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_9049096.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_9049096.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9049096.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: 1.73, per 1000 atoms: 0.51 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: 0.50 Conformation dependent library (CDL) restraints added in 117.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 396 0.89 - 1.15: 1225 1.15 - 1.41: 621 1.41 - 1.67: 874 1.67 - 1.93: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.236 1.432 -0.195 9.70e-03 1.06e+04 4.05e+02 bond pdb=" C LYS A 122 " pdb=" O LYS A 122 " ideal model delta sigma weight residual 1.235 1.015 0.221 1.21e-02 6.83e+03 3.32e+02 bond pdb=" C LEU A 172 " pdb=" N ASN A 173 " ideal model delta sigma weight residual 1.332 1.581 -0.249 1.39e-02 5.18e+03 3.22e+02 bond pdb=" N ILE A 105 " pdb=" CA ILE A 105 " ideal model delta sigma weight residual 1.457 1.659 -0.202 1.14e-02 7.69e+03 3.13e+02 bond pdb=" CA VAL A 51 " pdb=" CB VAL A 51 " ideal model delta sigma weight residual 1.537 1.331 0.206 1.17e-02 7.31e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 2954 4.32 - 8.63: 1867 8.63 - 12.95: 762 12.95 - 17.26: 172 17.26 - 21.58: 22 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.29 108.55 10.74 6.50e-01 2.37e+00 2.73e+02 angle pdb=" N ILE A 168 " pdb=" CA ILE A 168 " pdb=" C ILE A 168 " ideal model delta sigma weight residual 110.74 95.89 14.85 9.10e-01 1.21e+00 2.66e+02 angle pdb=" C ALA A 107 " pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 121.13 132.71 -11.58 7.30e-01 1.88e+00 2.52e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH1 ARG A 5 " ideal model delta sigma weight residual 121.50 135.02 -13.52 1.00e+00 1.00e+00 1.83e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 131.75 -10.52 8.10e-01 1.52e+00 1.69e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.49: 1291 16.49 - 32.96: 123 32.96 - 49.44: 51 49.44 - 65.91: 14 65.91 - 82.39: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ARG A 48 " pdb=" N ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual -122.60 -141.31 18.71 0 2.50e+00 1.60e-01 5.60e+01 dihedral pdb=" C THR A 110 " pdb=" N THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual -122.00 -140.31 18.31 0 2.50e+00 1.60e-01 5.36e+01 dihedral pdb=" C VAL A 51 " pdb=" N VAL A 51 " pdb=" CA VAL A 51 " pdb=" CB VAL A 51 " ideal model delta harmonic sigma weight residual -122.00 -139.83 17.83 0 2.50e+00 1.60e-01 5.09e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.229: 92 0.229 - 0.454: 87 0.454 - 0.679: 45 0.679 - 0.904: 16 0.904 - 1.129: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.46 -1.13 2.00e-01 2.50e+01 3.19e+01 chirality pdb=" CB THR A 124 " pdb=" CA THR A 124 " pdb=" OG1 THR A 124 " pdb=" CG2 THR A 124 " both_signs ideal model delta sigma weight residual False 2.55 1.42 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ILE A 168 " pdb=" N ILE A 168 " pdb=" C ILE A 168 " pdb=" CB ILE A 168 " both_signs ideal model delta sigma weight residual False 2.43 3.36 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.186 9.50e-02 1.11e+02 9.10e-02 1.03e+02 pdb=" NE ARG A 156 " -0.093 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " 0.109 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " -0.054 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " 0.055 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " 0.074 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " -0.030 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " 0.026 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.046 9.50e-02 1.11e+02 6.85e-02 1.01e+02 pdb=" NE ARG A 48 " 0.093 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " 