Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7445011.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=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 { 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_7445011.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7445011.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.29, per 1000 atoms: 0.38 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 136.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 565 0.92 - 1.17: 1086 1.17 - 1.43: 689 1.43 - 1.69: 779 1.69 - 1.95: 34 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.448 1.633 -0.185 9.00e-03 1.23e+04 4.22e+02 bond pdb=" C THR A 125 " pdb=" O THR A 125 " ideal model delta sigma weight residual 1.234 1.453 -0.218 1.20e-02 6.94e+03 3.31e+02 bond pdb=" N VAL A 8 " pdb=" CA VAL A 8 " ideal model delta sigma weight residual 1.459 1.673 -0.214 1.24e-02 6.50e+03 2.97e+02 bond pdb=" CA GLU A 147 " pdb=" C GLU A 147 " ideal model delta sigma weight residual 1.522 1.315 0.206 1.21e-02 6.83e+03 2.91e+02 bond pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 1.459 1.661 -0.202 1.20e-02 6.94e+03 2.82e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.72: 3178 4.72 - 9.43: 1878 9.43 - 14.15: 614 14.15 - 18.86: 95 18.86 - 23.58: 12 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 107.20 121.65 -14.45 1.00e+00 1.00e+00 2.09e+02 angle pdb=" ND1 HIS A 138 " pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 106.10 92.21 13.89 1.00e+00 1.00e+00 1.93e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.45 121.18 -10.73 7.80e-01 1.64e+00 1.89e+02 angle pdb=" O BLYS A 175 " pdb=" C BLYS A 175 " pdb=" N GLU A 176 " ideal model delta sigma weight residual 122.09 136.56 -14.47 1.08e+00 8.57e-01 1.79e+02 angle pdb=" CA AGLY A 65 " pdb=" C AGLY A 65 " pdb=" O AGLY A 65 " ideal model delta sigma weight residual 121.62 108.23 13.39 1.05e+00 9.07e-01 1.63e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 1290 16.90 - 33.81: 133 33.81 - 50.71: 36 50.71 - 67.62: 21 67.62 - 84.52: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 144.63 -21.83 0 2.50e+00 1.60e-01 7.62e+01 dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -143.56 20.96 0 2.50e+00 1.60e-01 7.03e+01 dihedral pdb=" C BGLU A 64 " pdb=" N BGLU A 64 " pdb=" CA BGLU A 64 " pdb=" CB BGLU A 64 " ideal model delta harmonic sigma weight residual -122.60 -101.66 -20.94 0 2.50e+00 1.60e-01 7.01e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 130 0.246 - 0.491: 67 0.491 - 0.737: 31 0.737 - 0.982: 11 0.982 - 1.228: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 42 " pdb=" N ASP A 42 " pdb=" C ASP A 42 " pdb=" CB ASP A 42 " both_signs ideal model delta sigma weight residual False 2.51 3.74 -1.23 2.00e-01 2.50e+01 3.77e+01 chirality pdb=" CA BGLU A 64 " pdb=" N BGLU A 64 " pdb=" C BGLU A 64 " pdb=" CB BGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" CA VAL A 8 " pdb=" N VAL A 8 " pdb=" C VAL A 8 " pdb=" CB VAL A 8 " both_signs ideal model delta sigma weight residual False 2.44 3.45 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.052 2.00e-02 2.50e+03 6.31e-02 1.19e+02 pdb=" CG PHE A 164 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.102 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.067 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.097 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.002 2.00e-02 2.50e+03 5.52e-02 9.14e+01 pdb=" CG TYR A 139 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.115 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.085 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.065 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.050 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.011 2.00e-02 2.50e+03 5.32e-02 8.49e+01 