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_4872201.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_4872201.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4872201.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 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: 1.59, per 1000 atoms: 0.47 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: 0.32 Conformation dependent library (CDL) restraints added in 103.1 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: 0.65 - 0.91: 524 0.91 - 1.17: 1127 1.17 - 1.44: 671 1.44 - 1.70: 811 1.70 - 1.96: 20 Bond restraints: 3153 Sorted by residual: bond pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 1.235 1.482 -0.246 1.14e-02 7.69e+03 4.67e+02 bond pdb=" N ALYS A 132 " pdb=" CA ALYS A 132 " ideal model delta sigma weight residual 1.459 1.674 -0.215 1.19e-02 7.06e+03 3.26e+02 bond pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.337 1.524 -0.188 1.11e-02 8.12e+03 2.86e+02 bond pdb=" CA TYR A 139 " pdb=" C TYR A 139 " ideal model delta sigma weight residual 1.522 1.315 0.207 1.23e-02 6.61e+03 2.84e+02 bond pdb=" C ASP A 68 " pdb=" N VAL A 69 " ideal model delta sigma weight residual 1.332 1.135 0.197 1.20e-02 6.94e+03 2.70e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 3002 4.36 - 8.72: 1849 8.72 - 13.08: 738 13.08 - 17.43: 165 17.43 - 21.79: 23 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 78 " pdb=" C GLY A 78 " pdb=" N ALA A 79 " ideal model delta sigma weight residual 122.18 135.54 -13.36 9.60e-01 1.09e+00 1.94e+02 angle pdb=" N VAL A 88 " pdb=" CA VAL A 88 " pdb=" C VAL A 88 " ideal model delta sigma weight residual 110.62 125.63 -15.01 1.14e+00 7.69e-01 1.73e+02 angle pdb=" CA ALA A 171 " pdb=" C ALA A 171 " pdb=" N LEU A 172 " ideal model delta sigma weight residual 117.30 102.54 14.76 1.16e+00 7.43e-01 1.62e+02 angle pdb=" N ALA A 179 " pdb=" CA ALA A 179 " pdb=" C ALA A 179 " ideal model delta sigma weight residual 111.28 124.70 -13.42 1.09e+00 8.42e-01 1.52e+02 angle pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 109.00 121.29 -12.29 1.00e+00 1.00e+00 1.51e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 1303 16.97 - 33.93: 121 33.93 - 50.89: 40 50.89 - 67.86: 14 67.86 - 84.82: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ARG A 98 " pdb=" N ARG A 98 " pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " ideal model delta harmonic sigma weight residual -122.60 -146.29 23.69 0 2.50e+00 1.60e-01 8.98e+01 dihedral pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " ideal model delta harmonic sigma weight residual 122.80 142.90 -20.10 0 2.50e+00 1.60e-01 6.46e+01 dihedral pdb=" C PRO A 73 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " pdb=" CB PRO A 73 " ideal model delta harmonic sigma weight residual -120.70 -102.12 -18.58 0 2.50e+00 1.60e-01 5.52e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.210: 100 0.210 - 0.420: 65 0.420 - 0.629: 47 0.629 - 0.838: 24 0.838 - 1.047: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLEU A 153 " pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CB BLEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.56 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" CA PHE A 119 " pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CB PHE A 119 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" CA LEU A 82 " pdb=" N LEU A 82 " pdb=" C LEU A 82 " pdb=" CB LEU A 82 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.37e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.236 9.50e-02 1.11e+02 1.05e-01 1.14e+02 pdb=" NE ARG A 28 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " 0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " -0.133 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " -0.026 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " 0.028 