0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.011 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.122 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.041 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.078 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.009 2.00e-02 2.50e+03 5.53e-02 9.18e+01 pdb=" CG TYR A 141 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.142 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.053 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.015 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 1220 2.35 - 2.91: 8224 2.91 - 3.47: 10514 3.47 - 4.04: 15150 4.04 - 4.60: 21582 Nonbonded interactions: 56690 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.783 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.840 2.270 nonbonded pdb=" H ASP A 49 " pdb=" HA ASP A 49 " model vdw 1.852 1.816 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.852 2.450 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.852 2.100 ... (remaining 56685 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_9049096_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= 0.2784 r_free= 0.1851 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.397557 | | target function (ml) not normalized (work): 71429.518843 | | target function (ml) not normalized (free): 3264.680149 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3180 0.2203 7.4828 5.0518| | 2: 3.63 - 2.88 1.00 2711 122 0.2626 0.1728 4.3318 4.3426| | 3: 2.88 - 2.52 1.00 2682 148 0.2578 0.1790 4.189 4.191| | 4: 2.52 - 2.29 1.00 2661 139 0.2548 0.1611 3.5161 3.6215| | 5: 2.29 - 2.13 1.00 2678 122 0.2671 0.1424 3.3919 3.4091| | 6: 2.13 - 2.00 1.00 2692 117 0.2738 0.1792 3.3125 3.3511| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.76 0.77 0.23 1324.57| | 2: 3.63 - 2.88 2711 122 0.83 23.99 1.31 0.23 1324.57| | 3: 2.88 - 2.52 2682 148 0.73 33.13 1.29 0.23 1324.57| | 4: 2.52 - 2.29 2661 139 0.93 11.58 1.29 0.26 138.31| | 5: 2.29 - 2.13 2678 122 0.92 13.71 1.32 0.26 138.31| | 6: 2.13 - 2.00 2692 117 0.90 16.48 1.34 0.26 138.31| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 138.31 max = 1324.57 mean = 738.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 19.45| |phase err.(test): min = 0.00 max = 89.94 mean = 19.73| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.250 1557 Z= 5.564 Angle : 5.272 17.218 2118 Z= 3.760 Chirality : 0.389 1.129 243 Planarity : 0.032 0.084 284 Dihedral : 13.915 82.386 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 31.89 % 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: -2.93 (0.44), residues: 224 helix: -2.86 (0.37), residues: 109 sheet: -0.74 (0.76), residues: 28 loop : -0.74 (0.51), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.103 0.025 ARG A 156 TYR 0.115 0.046 TYR A 141 PHE 0.110 0.045 PHE A 164 HIS 0.058 0.032 HIS A 115 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= 0.2784 r_free= 0.1851 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.397557 | | target function (ml) not normalized (work): 71429.518843 | | target function (ml) not normalized (free): 3264.680149 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3363 percent. r_work = 0.2918 r_free = 0.1996 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2918 0.1996 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2918 0.1996 n_refl.: 17050 remove outliers: r(all,work,free)=0.2160 0.2170 0.1996 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2132 0.2142 0.1978 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1613 0.1610 0.1674 n_refl.: 17045 remove outliers: r(all,work,free)=0.1612 0.1609 0.1674 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4019 394.867 362.395 0.653 1.015 0.397 11.894-9.307 99.02 97 4 0.1873 633.774 615.121 0.930 1.016 0.380 9.237-7.194 