Starting phenix.refine on Sun Dec 29 09:10:02 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=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_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 = 3 } } 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: 2.09, per 1000 atoms: 0.62 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: 0.39 Conformation dependent library (CDL) restraints added in 140.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.55 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 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_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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3616 r_free= 0.2027 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471969 | | target function (ml) not normalized (work): 22046.806095 | | target function (ml) not normalized (free): 1149.934245 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3796 0.2254 4.8541 4.92| | 2: 3.78 - 3.00 1.00 2430 110 0.3397 0.1643 4.0789 4.1027| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.78 0.83 0.13 6617.47| | 2: 3.78 - 3.00 2430 110 0.94 11.10 1.48 0.26 446.28| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 375.48 max = 12076.63 mean = 3575.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.21| |phase err.(test): min = 0.00 max = 89.94 mean = 32.99| |-----------------------------------------------------------------------------| ----------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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3616 r_free= 0.2027 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471969 | | target function (ml) not normalized (work): 22046.806095 | | target function (ml) not normalized (free): 1149.934245 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3571 0.3648 0.2138 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3571 0.3648 0.2138 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2548 0.2138 n_refl.: 5178 overall B=-2.82 to atoms: r(all,work,free)=0.2417 0.2438 0.2089 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1564 0.1562 0.1592 n_refl.: 5178 remove outliers: r(all,work,free)=0.1559 0.1558 0.1592 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 0.3807 449.942 410.787 0.672 1.067 0.408 11.894-9.307 99.02 97 4 0.1874 714.769 697.491 0.942 1.063 0.399 9.237-7.194 100.00 213 7 0.2201 584.539 576.571 0.967 1.056 0.348 7.162-5.571 100.00 427 22 0.2338 438.626 424.357 0.937 1.044 0.336 5.546-4.326 100.00 867 58 0.1372 602.171 596.455 0.981 1.023 0.226 4.315-3.360 100.00 1859 96 0.1311 572.671 567.355 1.055 0.989 0.189 3.356-3.002 100.00 1373 60 0.1592 441.095 435.043 1.065 0.955 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6112 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1558 r_free=0.1592 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=0.1559 r_free=0.1595 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.304171 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.831484 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 0.1162 0.1797 0.0635 0.009 1.0 2.2 0.5 0.0 0 9.152 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 17.97 6.35 3.013 16.036 1.831 0.018 10.23 17.89 7.66 4.976 16.245 1.831 0.015 Individual atomic B min max mean iso aniso Overall: 2.30 111.48 17.46 5.32 1785 0 Protein: 2.30 111.06 14.77 5.31 1519 0 Water: 4.04 111.48 33.11 N/A 258 0 Other: 16.93 38.05 23.93 N/A 8 0 Chain A: 2.30 111.48 17.46 N/A 1785 0 Histogram: Values Number of atoms 2.30 - 13.22 913 13.22 - 24.14 487 24.14 - 35.05 190 35.05 - 45.97 108 45.97 - 56.89 55 56.89 - 67.81 15 67.81 - 78.72 8 78.72 - 89.64 5 89.64 - 100.56 1 100.56 - 111.48 3 =========================== Idealize ADP of riding H ========================== r_work=0.1023 r_free=0.1789 r_work=0.1017 r_free=0.1796 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.1796 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 = 0.1010 r_free = 0.1794 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.16 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= 0.1010 r_free= 0.1794 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013867 | | target function (ls_wunit_k1) not normalized (work): 68.278999 | | target function (ls_wunit_k1) not normalized (free): 10.426167 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1050 0.1010 0.1794 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2095 0.2094 0.2223 n_refl.: 5176 remove outliers: r(all,work,free)=0.2095 0.2094 0.2223 n_refl.: 5176 overall B=-0.97 to atoms: r(all,work,free)=0.2053 0.2051 0.2212 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1048 0.1008 0.1783 n_refl.: 5176 remove outliers: r(all,work,free)=0.1048 0.1008 0.1783 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 0.3369 329.677 311.899 0.673 1.021 0.387 11.894-9.307 99.02 97 4 0.1509 523.718 515.891 0.975 1.021 0.371 9.237-7.194 100.00 213 7 0.1670 428.297 427.329 1.007 1.019 0.311 7.162-5.571 100.00 427 22 0.1621 321.385 318.177 0.973 1.015 0.302 5.546-4.326 100.00 867 58 0.0905 441.216 437.998 0.994 1.008 0.197 4.315-3.360 100.00 1859 96 0.0760 419.601 419.451 1.046 0.996 0.183 3.356-3.002 100.00 1373 60 0.0995 323.194 321.936 1.026 0.984 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4928 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1008 r_free=0.1783 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=0.1010 r_free=0.1783 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1783 | n_water=258 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1043 r_free=0.1765 | n_water=248 | time (s): 19.690 (total time: 20.410) Filter (q & B) r_work=0.1044 r_free=0.1769 | n_water=245 | time (s): 1.450 (total time: 21.860) Compute maps r_work=0.1044 r_free=0.1769 | n_water=245 | time (s): 0.580 (total time: 22.440) Filter (map) r_work=0.1375 r_free=0.1799 | n_water=138 | time (s): 1.770 (total time: 24.210) Find peaks r_work=0.1375 r_free=0.1799 | n_water=138 | time (s): 0.470 (total time: 24.680) Add new water r_work=0.1738 r_free=0.2085 | n_water=227 | time (s): 1.750 (total time: 26.430) Refine new water occ: r_work=0.1180 r_free=0.1672 adp: r_work=0.1156 r_free=0.1687 occ: r_work=0.1153 r_free=0.1660 adp: r_work=0.1142 r_free=0.1675 occ: r_work=0.1139 r_free=0.1665 adp: r_work=0.1138 r_free=0.1669 ADP+occupancy (water only), MIN, final r_work=0.1138 r_free=0.1669 r_work=0.1138 r_free=0.1669 | n_water=227 | time (s): 3.970 (total time: 30.400) Filter (q & B) r_work=0.1138 r_free=0.1666 | n_water=226 | time (s): 1.250 (total time: 31.650) Filter (dist only) r_work=0.1138 r_free=0.1666 | n_water=226 | time (s): 15.530 (total time: 47.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.821520 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.713642 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 0.1022 0.1812 0.0790 0.009 1.0 5.4 0.5 0.6 0 11.411 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.22 18.12 7.90 4.688 16.838 2.714 0.014 9.53 18.66 9.13 5.617 17.292 2.714 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 109.29 16.74 6.72 1753 0 Protein: 0.00 109.29 15.16 6.71 1519 0 Water: 0.00 63.14 27.12 N/A 226 0 Other: 11.52 35.80 23.27 N/A 8 0 Chain A: 0.00 109.29 15.88 N/A 1665 0 Chain S: 3.91 61.82 32.96 N/A 88 0 Histogram: Values Number of atoms 0.00 - 10.93 710 10.93 - 21.86 637 21.86 - 32.79 220 32.79 - 43.71 104 43.71 - 54.64 45 54.64 - 65.57 23 65.57 - 76.50 8 76.50 - 87.43 2 87.43 - 98.36 2 98.36 - 109.