Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4279219.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4279219.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4279219.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.82, per 1000 atoms: 0.54 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: 0.45 Conformation dependent library (CDL) restraints added in 110.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.64 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: 540 0.91 - 1.18: 1116 1.18 - 1.44: 680 1.44 - 1.70: 797 1.70 - 1.96: 20 Bond restraints: 3153 Sorted by residual: bond pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.374 1.109 0.265 1.10e-02 8.26e+03 5.80e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.534 1.674 -0.140 6.80e-03 2.16e+04 4.22e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.237 1.031 0.206 1.13e-02 7.83e+03 3.32e+02 bond pdb=" C MET A 17 " pdb=" O MET A 17 " ideal model delta sigma weight residual 1.236 1.037 0.200 1.15e-02 7.56e+03 3.02e+02 bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.518 1.351 0.167 1.00e-02 1.00e+04 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 3244 4.79 - 9.58: 1845 9.58 - 14.36: 584 14.36 - 19.15: 98 19.15 - 23.94: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 133.71 -12.48 8.10e-01 1.52e+00 2.38e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 123.03 107.07 15.96 1.11e+00 8.12e-01 2.07e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.29 110.25 9.04 6.50e-01 2.37e+00 1.93e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.45 112.85 9.60 7.20e-01 1.93e+00 1.78e+02 angle pdb=" N GLY A 174 " pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 112.04 125.10 -13.06 1.02e+00 9.61e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 1284 16.41 - 32.82: 133 32.82 - 49.22: 42 49.22 - 65.63: 18 65.63 - 82.04: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 25 " pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual -122.00 -143.48 21.48 0 2.50e+00 1.60e-01 7.38e+01 dihedral pdb=" N CYS A 46 " pdb=" C CYS A 46 " pdb=" CA CYS A 46 " pdb=" CB CYS A 46 " ideal model delta harmonic sigma weight residual 122.80 140.35 -17.55 0 2.50e+00 1.60e-01 4.93e+01 dihedral pdb=" C CYS A 46 " pdb=" N CYS A 46 " pdb=" CA CYS A 46 " pdb=" CB CYS A 46 " ideal model delta harmonic sigma weight residual -122.60 -139.63 17.03 0 2.50e+00 1.60e-01 4.64e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 89 0.198 - 0.396: 95 0.396 - 0.593: 35 0.593 - 0.791: 15 0.791 - 0.989: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 112 " pdb=" CB LEU A 112 " pdb=" CD1 LEU A 112 " pdb=" CD2 LEU A 112 " both_signs ideal model delta sigma weight residual False -2.59 -1.60 -0.99 2.00e-01 2.50e+01 2.44e+01 chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.41 -0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.48 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.070 2.00e-02 2.50e+03 5.69e-02 9.72e+01 pdb=" CG PHE A 119 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.120 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.035 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.081 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.057 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.036 2.00e-02 2.50e+03 5.37e-02 8.66e+01 pdb=" CG BTYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.044 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.054 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.092 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.045 9.50e-02 