100.00 213 7 0.2189 518.363 508.235 0.957 1.016 0.371 7.162-5.571 100.00 427 22 0.2323 389.032 376.489 0.922 1.014 0.280 5.546-4.326 100.00 867 58 0.1379 534.079 528.812 0.957 1.011 0.235 4.315-3.360 100.00 1859 96 0.1281 507.914 503.548 1.017 1.007 0.212 3.356-2.611 100.00 3867 181 0.1654 333.671 329.069 1.012 0.999 0.061 2.608-2.000 99.99 8818 434 0.1647 217.496 213.669 1.035 0.986 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4664 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1609 r_free=0.1674 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 3 r_work=0.1616 r_free=0.1681 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.832193 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.891064 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 0.1633 0.0282 0.009 1.0 1.3 0.5 0.0 0 11.916 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.33 2.82 3.013 18.448 0.891 0.023 12.77 16.54 3.77 3.614 18.719 0.891 0.020 Individual atomic B min max mean iso aniso Overall: 6.32 113.89 19.99 4.05 1785 0 Protein: 6.32 112.58 17.24 4.05 1519 0 Water: 8.77 113.89 35.98 N/A 258 0 Other: 22.01 36.40 26.51 N/A 8 0 Chain A: 6.32 113.89 19.99 N/A 1785 0 Histogram: Values Number of atoms 6.32 - 17.07 1092 17.07 - 27.83 337 27.83 - 38.59 185 38.59 - 49.35 96 49.35 - 60.10 47 60.10 - 70.86 14 70.86 - 81.62 6 81.62 - 92.37 5 92.37 - 103.13 0 103.13 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1654 r_work=0.1280 r_free=0.1662 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1662 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 = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1275 r_free= 0.1655 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020030 | | target function (ls_wunit_k1) not normalized (work): 325.219127 | | target function (ls_wunit_k1) not normalized (free): 26.966796 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1655 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1916 0.1916 0.1982 n_refl.: 17044 remove outliers: r(all,work,free)=0.1916 0.1916 0.1982 n_refl.: 17044 overall B=-0.38 to atoms: r(all,work,free)=0.1887 0.1887 0.1967 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1276 0.1643 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1274 0.1643 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 0.3553 303.148 280.170 0.635 1.000 0.370 11.894-9.307 99.02 97 4 0.1709 487.566 478.771 0.930 0.999 0.367 9.237-7.194 100.00 213 7 0.1831 398.779 396.095 0.972 0.998 0.351 7.162-5.571 100.00 427 22 0.1828 299.284 294.523 0.942 0.997 0.264 5.546-4.326 100.00 867 58 0.1042 410.869 408.917 0.971 0.995 0.210 4.315-3.360 100.00 1859 96 0.0929 390.741 390.610 1.031 0.992 0.191 3.356-2.611 100.00 3867 181 0.1300 256.694 255.299 1.028 0.986 0.091 2.608-2.000 99.99 8818 434 0.1347 167.321 165.582 1.038 0.977 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3719 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1643 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1276 r_free=0.1643 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1643 | n_water=258 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1286 r_free=0.1634 | n_water=252 | time (s): 20.400 (total time: 21.070) Filter (q & B) r_work=0.1286 r_free=0.1635 | n_water=250 | time (s): 2.160 (total time: 23.230) Compute maps r_work=0.1286 r_free=0.1635 | n_water=250 | time (s): 0.750 (total time: 23.980) Filter (map) r_work=0.1316 r_free=0.1629 | n_water=215 | time (s): 1.700 (total time: 25.680) Find peaks r_work=0.1316 r_free=0.1629 | n_water=215 | time (s): 0.430 (total time: 26.110) Add new water r_work=0.1524 r_free=0.1877 | n_water=370 | time (s): 1.470 (total time: 27.580) Refine new water occ: r_work=0.1330 r_free=0.1595 adp: r_work=0.1274 r_free=0.1598 occ: r_work=0.1279 r_free=0.1555 adp: r_work=0.1246 r_free=0.1561 occ: r_work=0.1247 r_free=0.1549 adp: r_work=0.1235 r_free=0.1547 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1547 r_work=0.1235 r_free=0.1547 | n_water=370 | time (s): 10.180 (total time: 37.760) Filter (q & B) r_work=0.1236 r_free=0.1544 | n_water=364 | time (s): 1.520 (total time: 39.280) Filter (dist only) r_work=0.1237 r_free=0.1547 | n_water=363 | time (s): 27.820 (total time: 67.