Starting phenix.refine on Sun Dec 29 09:24:42 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=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" 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" } 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: 1.40, per 1000 atoms: 0.41 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: 0.28 Conformation dependent library (CDL) restraints added in 104.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 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 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2781 r_free= 0.1845 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.400691 | | target function (ml) not normalized (work): 71480.420767 | | target function (ml) not normalized (free): 3276.452974 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3186 0.2213 7.5148 5.0553| | 2: 3.63 - 2.88 1.00 2711 122 0.2628 0.1658 4.3282 4.3014| | 3: 2.88 - 2.52 1.00 2682 148 0.2571 0.1679 4.1845 4.1882| | 4: 2.52 - 2.29 1.00 2661 139 0.2533 0.1601 3.5031 3.5889| | 5: 2.29 - 2.13 1.00 2678 122 0.2630 0.1523 3.3956 3.522| | 6: 2.13 - 2.00 1.00 2692 117 0.2767 0.1936 3.3151 3.4145| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.64 2819 159 0.88 17.59 0.77 0.23 1313.94| | 2: 3.63 - 2.88 2711 122 0.83 23.97 1.31 0.23 1313.94| | 3: 2.88 - 2.52 2682 148 0.73 33.12 1.29 0.23 1313.94| | 4: 2.52 - 2.29 2661 139 0.93 11.69 1.30 0.26 142.26| | 5: 2.29 - 2.13 2678 122 0.92 13.79 1.32 0.26 142.26| | 6: 2.13 - 2.00 2692 117 0.90 16.70 1.34 0.26 142.26| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 142.26 max = 1313.94 mean = 734.63| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 19.48| |phase err.(test): min = 0.00 max = 89.47 mean = 19.93| |-----------------------------------------------------------------------------| ----------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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2781 r_free= 0.1845 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.400691 | | target function (ml) not normalized (work): 71480.420767 | | target function (ml) not normalized (free): 3276.452974 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3449 percent. r_work = 0.2916 r_free = 0.1983 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2863 0.2916 0.1983 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2863 0.2916 0.1983 n_refl.: 17050 remove outliers: r(all,work,free)=0.2153 0.2163 0.1983 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2125 0.2135 0.1966 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1610 0.1607 0.1671 n_refl.: 17045 remove outliers: r(all,work,free)=0.1609 0.1606 0.1671 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4048 394.702 362.786 0.646 1.011 0.397 11.894-9.307 99.02 97 4 0.1860 633.508 612.863 0.928 1.012 0.375 9.237-7.194 100.00 213 7 0.2215 518.146 508.912 0.964 1.012 0.371 7.162-5.571 100.00 427 22 0.2239 388.869 376.514 0.927 1.011 0.321 5.546-4.326 100.00 867 58 0.1408 533.855 528.699 0.960 1.009 0.205 4.315-3.360 100.00 1859 96 0.1308 507.701 504.179 1.016 1.006 0.181 3.356-2.611 100.00 3867 181 0.1649 333.531 328.831 1.014 1.000 0.071 2.608-2.000 99.99 8818 434 0.1629 217.405 213.441 1.031 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4828 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1606 r_free=0.1671 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1606 r_free=0.1671 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.329167 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.870898 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1353 