pdb=" CG PHE A 119 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.134 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.016 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.012 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 801 2.28 - 2.86: 7823 2.86 - 3.44: 10644 3.44 - 4.02: 15320 4.02 - 4.60: 22098 Nonbonded interactions: 56686 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.701 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.791 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.823 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.826 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O LEU A 185 " pdb=" H GLY A 159 " model vdw sym.op. 1.826 2.450 x-y,-y,-z-4/3 ... (remaining 56681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 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_7445011_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2790 r_free= 0.1873 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406814 | | target function (ml) not normalized (work): 71579.876602 | | target function (ml) not normalized (free): 3289.162844 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3187 0.2158 7.4857 5.0294| | 2: 3.63 - 2.88 1.00 2711 122 0.2646 0.1840 4.3356 4.336| | 3: 2.88 - 2.52 1.00 2682 148 0.2541 0.1707 4.184 4.1965| | 4: 2.52 - 2.29 1.00 2661 139 0.2559 0.1589 3.5106 3.6328| | 5: 2.29 - 2.13 1.00 2678 122 0.2695 0.1636 3.4259 3.508| | 6: 2.13 - 2.00 1.00 2692 117 0.2744 0.1902 3.338 3.4743| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.72 0.77 0.23 1317.83| | 2: 3.63 - 2.88 2711 122 0.82 24.03 1.32 0.23 1317.83| | 3: 2.88 - 2.52 2682 148 0.73 33.13 1.28 0.23 1317.83| | 4: 2.52 - 2.29 2661 139 0.92 12.51 1.30 0.26 152.27| | 5: 2.29 - 2.13 2678 122 0.91 14.61 1.32 0.26 152.27| | 6: 2.13 - 2.00 2692 117 0.89 17.36 1.33 0.26 152.27| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 152.27 max = 1317.83 mean = 741.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 19.89| |phase err.(test): min = 0.00 max = 89.67 mean = 19.97| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.280 1557 Z= 5.469 Angle : 5.315 16.752 2118 Z= 3.778 Chirality : 0.375 1.228 243 Planarity : 0.032 0.101 284 Dihedral : 13.984 84.523 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 23.24 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.48), residues: 224 helix: -1.85 (0.42), residues: 103 sheet: 0.01 (0.93), residues: 28 loop : -0.27 (0.54), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.078 0.024 ARG A 48 TYR 0.104 0.035 TYR A 139 PHE 0.107 0.042 PHE A 164 HIS 0.084 0.038 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2790 r_free= 0.1873 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.406814 | | target function (ml) not normalized (work): 71579.876602 | | target function (ml) not normalized (free): 3289.162844 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3122 percent. r_work = 0.2921 r_free = 0.2039 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2869 0.2921 0.2039 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2869 0.2921 0.2039 n_refl.: 17050 remove outliers: r(all,work,free)=0.2158 0.2167 0.2039 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2131 0.2139 0.2023 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1610 0.1605 0.1713 n_refl.: 17045 remove outliers: r(all,work,free)=0.1608 0.1603 0.1713 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3916 399.094 360.526 0.644 1.017 0.403 11.894-9.307 99.02 97 4 0.1868 633.856 614.112 0.918 1.019 0.390 9.237-7.194 100.00 213 7 0.2111 518.430 510.728 0.955 1.018 0.361 7.162-5.571 100.00 427 22 0.2280 389.083 374.816 0.921 1.017 0.321 5.546-4.326 100.00 867 58 0.1392 534.148 527.241 0.957 1.014 0.241 4.315-3.360 100.00 1859 96 0.1294 507.980 