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.363266 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.974528 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 0.1204 0.1557 0.0353 0.008 0.9 2.6 0.5 0.0 0 12.182 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 15.57 3.53 4.161 21.104 0.975 0.018 11.91 15.89 3.98 4.190 21.377 0.975 0.017 Individual atomic B min max mean iso aniso Overall: 6.77 107.19 21.39 4.26 1890 0 Protein: 6.77 107.19 17.76 4.25 1519 0 Water: 8.84 68.16 36.31 N/A 363 0 Other: 24.81 45.40 35.03 N/A 8 0 Chain A: 6.77 107.19 19.58 N/A 1742 0 Chain S: 19.14 63.45 42.81 N/A 148 0 Histogram: Values Number of atoms 6.77 - 16.81 1026 16.81 - 26.86 376 26.86 - 36.90 226 36.90 - 46.94 152 46.94 - 56.98 71 56.98 - 67.02 27 67.02 - 77.07 4 77.07 - 87.11 6 87.11 - 97.15 0 97.15 - 107.19 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1589 r_work=0.1192 r_free=0.1590 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1590 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1592 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= 0.1191 r_free= 0.1592 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.016975 | | target function (ls_wunit_k1) not normalized (work): 275.594308 | | target function (ls_wunit_k1) not normalized (free): 24.912394 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1191 0.1592 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1759 0.1752 0.1910 n_refl.: 17042 remove outliers: r(all,work,free)=0.1759 0.1752 0.1910 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1734 0.1728 0.1894 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1186 0.1591 n_refl.: 17042 remove outliers: r(all,work,free)=0.1204 0.1185 0.1591 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 0.3293 299.988 283.309 0.606 1.005 0.350 11.894-9.307 99.02 97 4 0.1524 487.566 484.028 0.916 1.005 0.350 9.237-7.194 100.00 213 7 0.1667 398.779 399.779 0.974 1.005 0.295 7.162-5.571 100.00 427 22 0.1514 299.284 296.269 0.931 1.005 0.245 5.546-4.326 100.00 867 58 0.0876 410.869 407.814 0.959 1.004 0.221 4.315-3.360 100.00 1859 96 0.0817 390.741 389.846 1.015 1.003 0.211 3.356-2.611 100.00 3867 181 0.1194 256.694 255.781 1.011 1.001 0.131 2.608-2.000 99.99 8818 434 0.1330 167.321 166.285 1.016 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3257 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1591 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1185 r_free=0.1591 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1591 | n_water=363 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1186 r_free=0.1596 | n_water=361 | time (s): 27.900 (total time: 28.540) Filter (q & B) r_work=0.1186 r_free=0.1596 | n_water=361 | time (s): 0.800 (total time: 29.340) Compute maps r_work=0.1186 r_free=0.1596 | n_water=361 | time (s): 0.660 (total time: 30.000) Filter (map) r_work=0.1253 r_free=0.1633 | n_water=270 | time (s): 1.840 (total time: 31.840) Find peaks r_work=0.1253 r_free=0.1633 | n_water=270 | time (s): 0.580 (total time: 32.420) Add new water r_work=0.1434 r_free=0.1811 | n_water=417 | time (s): 2.020 (total time: 34.440) Refine new water occ: r_work=0.1241 r_free=0.1598 adp: r_work=0.1234 r_free=0.1604 occ: r_work=0.1216 r_free=0.1569 adp: r_work=0.1206 r_free=0.1574 occ: r_work=0.1198 r_free=0.1554 adp: r_work=0.1189 r_free=0.1557 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1557 r_work=0.1189 r_free=0.1557 | n_water=417 | time (s): 25.710 (total time: 60.150) Filter (q & B) r_work=0.1192 r_free=0.1558 | n_water=408 | time (s): 1.660 (total time: 61.810) Filter (dist only) r_work=0.1192 r_free=0.1558 | n_water=408 | time (s): 32.260 (total time: 94.