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.0953 r_free=0.1866 r_work=0.0949 r_free=0.1866 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0949 r_free = 0.1866 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0948 r_free = 0.1876 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.30 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= 0.0948 r_free= 0.1876 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.012252 | | target function (ls_wunit_k1) not normalized (work): 60.327267 | | target function (ls_wunit_k1) not normalized (free): 10.706955 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0995 0.0948 0.1876 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2134 0.2138 0.2212 n_refl.: 5176 remove outliers: r(all,work,free)=0.2134 0.2138 0.2212 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2134 0.2138 0.2212 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0999 0.0952 0.1887 n_refl.: 5176 remove outliers: r(all,work,free)=0.0997 0.0949 0.1887 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 0.3307 326.900 314.127 0.672 1.008 0.364 11.894-9.307 99.02 97 4 0.1491 523.718 518.512 0.987 1.010 0.360 9.237-7.194 100.00 213 7 0.1489 428.297 431.676 1.019 1.010 0.300 7.162-5.571 100.00 427 22 0.1448 321.385 319.813 0.990 1.008 0.290 5.546-4.326 100.00 867 58 0.0800 441.216 438.519 1.009 1.005 0.216 4.315-3.360 100.00 1859 96 0.0736 419.601 419.404 1.061 0.998 0.207 3.356-3.002 100.00 1373 60 0.0974 323.194 321.762 1.037 0.992 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.3268 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0949 r_free=0.1887 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0950 r_free=0.1889 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0950 r_free=0.1889 | n_water=226 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0973 r_free=0.1885 | n_water=221 | time (s): 16.390 (total time: 17.050) Filter (q & B) r_work=0.1026 r_free=0.1886 | n_water=219 | time (s): 1.890 (total time: 18.940) Compute maps r_work=0.1026 r_free=0.1886 | n_water=219 | time (s): 0.540 (total time: 19.480) Filter (map) r_work=0.1300 r_free=0.1891 | n_water=145 | time (s): 1.580 (total time: 21.060) Find peaks r_work=0.1300 r_free=0.1891 | n_water=145 | time (s): 0.380 (total time: 21.440) Add new water r_work=0.1673 r_free=0.2298 | n_water=230 | time (s): 1.160 (total time: 22.600) Refine new water occ: r_work=0.1074 r_free=0.1884 adp: r_work=0.1068 r_free=0.1899 occ: r_work=0.1058 r_free=0.1880 adp: r_work=0.1057 r_free=0.1884 occ: r_work=0.1050 r_free=0.1863 adp: r_work=0.1048 r_free=0.1869 ADP+occupancy (water only), MIN, final r_work=0.1048 r_free=0.1869 r_work=0.1048 r_free=0.1869 | n_water=230 | time (s): 11.560 (total time: 34.160) Filter (q & B) r_work=0.1048 r_free=0.1869 | n_water=230 | time (s): 0.910 (total time: 35.070) Filter (dist only) r_work=0.1060 r_free=0.1870 | n_water=227 | time (s): 18.710 (total time: 53.