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_8565654.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8565654.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8565654.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" } 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 3 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: 2.21, per 1000 atoms: 0.65 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: 0.52 Conformation dependent library (CDL) restraints added in 107.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 605 0.93 - 1.19: 1066 1.19 - 1.46: 792 1.46 - 1.73: 674 1.73 - 2.00: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.090 0.236 1.10e-02 8.26e+03 4.59e+02 bond pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " ideal model delta sigma weight residual 1.326 1.553 -0.227 1.10e-02 8.26e+03 4.25e+02 bond pdb=" N ALA A 129 " pdb=" CA ALA A 129 " ideal model delta sigma weight residual 1.456 1.213 0.243 1.31e-02 5.83e+03 3.45e+02 bond pdb=" N GLN A 95 " pdb=" CA GLN A 95 " ideal model delta sigma weight residual 1.459 1.676 -0.217 1.17e-02 7.31e+03 3.45e+02 bond pdb=" N GLU A 116 " pdb=" CA GLU A 116 " ideal model delta sigma weight residual 1.462 1.728 -0.266 1.46e-02 4.69e+03 3.33e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 3279 4.95 - 9.89: 1859 9.89 - 14.84: 558 14.84 - 19.79: 75 19.79 - 24.73: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 48 " pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 119.20 133.63 -14.43 9.00e-01 1.23e+00 2.57e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.29 111.06 11.23 8.10e-01 1.52e+00 1.92e+02 angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.27 107.28 15.99 1.16e+00 7.43e-01 1.90e+02 angle pdb=" N ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta sigma weight residual 111.21 126.28 -15.07 1.17e+00 7.31e-01 1.66e+02 angle pdb=" C GLY A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 119.87 106.77 13.10 1.04e+00 9.25e-01 1.59e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 1322 17.39 - 34.77: 104 34.77 - 52.15: 37 52.15 - 69.54: 14 69.54 - 86.92: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C HIS A 115 " pdb=" N HIS A 115 " pdb=" CA HIS A 115 " pdb=" CB HIS A 115 " ideal model delta harmonic sigma weight residual -122.60 -144.72 22.12 0 2.50e+00 1.60e-01 7.83e+01 dihedral pdb=" N ARG A 27 " pdb=" C ARG A 27 " pdb=" CA ARG A 27 " pdb=" CB ARG A 27 " ideal model delta harmonic sigma weight residual 122.80 141.55 -18.75 0 2.50e+00 1.60e-01 5.63e+01 dihedral pdb=" C LYS A 62 " pdb=" N LYS A 62 " pdb=" CA LYS A 62 " pdb=" CB LYS A 62 " ideal model delta harmonic sigma weight residual -122.60 -139.92 17.32 0 2.50e+00 1.60e-01 4.80e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.242: 107 0.242 - 0.482: 79 0.482 - 0.723: 40 0.723 - 0.964: 14 0.964 - 1.204: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 104 " pdb=" N ALA A 104 " pdb=" C ALA A 104 " pdb=" CB ALA A 104 " both_signs ideal model delta sigma weight residual False 2.48 3.69 -1.20 2.00e-01 2.50e+01 3.63e+01 chirality pdb=" CB VAL A 186 " pdb=" CA VAL A 186 " pdb=" CG1 VAL A 186 " pdb=" CG2 VAL A 186 " both_signs ideal model delta sigma weight residual False -2.63 -1.56 -1.07 2.00e-01 2.50e+01 2.86e+01 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 -1.58 -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=" CD ARG A 28 " 0.166 9.50e-02 1.11e+02 9.29e-02 1.29e+02 pdb=" NE ARG A 28 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.104 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " -0.038 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " 0.057 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " 0.142 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " -0.047 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.083 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.021 2.00e-02 2.50e+03 6.00e-02 1.08e+02 pdb=" CG PHE A 119 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.074 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.117 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.120 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " -0.041 2.00e-02 2.50e+03 6.26e-02 8.81e+01 pdb=" CG HIS A 138 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.071 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.148 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " 0.013 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.040 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.015 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 716 2.26 - 2.85: 7771 2.85 - 3.43: 10628 3.43 - 4.02: 15312 4.02 - 4.60: 22148 Nonbonded interactions: 56575 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.681 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.808 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.810 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.813 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.833 2.450 ... (remaining 56570 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_8565654_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= 0.3609 r_free= 0.2035 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467734 | | target function (ml) not normalized (work): 22025.930892 | | target function (ml) not normalized (free): 1146.104934 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3794 0.2295 4.8526 4.9334| | 2: 3.78 - 3.00 1.00 2430 110 0.3384 0.1595 4.0718 4.0506| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.66 0.83 0.13 6599.36| | 2: 3.78 - 3.00 2430 110 0.94 11.25 1.48 0.26 446.84| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 378.36 max = 12051.49 mean = 3566.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.22| |phase err.(test): min = 0.00 max = 89.91 mean = 33.67| |-----------------------------------------------------------------------------| ----------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 0.266 1557 Z= 5.534 Angle : 5.258 23.015 2118 Z= 3.666 Chirality : 0.408 1.204 243 Planarity : 0.033 0.139 284 Dihedral : 14.100 86.919 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 36.22 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.30 (0.48), residues: 224 helix: -3.20 (0.32), residues: 109 sheet: -0.60 (0.84), residues: 38 loop : -1.00 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.021 ARG A 98 TYR 0.083 0.039 TYR A 141 PHE 0.141 0.039 PHE A 119 HIS 0.104 0.040 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= 0.3609 r_free= 0.2035 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.467734 | | target function (ml) not normalized (work): 22025.930892 | | target function (ml) not normalized (free): 1146.104934 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3565 0.3641 0.2098 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3565 0.3641 0.2098 n_refl.: 5182 remove outliers: r(all,work,free)=0.2517 0.2541 0.2098 n_refl.: 5178 overall B=-2.85 to atoms: r(all,work,free)=0.2408 0.2429 0.2049 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1558 0.1557 0.1573 n_refl.: 5178 remove outliers: r(all,work,free)=0.1556 0.1555 0.1573 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.3998 444.986 409.030 0.641 1.080 0.392 11.894-9.307 99.02 97 4 0.1864 714.371 692.210 0.925 1.076 0.372 9.237-7.194 100.00 213 7 0.2218 584.214 574.543 0.967 1.067 0.374 7.162-5.571 100.00 427 22 0.2242 438.381 