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.127 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " -0.006 2.00e-02 2.50e+03 7.02e-02 1.11e+02 pdb=" CG HIS A 126 " 0.071 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.100 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.059 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.108 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.104 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.074 9.50e-02 1.11e+02 7.15e-02 1.02e+02 pdb=" NE ARG A 48 " 0.073 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.092 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " 0.127 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.036 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.084 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.021 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.046 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 784 2.28 - 2.86: 7835 2.86 - 3.44: 10609 3.44 - 4.02: 15298 4.02 - 4.60: 22050 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.698 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.701 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.802 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.808 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.825 2.450 ... (remaining 56571 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_4872201_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= 0.2792 r_free= 0.1816 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.396284 | | target function (ml) not normalized (work): 71408.846284 | | target function (ml) not normalized (free): 3272.285374 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3194 0.2144 7.4696 5.0506| | 2: 3.63 - 2.88 1.00 2711 122 0.2638 0.1728 4.334 4.3197| | 3: 2.88 - 2.52 1.00 2682 148 0.2594 0.1616 4.1884 4.1898| | 4: 2.52 - 2.29 1.00 2661 139 0.2544 0.1571 3.4969 3.5968| | 5: 2.29 - 2.13 1.00 2678 122 0.2660 0.1491 3.4083 3.4631| | 6: 2.13 - 2.00 1.00 2692 117 0.2738 0.1920 3.3196 3.4162| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 1324.51| | 2: 3.63 - 2.88 2711 122 0.82 24.13 1.32 0.23 1324.51| | 3: 2.88 - 2.52 2682 148 0.73 33.23 1.29 0.23 1324.51| | 4: 2.52 - 2.29 2661 139 0.93 11.61 1.30 0.26 137.46| | 5: 2.29 - 2.13 2678 122 0.92 13.47 1.32 0.26 137.46| | 6: 2.13 - 2.00 2692 117 0.90 16.27 1.33 0.26 137.46| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 137.46 max = 1324.51 mean = 737.60| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.74 mean = 19.41| |phase err.(test): min = 0.00 max = 89.74 mean = 19.88| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.246 1557 Z= 5.439 Angle : 5.305 18.369 2118 Z= 3.695 Chirality : 0.396 1.047 243 Planarity : 0.032 0.102 284 Dihedral : 13.954 84.819 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 35.14 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.48), residues: 224 helix: -2.10 (0.39), residues: 109 sheet: -0.17 (1.02), residues: 28 loop : -0.93 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.109 0.023 ARG A 48 TYR 0.093 0.034 TYR A 141 PHE 0.108 0.039 PHE A 119 HIS 0.058 0.027 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2792 r_free= 0.1816 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.396284 | | target function (ml) not normalized (work): 71408.846284 | | target function (ml) not normalized (free): 3272.285374 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2790 percent. r_work = 0.2919 r_free = 0.1975 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2919 0.1975 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2919 0.1975 n_refl.: 17050 remove outliers: r(all,work,free)=0.2154 0.2166 0.1975 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2128 0.2139 0.1962 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1617 0.1614 0.1675 n_refl.: 17045 remove outliers: r(all,work,free)=0.1615 0.1612 0.1675 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 0.3894 398.783 361.241 0.652 1.013 0.397 11.894-9.307 99.02 97 4 0.1885 633.361 614.905 0.930 1.014 0.380 9.237-7.194 100.00 213 7 0.2183 518.026 508.793 0.962 1.013 0.361 7.162-5.571 100.00 427 22 0.2326 388.779 377.717 0.917 1.012 0.285 5.546-4.326 100.00 867 58 0.1387 533.731 528.954 0.957 1.010 0.215 4.315-3.360 100.00 1859 96 0.1312 507.583 503.577 1.017 1.006 0.191 3.356-2.611 100.00 3867 181 0.1656 333.453 328.704 1.014 0.999 0.034 2.608-2.000 99.99 8818 434 0.1638 217.354 213.651 1.029 0.988 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4250 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1612 r_free=0.1675 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=0.1613 r_free=0.1678 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.959673 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.836781 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 0.1351 0.1632 0.0282 0.008 1.0 0.6 0.5 0.0 0 10.980 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.32 2.82 3.013 18.459 0.837 0.023 12.77 16.54 3.77 3.628 18.716 0.837 0.020 Individual atomic B min max mean iso aniso Overall: 6.10 113.90 19.97 4.09 1785 0 Protein: 6.10 113.08 17.21 4.09 1519 0 Water: 8.94 113.90 36.06 N/A 258 0 Other: 22.05 37.35 26.51 N/A 8 0 Chain A: 6.10 113.90 19.97 N/A 1785 0 Histogram: Values Number of atoms 6.10 - 16.88 1075 16.88 - 27.66 352 27.66 - 38.44 183 38.44 - 49.22 101 49.22 - 60.00 47 60.00 - 70.78 12 70.78 - 81.56 7 81.56 - 92.34 4 92.34 - 103.12 1 103.12 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1654 r_work=0.1281 r_free=0.1663 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1663 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 = 0.1275 r_free = 0.1655 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.23 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= 0.1275 r_free= 0.1655 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019918 | | target function (ls_wunit_k1) not normalized (work): 323.394652 | | target function (ls_wunit_k1) not normalized (free): 27.042946 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1655 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1900 0.1898 0.1990 n_refl.: 17043 remove outliers: r(all,work,free)=0.1900 0.1898 0.1990 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1873 0.1870 0.1974 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1294 0.1276 0.1650 n_refl.: 17043 remove outliers: r(all,work,free)=0.1293 0.1275 0.1650 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 0.3551 304.491 283.961 0.641 1.010 0.380 11.894-9.307 99.02 97 4 0.1693 487.713 476.717 0.919 1.010 0.380 9.237-7.194 100.00 213 7 0.1816 398.900 395.798 0.958 1.010 0.351 7.162-5.571 100.00 427 22 0.1855 299.375 294.173 0.928 1.009 0.259 5.546-4.326 100.00 867 58 0.1044 410.993 408.710 0.957 1.007 0.205 4.315-3.360 100.00 1859 96 0.0925 390.859 390.516 1.016 1.005 0.191 3.356-2.611 100.00 3867 181 0.1298 256.772 255.558 1.015 1.000 0.091 2.608-2.000 99.99 8818 434 0.1351 167.371 165.862 1.022 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3724 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1650 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=0.1275 r_free=0.1648 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1648 | n_water=258 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1281 r_free=0.1641 | n_water=253 | time (s): 20.060 (total time: 20.960) Filter (q & B) r_work=0.1281 r_free=0.1641 | n_water=251 | time (s): 1.380 (total time: 22.340) Compute maps r_work=0.1281 r_free=0.1641 | n_water=251 | time (s): 0.620 (total time: 22.960) Filter (map) r_work=0.1317 r_free=0.1642 | n_water=213 | time (s): 1.720 (total time: 24.680) Find peaks r_work=0.1317 r_free=0.1642 | n_water=213 | time (s): 