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.082261 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.202633 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 0.0965 0.1917 0.0952 0.011 1.1 4.5 0.5 0.6 0 0.541 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.65 19.17 9.52 5.572 17.945 0.203 5.187 9.21 19.04 9.84 7.222 17.911 0.203 5.095 Individual atomic B min max mean iso aniso Overall: 0.00 108.81 16.40 8.82 1754 0 Protein: 0.00 108.81 15.22 8.80 1519 0 Water: 0.00 57.78 24.08 N/A 227 0 Other: 8.18 38.93 23.21 N/A 8 0 Chain A: 0.00 108.81 15.85 N/A 1649 0 Chain S: 0.00 54.37 25.07 N/A 105 0 Histogram: Values Number of atoms 0.00 - 10.88 685 10.88 - 21.76 658 21.76 - 32.64 236 32.64 - 43.52 107 43.52 - 54.40 33 54.40 - 65.28 19 65.28 - 76.16 8 76.16 - 87.05 4 87.05 - 97.93 3 97.93 - 108.81 1 =========================== Idealize ADP of riding H ========================== r_work=0.0921 r_free=0.1904 r_work=0.0926 r_free=0.1914 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0926 r_free = 0.1914 target_work(ml) = 5.099 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0916 r_free = 0.1895 target_work(ml) = 5.091 | | occupancies: max = 1.00 min = 0.30 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= 0.0916 r_free= 0.1895 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.091186 | | target function (ml) not normalized (work): 25063.910124 | | target function (ml) not normalized (free): 1865.363177 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0965 0.0916 0.1895 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2152 0.2161 0.2158 n_refl.: 5175 remove outliers: r(all,work,free)=0.2152 0.2161 0.2158 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2152 0.2161 0.2158 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0955 0.0907 0.1879 n_refl.: 5175 remove outliers: r(all,work,free)=0.0953 0.0904 0.1879 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 0.3556 329.074 293.760 0.595 0.994 0.340 11.894-9.307 99.02 97 4 0.1768 523.718 512.173 0.955 0.998 0.335 9.237-7.194 100.00 213 7 0.1928 428.297 424.890 1.000 0.999 0.304 7.162-5.571 100.00 427 22 0.1892 321.385 313.730 0.979 1.000 0.280 5.546-4.326 100.00 867 58 0.0930 441.216 434.959 1.002 1.001 0.220 4.315-3.360 100.00 1859 96 0.0605 419.601 419.297 1.062 1.002 0.220 3.356-3.002 100.00 1373 60 0.0623 323.194 322.539 1.036 1.003 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.5871 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0904 r_free=0.1879 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0906 r_free=0.1878 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0906 r_free=0.1878 | n_water=227 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.0924 r_free=0.1894 | n_water=223 | time (s): 17.990 (total time: 18.700) Filter (q & B) r_work=0.0956 r_free=0.1906 | n_water=222 | time (s): 1.390 (total time: 20.090) Compute maps r_work=0.0956 r_free=0.1906 | n_water=222 | time (s): 0.440 (total time: 20.530) Filter (map) r_work=0.1243 r_free=0.1916 | n_water=154 | time (s): 1.310 (total time: 21.840) Find peaks r_work=0.1243 r_free=0.1916 | n_water=154 | time (s): 0.540 (total time: 22.380) Add new water r_work=0.1526 r_free=0.2178 | n_water=219 | time (s): 1.580 (total time: 23.960) Refine new water occ: r_work=0.1011 r_free=0.1878 adp: r_work=0.1007 r_free=0.1886 occ: r_work=0.1002 r_free=0.1876 adp: r_work=0.1001 r_free=0.1879 occ: r_work=0.0997 r_free=0.1868 adp: r_work=0.0997 r_free=0.1868 ADP+occupancy (water only), MIN, final r_work=0.0997 r_free=0.1868 r_work=0.0997 r_free=0.1868 | n_water=219 | time (s): 7.590 (total time: 31.550) Filter (q & B) r_work=0.0997 r_free=0.1867 | n_water=218 | time (s): 1.920 (total time: 33.470) Filter (dist only) r_work=0.1001 r_free=0.1862 | n_water=217 | time (s): 17.150 (total time: 50.