424.379 0.933 1.053 0.326 5.546-4.326 100.00 867 58 0.1391 601.835 595.042 0.977 1.029 0.210 4.315-3.360 100.00 1859 96 0.1317 572.352 566.824 1.055 0.988 0.179 3.356-3.002 100.00 1373 60 0.1570 440.850 433.954 1.076 0.948 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.6678 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1555 r_free=0.1573 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1555 r_free=0.1573 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.892033 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.754238 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 0.1157 0.1755 0.0598 0.009 1.0 3.2 0.5 0.0 0 9.446 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 17.55 5.98 3.012 16.004 1.754 0.018 10.20 17.66 7.47 4.867 16.220 1.754 0.015 Individual atomic B min max mean iso aniso Overall: 2.17 111.44 17.44 5.22 1785 0 Protein: 2.17 110.36 14.74 5.21 1519 0 Water: 4.01 111.44 33.16 N/A 258 0 Other: 16.59 37.65 23.63 N/A 8 0 Chain A: 2.17 111.44 17.44 N/A 1785 0 Histogram: Values Number of atoms 2.17 - 13.10 917 13.10 - 24.03 483 24.03 - 34.96 189 34.96 - 45.88 106 45.88 - 56.81 58 56.81 - 67.74 16 67.74 - 78.66 7 78.66 - 89.59 5 89.59 - 100.52 1 100.52 - 111.44 3 =========================== Idealize ADP of riding H ========================== r_work=0.1020 r_free=0.1766 r_work=0.1013 r_free=0.1773 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1013 r_free = 0.1773 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 = 0.1003 r_free = 0.1755 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1003 r_free= 0.1755 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013854 | | target function (ls_wunit_k1) not normalized (work): 68.232870 | | target function (ls_wunit_k1) not normalized (free): 10.056773 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1040 0.1003 0.1755 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2100 0.2099 0.2224 n_refl.: 5177 remove outliers: r(all,work,free)=0.2100 0.2099 0.2224 n_refl.: 5177 overall B=-0.99 to atoms: r(all,work,free)=0.2058 0.2056 0.2211 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1042 0.1005 0.1747 n_refl.: 5177 remove outliers: r(all,work,free)=0.1040 0.1002 0.1747 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 0.3368 323.970 307.729 0.647 1.025 0.365 11.894-9.307 99.02 97 4 0.1560 524.571 515.457 0.971 1.025 0.361 9.237-7.194 100.00 213 7 0.1719 428.995 428.387 1.012 1.022 0.321 7.162-5.571 100.00 427 22 0.1573 321.908 318.570 0.976 1.017 0.302 5.546-4.326 100.00 867 58 0.0890 441.935 439.433 0.993 1.009 0.192 4.315-3.360 100.00 1859 96 0.0753 420.284 419.953 1.047 0.996 0.183 3.356-3.002 100.00 1373 60 0.0997 323.721 322.284 1.030 0.982 0.041 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.5105 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1002 r_free=0.1747 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1005 r_free=0.1747 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1005 r_free=0.1747 | n_water=258 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1021 r_free=0.1734 | n_water=252 | time (s): 21.250 (total time: 21.940) Filter (q & B) r_work=0.1022 r_free=0.1737 | n_water=250 | time (s): 1.460 (total time: 23.400) Compute maps r_work=0.1022 r_free=0.1737 | n_water=250 | time (s): 0.600 (total time: 24.000) Filter (map) r_work=0.1308 r_free=0.1842 | n_water=155 | time (s): 1.990 (total time: 25.990) Find peaks r_work=0.1308 r_free=0.1842 | n_water=155 | time (s): 0.450 (total time: 26.440) Add new water r_work=0.1638 r_free=0.2103 | n_water=241 | time (s): 1.310 (total time: 27.750) Refine new water occ: r_work=0.1150 r_free=0.1664 adp: r_work=0.1121 r_free=0.1678 occ: r_work=0.1119 r_free=0.1649 adp: r_work=0.1106 r_free=0.1667 occ: r_work=0.1105 r_free=0.1658 adp: r_work=0.1105 r_free=0.1658 ADP+occupancy (water only), MIN, final r_work=0.1105 r_free=0.1658 r_work=0.1105 r_free=0.1658 | n_water=241 | time (s): 3.570 (total time: 31.320) Filter (q & B) r_work=0.1106 r_free=0.1666 | n_water=240 | time (s): 1.360 (total time: 32.680) Filter (dist only) r_work=0.1114 r_free=0.1665 | n_water=237 | time (s): 17.080 (total time: 49.