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.002953 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.145038 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 0.1174 0.1596 0.0421 0.009 1.0 2.6 0.5 0.0 0 1.001 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.74 15.96 4.21 4.334 21.578 0.145 5.002 11.55 15.92 4.38 4.908 21.451 0.145 4.979 Individual atomic B min max mean iso aniso Overall: 6.50 103.48 20.87 4.62 1935 0 Protein: 6.50 103.48 16.95 4.61 1519 0 Water: 7.77 62.37 35.15 N/A 408 0 Other: 27.80 47.96 36.74 N/A 8 0 Chain A: 6.50 103.48 18.72 N/A 1736 0 Chain S: 14.84 62.37 39.60 N/A 199 0 Histogram: Values Number of atoms 6.50 - 16.19 1063 16.19 - 25.89 349 25.89 - 35.59 219 35.59 - 45.29 188 45.29 - 54.99 70 54.99 - 64.69 33 64.69 - 74.39 4 74.39 - 84.08 4 84.08 - 93.78 3 93.78 - 103.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1592 r_work=0.1155 r_free=0.1592 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1155 r_free = 0.1592 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1589 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.20 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= 0.1146 r_free= 0.1589 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.971486 | | target function (ml) not normalized (work): 80707.107614 | | target function (ml) not normalized (free): 4194.249777 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1167 0.1146 0.1589 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1671 0.1664 0.1857 n_refl.: 17041 remove outliers: r(all,work,free)=0.1671 0.1664 0.1857 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1646 0.1638 0.1847 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1166 0.1145 0.1586 n_refl.: 17041 remove outliers: r(all,work,free)=0.1165 0.1144 0.1586 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 0.3510 296.427 277.631 0.562 1.003 0.340 11.894-9.307 99.02 97 4 0.1768 487.566 481.204 0.909 1.004 0.340 9.237-7.194 100.00 213 7 0.1737 398.779 400.202 0.986 1.004 0.249 7.162-5.571 100.00 427 22 0.1635 299.284 294.020 0.938 1.004 0.221 5.546-4.326 100.00 867 58 0.0950 410.869 407.370 0.967 1.004 0.221 4.315-3.360 100.00 1859 96 0.0893 390.741 388.246 1.012 1.003 0.211 3.356-2.611 100.00 3867 181 0.1278 256.694 254.135 1.011 1.001 0.131 2.608-2.000 99.99 8818 434 0.1087 167.321 165.921 1.013 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3196 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1144 r_free=0.1586 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1144 r_free=0.1586 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1144 r_free=0.1586 | n_water=408 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1144 r_free=0.1586 | n_water=408 | time (s): 32.990 (total time: 33.650) Filter (q & B) r_work=0.1144 r_free=0.1586 | n_water=407 | time (s): 1.520 (total time: 35.170) Compute maps r_work=0.1144 r_free=0.1586 | n_water=407 | time (s): 0.500 (total time: 35.670) Filter (map) r_work=0.1198 r_free=0.1580 | n_water=313 | time (s): 1.610 (total time: 37.280) Find peaks r_work=0.1198 r_free=0.1580 | n_water=313 | time (s): 0.450 (total time: 37.730) Add new water r_work=0.1340 r_free=0.1679 | n_water=462 | time (s): 1.450 (total time: 39.180) Refine new water occ: r_work=0.1174 r_free=0.1525 adp: r_work=0.1164 r_free=0.1525 occ: r_work=0.1152 r_free=0.1504 adp: r_work=0.1139 r_free=0.1505 occ: r_work=0.1135 r_free=0.1496 adp: r_work=0.1125 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1125 r_free=0.1493 r_work=0.1125 r_free=0.1493 | n_water=462 | time (s): 30.480 (total time: 69.660) Filter (q & B) r_work=0.1129 r_free=0.1503 | n_water=450 | time (s): 1.820 (total time: 71.480) Filter (dist only) r_work=0.1129 r_free=0.1503 | n_water=450 | time (s): 33.220 (total time: 104.