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.052091 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.234982 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 0.0915 0.1900 0.0985 0.011 1.1 6.4 0.5 0.0 0 0.526 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.15 19.00 9.85 6.891 17.928 0.235 5.073 8.90 19.06 10.17 7.956 18.021 0.235 5.010 Individual atomic B min max mean iso aniso Overall: 0.00 107.08 16.52 10.23 1744 0 Protein: 0.00 107.08 15.55 10.20 1519 0 Water: 0.00 52.78 23.07 N/A 217 0 Other: 6.43 37.63 23.15 N/A 8 0 Chain A: 0.00 107.08 16.12 N/A 1642 0 Chain S: 0.00 48.49 23.07 N/A 102 0 Histogram: Values Number of atoms 0.00 - 10.71 653 10.71 - 21.42 660 21.42 - 32.12 250 32.12 - 42.83 111 42.83 - 53.54 38 53.54 - 64.25 13 64.25 - 74.96 8 74.96 - 85.67 5 85.67 - 96.37 4 96.37 - 107.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.0890 r_free=0.1906 r_work=0.0894 r_free=0.1906 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0894 r_free = 0.1906 target_work(ml) = 5.014 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0885 r_free = 0.1896 target_work(ml) = 5.007 | | occupancies: max = 1.00 min = 0.30 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= 0.0885 r_free= 0.1896 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 5.006564 | | target function (ml) not normalized (work): 24642.310065 | | target function (ml) not normalized (free): 2130.725152 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0937 0.0885 0.1896 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2118 0.2117 0.2256 n_refl.: 5174 remove outliers: r(all,work,free)=0.2118 0.2117 0.2256 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2118 0.2117 0.2256 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0942 0.0891 0.1899 n_refl.: 5174 remove outliers: r(all,work,free)=0.0942 0.0891 0.1899 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 0.3620 329.074 300.749 0.612 0.986 0.327 11.894-9.307 99.02 97 4 0.1807 523.718 508.079 0.952 0.991 0.324 9.237-7.194 100.00 213 7 0.2079 428.297 419.880 1.001 0.994 0.300 7.162-5.571 100.00 427 22 0.1979 321.385 313.115 0.988 0.996 0.290 5.546-4.326 100.00 867 58 0.0970 441.216 435.382 1.013 0.998 0.209 4.315-3.360 100.00 1859 96 0.0591 419.601 419.617 1.080 1.000 0.173 3.356-3.002 100.00 1373 60 0.0491 323.194 323.177 1.059 1.003 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4178 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0891 r_free=0.1899 After: r_work=0.0893 r_free=0.1898 ================================== NQH flips ================================== r_work=0.0893 r_free=0.1898 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0893 r_free=0.1902 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0893 r_free=0.1902 | n_water=217 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.0918 r_free=0.1912 | n_water=210 | time (s): 16.170 (total time: 16.880) Filter (q & B) r_work=0.1030 r_free=0.1935 | n_water=206 | time (s): 1.410 (total time: 18.290) Compute maps r_work=0.1030 r_free=0.1935 | n_water=206 | time (s): 0.490 (total time: 18.780) Filter (map) r_work=0.1296 r_free=0.1994 | n_water=151 | time (s): 1.680 (total time: 20.460) Find peaks r_work=0.1296 r_free=0.1994 | n_water=151 | time (s): 0.580 (total time: 21.040) Add new water r_work=0.1577 r_free=0.2294 | n_water=224 | time (s): 1.650 (total time: 22.690) Refine new water occ: r_work=0.1009 r_free=0.1875 adp: r_work=0.0996 r_free=0.1881 occ: r_work=0.0989 r_free=0.1867 adp: r_work=0.0988 r_free=0.1877 occ: r_work=0.0982 r_free=0.1862 adp: r_work=0.0980 r_free=0.1872 ADP+occupancy (water only), MIN, final r_work=0.0980 r_free=0.1872 r_work=0.0980 r_free=0.1872 | n_water=224 | time (s): 9.810 (total time: 32.500) Filter (q & B) r_work=0.0981 r_free=0.1870 | n_water=223 | time (s): 1.850 (total time: 34.350) Filter (dist only) r_work=0.0981 r_free=0.1870 | n_water=223 | time (s): 15.400 (total time: 49.