_weight: 0.1029 0.1765 0.009 0.980 0.0 108.2 16.4 223 n/a 3_xyzrec: 0.0946 0.1785 0.011 1.074 0.0 108.2 16.4 223 n/a 3_adp: 0.0908 0.1760 0.011 1.074 0.0 106.5 16.4 223 n/a 3_regHadp: 0.0912 0.1765 0.011 1.074 0.0 106.5 16.4 223 n/a 3_occ: 0.0899 0.1751 0.011 1.074 0.0 106.5 16.4 223 n/a 4_bss: 0.0893 0.1748 0.011 1.074 0.0 106.5 16.4 223 n/a 4_settarget: 0.0893 0.1748 0.011 1.074 0.0 106.5 16.4 223 n/a 4_updatecdl: 0.0893 0.1748 0.011 1.073 0.0 106.5 16.4 223 n/a 4_nqh: 0.0901 0.1737 0.011 1.073 0.0 106.5 16.4 223 n/a 4_sol: 0.0988 0.1772 0.011 1.073 0.0 106.5 16.4 222 n/a 4_weight: 0.0988 0.1772 0.011 1.073 0.0 106.5 16.4 222 n/a 4_xyzrec: 0.0906 0.1819 0.011 1.070 0.0 106.5 16.4 222 n/a 4_adp: 0.0884 0.1847 0.011 1.070 0.0 104.3 16.7 222 n/a 4_regHadp: 0.0888 0.1857 0.011 1.070 0.0 104.3 16.7 222 n/a 4_occ: 0.0879 0.1843 0.011 1.070 0.0 104.3 16.7 222 n/a 5_bss: 0.0876 0.1839 0.011 1.070 0.0 104.3 16.7 222 n/a 5_settarget: 0.0876 0.1839 0.011 1.070 0.0 104.3 16.7 222 n/a 5_updatecdl: 0.0876 0.1839 0.011 1.079 0.0 104.3 16.7 222 n/a 5_setrh: 0.0879 0.1838 0.011 1.079 0.0 104.3 16.7 222 n/a 5_nqh: 0.0879 0.1839 0.011 1.079 0.0 104.3 16.7 222 n/a 5_sol: 0.0976 0.1790 0.011 1.079 0.0 104.3 16.8 222 n/a 5_weight: 0.0976 0.1790 0.011 1.079 0.0 104.3 16.8 222 n/a 5_xyzrec: 0.0924 0.1819 0.011 1.146 0.0 104.3 16.8 222 n/a 5_adp: 0.0905 0.1842 0.011 1.146 0.0 103.0 17.1 222 n/a 5_regHadp: 0.0907 0.1845 0.011 1.146 0.0 103.0 17.1 222 n/a 5_occ: 0.0900 0.1842 0.011 1.146 0.0 103.0 17.1 222 n/a end: 0.0900 0.1841 0.011 1.146 0.0 103.0 17.1 222 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7445011_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7445011_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1900 Refinement macro-cycles (run) : 478.8400 Write final files (write_after_run_outputs) : 11.1600 Total : 493.1900 Total CPU time: 8.60 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:57 PST -0800 (1735492737.55 s) Start R-work = 0.1542, R-free = 0.1643 Final R-work = 0.0900, R-free = 0.1841 =============================================================================== Job complete usr+sys time: 524.54 seconds wall clock time: 9 minutes 6.69 seconds (546.69 seconds total)