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.002873 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160871 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 0.1555 0.0441 0.010 1.0 5.1 0.5 0.0 0 1.001 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.13 15.55 4.41 4.452 21.103 0.161 4.953 11.03 15.54 4.51 4.661 21.132 0.161 4.944 Individual atomic B min max mean iso aniso Overall: 5.54 99.97 21.05 4.85 1977 0 Protein: 5.54 99.97 16.52 4.84 1519 0 Water: 8.39 63.36 36.10 N/A 450 0 Other: 27.30 46.31 34.93 N/A 8 0 Chain A: 5.54 99.97 18.23 N/A 1735 0 Chain S: 16.89 63.36 41.32 N/A 242 0 Histogram: Values Number of atoms 5.54 - 14.99 999 14.99 - 24.43 390 24.43 - 33.87 213 33.87 - 43.31 196 43.31 - 52.76 118 52.76 - 62.20 40 62.20 - 71.64 11 71.64 - 81.08 3 81.08 - 90.53 4 90.53 - 99.97 3 =========================== Idealize ADP of riding H ========================== r_work=0.1103 r_free=0.1554 r_work=0.1103 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1103 r_free = 0.1554 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1094 r_free = 0.1551 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.15 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= 0.1094 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.939817 | | target function (ml) not normalized (work): 80188.044774 | | target function (ml) not normalized (free): 4180.330798 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1116 0.1094 0.1551 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1594 0.1582 0.1860 n_refl.: 17040 remove outliers: r(all,work,free)=0.1594 0.1582 0.1860 n_refl.: 17040 overall B=-0.28 to atoms: r(all,work,free)=0.1577 0.1564 0.1852 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1115 0.1093 0.1545 n_refl.: 17040 remove outliers: r(all,work,free)=0.1115 0.1093 0.1545 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 0.3526 296.427 275.914 0.554 1.002 0.330 11.894-9.307 99.02 97 4 0.1746 487.566 481.515 0.915 1.004 0.304 9.237-7.194 100.00 213 7 0.1675 398.779 400.813 0.987 1.004 0.230 7.162-5.571 100.00 427 22 0.1444 299.284 294.364 0.938 1.004 0.215 5.546-4.326 100.00 867 58 0.0887 410.869 407.754 0.966 1.003 0.211 4.315-3.360 100.00 1859 96 0.0843 390.741 388.621 1.006 1.003 0.201 3.356-2.611 100.00 3867 181 0.1229 256.694 254.454 1.004 1.001 0.068 2.608-2.000 99.99 8818 434 0.1047 167.321 166.114 1.000 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9632 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1093 r_free=0.1545 After: r_work=0.1095 r_free=0.1544 ================================== NQH flips ================================== r_work=0.1095 r_free=0.1544 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1095 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1095 r_free=0.1544 | n_water=450 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1095 r_free=0.1546 | n_water=449 | time (s): 37.310 (total time: 38.050) Filter (q & B) r_work=0.1096 r_free=0.1548 | n_water=448 | time (s): 2.140 (total time: 40.190) Compute maps r_work=0.1096 r_free=0.1548 | n_water=448 | time (s): 0.570 (total time: 40.760) Filter (map) r_work=0.1175 r_free=0.1561 | n_water=330 | time (s): 1.710 (total time: 42.470) Find peaks r_work=0.1175 r_free=0.1561 | n_water=330 | time (s): 0.420 (total time: 42.890) Add new water r_work=0.1304 r_free=0.1665 | n_water=466 | time (s): 1.650 (total time: 44.540) Refine new water occ: r_work=0.1147 r_free=0.1534 adp: r_work=0.1139 r_free=0.1536 occ: r_work=0.1124 r_free=0.1516 adp: r_work=0.1115 r_free=0.1515 occ: r_work=0.1106 r_free=0.1506 adp: r_work=0.1099 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1099 r_free=0.1506 r_work=0.1099 r_free=0.1506 | n_water=466 | time (s): 25.050 (total time: 69.590) Filter (q & B) r_work=0.1102 r_free=0.1508 | n_water=458 | time (s): 2.390 (total time: 71.980) Filter (dist only) r_work=0.1102 r_free=0.1508 | n_water=458 | time (s): 34.290 (total time: 106.