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.926236 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.235062 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 0.1865 0.0941 0.011 1.1 7.7 0.5 0.0 0 0.463 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.24 18.65 9.41 7.816 18.280 0.235 5.041 9.08 18.79 9.71 8.864 18.388 0.235 4.989 Individual atomic B min max mean iso aniso Overall: 0.00 105.85 16.95 11.63 1750 0 Protein: 0.00 105.85 15.90 11.58 1519 0 Water: 0.00 60.92 23.86 N/A 223 0 Other: 3.71 37.10 22.52 N/A 8 0 Chain A: 0.00 105.85 16.39 N/A 1635 0 Chain S: 0.00 60.92 24.92 N/A 115 0 Histogram: Values Number of atoms 0.00 - 10.59 616 10.59 - 21.17 662 21.17 - 31.76 274 31.76 - 42.34 109 42.34 - 52.93 47 52.93 - 63.51 19 63.51 - 74.10 11 74.10 - 84.68 4 84.68 - 95.27 6 95.27 - 105.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.0908 r_free=0.1879 r_work=0.0913 r_free=0.1879 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0913 r_free = 0.1879 target_work(ml) = 4.995 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0903 r_free = 0.1859 target_work(ml) = 4.989 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0903 r_free= 0.1859 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 4.988774 | | target function (ml) not normalized (work): 24554.747790 | | target function (ml) not normalized (free): 2131.968717 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1267 0.1830 5.5399 6.2739| | 2: 3.78 - 3.00 1.00 2430 110 0.0459 0.1908 4.4236 11.283| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.92 12.20 1.00 0.98 13223.86| | 2: 3.78 - 3.00 2430 110 0.99 2.05 1.00 1.00 1013.90| |alpha: min = 0.96 max = 1.00 mean = 0.99| |beta: min = 658.80 max = 21989.34 mean = 7195.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.67 mean = 7.19| |phase err.(test): min = 0.00 max = 80.39 mean = 7.30| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0952 0.0903 0.1859 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2147 0.2147 0.2248 n_refl.: 5174 remove outliers: r(all,work,free)=0.2147 0.2147 0.2248 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2147 0.2147 0.2248 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0952 0.0902 0.1859 n_refl.: 5174 remove outliers: r(all,work,free)=0.0952 0.0902 0.1859 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 0.3703 329.074 293.856 0.631 0.985 0.325 11.894-9.307 99.02 97 4 0.1825 523.718 513.134 1.007 0.992 0.321 9.237-7.194 100.00 213 7 0.2205 428.297 420.609 1.050 0.995 0.300 7.162-5.571 100.00 427 22 0.2057 321.385 313.280 1.030 0.997 0.280 5.546-4.326 100.00 867 58 0.1043 441.216 433.826 1.063 0.999 0.200 4.315-3.360 100.00 1859 96 0.0583 419.601 420.068 1.146 1.002 0.200 3.356-3.002 100.00 1373 60 0.0436 323.194 322.856 1.126 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.3925 ================= 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 : 0.3616 0.2027 0.083 5.460 8.8 119.3 19.9 258 0.000 1_bss: 0.1558 0.1592 0.083 5.460 6.0 116.5 17.1 258 0.000 