1.11e+02 6.26e-02 8.32e+01 pdb=" NE ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.051 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.093 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.108 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " 0.084 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.36: 1297 2.36 - 2.92: 8286 2.92 - 3.48: 10469 3.48 - 4.04: 15144 4.04 - 4.60: 21483 Nonbonded interactions: 56679 Sorted by model distance: nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.794 2.450 nonbonded pdb="HH12 ARG A 5 " pdb=" O BGLU A 64 " model vdw 1.829 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.833 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.833 2.100 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.850 2.450 ... (remaining 56674 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_4279219_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= 0.2786 r_free= 0.1812 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411665 | | target function (ml) not normalized (work): 71658.678154 | | target function (ml) not normalized (free): 3273.702095 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3206 0.2144 7.5899 5.0286| | 2: 3.63 - 2.88 1.00 2711 122 0.2643 0.1666 4.3244 4.3314| | 3: 2.88 - 2.52 1.00 2682 148 0.2543 0.1629 4.1768 4.1665| | 4: 2.52 - 2.29 1.00 2661 139 0.2542 0.1471 3.4926 3.5884| | 5: 2.29 - 2.13 1.00 2678 122 0.2651 0.1573 3.3943 3.4606| | 6: 2.13 - 2.00 1.00 2692 117 0.2727 0.2038 3.3259 3.4881| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.42 0.77 0.23 1277.42| | 2: 3.63 - 2.88 2711 122 0.83 23.66 1.31 0.23 1277.42| | 3: 2.88 - 2.52 2682 148 0.74 32.51 1.28 0.23 1277.42| | 4: 2.52 - 2.29 2661 139 0.93 11.86 1.30 0.26 141.40| | 5: 2.29 - 2.13 2678 122 0.92 13.76 1.32 0.26 141.40| | 6: 2.13 - 2.00 2692 117 0.90 16.66 1.33 0.26 141.40| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 141.40 max = 1277.42 mean = 715.74| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.93 mean = 19.31| |phase err.(test): min = 0.00 max = 89.04 mean = 19.55| |-----------------------------------------------------------------------------| ----------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 0.265 1557 Z= 5.480 Angle : 5.250 16.235 2118 Z= 3.755 Chirality : 0.363 0.989 243 Planarity : 0.033 0.112 284 Dihedral : 13.970 82.037 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 29.19 % 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: -2.70 (0.47), residues: 224 helix: -2.63 (0.39), residues: 102 sheet: -0.96 (0.92), residues: 28 loop : -0.76 (0.53), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.013 ARG A 27 TYR 0.078 0.033 TYR A 141 PHE 0.088 0.037 PHE A 162 HIS 0.088 0.049 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2786 r_free= 0.1812 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411665 | | target function (ml) not normalized (work): 71658.678154 | | target function (ml) not normalized (free): 3273.702095 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2775 percent. r_work = 0.2914 r_free = 0.1994 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2861 0.2914 0.1994 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2861 0.2914 0.1994 n_refl.: 17050 remove outliers: r(all,work,free)=0.2149 0.2159 0.1994 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2123 0.2133 0.1974 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1610 0.1609 0.1649 n_refl.: 17045 remove outliers: r(all,work,free)=0.1608 0.1606 0.1649 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 0.3886 