0.640 (total time: 25.320) Add new water r_work=0.1528 r_free=0.1898 | n_water=369 | time (s): 1.950 (total time: 27.270) Refine new water occ: r_work=0.1325 r_free=0.1566 adp: r_work=0.1268 r_free=0.1574 occ: r_work=0.1273 r_free=0.1528 adp: r_work=0.1241 r_free=0.1540 occ: r_work=0.1242 r_free=0.1531 adp: r_work=0.1233 r_free=0.1534 ADP+occupancy (water only), MIN, final r_work=0.1233 r_free=0.1534 r_work=0.1233 r_free=0.1534 | n_water=369 | time (s): 9.830 (total time: 37.100) Filter (q & B) r_work=0.1234 r_free=0.1535 | n_water=363 | time (s): 2.210 (total time: 39.310) Filter (dist only) r_work=0.1235 r_free=0.1538 | n_water=362 | time (s): 27.350 (total time: 66.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.432581 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.984178 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 0.1209 0.1593 0.0384 0.008 0.9 2.9 0.5 0.0 0 12.216 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 15.93 3.84 4.177 21.033 0.984 0.018 11.93 16.19 4.27 4.247 21.306 0.984 0.017 Individual atomic B min max mean iso aniso Overall: 6.78 107.70 21.32 4.39 1889 0 Protein: 6.78 107.70 17.75 4.38 1519 0 Water: 8.48 68.20 35.96 N/A 362 0 Other: 25.24 45.19 36.05 N/A 8 0 Chain A: 6.78 107.70 19.51 N/A 1740 0 Chain S: 18.86 64.02 42.45 N/A 149 0 Histogram: Values Number of atoms 6.78 - 16.88 1028 16.88 - 26.97 377 26.97 - 37.06 226 37.06 - 47.15 153 47.15 - 57.24 67 57.24 - 67.33 25 67.33 - 77.43 5 77.43 - 87.52 5 87.52 - 97.61 1 97.61 - 107.70 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1619 r_work=0.1193 r_free=0.1621 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1621 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1613 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 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= 0.1190 r_free= 0.1613 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016892 | | target function (ls_wunit_k1) not normalized (work): 274.236587 | | target function (ls_wunit_k1) not normalized (free): 24.938381 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1190 0.1613 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1803 0.1799 0.1961 n_refl.: 17042 remove outliers: r(all,work,free)=0.1803 0.1799 0.1961 n_refl.: 17042 overall B=-0.51 to atoms: r(all,work,free)=0.1769 0.1764 0.1939 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1185 0.1607 n_refl.: 17042 remove outliers: r(all,work,free)=0.1204 0.1184 0.1607 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 0.3216 306.516 283.472 0.619 1.007 0.364 11.894-9.307 99.02 97 4 0.1559 487.713 482.220 0.919 1.007 0.360 9.237-7.194 100.00 213 7 0.1683 398.900 398.841 0.971 1.006 0.311 7.162-5.571 100.00 427 22 0.1529 299.375 296.710 0.937 1.006 0.251 5.546-4.326 100.00 867 58 0.0853 410.993 408.262 0.958 1.005 0.211 4.315-3.360 100.00 1859 96 0.0815 390.859 390.043 1.014 1.004 0.202 3.356-2.611 100.00 3867 181 0.1190 256.772 255.856 1.008 1.001 0.142 2.608-2.000 99.99 8818 434 0.1333 167.371 166.341 1.010 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1459 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1184 r_free=0.1607 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1184 r_free=0.1607 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1607 | n_water=362 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1184 r_free=0.1609 | n_water=359 | time (s): 30.520 (total time: 31.240) Filter (q & B) r_work=0.1184 r_free=0.1609 | n_water=359 | time (s): 1.160 (total time: 32.400) Compute maps r_work=0.1184 r_free=0.1609 | n_water=359 | time (s): 0.660 (total time: 33.060) Filter (map) r_work=0.1252 r_free=0.1643 | n_water=261 | time (s): 1.900 (total time: 34.960) Find peaks r_work=0.1252 r_free=0.1643 | n_water=261 | time (s): 0.570 (total time: 35.530) Add new water r_work=0.1446 r_free=0.1830 | n_water=408 | time (s): 1.510 (total time: 37.040) Refine new water occ: r_work=0.1246 r_free=0.1589 adp: r_work=0.1239 r_free=0.1595 occ: r_work=0.1219 r_free=0.1555 adp: r_work=0.1209 r_free=0.1563 occ: r_work=0.1201 r_free=0.1540 adp: r_work=0.1191 r_free=0.1542 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1542 r_work=0.1191 r_free=0.1542 | n_water=408 | time (s): 42.310 (total time: 79.350) Filter (q & B) r_work=0.1194 r_free=0.1546 | n_water=399 | time (s): 1.460 (total time: 80.810) Filter (dist only) r_work=0.1194 r_free=0.1546 | n_water=399 | time (s): 30.120 (total time: 110.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.932513 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.149383 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 0.1176 0.1565 0.0389 0.009 1.0 3.8 0.5 0.0 0 0.966 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 15.65 3.89 4.410 21.393 0.149 5.003 11.57 15.65 4.07 4.923 21.271 0.149 4.979 Individual atomic B min max mean iso aniso Overall: 6.33 105.70 20.63 4.61 1926 0 Protein: 6.33 105.70 16.81 4.61 1519 0 Water: 8.64 60.29 34.86 N/A 399 0 Other: 26.58 45.13 34.79 N/A 8 0 Chain A: 6.33 105.70 18.55 N/A 1736 0 Chain S: 20.31 60.29 39.58 N/A 190 0 Histogram: Values Number of atoms 6.33 - 16.27 1081 16.27 - 26.20 340 26.20 - 36.14 220 36.14 - 46.08 182 46.08 - 56.01 67 56.01 - 65.95 23 65.95 - 75.89 5 75.89 - 85.82 3 85.82 - 95.76 3 95.76 - 105.70 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1565 r_work=0.1158 r_free=0.1565 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1565 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1148 r_free = 0.1558 target_work(ml) = 4.973 | | 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= 0.1148 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.972837 | | target function (ml) not normalized (work): 80729.040684 | | target function (ml) not normalized (free): 4194.362738 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1168 0.1148 0.1558 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1647 0.1639 0.1843 n_refl.: 17041 remove outliers: r(all,work,free)=0.1647 0.1639 0.1843 n_refl.: 17041 overall B=-0.42 to atoms: r(all,work,free)=0.1620 0.1611 0.1829 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1144 0.1553 n_refl.: 17041 remove outliers: r(all,work,free)=0.1163 0.1143 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 0.3482 303.025 280.668 0.572 1.006 0.340 11.894-9.307 99.02 97 4 0.1736 487.713 480.902 0.910 1.007 0.330 9.237-7.194 100.00 213 7 0.1847 398.900 399.110 0.982 1.007 0.244 7.162-5.571 100.00 427 22 0.1614 299.375 294.445 0.941 1.007 0.211 5.546-4.326 100.00 867 58 0.0943 410.993 407.188 0.963 1.006 0.201 4.315-3.360 100.00 1859 96 0.0882 390.859 388.481 1.011 1.004 0.202 3.356-2.611 100.00 3867 181 0.1275 256.772 254.629 1.010 1.001 0.142 2.608-2.000 99.99 8818 434 0.1089 167.371 165.940 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1537 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1553 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1143 r_free=0.1553 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1553 | n_water=399 | time (s): 0.860 (total time: 0.860) Filter (dist) r_work=0.1143 r_free=0.1553 | n_water=399 | time (s): 29.660 (total time: 30.520) Filter (q & B) r_work=0.1143 r_free=0.1552 | n_water=398 | time (s): 1.600 (total time: 32.120) Compute maps r_work=0.1143 r_free=0.1552 | n_water=398 | time (s): 0.730 (total time: 32.850) Filter (map) r_work=0.1196 r_free=0.1602 | n_water=313 | time (s): 2.140 (total time: 34.990) Find peaks r_work=0.1196 r_free=0.1602 | n_water=313 | time (s): 0.650 (total time: 35.640) Add new water r_work=0.1329 r_free=0.1736 | n_water=452 | time (s): 1.830 (total time: 37.470) Refine new water occ: r_work=0.1168 r_free=0.1538 adp: r_work=0.1160 r_free=0.1542 occ: r_work=0.1145 r_free=0.1513 adp: r_work=0.1136 r_free=0.1515 occ: r_work=0.1131 r_free=0.1502 adp: r_work=0.1123 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1503 r_work=0.1123 r_free=0.1503 | n_water=452 | time (s): 36.440 (total time: 73.910) Filter (q & B) r_work=0.1127 r_free=0.1510 | n_water=442 | time (s): 2.160 (total time: 76.070) Filter (dist only) r_work=0.1130 r_free=0.1514 | n_water=441 | time (s): 35.120 (total time: 111.