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.075970 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.599415 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 0.0998 0.1760 0.0762 0.009 1.0 4.8 0.5 0.6 0 12.038 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.98 17.60 7.62 4.616 16.807 2.599 0.014 9.34 17.98 8.65 5.423 17.233 2.599 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.09 16.74 6.40 1764 0 Protein: 0.00 106.09 15.05 6.38 1519 0 Water: 0.00 62.74 27.14 N/A 237 0 Other: 17.26 44.94 29.12 N/A 8 0 Chain A: 0.00 106.09 15.91 N/A 1680 0 Chain S: 5.04 58.20 33.23 N/A 84 0 Histogram: Values Number of atoms 0.00 - 10.61 654 10.61 - 21.22 676 21.22 - 31.83 219 31.83 - 42.43 129 42.43 - 53.04 41 53.04 - 63.65 27 63.65 - 74.26 10 74.26 - 84.87 3 84.87 - 95.48 3 95.48 - 106.09 2 =========================== Idealize ADP of riding H ========================== r_work=0.0934 r_free=0.1798 r_work=0.0931 r_free=0.1802 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0931 r_free = 0.1802 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0930 r_free = 0.1799 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.28 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= 0.0930 r_free= 0.1799 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011999 | | target function (ls_wunit_k1) not normalized (work): 59.080830 | | target function (ls_wunit_k1) not normalized (free): 9.869249 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0974 0.0930 0.1799 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2099 0.2102 0.2185 n_refl.: 5176 remove outliers: r(all,work,free)=0.2099 0.2102 0.2185 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2099 0.2102 0.2185 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0975 0.0931 0.1805 n_refl.: 5176 remove outliers: r(all,work,free)=0.0975 0.0931 0.1805 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 0.3304 323.970 309.707 0.651 1.006 0.360 11.894-9.307 99.02 97 4 0.1556 524.571 520.373 0.987 1.008 0.350 9.237-7.194 100.00 213 7 0.1479 428.995 429.953 1.026 1.008 0.295 7.162-5.571 100.00 427 22 0.1420 321.908 319.814 0.996 1.006 0.290 5.546-4.326 100.00 867 58 0.0790 441.935 439.258 1.011 1.003 0.230 4.315-3.360 100.00 1859 96 0.0710 420.284 419.917 1.057 0.999 0.190 3.356-3.002 100.00 1373 60 0.0949 323.721 322.794 1.033 0.995 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.2534 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0931 r_free=0.1805 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0931 r_free=0.1805 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0931 r_free=0.1805 | n_water=237 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.0951 r_free=0.1793 | n_water=233 | time (s): 18.800 (total time: 19.490) Filter (q & B) r_work=0.1045 r_free=0.1769 | n_water=230 | time (s): 1.970 (total time: 21.460) Compute maps r_work=0.1045 r_free=0.1769 | n_water=230 | time (s): 0.660 (total time: 22.120) Filter (map) r_work=0.1308 r_free=0.1811 | n_water=158 | time (s): 1.600 (total time: 23.720) Find peaks r_work=0.1308 r_free=0.1811 | n_water=158 | time (s): 0.600 (total time: 24.320) Add new water r_work=0.1631 r_free=0.2142 | n_water=235 | time (s): 1.550 (total time: 25.870) Refine