0.1649 0.0297 0.009 1.0 0.6 0.5 0.0 0 11.165 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.49 2.97 3.012 18.444 0.871 0.023 12.80 16.70 3.90 3.634 18.713 0.871 0.020 Individual atomic B min max mean iso aniso Overall: 5.98 113.88 19.98 4.10 1785 0 Protein: 5.98 113.08 17.21 4.10 1519 0 Water: 8.87 113.88 36.09 N/A 258 0 Other: 21.19 37.72 26.17 N/A 8 0 Chain A: 5.98 113.88 19.98 N/A 1785 0 Histogram: Values Number of atoms 5.98 - 16.77 1067 16.77 - 27.56 355 27.56 - 38.35 187 38.35 - 49.14 100 49.14 - 59.93 49 59.93 - 70.72 12 70.72 - 81.51 7 81.51 - 92.30 4 92.30 - 103.09 1 103.09 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1280 r_free=0.1670 r_work=0.1283 r_free=0.1677 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1283 r_free = 0.1677 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1278 r_free = 0.1670 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1278 r_free= 0.1670 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020022 | | target function (ls_wunit_k1) not normalized (work): 325.090186 | | target function (ls_wunit_k1) not normalized (free): 27.129125 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1297 0.1278 0.1670 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1913 0.1912 0.1983 n_refl.: 17044 remove outliers: r(all,work,free)=0.1913 0.1912 0.1983 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1884 0.1883 0.1967 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1296 0.1277 0.1660 n_refl.: 17044 remove outliers: r(all,work,free)=0.1294 0.1276 0.1660 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3540 303.484 281.644 0.620 1.009 0.370 11.894-9.307 99.02 97 4 0.1664 488.107 477.529 0.915 1.010 0.370 9.237-7.194 100.00 213 7 0.1830 399.222 396.710 0.959 1.010 0.351 7.162-5.571 100.00 427 22 0.1822 299.616 294.889 0.937 1.009 0.301 5.546-4.326 100.00 867 58 0.1039 411.325 409.243 0.957 1.007 0.200 4.315-3.360 100.00 1859 96 0.0922 391.174 390.686 1.017 1.005 0.181 3.356-2.611 100.00 3867 181 0.1304 256.979 255.719 1.016 1.000 0.091 2.608-2.000 99.99 8818 434 0.1355 167.506 166.023 1.023 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4011 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1660 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1660 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1660 | n_water=258 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1280 r_free=0.1654 | n_water=253 | time (s): 20.990 (total time: 21.620) Filter (q & B) r_work=0.1280 r_free=0.1652 | n_water=251 | time (s): 1.780 (total time: 23.400) Compute maps r_work=0.1280 r_free=0.1652 | n_water=251 | time (s): 0.740 (total time: 24.140) Filter (map) r_work=0.1322 r_free=0.1644 | n_water=210 | time (s): 1.970 (total time: 26.110) Find peaks r_work=0.1322 r_free=0.1644 | n_water=210 | time (s): 0.490 (total time: 26.600) Add new water r_work=0.1545 r_free=0.1892 | n_water=375 | time (s): 1.980 (total time: 28.580) Refine new water occ: r_work=0.1330 r_free=0.1576 adp: r_work=0.1269 r_free=0.1566 occ: r_work=0.1275 r_free=0.1537 adp: r_work=0.1242 r_free=0.1542 occ: r_work=0.1244 r_free=0.1541 adp: r_work=0.1231 r_free=0.1536 ADP+occupancy (water only), MIN, final r_work=0.1231 r_free=0.1536 r_work=0.1231 r_free=0.1536 | n_water=375 | time (s): 17.760 (total time: 46.340) Filter (q & B) r_work=0.1234 r_free=0.1538 | n_water=366 | time (s): 2.040 (total time: 48.380) Filter (dist only) r_work=0.1234 r_free=0.1538 | n_water=366 | time (s): 27.150 (total time: 75.