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.991316 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.167689 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 0.1115 0.1578 0.0463 0.010 1.0 3.2 0.5 0.0 0 0.996 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.15 15.78 4.63 4.442 20.845 0.168 4.961 11.04 15.62 4.58 4.649 20.888 0.168 4.951 Individual atomic B min max mean iso aniso Overall: 5.69 103.32 20.79 4.84 1968 0 Protein: 5.69 103.32 16.35 4.84 1519 0 Water: 8.44 64.99 35.85 N/A 441 0 Other: 25.92 43.25 33.48 N/A 8 0 Chain A: 5.69 103.32 18.04 N/A 1734 0 Chain S: 13.05 64.99 41.21 N/A 234 0 Histogram: Values Number of atoms 5.69 - 15.45 1058 15.45 - 25.21 355 25.21 - 34.98 219 34.98 - 44.74 189 44.74 - 54.50 96 54.50 - 64.27 35 64.27 - 74.03 7 74.03 - 83.79 4 83.79 - 93.55 3 93.55 - 103.32 2 =========================== Idealize ADP of riding H ========================== r_work=0.1104 r_free=0.1562 r_work=0.1104 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1104 r_free = 0.1563 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1097 r_free = 0.1571 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.23 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= 0.1097 r_free= 0.1571 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.948109 | | target function (ml) not normalized (work): 80322.660671 | | target function (ml) not normalized (free): 4189.349269 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1120 0.1097 0.1571 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1564 0.1549 0.1869 n_refl.: 17040 remove outliers: r(all,work,free)=0.1564 0.1549 0.1869 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1548 0.1533 0.1860 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1118 0.1096 0.1569 n_refl.: 17040 remove outliers: r(all,work,free)=0.1118 0.1096 0.1569 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 0.3621 303.025 277.158 0.554 1.004 0.328 11.894-9.307 99.02 97 4 0.1719 487.713 481.547 0.914 1.004 0.320 9.237-7.194 100.00 213 7 0.1721 398.900 400.745 0.984 1.004 0.225 7.162-5.571 100.00 427 22 0.1541 299.375 294.099 0.941 1.004 0.206 5.546-4.326 100.00 867 58 0.0903 410.993 407.294 0.962 1.004 0.201 4.315-3.360 100.00 1859 96 0.0846 390.859 388.881 1.005 1.003 0.201 3.356-2.611 100.00 3867 181 0.1215 256.772 254.802 1.003 1.001 0.121 2.608-2.000 99.99 8818 434 0.1045 167.371 166.141 0.997 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8893 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1096 r_free=0.1569 After: r_work=0.1098 r_free=0.1568 ================================== NQH flips ================================== r_work=0.1098 r_free=0.1568 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1098 r_free=0.1568 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1098 r_free=0.1568 | n_water=441 | time (s): 0.780 (total time: 0.780) Filter (dist) r_work=0.1098 r_free=0.1558 | n_water=440 | time (s): 37.670 (total time: 38.450) Filter (q & B) r_work=0.1098 r_free=0.1558 | n_water=440 | time (s): 0.790 (total time: 39.240) Compute maps r_work=0.1098 r_free=0.1558 | n_water=440 | time (s): 0.550 (total time: 39.790) Filter (map) r_work=0.1176 r_free=0.1569 | n_water=341 | time (s): 1.910 (total time: 41.700) Find peaks r_work=0.1176 r_free=0.1569 | n_water=341 | time (s): 0.610 (total time: 42.310) Add new water r_work=0.1298 r_free=0.1678 | n_water=482 | time (s): 2.130 (total time: 44.440) Refine new water occ: r_work=0.1136 r_free=0.1506 adp: r_work=0.1130 r_free=0.1512 occ: r_work=0.1116 r_free=0.1485 adp: r_work=0.1108 r_free=0.1490 occ: r_work=0.1101 r_free=0.1472 adp: r_work=0.1095 r_free=0.1474 ADP+occupancy (water only), MIN, final r_work=0.1095 r_free=0.1474 r_work=0.1095 r_free=0.1474 | n_water=482 | time (s): 33.150 (total time: 77.590) Filter (q & B) r_work=0.1099 r_free=0.1486 | n_water=469 | time (s): 2.310 (total time: 79.900) Filter (dist only) r_work=0.1099 r_free=0.1488 | n_water=468 | time (s): 37.760 (total time: 117.