1_settarget: 0.1558 0.1592 0.083 5.460 6.0 116.5 17.1 258 0.000 1_nqh: 0.1559 0.1595 0.083 5.460 6.0 116.5 17.1 258 0.006 1_weight: 0.1559 0.1595 0.083 5.460 6.0 116.5 17.1 258 0.006 1_xyzrec: 0.1162 0.1797 0.009 0.957 6.0 116.5 17.1 258 0.217 1_adp: 0.1023 0.1789 0.009 0.957 2.3 111.5 17.5 258 0.217 1_regHadp: 0.1017 0.1796 0.009 0.957 2.3 111.5 17.5 258 0.217 1_occ: 0.1010 0.1794 0.009 0.957 2.3 111.5 17.5 258 0.217 2_bss: 0.1008 0.1783 0.009 0.957 1.3 110.5 16.5 258 0.217 2_settarget: 0.1008 0.1783 0.009 0.957 1.3 110.5 16.5 258 0.217 2_updatecdl: 0.1008 0.1783 0.009 0.979 1.3 110.5 16.5 258 0.217 2_nqh: 0.1010 0.1783 0.009 0.979 1.3 110.5 16.5 258 0.211 2_sol: 0.1138 0.1666 0.009 0.979 1.3 110.1 15.9 226 n/a 2_weight: 0.1138 0.1666 0.009 0.979 1.3 110.1 15.9 226 n/a 2_xyzrec: 0.1022 0.1812 0.009 0.979 1.3 110.1 15.9 226 n/a 2_adp: 0.0953 0.1866 0.009 0.979 0.0 109.3 16.7 226 n/a 2_regHadp: 0.0949 0.1866 0.009 0.979 0.0 109.3 16.7 226 n/a 2_occ: 0.0948 0.1876 0.009 0.979 0.0 109.3 16.7 226 n/a 3_bss: 0.0949 0.1887 0.009 0.979 0.0 109.3 16.7 226 n/a 3_settarget: 0.0949 0.1887 0.009 0.979 0.0 109.3 16.7 226 n/a 3_updatecdl: 0.0949 0.1887 0.009 0.987 0.0 109.3 16.7 226 n/a 3_nqh: 0.0950 0.1889 0.009 0.987 0.0 109.3 16.7 226 n/a 3_sol: 0.1060 0.1870 0.009 0.987 0.0 109.3 16.5 227 n/a 3_weight: 0.1060 0.1870 0.009 0.987 0.0 109.3 16.5 227 n/a 3_xyzrec: 0.0965 0.1917 0.011 1.064 0.0 109.3 16.5 227 n/a 3_adp: 0.0921 0.1904 0.011 1.064 0.0 108.8 16.4 227 n/a 3_regHadp: 0.0926 0.1914 0.011 1.064 0.0 108.8 16.4 227 n/a 3_occ: 0.0916 0.1895 0.011 1.064 0.0 108.8 16.4 227 n/a 4_bss: 0.0904 0.1879 0.011 1.064 0.0 108.8 16.4 227 n/a 4_settarget: 0.0904 0.1879 0.011 1.064 0.0 108.8 16.4 227 n/a 4_updatecdl: 0.0904 0.1879 0.011 1.078 0.0 108.8 16.4 227 n/a 4_nqh: 0.0906 0.1878 0.011 1.078 0.0 108.8 16.4 227 n/a 4_sol: 0.1001 0.1862 0.011 1.078 0.0 108.8 16.3 217 n/a 4_weight: 0.1001 0.1862 0.011 1.078 0.0 108.8 16.3 217 n/a 4_xyzrec: 0.0915 0.1900 0.011 1.077 0.0 108.8 16.3 217 n/a 4_adp: 0.0890 0.1906 0.011 1.077 0.0 107.1 16.5 217 n/a 4_regHadp: 0.0894 0.1906 0.011 1.077 0.0 107.1 16.5 217 n/a 4_occ: 0.0885 0.1896 0.011 1.077 0.0 107.1 16.5 217 n/a 5_bss: 0.0891 0.1899 0.011 1.077 0.0 107.1 16.5 217 n/a 5_settarget: 0.0891 0.1899 0.011 1.077 0.0 107.1 16.5 217 n/a 5_updatecdl: 0.0891 0.1899 0.011 1.084 0.0 107.1 16.5 217 n/a 5_setrh: 0.0893 0.1898 0.011 1.084 0.0 107.1 16.5 217 n/a 5_nqh: 0.0893 0.1902 0.011 1.084 0.0 107.1 16.5 217 n/a 5_sol: 0.0981 0.1870 0.011 1.084 0.0 107.1 16.7 223 n/a 5_weight: 0.0981 0.1870 0.011 1.084 0.0 107.1 16.7 223 n/a 5_xyzrec: 0.0924 0.1865 0.011 1.112 0.0 107.1 16.7 223 n/a 5_adp: 0.0908 0.1879 0.011 1.112 0.0 105.9 16.9 223 n/a 5_regHadp: 0.0913 0.1879 0.011 1.112 0.0 105.9 16.9 223 n/a 5_occ: 0.0903 0.1859 0.011 1.112 0.0 105.9 16.9 223 n/a end: 0.0902 0.1859 0.011 1.112 0.0 105.9 16.9 223 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3867824_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3867824_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0700 Refinement macro-cycles (run) : 464.5900 Write final files (write_after_run_outputs) : 12.0400 Total : 480.7000 Total CPU time: 8.41 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:45 PST -0800 (1735492725.21 s) Start R-work = 0.1558, R-free = 0.1592 Final R-work = 0.0902, R-free = 0.1859 =============================================================================== Job complete usr+sys time: 513.43 seconds wall clock time: 8 minutes 55.11 seconds (535.11 seconds total)