504.621 1.014 1.008 0.201 3.356-2.611 100.00 3867 181 0.1633 333.714 329.011 1.010 0.999 0.091 2.608-2.000 99.99 8818 434 0.1646 217.524 213.400 1.037 0.982 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4312 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1603 r_free=0.1713 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN Total number of N/Q/H flips: 3 r_work=0.1605 r_free=0.1721 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.867419 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.037543 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 0.1349 0.1634 0.0284 0.009 1.0 1.0 0.5 0.0 0 11.934 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.49 16.34 2.84 3.013 18.457 1.038 0.023 12.74 16.57 3.83 3.676 18.707 1.038 0.020 Individual atomic B min max mean iso aniso Overall: 5.92 113.90 19.96 4.16 1785 0 Protein: 5.92 113.00 17.19 4.16 1519 0 Water: 7.99 113.90 36.04 N/A 258 0 Other: 21.69 37.35 26.26 N/A 8 0 Chain A: 5.92 113.90 19.96 N/A 1785 0 Histogram: Values Number of atoms 5.92 - 16.71 1071 16.71 - 27.51 350 27.51 - 38.31 188 38.31 - 49.11 96 49.11 - 59.91 52 59.91 - 70.70 13 70.70 - 81.50 7 81.50 - 92.30 4 92.30 - 103.10 1 103.10 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1274 r_free=0.1657 r_work=0.1277 r_free=0.1664 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1277 r_free = 0.1664 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 = 0.1272 r_free = 0.1659 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1272 r_free= 0.1659 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019901 | | target function (ls_wunit_k1) not normalized (work): 323.119345 | | target function (ls_wunit_k1) not normalized (free): 27.342508 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1272 0.1659 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1908 0.1906 0.1992 n_refl.: 17043 remove outliers: r(all,work,free)=0.1908 0.1906 0.1992 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1880 0.1878 0.1975 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1290 0.1272 0.1651 n_refl.: 17043 remove outliers: r(all,work,free)=0.1290 0.1272 0.1651 n_refl.: 17043 ======================== 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 0.3578 306.963 286.086 0.654 1.014 0.393 11.894-9.307 99.02 97 4 0.1685 487.530 477.890 0.916 1.014 0.380 9.237-7.194 100.00 213 7 0.1835 398.750 395.368 0.955 1.014 0.351 7.162-5.571 100.00 427 22 0.1822 299.263 294.158 0.925 1.012 0.301 5.546-4.326 100.00 867 58 0.1046 410.840 408.252 0.953 1.010 0.210 4.315-3.360 100.00 1859 96 0.0929 390.712 390.320 1.014 1.006 0.191 3.356-2.611 100.00 3867 181 0.1292 256.676 255.369 1.013 0.999 0.091 2.608-2.000 99.99 8818 434 0.1347 167.309 165.825 1.026 0.987 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3496 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1651 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1276 r_free=0.1653 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1653 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1284 r_free=0.1643 | n_water=253 | time (s): 19.470 (total time: 20.130) Filter (q & B) r_work=0.1284 r_free=0.1643 | n_water=251 | time (s): 1.530 (total time: 21.660) Compute maps r_work=0.1284 r_free=0.1643 | n_water=251 | time (s): 0.780 (total time: 22.440) Filter (map) r_work=0.1326 r_free=0.1634 | n_water=206 | time (s): 2.160 (total time: 24.600) Find peaks r_work=0.1326 r_free=0.1634 | n_water=206 | time (s): 0.560 (total time: 25.160) Add new water r_work=0.1551 r_free=0.1868 | n_water=366 | time (s): 1.940 (total time: 27.100) Refine new water occ: r_work=0.1341 r_free=0.1577 adp: r_work=0.1283 r_free=0.1569 occ: r_work=0.1288 r_free=0.1546 adp: r_work=0.1255 r_free=0.1547 occ: r_work=0.1257 r_free=0.1544 adp: r_work=0.1246 r_free=0.1545 ADP+occupancy (water only), MIN, final r_work=0.1246 r_free=0.1545 r_work=0.1246 r_free=0.1545 | n_water=366 | time (s): 15.380 (total time: 42.480) Filter (q & B) r_work=0.1247 r_free=0.1554 | n_water=358 | time (s): 2.220 (total time: 44.700) Filter (dist only) r_work=0.1247 r_free=0.1554 | n_water=357 | time (s): 27.780 (total time: 72.