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.081614 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.189535 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 0.1120 0.1513 0.0393 0.010 1.1 6.7 0.5 0.0 0 1.041 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.20 15.13 3.93 4.545 20.845 0.190 4.945 11.09 15.15 4.06 4.610 20.929 0.190 4.939 Individual atomic B min max mean iso aniso Overall: 5.54 99.41 21.02 5.05 1985 0 Protein: 5.54 99.41 16.29 5.03 1519 0 Water: 8.11 65.50 36.43 N/A 458 0 Other: 26.58 44.26 35.05 N/A 8 0 Chain A: 5.54 99.41 17.98 N/A 1735 0 Chain S: 15.59 65.50 42.05 N/A 250 0 Histogram: Values Number of atoms 5.54 - 14.92 1017 14.92 - 24.31 373 24.31 - 33.70 207 33.70 - 43.08 202 43.08 - 52.47 127 52.47 - 61.86 36 61.86 - 71.25 13 71.25 - 80.63 2 80.63 - 90.02 4 90.02 - 99.41 4 =========================== Idealize ADP of riding H ========================== r_work=0.1109 r_free=0.1515 r_work=0.1109 r_free=0.1515 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1109 r_free = 0.1515 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1508 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1101 r_free= 0.1508 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.935995 | | target function (ml) not normalized (work): 80126.014163 | | target function (ml) not normalized (free): 4166.323806 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1106 0.1395 5.4458 5.6529| | 2: 3.63 - 2.88 1.00 2711 122 0.1078 0.1433 5.208 5.3329| | 3: 2.88 - 2.52 1.00 2681 148 0.1356 0.1722 5.1282 5.2133| | 4: 2.52 - 2.29 1.00 2661 139 0.0929 0.1508 4.6321 4.9521| | 5: 2.29 - 2.13 1.00 2678 122 0.0961 0.1465 4.5903 4.886| | 6: 2.13 - 2.00 1.00 2692 117 0.1133 0.1777 4.5828 4.7941| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 8.82 1.00 0.96 6315.32| | 2: 3.63 - 2.88 2711 122 0.92 12.79 1.01 0.96 6315.32| | 3: 2.88 - 2.52 2681 148 0.88 18.90 0.99 0.96 6315.32| | 4: 2.52 - 2.29 2661 139 0.93 12.29 1.01 0.97 2177.48| | 5: 2.29 - 2.13 2678 122 0.91 14.35 1.00 0.97 2177.48| | 6: 2.13 - 2.00 2692 117 0.89 17.17 0.99 0.97 2177.48| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2177.48 max = 6315.32 mean = 4268.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.95 mean = 14.01| |phase err.(test): min = 0.00 max = 89.91 mean = 13.77| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1101 0.1508 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1579 0.1568 0.1815 n_refl.: 17040 remove outliers: r(all,work,free)=0.1579 0.1568 0.1815 n_refl.: 17040 overall B=-0.23 to atoms: r(all,work,free)=0.1565 0.1553 0.1808 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1102 0.1508 n_refl.: 17040 remove outliers: r(all,work,free)=0.1121 0.1102 0.1508 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 0.3470 296.427 280.199 0.547 1.004 0.318 11.894-9.307 99.02 97 4 0.1674 487.566 480.829 0.910 1.005 0.310 9.237-7.194 100.00 213 7 0.1743 398.779 401.674 0.987 1.005 0.225 7.162-5.571 100.00 427 22 0.1561 299.284 293.511 0.932 1.005 0.210 5.546-4.326 100.00 867 58 0.0917 410.869 407.931 0.964 1.004 0.201 4.315-3.360 100.00 1859 96 0.0869 390.741 388.685 1.002 1.003 0.201 3.356-2.611 100.00 3867 181 0.1230 256.694 254.400 1.002 1.001 0.053 2.608-2.000 99.99 8818 434 0.1039 167.321 