new water occ: r_work=0.1055 r_free=0.1752 adp: r_work=0.1046 r_free=0.1769 occ: r_work=0.1037 r_free=0.1750 adp: r_work=0.1036 r_free=0.1757 occ: r_work=0.1028 r_free=0.1738 adp: r_work=0.1026 r_free=0.1744 ADP+occupancy (water only), MIN, final r_work=0.1026 r_free=0.1744 r_work=0.1026 r_free=0.1744 | n_water=235 | time (s): 10.460 (total time: 36.330) Filter (q & B) r_work=0.1026 r_free=0.1744 | n_water=235 | time (s): 1.140 (total time: 37.470) Filter (dist only) r_work=0.1033 r_free=0.1742 | n_water=233 | time (s): 17.440 (total time: 54.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.084559 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.226672 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 0.1831 0.0908 0.011 1.1 4.8 0.5 0.6 0 0.542 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.24 18.31 9.08 5.356 17.874 0.227 5.154 8.81 18.43 9.62 7.078 17.875 0.227 5.061 Individual atomic B min max mean iso aniso Overall: 0.00 106.56 16.54 8.72 1760 0 Protein: 0.00 106.56 15.13 8.70 1519 0 Water: 0.00 57.74 25.14 N/A 233 0 Other: 20.99 53.37 33.35 N/A 8 0 Chain A: 0.00 106.56 15.92 N/A 1661 0 Chain S: 0.00 55.36 26.99 N/A 99 0 Histogram: Values Number of atoms 0.00 - 10.66 672 10.66 - 21.31 665 21.31 - 31.97 221 31.97 - 42.63 127 42.63 - 53.28 37 53.28 - 63.94 18 63.94 - 74.59 12 74.59 - 85.25 3 85.25 - 95.91 4 95.91 - 106.56 1 =========================== Idealize ADP of riding H ========================== r_work=0.0881 r_free=0.1843 r_work=0.0887 r_free=0.1850 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0887 r_free = 0.1850 target_work(ml) = 5.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1837 target_work(ml) = 5.060 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1837 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.059510 | | target function (ml) not normalized (work): 24913.024983 | | target function (ml) not normalized (free): 1862.867886 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0930 0.0881 0.1837 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2111 0.2118 0.2152 n_refl.: 5176 remove outliers: r(all,work,free)=0.2111 0.2118 0.2152 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2111 0.2118 0.2152 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0922 0.0874 0.1830 n_refl.: 5176 remove outliers: r(all,work,free)=0.0920 0.0872 0.1830 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 0.3570 326.087 296.474 0.604 0.994 0.350 11.894-9.307 99.02 97 4 0.1766 524.571 513.956 0.955 0.996 0.335 9.237-7.194 100.00 213 7 0.1859 428.995 424.301 1.000 0.998 0.290 7.162-5.571 100.00 427 22 0.1787 321.908 313.138 0.979 0.999 0.290 5.546-4.326 100.00 867 58 0.0885 441.935 436.666 0.996 1.000 0.250 4.315-3.360 100.00 1859 96 0.0574 420.284 419.830 1.046 1.003 0.200 3.356-3.002 100.00 1373 60 0.0625 323.721 323.779 1.022 1.005 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-5.9802 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0872 r_free=0.1830 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=0.0875 r_free=0.1822 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0875 r_free=0.1822 | n_water=233 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0882 r_free=0.1810 | n_water=231 | time (s): 20.160 (total time: 20.670) Filter (q & B) r_work=0.0959 r_free=0.1832 | n_water=229 | time (s): 1.780 (total time: 22.450) Compute maps r_work=0.0959 r_free=0.1832 | n_water=229 | time (s): 0.530 (total time: 22.980) Filter (map) r_work=0.1247 r_free=0.1911 | n_water=158 | time (s): 1.470 (total time: 24.450) Find peaks r_work=0.1247 r_free=0.1911 | n_water=158 | time (s): 0.580 (total time: 25.030) Add new water r_work=0.1574 r_free=0.2230 | n_water=231 | time (s): 1.310 (total time: 26.340) Refine new water occ: r_work=0.1006 r_free=0.1858 adp: r_work=0.0999 r_free=0.1874 occ: r_work=0.0989 r_free=0.1854 adp: r_work=0.0990 r_free=0.1865 occ: r_work=0.0981 r_free=0.1846 adp: r_work=0.0981 r_free=0.1856 ADP+occupancy (water only), MIN, final r_work=0.0981 r_free=0.1856 r_work=0.0981 r_free=0.1856 | n_water=231 | time (s): 6.050 (total time: 32.390) Filter (q & B) r_work=0.0981 r_free=0.1856 | n_water=231 | time (s): 1.050 (total time: 33.440) Filter (dist only) r_work=0.0993 r_free=0.1839 | n_water=229 | time (s): 19.600 (total time: 53.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.007133 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.270280 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 0.0911 0.1843 0.0932 0.011 1.0 4.2 0.5 0.0 0 0.504 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.11 18.43 9.32 6.816 17.948 0.270 5.045 8.86 18.52 9.66 8.194 18.086 0.270 4.980 Individual atomic B min max mean iso aniso Overall: 0.00 106.47 16.79 10.70 1756 0 Protein: 0.00 106.47 15.55 10.67 1519 0 Water: 0.00 55.52 24.36 N/A 229 0 Other: 23.96 59.12 35.99 N/A 8 0 Chain A: 0.00 106.47 16.21 N/A 1651 0 Chain S: 0.00 51.48 25.88 N/A 105 0 Histogram: Values Number of atoms 0.00 - 10.65 648 10.65 - 21.29 650 21.29 - 31.94 252 31.94 - 42.59 123 42.59 - 53.24 50 53.24 - 63.88 12 63.88 - 74.53 10 74.53 - 85.18 6 85.18 - 95.83 3 95.83 - 106.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.0886 r_free=0.1852 r_work=0.0890 r_free=0.1857 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0890 r_free = 0.1857 target_work(ml) = 4.985 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0880 r_free = 0.1842 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0880 r_free= 0.1842 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.979259 | | target function (ml) not normalized (work): 24512.890295 | | target function (ml) not normalized (free): 2092.170224 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0928 0.0880 0.1842 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2084 0.2086 0.2179 n_refl.: 5175 remove outliers: r(all,work,free)=0.2084 0.2086 0.2179 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2084 0.2086 0.2179 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0927 0.0878 0.1843 n_refl.: 5175 remove outliers: r(all,work,free)=0.0927 0.0878 0.1843 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 0.3779 326.087 291.066 0.575 0.988 0.326 11.894-9.307 99.02 97 4 0.1868 524.571 519.819 0.979 0.992 0.323 9.237-7.194 100.00 213 7 0.2079 428.995 422.203 1.011 0.995 0.284 7.162-5.571 100.00 427 22 0.2043 321.908 312.024 0.991 0.996 0.270 5.546-4.326 100.00 867 58 0.0950 441.935 435.160 1.011 0.999 0.230 4.315-3.360 100.00 1859 96 0.0565 420.284 419.891 1.076 1.003 0.210 3.356-3.002 100.00 1373 60 0.0463 323.721 324.141 1.054 1.006 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.3703 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0878 r_free=0.1843 After: r_work=0.0881 r_free=0.1842 ================================== NQH flips ================================== r_work=0.0881 r_free=0.1842 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=0.0881 r_free=0.1843 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0881 r_free=0.1843 | n_water=229 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.0898 r_free=0.1844 | n_water=225 | time (s): 18.780 (total time: 19.280) Filter (q & B) r_work=0.1039 r_free=0.1903 | n_water=221 | time (s): 1.810 (total time: 21.090) Compute maps r_work=0.1039 r_free=0.1903 | n_water=221 | time (s): 0.580 (total time: 21.670) Filter (map) r_work=0.1261 r_free=0.1927 | n_water=163 | time (s): 