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.542579 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.994856 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 0.1219 0.1604 0.0385 0.008 0.9 2.2 0.5 0.0 0 12.271 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 16.04 3.85 4.213 21.009 0.995 0.018 12.02 16.23 4.22 4.261 21.233 0.995 0.018 Individual atomic B min max mean iso aniso Overall: 6.78 107.62 21.19 4.26 1884 0 Protein: 6.78 107.62 17.65 4.25 1519 0 Water: 8.61 65.80 35.91 N/A 357 0 Other: 24.87 46.31 35.83 N/A 8 0 Chain A: 6.78 107.62 19.26 N/A 1733 0 Chain S: 18.56 64.47 43.28 N/A 151 0 Histogram: Values Number of atoms 6.78 - 16.86 1034 16.86 - 26.95 374 26.95 - 37.03 219 37.03 - 47.12 151 47.12 - 57.20 76 57.20 - 67.28 19 67.28 - 77.37 4 77.37 - 87.45 3 87.45 - 97.54 2 97.54 - 107.62 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1623 r_work=0.1203 r_free=0.1625 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1625 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1624 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1199 r_free= 0.1624 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017345 | | target function (ls_wunit_k1) not normalized (work): 281.608677 | | target function (ls_wunit_k1) not normalized (free): 25.527388 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1199 0.1624 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1807 0.1801 0.1963 n_refl.: 17043 remove outliers: r(all,work,free)=0.1807 0.1801 0.1963 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1772 0.1766 0.1940 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1194 0.1616 n_refl.: 17043 remove outliers: r(all,work,free)=0.1213 0.1193 0.1616 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 0.3319 306.401 279.734 0.613 1.006 0.360 11.894-9.307 99.02 97 4 0.1594 487.530 482.536 0.917 1.007 0.347 9.237-7.194 100.00 213 7 0.1719 398.750 397.386 0.970 1.006 0.290 7.162-5.571 100.00 427 22 0.1595 299.263 295.439 0.934 1.006 0.271 5.546-4.326 100.00 867 58 0.0888 410.840 407.789 0.959 1.005 0.206 4.315-3.360 100.00 1859 96 0.0818 390.712 390.132 1.016 1.003 0.202 3.356-2.611 100.00 3867 181 0.1199 256.676 255.756 1.009 1.001 0.091 2.608-2.000 99.99 8818 434 0.1330 167.309 166.267 1.010 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1527 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1616 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1616 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1616 | n_water=357 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1196 r_free=0.1615 | n_water=355 | time (s): 27.650 (total time: 28.290) Filter (q & B) r_work=0.1196 r_free=0.1615 | n_water=355 | time (s): 0.840 (total time: 29.130) Compute maps r_work=0.1196 r_free=0.1615 | n_water=355 | time (s): 0.630 (total time: 29.760) Filter (map) r_work=0.1269 r_free=0.1625 | n_water=259 | time (s): 1.540 (total time: 31.300) Find peaks r_work=0.1269 r_free=0.1625 | n_water=259 | time (s): 0.410 (total time: 31.710) Add new water r_work=0.1462 r_free=0.1781 | n_water=410 | time (s): 1.590 (total time: 33.300) Refine new water occ: r_work=0.1244 r_free=0.1552 adp: r_work=0.1235 r_free=0.1554 occ: r_work=0.1217 r_free=0.1530 adp: r_work=0.1204 r_free=0.1532 occ: r_work=0.1197 r_free=0.1523 adp: r_work=0.1187 r_free=0.1522 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1522 r_work=0.1187 r_free=0.1522 | n_water=410 | time (s): 34.340 (total time: 67.640) Filter (q & B) r_work=0.1191 r_free=0.1524 | n_water=401 | time (s): 2.180 (total time: 69.820) Filter (dist only) r_work=0.1191 r_free=0.1525 | n_water=400 | time (s): 31.600 (total time: 101.