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.272124 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.984582 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1213 0.1578 0.0365 0.008 0.9 2.2 0.5 0.0 0 11.636 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 15.78 3.65 4.182 21.103 0.985 0.018 12.00 15.90 3.90 4.177 21.340 0.985 0.018 Individual atomic B min max mean iso aniso Overall: 6.80 107.69 21.37 4.23 1893 0 Protein: 6.80 107.69 17.72 4.23 1519 0 Water: 8.71 65.77 36.40 N/A 366 0 Other: 21.58 34.99 27.35 N/A 8 0 Chain A: 6.80 107.69 19.40 N/A 1737 0 Chain S: 18.17 65.76 43.35 N/A 156 0 Histogram: Values Number of atoms 6.80 - 16.89 1040 16.89 - 26.97 370 26.97 - 37.06 219 37.06 - 47.15 153 47.15 - 57.24 75 57.24 - 67.33 26 67.33 - 77.42 3 77.42 - 87.51 4 87.51 - 97.60 1 97.60 - 107.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1590 r_work=0.1201 r_free=0.1589 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1589 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1593 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1200 r_free= 0.1593 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017149 | | target function (ls_wunit_k1) not normalized (work): 278.419873 | | target function (ls_wunit_k1) not normalized (free): 23.555459 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1200 0.1593 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1757 0.1751 0.1912 n_refl.: 17042 remove outliers: r(all,work,free)=0.1757 0.1751 0.1912 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1733 0.1726 0.1897 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1193 0.1582 n_refl.: 17042 remove outliers: r(all,work,free)=0.1211 0.1192 0.1582 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3365 300.321 285.459 0.589 1.002 0.340 11.894-9.307 99.02 97 4 0.1524 488.107 484.727 0.913 1.003 0.337 9.237-7.194 100.00 213 7 0.1659 399.222 400.591 0.973 1.003 0.290 7.162-5.571 100.00 427 22 0.1567 299.616 295.604 0.943 1.003 0.271 5.546-4.326 100.00 867 58 0.0884 411.325 409.143 0.961 1.003 0.205 4.315-3.360 100.00 1859 96 0.0825 391.174 390.178 1.016 1.003 0.191 3.356-2.611 100.00 3867 181 0.1207 256.979 256.103 1.011 1.002 0.063 2.608-2.000 99.99 8818 434 0.1328 167.506 166.557 1.014 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3609 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1582 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1582 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1582 | n_water=366 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1192 r_free=0.1583 | n_water=365 | time (s): 30.250 (total time: 30.980) Filter (q & B) r_work=0.1192 r_free=0.1583 | n_water=365 | time (s): 1.120 (total time: 32.100) Compute maps r_work=0.1192 r_free=0.1583 | n_water=365 | time (s): 0.680 (total time: 32.780) Filter (map) r_work=0.1260 r_free=0.1621 | n_water=266 | time (s): 1.640 (total time: 34.420) Find peaks r_work=0.1260 r_free=0.1621 | n_water=266 | time (s): 0.470 (total time: 34.890) Add new water r_work=0.1432 r_free=0.1766 | n_water=407 | time (s): 1.710 (total time: 36.600) Refine new water occ: r_work=0.1242 r_free=0.1553 adp: r_work=0.1233 r_free=0.1558 occ: r_work=0.1217 r_free=0.1529 adp: r_work=0.1205 r_free=0.1533 occ: r_work=0.1198 r_free=0.1519 adp: r_work=0.1189 r_free=0.1522 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1522 r_work=0.1189 r_free=0.1522 | n_water=407 | time (s): 38.660 (total time: 75.260) Filter (q & B) r_work=0.1191 r_free=0.1525 | n_water=400 | time (s): 1.810 (total time: 77.070) Filter (dist only) r_work=0.1190 r_free=0.1528 | n_water=398 | time (s): 32.030 (total time: 109.