398.940 361.367 0.653 1.018 0.403 11.894-9.307 99.02 97 4 0.1868 633.612 613.516 0.923 1.018 0.385 9.237-7.194 100.00 213 7 0.2121 518.231 510.188 0.947 1.017 0.355 7.162-5.571 100.00 427 22 0.2337 388.933 375.679 0.917 1.016 0.289 5.546-4.326 100.00 867 58 0.1401 533.942 529.430 0.959 1.013 0.251 4.315-3.360 100.00 1859 96 0.1305 507.784 503.263 1.015 1.008 0.191 3.356-2.611 100.00 3867 181 0.1653 333.585 329.445 1.011 0.999 0.061 2.608-2.000 99.99 8818 434 0.1630 217.440 213.504 1.034 0.984 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4115 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1606 r_free=0.1649 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1610 r_free=0.1657 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.355911 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.969870 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 0.1350 0.1648 0.0298 0.009 1.0 1.3 0.5 0.0 0 11.678 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.48 2.98 3.013 18.463 0.970 0.022 12.76 16.68 3.92 3.654 18.699 0.970 0.020 Individual atomic B min max mean iso aniso Overall: 6.00 113.90 19.94 4.13 1785 0 Protein: 6.00 113.04 17.16 4.14 1519 0 Water: 9.00 113.90 36.08 N/A 258 0 Other: 21.93 36.96 26.66 N/A 8 0 Chain A: 6.00 113.90 19.94 N/A 1785 0 Histogram: Values Number of atoms 6.00 - 16.79 1077 16.79 - 27.58 348 27.58 - 38.37 185 38.37 - 49.16 98 49.16 - 59.95 50 59.95 - 70.74 12 70.74 - 81.53 7 81.53 - 92.32 4 92.32 - 103.11 1 103.11 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1668 r_work=0.1279 r_free=0.1677 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1677 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1274 r_free = 0.1666 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 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= 0.1274 r_free= 0.1666 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019875 | | target function (ls_wunit_k1) not normalized (work): 322.694776 | | target function (ls_wunit_k1) not normalized (free): 27.779441 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1274 0.1666 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1902 0.1900 0.1994 n_refl.: 17043 remove outliers: r(all,work,free)=0.1902 0.1900 0.1994 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1866 0.1863 0.1974 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1291 0.1273 0.1657 n_refl.: 17043 remove outliers: r(all,work,free)=0.1290 0.1271 0.1657 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 0.3407 306.713 281.718 0.629 1.006 0.368 11.894-9.307 99.02 97 4 0.1698 488.026 477.305 0.921 1.007 0.367 9.237-7.194 100.00 213 7 0.1829 399.156 395.466 0.960 1.007 0.351 7.162-5.571 100.00 427 22 0.1855 299.567 294.108 0.930 1.006 0.291 5.546-4.326 100.00 867 58 0.1046 411.258 408.605 0.958 1.005 0.210 4.315-3.360 100.00 1859 96 0.0927 391.110 390.578 1.016 1.004 0.192 3.356-2.611 100.00 3867 181 0.1291 256.937 255.636 1.009 1.001 0.081 2.608-2.000 99.99 8818 434 0.1347 167.479 166.127 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1473 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1657 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1273 r_free=0.1656 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1656 | n_water=258 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1281 r_free=0.1648 | n_water=252 | time (s): 21.000 (total time: 21.640) Filter (q & B) r_work=0.1281 r_free=0.1649 | n_water=250 | time (s): 1.660 (total time: 23.300) Compute maps r_work=0.1281 r_free=0.1649 | n_water=250 | time (s): 0.560 (total time: 