1.520 (total time: 23.190) Find peaks r_work=0.1261 r_free=0.1927 | n_water=163 | time (s): 0.550 (total time: 23.740) Add new water r_work=0.1526 r_free=0.2187 | n_water=226 | time (s): 1.750 (total time: 25.490) Refine new water occ: r_work=0.1018 r_free=0.1867 adp: r_work=0.1007 r_free=0.1871 occ: r_work=0.0999 r_free=0.1865 adp: r_work=0.1000 r_free=0.1867 occ: r_work=0.0992 r_free=0.1864 adp: r_work=0.0992 r_free=0.1865 ADP+occupancy (water only), MIN, final r_work=0.0992 r_free=0.1865 r_work=0.0992 r_free=0.1865 | n_water=226 | time (s): 12.120 (total time: 37.610) Filter (q & B) r_work=0.0992 r_free=0.1865 | n_water=225 | time (s): 1.560 (total time: 39.170) Filter (dist only) r_work=0.1005 r_free=0.1877 | n_water=223 | time (s): 18.810 (total time: 57.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.990239 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.211048 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 0.0940 0.1917 0.0978 0.010 1.1 9.0 0.5 0.0 0 0.495 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.40 19.17 9.78 8.124 18.304 0.211 5.059 9.18 19.41 10.23 8.849 18.434 0.211 5.001 Individual atomic B min max mean iso aniso Overall: 0.00 107.79 17.06 11.61 1750 0 Protein: 0.00 107.79 15.93 11.58 1519 0 Water: 0.00 57.81 23.97 N/A 223 0 Other: 19.92 54.12 37.78 N/A 8 0 Chain A: 0.00 107.79 16.46 N/A 1641 0 Chain S: 0.00 57.81 26.05 N/A 109 0 Histogram: Values Number of atoms 0.00 - 10.78 642 10.78 - 21.56 640 21.56 - 32.34 265 32.34 - 43.11 119 43.11 - 53.89 46 53.89 - 64.67 16 64.67 - 75.45 9 75.45 - 86.23 6 86.23 - 97.01 5 97.01 - 107.79 2 =========================== Idealize ADP of riding H ========================== r_work=0.0918 r_free=0.1941 r_work=0.0923 r_free=0.1945 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0923 r_free = 0.1945 target_work(ml) = 5.007 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0919 r_free = 0.1933 target_work(ml) = 5.003 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0919 r_free= 0.1933 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.003216 | | target function (ml) not normalized (work): 24630.832826 | | target function (ml) not normalized (free): 2169.117944 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1294 0.1847 5.5591 6.1261| | 2: 3.78 - 3.00 1.00 2430 110 0.0461 0.2079 4.433 11.811| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2493 142 0.91 12.77 1.00 0.97 14200.66| | 2: 3.78 - 3.00 2430 110 0.99 2.06 1.01 1.00 1029.26| |alpha: min = 0.96 max = 1.01 mean = 0.99| |beta: min = 667.84 max = 23853.39 mean = 7699.24| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.50 mean = 7.48| |phase err.(test): min = 0.00 max = 83.73 mean = 7.91| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0969 0.0919 0.1933 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2152 0.2149 0.2322 n_refl.: 5175 remove outliers: r(all,work,free)=0.2152 0.2149 0.2322 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2152 0.2149 0.2322 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0966 0.0916 0.1930 n_refl.: 5175 remove outliers: r(all,work,free)=0.0966 0.0916 0.1930 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 0.3958 326.087 291.775 0.601 0.985 0.315 11.894-9.307 99.02 97 4 0.1970 524.571 510.558 1.011 0.990 0.311 9.237-7.194 100.00 213 7 0.2235 428.995 417.107 1.056 0.994 0.290 7.162-5.571 100.00 427 22 0.2109 321.908 311.653 1.041 0.996 0.280 5.546-4.326 100.00 867 58 0.1023 441.935 436.432 1.067 0.999 0.220 4.315-3.360 100.00 1859 96 0.0591 420.284 420.009 1.151 1.002 0.210 3.356-3.002 100.00 1373 60 0.0444 323.721 324.006 1.130 1.006 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.6100 ================= 