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.842938 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.169599 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 0.1172 0.1536 0.0364 0.009 1.0 4.2 0.5 0.0 0 0.921 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.72 15.36 3.64 4.331 21.336 0.170 4.994 11.52 15.45 3.93 4.934 21.287 0.170 4.972 Individual atomic B min max mean iso aniso Overall: 6.39 103.81 20.75 4.82 1927 0 Protein: 6.39 103.81 16.84 4.80 1519 0 Water: 8.44 63.77 35.27 N/A 400 0 Other: 27.98 48.37 36.97 N/A 8 0 Chain A: 6.39 103.81 18.51 N/A 1730 0 Chain S: 15.77 63.77 40.39 N/A 197 0 Histogram: Values Number of atoms 6.39 - 16.13 1071 16.13 - 25.88 336 25.88 - 35.62 219 35.62 - 45.36 178 45.36 - 55.10 82 55.10 - 64.84 28 64.84 - 74.58 4 74.58 - 84.33 4 84.33 - 94.07 3 94.07 - 103.81 2 =========================== Idealize ADP of riding H ========================== r_work=0.1152 r_free=0.1545 r_work=0.1152 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1152 r_free = 0.1546 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1550 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.27 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= 0.1143 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.967216 | | target function (ml) not normalized (work): 80637.781805 | | target function (ml) not normalized (free): 4186.919490 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1162 0.1143 0.1550 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1648 0.1635 0.1937 n_refl.: 17041 remove outliers: r(all,work,free)=0.1648 0.1635 0.1937 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1624 0.1611 0.1923 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1162 0.1142 0.1554 n_refl.: 17041 remove outliers: r(all,work,free)=0.1161 0.1141 0.1554 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 0.3612 302.911 278.427 0.571 1.007 0.340 11.894-9.307 99.02 97 4 0.1737 487.530 480.547 0.912 1.007 0.340 9.237-7.194 100.00 213 7 0.1792 398.750 400.272 0.982 1.007 0.256 7.162-5.571 100.00 427 22 0.1618 299.263 294.476 0.941 1.007 0.252 5.546-4.326 100.00 867 58 0.0929 410.840 407.368 0.966 1.006 0.202 4.315-3.360 100.00 1859 96 0.0883 390.712 388.653 1.012 1.004 0.182 3.356-2.611 100.00 3867 181 0.1268 256.676 254.439 1.010 1.000 0.121 2.608-2.000 99.99 8818 434 0.1091 167.309 165.842 1.013 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1632 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1141 r_free=0.1554 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1142 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1550 | n_water=400 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1142 r_free=0.1550 | n_water=400 | time (s): 31.090 (total time: 31.710) Filter (q & B) r_work=0.1142 r_free=0.1550 | n_water=400 | time (s): 1.250 (total time: 32.960) Compute maps r_work=0.1142 r_free=0.1550 | n_water=400 | time (s): 0.700 (total time: 33.660) Filter (map) r_work=0.1204 r_free=0.1543 | n_water=319 | time (s): 1.950 (total time: 35.610) Find peaks r_work=0.1204 r_free=0.1543 | n_water=319 | time (s): 0.640 (total time: 36.250) Add new water r_work=0.1347 r_free=0.1674 | n_water=468 | time (s): 1.910 (total time: 38.160) Refine new water occ: r_work=0.1176 r_free=0.1517 adp: r_work=0.1169 r_free=0.1518 occ: r_work=0.1149 r_free=0.1499 adp: r_work=0.1141 r_free=0.1498 occ: r_work=0.1131 r_free=0.1491 adp: r_work=0.1124 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1124 r_free=0.1491 r_work=0.1124 r_free=0.1491 | n_water=468 | time (s): 32.710 (total time: 70.870) Filter (q & B) r_work=0.1127 r_free=0.1498 | n_water=457 | time (s): 2.360 (total time: 73.230) Filter (dist only) r_work=0.1127 r_free=0.1498 | n_water=457 | time (s): 35.910 (total time: 109.