23.860) Filter (map) r_work=0.1315 r_free=0.1633 | n_water=211 | time (s): 1.670 (total time: 25.530) Find peaks r_work=0.1315 r_free=0.1633 | n_water=211 | time (s): 0.560 (total time: 26.090) Add new water r_work=0.1528 r_free=0.1856 | n_water=369 | time (s): 1.540 (total time: 27.630) Refine new water occ: r_work=0.1328 r_free=0.1582 adp: r_work=0.1274 r_free=0.1585 occ: r_work=0.1278 r_free=0.1552 adp: r_work=0.1248 r_free=0.1564 occ: r_work=0.1250 r_free=0.1559 adp: r_work=0.1237 r_free=0.1560 ADP+occupancy (water only), MIN, final r_work=0.1237 r_free=0.1560 r_work=0.1237 r_free=0.1560 | n_water=369 | time (s): 11.370 (total time: 39.000) Filter (q & B) r_work=0.1240 r_free=0.1566 | n_water=359 | time (s): 1.650 (total time: 40.650) Filter (dist only) r_work=0.1240 r_free=0.1569 | n_water=358 | time (s): 28.590 (total time: 69.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.385347 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.010344 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 0.1214 0.1614 0.0401 0.008 0.9 2.2 0.5 0.0 0 11.693 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 16.14 4.01 4.199 20.876 1.010 0.018 11.97 16.40 4.42 4.268 21.153 1.010 0.018 Individual atomic B min max mean iso aniso Overall: 6.66 107.54 21.15 4.33 1885 0 Protein: 6.66 107.54 17.57 4.33 1519 0 Water: 8.43 66.45 36.04 N/A 358 0 Other: 25.28 44.53 34.58 N/A 8 0 Chain A: 6.66 107.54 19.32 N/A 1738 0 Chain S: 17.55 66.45 42.85 N/A 147 0 Histogram: Values Number of atoms 6.66 - 16.74 1043 16.74 - 26.83 360 26.83 - 36.92 216 36.92 - 47.01 161 47.01 - 57.10 64 57.10 - 67.18 31 67.18 - 77.27 3 77.27 - 87.36 3 87.36 - 97.45 2 97.45 - 107.54 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1640 r_work=0.1199 r_free=0.1639 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1639 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1634 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1196 r_free= 0.1634 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016953 | | target function (ls_wunit_k1) not normalized (work): 275.208415 | | target function (ls_wunit_k1) not normalized (free): 25.491731 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1196 0.1634 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1746 0.1735 0.1973 n_refl.: 17041 remove outliers: r(all,work,free)=0.1746 0.1735 0.1973 n_refl.: 17041 overall B=-0.41 to atoms: r(all,work,free)=0.1720 0.1709 0.1955 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1193 0.1626 n_refl.: 17041 remove outliers: r(all,work,free)=0.1214 0.1193 0.1626 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 0.3223 306.713 286.267 0.606 1.006 0.350 11.894-9.307 99.02 97 4 0.1510 488.026 487.218 0.917 1.007 0.338 9.237-7.194 100.00 213 7 0.1638 399.156 400.847 0.975 1.006 0.293 7.162-5.571 100.00 427 22 0.1528 299.567 296.748 0.936 1.006 0.281 5.546-4.326 100.00 867 58 0.0884 411.258 408.299 0.960 1.005 0.206 4.315-3.360 100.00 1859 96 0.0830 391.110 390.348 1.014 1.003 0.201 3.356-2.611 100.00 3867 181 0.1206 256.937 256.254 1.010 1.000 0.101 2.608-2.000 99.99 8818 434 0.1336 167.479 166.349 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1454 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1626 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=0.1195 r_free=0.1627 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1627 | n_water=358 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1195 r_free=0.1630 | n_water=357 | time (s): 26.510 (total time: 27.110) Filter (q & B) r_work=0.1195 r_free=0.1630 | n_water=357 | time (s): 