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.009168 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.155862 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1168 0.1521 0.0352 0.009 1.0 4.2 0.5 0.0 0 1.005 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.68 15.21 3.52 4.318 21.480 0.156 4.987 11.48 15.32 3.85 4.821 21.433 0.156 4.964 Individual atomic B min max mean iso aniso Overall: 6.24 105.68 20.92 4.67 1925 0 Protein: 6.24 105.68 17.04 4.67 1519 0 Water: 9.12 66.97 35.60 N/A 398 0 Other: 21.05 38.90 27.41 N/A 8 0 Chain A: 6.24 105.68 18.76 N/A 1735 0 Chain S: 17.39 66.97 40.65 N/A 190 0 Histogram: Values Number of atoms 6.24 - 16.18 1061 16.18 - 26.13 348 26.13 - 36.07 224 36.07 - 46.01 176 46.01 - 55.96 75 55.96 - 65.90 27 65.90 - 75.85 7 75.85 - 85.79 2 85.79 - 95.74 3 95.74 - 105.68 2 =========================== Idealize ADP of riding H ========================== r_work=0.1148 r_free=0.1532 r_work=0.1148 r_free=0.1534 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1148 r_free = 0.1534 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1532 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1140 r_free= 0.1532 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.957142 | | target function (ml) not normalized (work): 80474.250090 | | target function (ml) not normalized (free): 4177.040543 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1159 0.1140 0.1532 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1672 0.1665 0.1851 n_refl.: 17041 remove outliers: r(all,work,free)=0.1672 0.1665 0.1851 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1646 0.1639 0.1838 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1138 0.1532 n_refl.: 17041 remove outliers: r(all,work,free)=0.1156 0.1137 0.1532 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3475 296.756 284.042 0.561 1.001 0.328 11.894-9.307 99.02 97 4 0.1726 488.107 483.420 0.909 1.003 0.320 9.237-7.194 100.00 213 7 0.1773 399.222 401.477 0.989 1.004 0.250 7.162-5.571 100.00 427 22 0.1551 299.616 294.291 0.943 1.004 0.241 5.546-4.326 100.00 867 58 0.0925 411.325 407.662 0.964 1.003 0.201 4.315-3.360 100.00 1859 96 0.0884 391.174 388.946 1.012 1.003 0.201 3.356-2.611 100.00 3867 181 0.1270 256.979 254.847 1.012 1.002 0.142 2.608-2.000 99.99 8818 434 0.1092 167.506 166.095 1.013 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3373 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1137 r_free=0.1532 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1137 r_free=0.1532 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1532 | n_water=398 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1141 r_free=0.1529 | n_water=397 | time (s): 35.820 (total time: 36.720) Filter (q & B) r_work=0.1141 r_free=0.1529 | n_water=397 | time (s): 0.990 (total time: 37.710) Compute maps r_work=0.1141 r_free=0.1529 | n_water=397 | time (s): 0.660 (total time: 38.370) Filter (map) r_work=0.1201 r_free=0.1565 | n_water=313 | time (s): 1.820 (total time: 40.190) Find peaks r_work=0.1201 r_free=0.1565 | n_water=313 | time (s): 0.450 (total time: 40.640) Add new water r_work=0.1339 r_free=0.1672 | n_water=459 | time (s): 1.600 (total time: 42.240) Refine new water occ: r_work=0.1169 r_free=0.1508 adp: r_work=0.1164 r_free=0.1515 occ: r_work=0.1147 r_free=0.1483 adp: r_work=0.1141 r_free=0.1492 occ: r_work=0.1132 r_free=0.1471 adp: r_work=0.1126 r_free=0.1478 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1478 r_work=0.1126 r_free=0.1478 | n_water=459 | time (s): 22.680 (total time: 64.920) Filter (q & B) r_work=0.1131 r_free=0.1493 | n_water=445 | time (s): 1.720 (total time: 66.640) Filter (dist only) r_work=0.1130 r_free=0.1495 | n_water=444 | time (s): 37.280 (total time: 103.