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.931011 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.177559 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 0.1113 0.1547 0.0434 0.010 1.0 4.5 0.5 0.0 0 0.966 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.13 15.47 4.34 4.559 21.044 0.178 4.954 11.02 15.44 4.41 4.716 21.099 0.178 4.946 Individual atomic B min max mean iso aniso Overall: 5.80 100.82 21.07 4.95 1984 0 Protein: 5.80 100.82 16.44 4.94 1519 0 Water: 8.50 64.32 36.18 N/A 457 0 Other: 26.82 47.00 35.47 N/A 8 0 Chain A: 5.80 100.82 18.05 N/A 1728 0 Chain S: 15.60 64.32 41.46 N/A 256 0 Histogram: Values Number of atoms 5.80 - 15.31 1033 15.31 - 24.81 368 24.81 - 34.31 223 34.31 - 43.81 174 43.81 - 53.31 131 53.31 - 62.81 36 62.81 - 72.31 9 72.31 - 81.82 4 81.82 - 91.32 2 91.32 - 100.82 4 =========================== Idealize ADP of riding H ========================== r_work=0.1102 r_free=0.1544 r_work=0.1102 r_free=0.1545 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1102 r_free = 0.1545 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1092 r_free = 0.1558 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.22 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= 0.1092 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.942563 | | target function (ml) not normalized (work): 80232.632394 | | target function (ml) not normalized (free): 4180.853584 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1114 0.1092 0.1558 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1553 0.1537 0.1875 n_refl.: 17040 remove outliers: r(all,work,free)=0.1553 0.1537 0.1875 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1538 0.1522 0.1866 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1112 0.1089 0.1553 n_refl.: 17040 remove outliers: r(all,work,free)=0.1112 0.1089 0.1553 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 0.3702 302.911 276.335 0.551 1.004 0.340 11.894-9.307 99.02 97 4 0.1770 487.530 480.198 0.911 1.004 0.340 9.237-7.194 100.00 213 7 0.1738 398.750 400.369 0.984 1.004 0.230 7.162-5.571 100.00 427 22 0.1514 299.263 293.024 0.937 1.004 0.220 5.546-4.326 100.00 867 58 0.0885 410.840 407.991 0.967 1.003 0.190 4.315-3.360 100.00 1859 96 0.0832 390.712 388.803 1.007 1.002 0.181 3.356-2.611 100.00 3867 181 0.1217 256.676 254.478 1.002 1.001 0.121 2.608-2.000 99.99 8818 434 0.1037 167.309 166.085 0.998 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9091 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1089 r_free=0.1553 After: r_work=0.1091 r_free=0.1552 ================================== NQH flips ================================== r_work=0.1091 r_free=0.1552 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=0.1091 r_free=0.1552 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1091 r_free=0.1552 | n_water=457 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1096 r_free=0.1550 | n_water=455 | time (s): 40.650 (total time: 41.390) Filter (q & B) r_work=0.1096 r_free=0.1550 | n_water=455 | time (s): 1.060 (total time: 42.450) Compute maps r_work=0.1096 r_free=0.1550 | n_water=455 | time (s): 0.560 (total time: 43.010) Filter (map) r_work=0.1177 r_free=0.1559 | n_water=344 | time (s): 1.840 (total time: 44.850) Find peaks r_work=0.1177 r_free=0.1559 | n_water=344 | time (s): 0.540 (total time: 45.390) Add new water r_work=0.1287 r_free=0.1651 | n_water=477 | time (s): 2.210 (total time: 47.600) Refine new water occ: r_work=0.1130 r_free=0.1515 adp: r_work=0.1122 r_free=0.1513 occ: r_work=0.1111 r_free=0.1501 adp: r_work=0.1102 r_free=0.1497 occ: r_work=0.1099 r_free=0.1490 adp: r_work=0.1092 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1092 r_free=0.1491 r_work=0.1092 r_free=0.1491 | n_water=477 | time (s): 35.440 (total time: 83.040) Filter (q & B) r_work=0.1098 r_free=0.1502 | n_water=462 | time (s): 1.960 (total time: 85.000) Filter (dist only) r_work=0.1098 r_free=0.1503 | n_water=461 | time (s): 37.660 (total time: 122.