0.820 (total time: 27.930) Compute maps r_work=0.1195 r_free=0.1630 | n_water=357 | time (s): 0.590 (total time: 28.520) Filter (map) r_work=0.1265 r_free=0.1632 | n_water=256 | time (s): 1.770 (total time: 30.290) Find peaks r_work=0.1265 r_free=0.1632 | n_water=256 | time (s): 0.470 (total time: 30.760) Add new water r_work=0.1448 r_free=0.1836 | n_water=400 | time (s): 1.440 (total time: 32.200) Refine new water occ: r_work=0.1252 r_free=0.1591 adp: r_work=0.1245 r_free=0.1594 occ: r_work=0.1226 r_free=0.1561 adp: r_work=0.1217 r_free=0.1564 occ: r_work=0.1209 r_free=0.1541 adp: r_work=0.1200 r_free=0.1546 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1546 r_work=0.1200 r_free=0.1546 | n_water=400 | time (s): 31.540 (total time: 63.740) Filter (q & B) r_work=0.1201 r_free=0.1558 | n_water=393 | time (s): 1.480 (total time: 65.220) Filter (dist only) r_work=0.1201 r_free=0.1558 | n_water=393 | time (s): 30.730 (total time: 95.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.825676 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.135095 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 0.1182 0.1564 0.0382 0.009 0.9 3.8 0.5 0.0 0 0.913 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.82 15.64 3.82 4.357 21.246 0.135 5.000 11.66 15.77 4.11 4.831 21.150 0.135 4.978 Individual atomic B min max mean iso aniso Overall: 6.35 105.02 20.54 4.60 1920 0 Protein: 6.35 105.02 16.83 4.60 1519 0 Water: 8.64 60.67 34.60 N/A 393 0 Other: 26.72 46.63 34.54 N/A 8 0 Chain A: 6.35 105.02 18.54 N/A 1733 0 Chain S: 17.05 60.67 39.09 N/A 187 0 Histogram: Values Number of atoms 6.35 - 16.22 1075 16.22 - 26.08 346 26.08 - 35.95 227 35.95 - 45.82 165 45.82 - 55.68 64 55.68 - 65.55 30 65.55 - 75.42 6 75.42 - 85.28 2 85.28 - 95.15 3 95.15 - 105.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1166 r_free=0.1577 r_work=0.1166 r_free=0.1578 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1166 r_free = 0.1578 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1155 r_free = 0.1570 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.15 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= 0.1155 r_free= 0.1570 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.972447 | | target function (ml) not normalized (work): 80722.699717 | | target function (ml) not normalized (free): 4192.072599 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1175 0.1155 0.1570 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1660 0.1654 0.1834 n_refl.: 17041 remove outliers: r(all,work,free)=0.1660 0.1654 0.1834 n_refl.: 17041 overall B=-0.46 to atoms: r(all,work,free)=0.1629 0.1622 0.1822 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1172 0.1152 0.1566 n_refl.: 17041 remove outliers: r(all,work,free)=0.1172 0.1152 0.1566 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 0.3497 306.713 283.882 0.570 1.004 0.340 11.894-9.307 99.02 97 4 0.1789 488.026 482.251 0.915 1.004 0.340 9.237-7.194 100.00 213 7 0.1878 399.156 400.295 0.989 1.004 0.255 7.162-5.571 100.00 427 22 0.1681 299.567 293.937 0.939 1.004 0.241 5.546-4.326 100.00 867 58 0.0968 411.258 407.555 0.967 1.004 0.201 4.315-3.360 100.00 1859 96 0.0893 391.110 388.732 1.013 1.003 0.202 3.356-2.611 100.00 3867 181 0.1278 256.937 254.809 1.010 1.002 0.132 2.608-2.000 99.99 8818 434 0.1087 167.479 166.105 1.008 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1625 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1152 r_free=0.1566 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=0.1152 r_free=0.1562 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1152 