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.974370 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.158824 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1121 0.1539 0.0418 0.010 1.0 4.2 0.5 0.0 0 0.987 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.21 15.39 4.18 4.494 21.123 0.159 4.952 11.10 15.43 4.33 4.646 21.186 0.159 4.946 Individual atomic B min max mean iso aniso Overall: 5.44 103.26 21.08 4.84 1971 0 Protein: 5.44 103.26 16.67 4.84 1519 0 Water: 8.79 62.22 36.05 N/A 444 0 Other: 20.86 37.87 27.12 N/A 8 0 Chain A: 5.44 103.26 18.34 N/A 1734 0 Chain S: 16.65 62.22 41.09 N/A 237 0 Histogram: Values Number of atoms 5.44 - 15.22 996 15.22 - 25.01 412 25.01 - 34.79 222 34.79 - 44.57 183 44.57 - 54.35 101 54.35 - 64.14 41 64.14 - 73.92 8 73.92 - 83.70 3 83.70 - 93.48 3 93.48 - 103.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1110 r_free=0.1543 r_work=0.1110 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1110 r_free = 0.1544 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1548 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.942091 | | target function (ml) not normalized (work): 80224.957249 | | target function (ml) not normalized (free): 4178.273953 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1123 0.1102 0.1548 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1596 0.1585 0.1856 n_refl.: 17040 remove outliers: r(all,work,free)=0.1596 0.1585 0.1856 n_refl.: 17040 overall B=-0.33 to atoms: r(all,work,free)=0.1575 0.1563 0.1844 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1100 0.1537 n_refl.: 17040 remove outliers: r(all,work,free)=0.1121 0.1100 0.1537 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3617 296.756 277.105 0.534 1.002 0.330 11.894-9.307 99.02 97 4 0.1847 488.107 482.107 0.906 1.003 0.300 9.237-7.194 100.00 213 7 0.1754 399.222 401.070 0.991 1.003 0.230 7.162-5.571 100.00 427 22 0.1568 299.616 294.161 0.941 1.003 0.230 5.546-4.326 100.00 867 58 0.0920 411.325 408.181 0.965 1.003 0.185 4.315-3.360 100.00 1859 96 0.0856 391.174 388.814 1.010 1.003 0.181 3.356-2.611 100.00 3867 181 0.1234 256.979 254.914 1.010 1.001 0.131 2.608-2.000 99.99 8818 434 0.1026 167.506 166.350 1.008 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1302 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1537 After: r_work=0.1102 r_free=0.1536 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1536 | n_water=444 | time (s): 0.880 (total time: 0.880) Filter (dist) r_work=0.1102 r_free=0.1536 | n_water=444 | time (s): 33.960 (total time: 34.840) Filter (q & B) r_work=0.1102 r_free=0.1536 | n_water=444 | time (s): 1.300 (total time: 36.140) Compute maps r_work=0.1102 r_free=0.1536 | n_water=444 | time (s): 0.770 (total time: 36.910) Filter (map) r_work=0.1171 r_free=0.1565 | n_water=340 | time (s): 1.760 (total time: 38.670) Find peaks r_work=0.1171 r_free=0.1565 | n_water=340 | time (s): 0.420 (total time: 39.090) Add new water r_work=0.1274 r_free=0.1663 | n_water=473 | time (s): 1.400 (total time: 40.490) Refine new water occ: r_work=0.1134 r_free=0.1494 adp: r_work=0.1127 r_free=0.1503 occ: r_work=0.1117 r_free=0.1482 adp: r_work=0.1109 r_free=0.1490 occ: r_work=0.1105 r_free=0.1477 adp: r_work=0.1099 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1099 r_free=0.1484 r_work=0.1099 r_free=0.1484 | n_water=473 | time (s): 34.900 (total time: 75.390) Filter (q & B) r_work=0.1103 r_free=0.1501 | n_water=460 | time (s): 1.620 (total time: 77.010) Filter (dist only) r_work=0.1103 r_free=0.1502 | n_water=459 | time (s): 36.070 (total time: 113.