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.916573 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.195104 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 0.1498 0.0385 0.011 1.0 4.5 0.5 0.0 0 0.958 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.13 14.98 3.85 4.527 20.705 0.195 4.942 11.03 14.94 3.92 4.617 20.787 0.195 4.935 Individual atomic B min max mean iso aniso Overall: 5.12 102.40 20.93 5.09 1995 0 Protein: 5.12 102.40 16.13 5.08 1519 0 Water: 8.10 66.31 36.28 N/A 468 0 Other: 25.52 43.52 32.99 N/A 8 0 Chain A: 5.12 102.40 17.79 N/A 1734 0 Chain S: 15.12 66.31 41.74 N/A 261 0 Histogram: Values Number of atoms 5.12 - 14.85 1021 14.85 - 24.58 387 24.58 - 34.31 226 34.31 - 44.03 178 44.03 - 53.76 127 53.76 - 63.49 37 63.49 - 73.22 10 73.22 - 82.94 2 82.94 - 92.67 4 92.67 - 102.40 3 =========================== Idealize ADP of riding H ========================== r_work=0.1103 r_free=0.1494 r_work=0.1102 r_free=0.1494 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1102 r_free = 0.1494 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1096 r_free = 0.1495 target_work(ml) = 4.931 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1096 r_free= 0.1495 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.931181 | | target function (ml) not normalized (work): 80047.855538 | | target function (ml) not normalized (free): 4166.191555 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1116 0.1363 5.4572 5.6584| | 2: 3.63 - 2.88 1.00 2711 122 0.1081 0.1557 5.2212 5.3977| | 3: 2.88 - 2.52 1.00 2681 148 0.1336 0.1598 5.1284 5.1833| | 4: 2.52 - 2.29 1.00 2661 139 0.0918 0.1446 4.6167 4.9092| | 5: 2.29 - 2.13 1.00 2678 122 0.0952 0.1505 4.5707 4.9011| | 6: 2.13 - 2.00 1.00 2692 117 0.1098 0.1758 4.5631 4.7911| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.08 1.00 0.96 6472.34| | 2: 3.63 - 2.88 2711 122 0.92 12.94 1.01 0.96 6472.34| | 3: 2.88 - 2.52 2681 148 0.87 19.09 0.99 0.96 6472.34| | 4: 2.52 - 2.29 2661 139 0.93 12.02 1.01 0.97 2091.18| | 5: 2.29 - 2.13 2678 122 0.91 14.10 1.00 0.97 2091.18| | 6: 2.13 - 2.00 2692 117 0.90 16.68 0.99 0.97 2091.18| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2091.18 max = 6472.34 mean = 4304.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.78 mean = 13.95| |phase err.(test): min = 0.00 max = 89.46 mean = 13.58| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1115 0.1096 0.1495 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1536 0.1525 0.1780 n_refl.: 17040 remove outliers: r(all,work,free)=0.1536 0.1525 0.1780 n_refl.: 17040 overall B=-0.21 to atoms: r(all,work,free)=0.1524 0.1513 0.1774 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1117 0.1098 0.1492 n_refl.: 17040 remove outliers: r(all,work,free)=0.1117 0.1098 0.1492 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 0.3694 303.025 276.267 0.540 1.001 0.330 11.894-9.307 99.02 97 4 0.1719 487.713 481.918 0.919 1.002 0.330 9.237-7.194 100.00 213 7 0.1717 398.900 400.975 0.991 1.003 0.210 7.162-5.571 100.00 427 22 0.1552 299.375 294.266 0.938 1.003 0.190 5.546-4.326 100.00 867 58 0.0914 410.993 407.602 0.965 1.002 0.190 4.315-3.360 100.00 1859 96 0.0888 390.859 389.074 1.004 1.002 0.171 3.356-2.611 100.00 3867 181 0.1221 256.772 254.590 1.000 1.001 0.111 