r_free=0.1562 | n_water=393 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1152 r_free=0.1562 | n_water=393 | time (s): 29.530 (total time: 30.240) Filter (q & B) r_work=0.1152 r_free=0.1563 | n_water=392 | time (s): 1.740 (total time: 31.980) Compute maps r_work=0.1152 r_free=0.1563 | n_water=392 | time (s): 0.770 (total time: 32.750) Filter (map) r_work=0.1200 r_free=0.1563 | n_water=316 | time (s): 2.230 (total time: 34.980) Find peaks r_work=0.1200 r_free=0.1563 | n_water=316 | time (s): 0.630 (total time: 35.610) Add new water r_work=0.1343 r_free=0.1680 | n_water=461 | time (s): 1.790 (total time: 37.400) Refine new water occ: r_work=0.1177 r_free=0.1527 adp: r_work=0.1170 r_free=0.1532 occ: r_work=0.1154 r_free=0.1505 adp: r_work=0.1145 r_free=0.1512 occ: r_work=0.1138 r_free=0.1489 adp: r_work=0.1130 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1493 r_work=0.1130 r_free=0.1493 | n_water=461 | time (s): 35.100 (total time: 72.500) Filter (q & B) r_work=0.1133 r_free=0.1497 | n_water=451 | time (s): 1.640 (total time: 74.140) Filter (dist only) r_work=0.1133 r_free=0.1497 | n_water=451 | time (s): 35.230 (total time: 109.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.974111 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.134845 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1116 0.1543 0.0426 0.010 1.0 3.5 0.5 0.0 0 0.987 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.43 4.26 4.438 20.860 0.135 4.952 11.07 15.40 4.34 4.627 20.864 0.135 4.945 Individual atomic B min max mean iso aniso Overall: 5.81 101.49 20.77 4.72 1978 0 Protein: 5.81 101.49 16.31 4.72 1519 0 Water: 8.36 63.39 35.56 N/A 451 0 Other: 25.67 45.31 33.28 N/A 8 0 Chain A: 5.81 101.49 17.95 N/A 1731 0 Chain S: 16.66 63.39 40.48 N/A 247 0 Histogram: Values Number of atoms 5.81 - 15.38 1041 15.38 - 24.95 375 24.95 - 34.52 215 34.52 - 44.08 197 44.08 - 53.65 100 53.65 - 63.22 36 63.22 - 72.79 4 72.79 - 82.36 5 82.36 - 91.92 3 91.92 - 101.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1540 r_work=0.1107 r_free=0.1541 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1107 r_free = 0.1541 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1545 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1545 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.942728 | | target function (ml) not normalized (work): 80240.245110 | | target function (ml) not normalized (free): 4180.643864 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1100 0.1545 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1553 0.1538 0.1851 n_refl.: 17041 remove outliers: r(all,work,free)=0.1553 0.1538 0.1851 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1537 0.1523 0.1843 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1119 0.1097 0.1541 n_refl.: 17041 remove outliers: r(all,work,free)=0.1118 0.1096 0.1541 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 0.3644 303.220 280.421 0.558 1.003 0.339 11.894-9.307 99.02 97 4 0.1808 488.026 480.626 0.912 1.004 0.338 9.237-7.194 100.00 213 7 0.1757 399.156 400.487 0.991 1.004 0.214 7.162-5.571 100.00 427 22 0.1574 299.567 293.720 0.937 1.004 0.203 5.546-4.326 100.00 867 58 0.0922 411.258 407.735 0.965 1.003 0.198 4.315-3.360 100.00 1859 96 0.0846 391.110 388.753 1.006 1.003 0.191 3.356-2.611 100.00 3867 181 0.1219 256.937 254.818 1.001 1.001 0.131 2.608-2.000 99.99 8818 434 0.1031 167.479 166.288 0.997 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.8904 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1096 r_free=0.1541 