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.932886 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.152042 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1116 0.1522 0.0406 0.010 1.1 4.8 0.5 0.0 0 0.966 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.22 4.06 4.555 20.890 0.152 4.935 11.11 15.11 4.01 4.536 21.013 0.152 4.927 Individual atomic B min max mean iso aniso Overall: 5.25 101.66 21.09 4.93 1986 0 Protein: 5.25 101.66 16.51 4.93 1519 0 Water: 8.64 65.38 36.14 N/A 459 0 Other: 19.52 35.80 26.38 N/A 8 0 Chain A: 5.25 101.66 18.14 N/A 1734 0 Chain S: 18.48 65.38 41.40 N/A 252 0 Histogram: Values Number of atoms 5.25 - 14.89 995 14.89 - 24.53 403 24.53 - 34.17 216 34.17 - 43.81 195 43.81 - 53.46 122 53.46 - 63.10 33 63.10 - 72.74 12 72.74 - 82.38 4 82.38 - 92.02 2 92.02 - 101.66 4 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1511 r_work=0.1111 r_free=0.1511 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1511 target_work(ml) = 4.927 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1106 r_free = 0.1513 target_work(ml) = 4.924 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1106 r_free= 0.1513 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.923859 | | target function (ml) not normalized (work): 79929.000052 | | target function (ml) not normalized (free): 4152.439853 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1121 0.1414 5.4532 5.6419| | 2: 3.63 - 2.88 1.00 2711 122 0.1097 0.1526 5.217 5.352| | 3: 2.88 - 2.52 1.00 2681 148 0.1350 0.1657 5.1218 5.193| | 4: 2.52 - 2.29 1.00 2661 139 0.0933 0.1522 4.6078 4.9339| | 5: 2.29 - 2.13 1.00 2678 122 0.0952 0.1452 4.557 4.8494| | 6: 2.13 - 2.00 1.00 2692 117 0.1114 0.1667 4.5564 4.7558| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 8.77 0.99 0.96 6249.88| | 2: 3.63 - 2.88 2711 122 0.93 12.66 1.01 0.96 6249.88| | 3: 2.88 - 2.52 2681 148 0.88 18.78 0.99 0.96 6249.88| | 4: 2.52 - 2.29 2661 139 0.93 11.64 1.01 0.99 1996.35| | 5: 2.29 - 2.13 2678 122 0.92 13.63 1.01 0.99 1996.35| | 6: 2.13 - 2.00 2692 117 0.90 16.24 1.00 0.99 1996.35| |alpha: min = 0.96 max = 0.99 mean = 0.97| |beta: min = 1996.35 max = 6249.88 mean = 4145.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.89 mean = 13.59| |phase err.(test): min = 0.00 max = 89.61 mean = 13.16| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1106 0.1513 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1595 0.1586 0.1823 n_refl.: 17040 remove outliers: r(all,work,free)=0.1595 0.1586 0.1823 n_refl.: 17040 overall B=-0.29 to atoms: r(all,work,free)=0.1577 0.1567 0.1811 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1106 0.1514 n_refl.: 17040 remove outliers: r(all,work,free)=0.1126 0.1106 0.1514 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3597 296.756 277.928 0.535 1.003 0.330 11.894-9.307 99.02 97 4 0.1813 488.107 482.545 0.909 1.004 0.294 9.237-7.194 100.00 213 7 0.1770 399.222 400.772 0.984 1.005 0.236 7.162-5.571 100.00 427 22 0.1565 299.616 294.573 0.938 1.005 0.214 5.546-4.326 100.00 867 58 0.0935 411.325 408.273 0.964 1.004 0.195 4.315-3.360 100.00 1859 96 0.0874 391.174 388.799 1.008 1.003 0.191 3.356-2.611 100.00 3867 181 0.1239 256.979 254.882 1.007 1.001 0.141 2.608-2.000 99.99 8818 434 0.1029 167.506 166.215 1.003 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0110 ================= 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 : 0.2781 0.1845 0.083 5.258 8.8 119.3 19.9 258 0.000 1_bss: 0.1606 0.1671 