165.950 0.993 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8046 ================= 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 : 0.2784 0.1851 0.082 5.272 8.8 119.3 19.9 258 0.000 1_bss: 0.1609 0.1674 0.082 5.272 8.4 118.9 19.5 258 0.000 1_settarget: 0.1609 0.1674 0.082 5.272 8.4 118.9 19.5 258 0.000 1_nqh: 0.1616 0.1681 0.082 5.272 8.4 118.9 19.5 258 0.010 1_weight: 0.1616 0.1681 0.082 5.272 8.4 118.9 19.5 258 0.010 1_xyzrec: 0.1351 0.1633 0.009 0.980 8.4 118.9 19.5 258 0.149 1_adp: 0.1277 0.1654 0.009 0.980 6.3 113.9 20.0 258 0.149 1_regHadp: 0.1280 0.1662 0.009 0.980 6.3 113.9 20.0 258 0.149 1_occ: 0.1275 0.1655 0.009 0.980 6.3 113.9 20.0 258 0.149 2_bss: 0.1274 0.1643 0.009 0.980 5.9 113.5 19.6 258 0.149 2_settarget: 0.1274 0.1643 0.009 0.980 5.9 113.5 19.6 258 0.149 2_updatecdl: 0.1274 0.1643 0.009 1.001 5.9 113.5 19.6 258 0.149 2_nqh: 0.1276 0.1643 0.009 1.001 5.9 113.5 19.6 258 0.143 2_sol: 0.1237 0.1547 0.009 1.001 5.9 112.2 20.9 363 n/a 2_weight: 0.1237 0.1547 0.009 1.001 5.9 112.2 20.9 363 n/a 2_xyzrec: 0.1204 0.1557 0.008 0.933 5.9 112.2 20.9 363 n/a 2_adp: 0.1191 0.1589 0.008 0.933 6.8 107.2 21.4 363 n/a 2_regHadp: 0.1192 0.1590 0.008 0.933 6.8 107.2 21.4 363 n/a 2_occ: 0.1191 0.1592 0.008 0.933 6.8 107.2 21.4 363 n/a 3_bss: 0.1185 0.1591 0.008 0.933 6.4 106.8 21.0 363 n/a 3_settarget: 0.1185 0.1591 0.008 0.933 6.4 106.8 21.0 363 n/a 3_updatecdl: 0.1185 0.1591 0.008 0.938 6.4 106.8 21.0 363 n/a 3_nqh: 0.1185 0.1591 0.008 0.938 6.4 106.8 21.0 363 n/a 3_sol: 0.1192 0.1558 0.008 0.938 6.4 106.8 21.1 408 n/a 3_weight: 0.1192 0.1558 0.008 0.938 6.4 106.8 21.1 408 n/a 3_xyzrec: 0.1174 0.1596 0.009 0.974 6.4 106.8 21.1 408 n/a 3_adp: 0.1155 0.1592 0.009 0.974 6.5 103.5 20.9 408 n/a 3_regHadp: 0.1155 0.1592 0.009 0.974 6.5 103.5 20.9 408 n/a 3_occ: 0.1146 0.1589 0.009 0.974 6.5 103.5 20.9 408 n/a 4_bss: 0.1144 0.1586 0.009 0.974 6.1 103.1 20.5 408 n/a 4_settarget: 0.1144 0.1586 0.009 0.974 6.1 103.1 20.5 408 n/a 4_updatecdl: 0.1144 0.1586 0.009 0.972 6.1 103.1 20.5 408 n/a 4_nqh: 0.1144 0.1586 0.009 0.972 6.1 103.1 20.5 408 n/a 4_sol: 0.1129 0.1503 0.009 0.972 6.1 103.1 21.0 450 n/a 4_weight: 0.1129 0.1503 0.009 0.972 6.1 103.1 21.0 450 n/a 4_xyzrec: 0.1113 0.1555 0.010 1.003 6.1 103.1 21.0 450 n/a 4_adp: 0.1103 0.1554 0.010 1.003 5.5 100.0 21.1 450 n/a 4_regHadp: 0.1103 0.1554 0.010 1.003 5.5 100.0 21.1 450 n/a 4_occ: 0.1094 0.1551 0.010 1.003 5.5 100.0 21.1 450 n/a 5_bss: 0.1093 0.1545 0.010 1.003 5.3 99.7 20.8 450 n/a 5_settarget: 0.1093 0.1545 0.010 1.003 5.3 99.7 20.8 450 n/a 5_updatecdl: 0.1093 0.1545 0.010 1.003 5.3 99.7 20.8 450 n/a 5_setrh: 0.1095 0.1544 0.010 1.003 5.3 99.7 20.8 450 n/a 5_nqh: 0.1095 0.1544 0.010 1.003 5.3 99.7 20.8 450 n/a 5_sol: 0.1102 0.1508 0.010 1.003 5.3 99.7 20.9 458 n/a 5_weight: 0.1102 0.1508 0.010 1.003 5.3 99.7 20.9 458 n/a 5_xyzrec: 0.1120 0.1513 0.010 1.051 5.3 99.7 20.9 458 n/a 5_adp: 0.1109 0.1515 0.010 1.051 5.5 99.4 21.0 458 n/a 5_regHadp: 0.1109 0.1515 0.010 1.051 5.5 99.4 21.0 458 n/a 5_occ: 0.1101 0.1508 0.010 1.051 5.5 99.4 21.0 458 n/a end: 0.1102 0.1508 0.010 1.051 5.3 99.2 20.8 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9049096_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9049096_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0900 Refinement macro-cycles (run) : 900.6200 Write final files (write_after_run_outputs) : 21.3700 Total : 925.0800 Total CPU time: 15.80 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:49 PST -0800 (1735494049.83 s) Start R-work = 0.1609, R-free = 0.1674 Final R-work = 0.1102, R-free = 0.1508 =============================================================================== Job complete usr+sys time: 974.71 seconds wall clock time: 16 minutes 38.20 seconds (998.20 seconds total)