After: r_work=0.1098 r_free=0.1539 ================================== NQH flips ================================== r_work=0.1098 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1098 r_free=0.1539 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1098 r_free=0.1539 | n_water=451 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1104 r_free=0.1535 | n_water=449 | time (s): 37.720 (total time: 38.520) Filter (q & B) r_work=0.1104 r_free=0.1535 | n_water=449 | time (s): 0.840 (total time: 39.360) Compute maps r_work=0.1104 r_free=0.1535 | n_water=449 | time (s): 0.740 (total time: 40.100) Filter (map) r_work=0.1170 r_free=0.1522 | n_water=348 | time (s): 1.760 (total time: 41.860) Find peaks r_work=0.1170 r_free=0.1522 | n_water=348 | time (s): 0.460 (total time: 42.320) Add new water r_work=0.1278 r_free=0.1620 | n_water=481 | time (s): 1.770 (total time: 44.090) Refine new water occ: r_work=0.1132 r_free=0.1498 adp: r_work=0.1127 r_free=0.1495 occ: r_work=0.1114 r_free=0.1482 adp: r_work=0.1107 r_free=0.1479 occ: r_work=0.1103 r_free=0.1473 adp: r_work=0.1097 r_free=0.1471 ADP+occupancy (water only), MIN, final r_work=0.1097 r_free=0.1471 r_work=0.1097 r_free=0.1471 | n_water=481 | time (s): 18.920 (total time: 63.010) Filter (q & B) r_work=0.1102 r_free=0.1483 | n_water=467 | time (s): 1.720 (total time: 64.730) Filter (dist only) r_work=0.1102 r_free=0.1485 | n_water=466 | time (s): 37.760 (total time: 102.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.935704 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.159598 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1121 0.1499 0.0378 0.011 1.1 6.7 0.5 0.0 0 0.968 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.21 14.99 3.78 4.451 20.610 0.160 4.944 11.12 14.92 3.81 4.543 20.698 0.160 4.935 Individual atomic B min max mean iso aniso Overall: 5.53 99.85 20.80 4.95 1993 0 Protein: 5.53 99.85 16.09 4.94 1519 0 Water: 8.27 64.25 35.93 N/A 466 0 Other: 26.06 44.03 33.57 N/A 8 0 Chain A: 5.53 99.85 17.74 N/A 1730 0 Chain S: 17.99 64.25 40.95 N/A 263 0 Histogram: Values Number of atoms 5.53 - 14.96 1039 14.96 - 24.39 366 24.39 - 33.83 211 33.83 - 43.26 205 43.26 - 52.69 115 52.69 - 62.12 33 62.12 - 71.56 14 71.56 - 80.99 3 80.99 - 90.42 3 90.42 - 99.85 4 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1492 r_work=0.1112 r_free=0.1492 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1492 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1487 target_work(ml) = 4.928 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1487 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.928464 | | target function (ml) not normalized (work): 80003.750750 | | target function (ml) not normalized (free): 4159.832631 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1128 0.1400 5.4597 5.6791| | 2: 3.63 - 2.88 1.00 2711 122 0.1071 0.1404 5.2082 5.3268| | 3: 2.88 - 2.52 1.00 2681 148 0.1344 0.1655 5.1211 5.1945| | 4: 2.52 - 2.29 1.00 2661 139 0.0933 0.1444 4.618 4.9052| | 5: 2.29 - 2.13 1.00 2678 122 0.0959 0.1512 4.57 4.9084| | 6: 2.13 - 2.00 1.00 2692 117 0.1118 0.1731 4.5639 4.7653| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.92 1.00 0.96 6296.35| | 2: 3.63 - 2.88 2711 122 0.92 12.69 1.01 0.96 6296.35| | 3: 2.88 - 2.52 2681 148 0.88 18.84 0.99 0.96 6296.35| | 4: 2.52 - 2.29 2661 139 0.93 11.94 1.01 0.97 2065.05| | 5: 2.29 - 2.13 2678 122 0.92 13.96 1.00 0.97 2065.05| | 6: 2.13 - 2.00 2692 117 0.90 16.60 0.99 0.97 2065.05| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2065.05 max = 6296.35 mean = 4202.