0.083 5.258 8.4 118.9 19.5 258 0.000 1_settarget: 0.1606 0.1671 0.083 5.258 8.4 118.9 19.5 258 0.000 1_nqh: 0.1606 0.1671 0.083 5.258 8.4 118.9 19.5 258 0.000 1_weight: 0.1606 0.1671 0.083 5.258 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1353 0.1649 0.009 0.960 8.4 118.9 19.5 258 0.153 1_adp: 0.1280 0.1670 0.009 0.960 6.0 113.9 20.0 258 0.153 1_regHadp: 0.1283 0.1677 0.009 0.960 6.0 113.9 20.0 258 0.153 1_occ: 0.1278 0.1670 0.009 0.960 6.0 113.9 20.0 258 0.153 2_bss: 0.1276 0.1660 0.009 0.960 5.6 113.5 19.6 258 0.153 2_settarget: 0.1276 0.1660 0.009 0.960 5.6 113.5 19.6 258 0.153 2_updatecdl: 0.1276 0.1660 0.009 0.977 5.6 113.5 19.6 258 0.153 2_nqh: 0.1276 0.1660 0.009 0.977 5.6 113.5 19.6 258 0.153 2_sol: 0.1234 0.1538 0.009 0.977 5.6 112.7 20.9 366 n/a 2_weight: 0.1234 0.1538 0.009 0.977 5.6 112.7 20.9 366 n/a 2_xyzrec: 0.1213 0.1578 0.008 0.904 5.6 112.7 20.9 366 n/a 2_adp: 0.1200 0.1590 0.008 0.904 6.8 107.7 21.4 366 n/a 2_regHadp: 0.1201 0.1589 0.008 0.904 6.8 107.7 21.4 366 n/a 2_occ: 0.1200 0.1593 0.008 0.904 6.8 107.7 21.4 366 n/a 3_bss: 0.1192 0.1582 0.008 0.904 6.4 107.3 21.0 366 n/a 3_settarget: 0.1192 0.1582 0.008 0.904 6.4 107.3 21.0 366 n/a 3_updatecdl: 0.1192 0.1582 0.008 0.910 6.4 107.3 21.0 366 n/a 3_nqh: 0.1192 0.1582 0.008 0.910 6.4 107.3 21.0 366 n/a 3_sol: 0.1190 0.1528 0.008 0.910 6.4 107.3 21.0 398 n/a 3_weight: 0.1190 0.1528 0.008 0.910 6.4 107.3 21.0 398 n/a 3_xyzrec: 0.1168 0.1521 0.009 0.985 6.4 107.3 21.0 398 n/a 3_adp: 0.1148 0.1532 0.009 0.985 6.2 105.7 20.9 398 n/a 3_regHadp: 0.1148 0.1534 0.009 0.985 6.2 105.7 20.9 398 n/a 3_occ: 0.1140 0.1532 0.009 0.985 6.2 105.7 20.9 398 n/a 4_bss: 0.1137 0.1532 0.009 0.985 5.9 105.3 20.5 398 n/a 4_settarget: 0.1137 0.1532 0.009 0.985 5.9 105.3 20.5 398 n/a 4_updatecdl: 0.1137 0.1532 0.009 0.982 5.9 105.3 20.5 398 n/a 4_nqh: 0.1137 0.1532 0.009 0.982 5.9 105.3 20.5 398 n/a 4_sol: 0.1130 0.1495 0.009 0.982 5.9 105.3 21.0 444 n/a 4_weight: 0.1130 0.1495 0.009 0.982 5.9 105.3 21.0 444 n/a 4_xyzrec: 0.1121 0.1539 0.010 0.982 5.9 105.3 21.0 444 n/a 4_adp: 0.1110 0.1543 0.010 0.982 5.4 103.3 21.1 444 n/a 4_regHadp: 0.1110 0.1544 0.010 0.982 5.4 103.3 21.1 444 n/a 4_occ: 0.1102 0.1548 0.010 0.982 5.4 103.3 21.1 444 n/a 5_bss: 0.1100 0.1537 0.010 0.982 5.1 102.9 20.8 444 n/a 5_settarget: 0.1100 0.1537 0.010 0.982 5.1 102.9 20.8 444 n/a 5_updatecdl: 0.1100 0.1537 0.010 0.985 5.1 102.9 20.8 444 n/a 5_setrh: 0.1102 0.1536 0.010 0.985 5.1 102.9 20.8 444 n/a 5_nqh: 0.1102 0.1536 0.010 0.985 5.1 102.9 20.8 444 n/a 5_sol: 0.1103 0.1502 0.010 0.985 5.1 102.9 20.9 459 n/a 5_weight: 0.1103 0.1502 0.010 0.985 5.1 102.9 20.9 459 n/a 5_xyzrec: 0.1116 0.1522 0.010 1.107 5.1 102.9 20.9 459 n/a 5_adp: 0.1111 0.1511 0.010 1.107 5.2 101.7 21.1 459 n/a 5_regHadp: 0.1111 0.1511 0.010 1.107 5.2 101.7 21.1 459 n/a 5_occ: 0.1106 0.1513 0.010 1.107 5.2 101.7 21.1 459 n/a end: 0.1106 0.1514 0.010 1.107 5.0 101.4 20.8 459 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8565654_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8565654_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8600 Refinement macro-cycles (run) : 921.2700 Write final files (write_after_run_outputs) : 19.4200 Total : 944.5500 Total CPU time: 16.10 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:07 PST -0800 (1735494067.47 s) Start R-work = 0.1606, R-free = 0.1671 Final R-work = 0.1106, R-free = 0.1514 =============================================================================== Job complete usr+sys time: 989.81 seconds wall clock time: 16 minutes 52.53 seconds (1012.53 seconds total)