2.608-2.000 99.99 8818 434 0.1021 167.371 165.960 0.987 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7403 ================= 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 : 0.2792 0.1816 0.081 5.305 8.8 119.3 19.9 258 0.000 1_bss: 0.1612 0.1675 0.081 5.305 8.4 118.9 19.5 258 0.000 1_settarget: 0.1612 0.1675 0.081 5.305 8.4 118.9 19.5 258 0.000 1_nqh: 0.1613 0.1678 0.081 5.305 8.4 118.9 19.5 258 0.003 1_weight: 0.1613 0.1678 0.081 5.305 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1351 0.1632 0.008 0.957 8.4 118.9 19.5 258 0.154 1_adp: 0.1277 0.1654 0.008 0.957 6.1 113.9 20.0 258 0.154 1_regHadp: 0.1281 0.1663 0.008 0.957 6.1 113.9 20.0 258 0.154 1_occ: 0.1275 0.1655 0.008 0.957 6.1 113.9 20.0 258 0.154 2_bss: 0.1275 0.1650 0.008 0.957 5.7 113.5 19.6 258 0.154 2_settarget: 0.1275 0.1650 0.008 0.957 5.7 113.5 19.6 258 0.154 2_updatecdl: 0.1275 0.1650 0.008 0.974 5.7 113.5 19.6 258 0.154 2_nqh: 0.1275 0.1648 0.008 0.974 5.7 113.5 19.6 258 0.151 2_sol: 0.1235 0.1538 0.008 0.974 5.7 112.7 20.8 362 n/a 2_weight: 0.1235 0.1538 0.008 0.974 5.7 112.7 20.8 362 n/a 2_xyzrec: 0.1209 0.1593 0.008 0.921 5.7 112.7 20.8 362 n/a 2_adp: 0.1193 0.1619 0.008 0.921 6.8 107.7 21.3 362 n/a 2_regHadp: 0.1193 0.1621 0.008 0.921 6.8 107.7 21.3 362 n/a 2_occ: 0.1190 0.1613 0.008 0.921 6.8 107.7 21.3 362 n/a 3_bss: 0.1184 0.1607 0.008 0.921 6.3 107.2 20.8 362 n/a 3_settarget: 0.1184 0.1607 0.008 0.921 6.3 107.2 20.8 362 n/a 3_updatecdl: 0.1184 0.1607 0.008 0.920 6.3 107.2 20.8 362 n/a 3_nqh: 0.1184 0.1607 0.008 0.920 6.3 107.2 20.8 362 n/a 3_sol: 0.1194 0.1546 0.008 0.920 6.3 107.2 20.9 399 n/a 3_weight: 0.1194 0.1546 0.008 0.920 6.3 107.2 20.9 399 n/a 3_xyzrec: 0.1176 0.1565 0.009 0.963 6.3 107.2 20.9 399 n/a 3_adp: 0.1157 0.1565 0.009 0.963 6.3 105.7 20.6 399 n/a 3_regHadp: 0.1158 0.1565 0.009 0.963 6.3 105.7 20.6 399 n/a 3_occ: 0.1148 0.1558 0.009 0.963 6.3 105.7 20.6 399 n/a 4_bss: 0.1143 0.1553 0.009 0.963 5.9 105.3 20.2 399 n/a 4_settarget: 0.1143 0.1553 0.009 0.963 5.9 105.3 20.2 399 n/a 4_updatecdl: 0.1143 0.1553 0.009 0.963 5.9 105.3 20.2 399 n/a 4_nqh: 0.1143 0.1553 0.009 0.963 5.9 105.3 20.2 399 n/a 4_sol: 0.1130 0.1514 0.009 0.963 5.9 105.3 20.7 441 n/a 4_weight: 0.1130 0.1514 0.009 0.963 5.9 105.3 20.7 441 n/a 4_xyzrec: 0.1115 0.1578 0.010 0.985 5.9 105.3 20.7 441 n/a 4_adp: 0.1104 0.1562 0.010 0.985 5.7 103.3 20.8 441 n/a 4_regHadp: 0.1104 0.1563 0.010 0.985 5.7 103.3 20.8 441 n/a 4_occ: 0.1097 0.1571 0.010 0.985 5.7 103.3 20.8 441 n/a 5_bss: 0.1096 0.1569 0.010 0.985 5.4 103.1 20.5 441 n/a 5_settarget: 0.1096 0.1569 0.010 0.985 5.4 103.1 20.5 441 n/a 5_updatecdl: 0.1096 0.1569 0.010 0.986 5.4 103.1 20.5 441 n/a 5_setrh: 0.1098 0.1568 0.010 0.986 5.4 103.1 20.5 441 n/a 5_nqh: 0.1098 0.1568 0.010 0.986 5.4 103.1 20.5 441 n/a 5_sol: 0.1099 0.1488 0.010 0.986 5.4 103.1 20.8 468 n/a 5_weight: 0.1099 0.1488 0.010 0.986 5.4 103.1 20.8 468 n/a 5_xyzrec: 0.1113 0.1498 0.011 1.021 5.4 103.1 20.8 468 n/a 5_adp: 0.1103 0.1494 0.011 1.021 5.1 102.4 20.9 468 n/a 5_regHadp: 0.1102 0.1494 0.011 1.021 5.1 102.4 20.9 468 n/a 5_occ: 0.1096 0.1495 0.011 1.021 5.1 102.4 20.9 468 n/a end: 0.1098 0.1492 0.011 1.021 4.9 102.2 20.7 468 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4872201_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4872201_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7900 Refinement macro-cycles (run) : 932.3900 Write final files (write_after_run_outputs) : 20.7800 Total : 956.9600 Total CPU time: 16.32 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:19 PST -0800 (1735494079.95 s) Start R-work = 0.1612, R-free = 0.1675 Final R-work = 0.1098, R-free = 0.1492 =============================================================================== Job complete usr+sys time: 999.93 seconds wall clock time: 17 minutes 2.58 seconds (1022.58 seconds total)