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 : 0.3609 0.2035 0.083 5.258 8.8 119.3 19.9 258 0.000 1_bss: 0.1555 0.1573 0.083 5.258 6.0 116.4 17.0 258 0.000 1_settarget: 0.1555 0.1573 0.083 5.258 6.0 116.4 17.0 258 0.000 1_nqh: 0.1555 0.1573 0.083 5.258 6.0 116.4 17.0 258 0.000 1_weight: 0.1555 0.1573 0.083 5.258 6.0 116.4 17.0 258 0.000 1_xyzrec: 0.1157 0.1755 0.009 0.969 6.0 116.4 17.0 258 0.215 1_adp: 0.1020 0.1766 0.009 0.969 2.2 111.4 17.4 258 0.215 1_regHadp: 0.1013 0.1773 0.009 0.969 2.2 111.4 17.4 258 0.215 1_occ: 0.1003 0.1755 0.009 0.969 2.2 111.4 17.4 258 0.215 2_bss: 0.1002 0.1747 0.009 0.969 1.2 110.5 16.5 258 0.215 2_settarget: 0.1002 0.1747 0.009 0.969 1.2 110.5 16.5 258 0.215 2_updatecdl: 0.1002 0.1747 0.009 0.994 1.2 110.5 16.5 258 0.215 2_nqh: 0.1005 0.1747 0.009 0.994 1.2 110.5 16.5 258 0.221 2_sol: 0.1114 0.1665 0.009 0.994 1.2 109.4 15.9 237 n/a 2_weight: 0.1114 0.1665 0.009 0.994 1.2 109.4 15.9 237 n/a 2_xyzrec: 0.0998 0.1760 0.009 1.004 1.2 109.4 15.9 237 n/a 2_adp: 0.0934 0.1798 0.009 1.004 0.0 106.1 16.7 237 n/a 2_regHadp: 0.0931 0.1802 0.009 1.004 0.0 106.1 16.7 237 n/a 2_occ: 0.0930 0.1799 0.009 1.004 0.0 106.1 16.7 237 n/a 3_bss: 0.0931 0.1805 0.009 1.004 0.0 106.1 16.7 237 n/a 3_settarget: 0.0931 0.1805 0.009 1.004 0.0 106.1 16.7 237 n/a 3_updatecdl: 0.0931 0.1805 0.009 1.010 0.0 106.1 16.7 237 n/a 3_nqh: 0.0931 0.1805 0.009 1.010 0.0 106.1 16.7 237 n/a 3_sol: 0.1033 0.1742 0.009 1.010 0.0 106.1 16.5 233 n/a 3_weight: 0.1033 0.1742 0.009 1.010 0.0 106.1 16.5 233 n/a 3_xyzrec: 0.0924 0.1831 0.011 1.083 0.0 106.1 16.5 233 n/a 3_adp: 0.0881 0.1843 0.011 1.083 0.0 106.6 16.5 233 n/a 3_regHadp: 0.0887 0.1850 0.011 1.083 0.0 106.6 16.5 233 n/a 3_occ: 0.0881 0.1837 0.011 1.083 0.0 106.6 16.5 233 n/a 4_bss: 0.0872 0.1830 0.011 1.083 0.0 106.6 16.5 233 n/a 4_settarget: 0.0872 0.1830 0.011 1.083 0.0 106.6 16.5 233 n/a 4_updatecdl: 0.0872 0.1830 0.011 1.084 0.0 106.6 16.5 233 n/a 4_nqh: 0.0875 0.1822 0.011 1.084 0.0 106.6 16.5 233 n/a 4_sol: 0.0993 0.1839 0.011 1.084 0.0 106.6 16.5 229 n/a 4_weight: 0.0993 0.1839 0.011 1.084 0.0 106.6 16.5 229 n/a 4_xyzrec: 0.0911 0.1843 0.011 1.033 0.0 106.6 16.5 229 n/a 4_adp: 0.0886 0.1852 0.011 1.033 0.0 106.5 16.8 229 n/a 4_regHadp: 0.0890 0.1857 0.011 1.033 0.0 106.5 16.8 229 n/a 4_occ: 0.0880 0.1842 0.011 1.033 0.0 106.5 16.8 229 n/a 5_bss: 0.0878 0.1843 0.011 1.033 0.0 106.5 16.8 229 n/a 5_settarget: 0.0878 0.1843 0.011 1.033 0.0 106.5 16.8 229 n/a 5_updatecdl: 0.0878 0.1843 0.011 1.041 0.0 106.5 16.8 229 n/a 5_setrh: 0.0881 0.1842 0.011 1.041 0.0 106.5 16.8 229 n/a 5_nqh: 0.0881 0.1843 0.011 1.041 0.0 106.5 16.8 229 n/a 5_sol: 0.1005 0.1877 0.011 1.041 0.0 106.5 16.8 223 n/a 5_weight: 0.1005 0.1877 0.011 1.041 0.0 106.5 16.8 223 n/a 5_xyzrec: 0.0940 0.1917 0.010 1.101 0.0 106.5 16.8 223 n/a 5_adp: 0.0918 0.1941 0.010 1.101 0.0 107.8 17.1 223 n/a 5_regHadp: 0.0923 0.1945 0.010 1.101 0.0 107.8 17.1 223 n/a 5_occ: 0.0919 0.1933 0.010 1.101 0.0 107.8 17.1 223 n/a end: 0.0916 0.1930 0.010 1.101 0.0 107.8 17.1 223 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8565654_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8565654_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0200 Refinement macro-cycles (run) : 483.1800 Write final files (write_after_run_outputs) : 10.8700 Total : 497.0700 Total CPU time: 8.67 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:01 PST -0800 (1735492741.48 s) Start R-work = 0.1555, R-free = 0.1573 Final R-work = 0.0916, R-free = 0.1930 =============================================================================== Job complete usr+sys time: 528.57 seconds wall clock time: 9 minutes 10.12 seconds (550.12 seconds total)