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.991654 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.171586 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 0.1105 0.1523 0.0418 0.010 1.1 4.2 0.5 0.0 0 0.996 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.05 15.23 4.18 4.599 20.781 0.172 4.937 10.96 15.10 4.14 4.640 20.836 0.172 4.930 Individual atomic B min max mean iso aniso Overall: 5.65 99.34 20.90 5.04 1988 0 Protein: 5.65 99.34 16.21 5.02 1519 0 Water: 8.27 65.26 36.10 N/A 461 0 Other: 26.65 46.50 34.84 N/A 8 0 Chain A: 5.65 99.34 17.77 N/A 1727 0 Chain S: 19.62 65.26 41.59 N/A 261 0 Histogram: Values Number of atoms 5.65 - 15.02 1031 15.02 - 24.39 360 24.39 - 33.76 214 33.76 - 43.13 201 43.13 - 52.50 124 52.50 - 61.86 35 61.86 - 71.23 14 71.23 - 80.60 0 80.60 - 89.97 4 89.97 - 99.34 5 =========================== Idealize ADP of riding H ========================== r_work=0.1096 r_free=0.1510 r_work=0.1096 r_free=0.1510 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1096 r_free = 0.1510 target_work(ml) = 4.930 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1089 r_free = 0.1520 target_work(ml) = 4.927 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1089 r_free= 0.1520 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.926947 | | target function (ml) not normalized (work): 79979.131703 | | target function (ml) not normalized (free): 4163.976587 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1101 0.1443 5.4408 5.6586| | 2: 3.63 - 2.88 1.00 2711 122 0.1058 0.1471 5.2075 5.366| | 3: 2.88 - 2.52 1.00 2681 148 0.1338 0.1673 5.1277 5.1971| | 4: 2.52 - 2.29 1.00 2661 139 0.0911 0.1493 4.6123 4.9184| | 5: 2.29 - 2.13 1.00 2678 122 0.0958 0.1469 4.5754 4.8909| | 6: 2.13 - 2.00 1.00 2692 117 0.1125 0.1751 4.5689 4.787| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.07 1.00 0.96 6438.00| | 2: 3.63 - 2.88 2711 122 0.92 12.93 1.01 0.96 6438.00| | 3: 2.88 - 2.52 2681 148 0.87 19.02 0.99 0.96 6438.00| | 4: 2.52 - 2.29 2661 139 0.93 12.09 1.01 0.97 2096.56| | 5: 2.29 - 2.13 2678 122 0.92 14.03 1.00 0.97 2096.56| | 6: 2.13 - 2.00 2692 117 0.89 16.78 0.99 0.97 2096.56| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2096.56 max = 6438.00 mean = 4290.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.92 mean = 13.95| |phase err.(test): min = 0.00 max = 86.87 mean = 13.66| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1110 0.1089 0.1520 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1537 0.1523 0.1838 n_refl.: 17040 remove outliers: r(all,work,free)=0.1537 0.1523 0.1838 n_refl.: 17040 overall B=-0.21 to atoms: r(all,work,free)=0.1525 0.1510 0.1831 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1110 0.1089 0.1519 n_refl.: 17040 remove outliers: r(all,work,free)=0.1110 0.1089 0.1519 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 0.3585 302.911 280.263 0.547 1.005 0.327 11.894-9.307 99.02 97 4 0.1692 487.530 482.734 0.912 1.005 0.325 9.237-7.194 100.00 213 7 0.1740 398.750 400.042 0.982 1.005 0.215 7.162-5.571 100.00 427 22 0.1546 299.263 292.545 0.933 1.005 0.200 5.546-4.326 100.00 867 58 0.0899 410.840 407.885 0.964 1.004 0.185 4.315-3.360 100.00 1859 96 0.0854 390.712 388.758 1.003 1.003 0.181 3.356-2.611 100.00 3867 181 0.1213 256.676 254.507 0.999 1.000 0.101 2.608-2.000 99.99 8818 434 0.1026 167.309 166.019 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7430 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2790 0.1873 0.083 5.315 8.8 119.3 19.9 258 0.000 1_bss: 0.1603 0.1713 0.083 5.315 8.4 118.9 19.5 258 0.000 1_settarget: 0.1603 0.1713 0.083 5.315 8.4 118.9 19.5 258 0.000 1_nqh: 0.1605 0.1721 0.083 5.315 8.4 118.9 19.5 258 0.010 1_weight: 0.1605 0.1721 0.083 5.315 8.4 118.9 19.5 258 0.010 1_xyzrec: 0.1349 0.1634 0.009 0.979 8.4 118.9 19.5 258 0.150 1_adp: 0.1274 0.1657 0.009 0.979 5.9 113.9 20.0 258 0.150 1_regHadp: 0.1277 0.1664 0.009 0.979 5.9 113.9 20.0 258 0.150 1_occ: 0.1272 0.1659 0.009 0.979 5.9 113.9 20.0 258 0.150 2_bss: 0.1272 0.1651 0.009 0.979 5.5 113.5 19.6 258 0.150 2_settarget: 0.1272 0.1651 0.009 0.979 5.5 113.5 19.6 258 0.150 2_updatecdl: 0.1272 0.1651 0.009 1.000 5.5 113.5 19.6 258 0.150 2_nqh: 0.1276 0.1653 0.009 1.000 5.5 113.5 19.6 258 0.144 2_sol: 0.1247 0.1554 0.009 1.000 5.5 112.6 20.8 357 n/a 2_weight: 0.1247 0.1554 0.009 1.000 5.5 112.6 20.8 357 n/a 2_xyzrec: 0.1219 0.1604 0.008 0.937 5.5 112.6 20.8 357 n/a 2_adp: 0.1202 0.1623 0.008 0.937 6.8 107.6 21.2 357 n/a 2_regHadp: 0.1203 0.1625 0.008 0.937 6.8 107.6 21.2 357 n/a 2_occ: 0.1199 0.1624 0.008 0.937 6.8 107.6 21.2 357 n/a 3_bss: 0.1193 0.1616 0.008 0.937 6.3 107.1 20.7 357 n/a 3_settarget: 0.1193 0.1616 0.008 0.937 6.3 107.1 20.7 357 n/a 3_updatecdl: 0.1193 0.1616 0.008 0.937 6.3 107.1 20.7 357 n/a 3_nqh: 0.1193 0.1616 0.008 0.937 6.3 107.1 20.7 357 n/a 3_sol: 0.1191 0.1525 0.008 0.937 6.3 107.1 20.8 400 n/a 3_weight: 0.1191 0.1525 0.008 0.937 6.3 107.1 20.8 400 n/a 3_xyzrec: 0.1172 0.1536 0.009 0.954 6.3 107.1 20.8 400 n/a 3_adp: 0.1152 0.1545 0.009 0.954 6.4 103.8 20.7 400 n/a 3_regHadp: 0.1152 0.1546 0.009 0.954 6.4 103.8 20.7 400 n/a 3_occ: 0.1143 0.1550 0.009 0.954 6.4 103.8 20.7 400 n/a 4_bss: 0.1141 0.1554 0.009 0.954 6.0 103.4 20.4 400 n/a 4_settarget: 0.1141 0.1554 0.009 0.954 6.0 103.4 20.4 400 n/a 4_updatecdl: 0.1141 0.1554 0.009 0.953 6.0 103.4 20.4 400 n/a 4_nqh: 0.1142 0.1550 0.009 0.953 6.0 103.4 20.4 400 n/a 4_sol: 0.1127 0.1498 0.009 0.953 6.0 103.4 21.0 457 n/a 4_weight: 0.1127 0.1498 0.009 0.953 6.0 103.4 21.0 457 n/a 4_xyzrec: 0.1113 0.1547 0.010 0.979 6.0 103.4 21.0 457 n/a 4_adp: 0.1102 0.1544 0.010 0.979 5.8 100.8 21.1 457 n/a 4_regHadp: 0.1102 0.1545 0.010 0.979 5.8 100.8 21.1 457 n/a 4_occ: 0.1092 0.1558 0.010 0.979 5.8 100.8 21.1 457 n/a 5_bss: 0.1089 0.1553 0.010 0.979 5.5 100.6 20.8 457 n/a 5_settarget: 0.1089 0.1553 0.010 0.979 5.5 100.6 20.8 457 n/a 5_updatecdl: 0.1089 0.1553 0.010 0.981 5.5 100.6 20.8 457 n/a 5_setrh: 0.1091 0.1552 0.010 0.981 5.5 100.6 20.8 457 n/a 5_nqh: 0.1091 0.1552 0.010 0.981 5.5 100.6 20.8 457 n/a 5_sol: 0.1098 0.1503 0.010 0.981 5.5 100.6 20.8 461 n/a 5_weight: 0.1098 0.1503 0.010 0.981 5.5 100.6 20.8 461 n/a 5_xyzrec: 0.1105 0.1523 0.010 1.051 5.5 100.6 20.8 461 n/a 5_adp: 0.1096 0.1510 0.010 1.051 5.7 99.3 20.9 461 n/a 5_regHadp: 0.1096 0.1510 0.010 1.051 5.7 99.3 20.9 461 n/a 5_occ: 0.1089 0.1520 0.010 1.051 5.7 99.3 20.9 461 n/a end: 0.1089 0.1519 0.010 1.051 5.4 99.1 20.7 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7445011_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7445011_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1100 Refinement macro-cycles (run) : 930.6400 Write final files (write_after_run_outputs) : 20.1500 Total : 953.9000 Total CPU time: 16.24 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:15 PST -0800 (1735494075.53 s) Start R-work = 0.1603, R-free = 0.1713 Final R-work = 0.1089, R-free = 0.1519 =============================================================================== Job complete usr+sys time: 998.01 seconds wall clock time: 17 minutes 0.62 seconds (1020.62 seconds total)