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.80 mean = 13.79| |phase err.(test): min = 0.00 max = 87.21 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1102 0.1487 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1543 0.1531 0.1794 n_refl.: 17040 remove outliers: r(all,work,free)=0.1543 0.1531 0.1794 n_refl.: 17040 overall B=-0.21 to atoms: r(all,work,free)=0.1531 0.1519 0.1787 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1103 0.1485 n_refl.: 17040 remove outliers: r(all,work,free)=0.1121 0.1103 0.1485 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 0.3542 303.220 281.850 0.555 1.005 0.340 11.894-9.307 99.02 97 4 0.1788 488.026 482.283 0.909 1.005 0.339 9.237-7.194 100.00 213 7 0.1765 399.156 401.708 0.989 1.006 0.208 7.162-5.571 100.00 427 22 0.1611 299.567 293.325 0.933 1.005 0.198 5.546-4.326 100.00 867 58 0.0937 411.258 408.177 0.963 1.005 0.180 4.315-3.360 100.00 1859 96 0.0865 391.110 388.936 1.002 1.003 0.171 3.356-2.611 100.00 3867 181 0.1217 256.937 254.852 0.998 1.001 0.058 2.608-2.000 99.99 8818 434 0.1035 167.479 166.238 0.989 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7190 ================= 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 : 0.2786 0.1812 0.082 5.250 8.8 119.3 19.9 258 0.000 1_bss: 0.1606 0.1649 0.082 5.250 8.5 118.9 19.5 258 0.000 1_settarget: 0.1606 0.1649 0.082 5.250 8.5 118.9 19.5 258 0.000 1_nqh: 0.1610 0.1657 0.082 5.250 8.5 118.9 19.5 258 0.006 1_weight: 0.1610 0.1657 0.082 5.250 8.5 118.9 19.5 258 0.006 1_xyzrec: 0.1350 0.1648 0.009 0.982 8.5 118.9 19.5 258 0.153 1_adp: 0.1276 0.1668 0.009 0.982 6.0 113.9 19.9 258 0.153 1_regHadp: 0.1279 0.1677 0.009 0.982 6.0 113.9 19.9 258 0.153 1_occ: 0.1274 0.1666 0.009 0.982 6.0 113.9 19.9 258 0.153 2_bss: 0.1271 0.1657 0.009 0.982 5.5 113.4 19.4 258 0.153 2_settarget: 0.1271 0.1657 0.009 0.982 5.5 113.4 19.4 258 0.153 2_updatecdl: 0.1271 0.1657 0.009 0.993 5.5 113.4 19.4 258 0.153 2_nqh: 0.1273 0.1656 0.009 0.993 5.5 113.4 19.4 258 0.147 2_sol: 0.1240 0.1569 0.009 0.993 5.5 112.5 20.6 358 n/a 2_weight: 0.1240 0.1569 0.009 0.993 5.5 112.5 20.6 358 n/a 2_xyzrec: 0.1214 0.1614 0.008 0.916 5.5 112.5 20.6 358 n/a 2_adp: 0.1197 0.1640 0.008 0.916 6.7 107.5 21.2 358 n/a 2_regHadp: 0.1199 0.1639 0.008 0.916 6.7 107.5 21.2 358 n/a 2_occ: 0.1196 0.1634 0.008 0.916 6.7 107.5 21.2 358 n/a 3_bss: 0.1193 0.1626 0.008 0.916 6.2 107.1 20.7 358 n/a 3_settarget: 0.1193 0.1626 0.008 0.916 6.2 107.1 20.7 358 n/a 3_updatecdl: 0.1193 0.1626 0.008 0.921 6.2 107.1 20.7 358 n/a 3_nqh: 0.1195 0.1627 0.008 0.921 6.2 107.1 20.7 358 n/a 3_sol: 0.1201 0.1558 0.008 0.921 6.2 107.1 20.7 393 n/a 3_weight: 0.1201 0.1558 0.008 0.921 6.2 107.1 20.7 393 n/a 3_xyzrec: 0.1182 0.1564 0.009 0.939 6.2 107.1 20.7 393 n/a 3_adp: 0.1166 0.1577 0.009 0.939 6.3 105.0 20.5 393 n/a 3_regHadp: 0.1166 0.1578 0.009 0.939 6.3 105.0 20.5 393 n/a 3_occ: 0.1155 0.1570 0.009 0.939 6.3 105.0 20.5 393 n/a 4_bss: 0.1152 0.1566 0.009 0.939 5.9 104.6 20.1 393 n/a 4_settarget: 0.1152 0.1566 0.009 0.939 5.9 104.6 20.1 393 n/a 4_updatecdl: 0.1152 0.1566 0.009 0.939 5.9 104.6 20.1 393 n/a 4_nqh: 0.1152 0.1562 0.009 0.939 5.9 104.6 20.1 393 n/a 4_sol: 0.1133 0.1497 0.009 0.939 5.9 104.6 20.8 451 n/a 4_weight: 0.1133 0.1497 0.009 0.939 5.9 104.6 20.8 451 n/a 4_xyzrec: 0.1116 0.1543 0.010 0.992 5.9 104.6 20.8 451 n/a 4_adp: 0.1107 0.1540 0.010 0.992 5.8 101.5 20.8 451 n/a 4_regHadp: 0.1107 0.1541 0.010 0.992 5.8 101.5 20.8 451 n/a 4_occ: 0.1100 0.1545 0.010 0.992 5.8 101.5 20.8 451 n/a 5_bss: 0.1096 0.1541 0.010 0.992 5.6 101.2 20.5 451 n/a 5_settarget: 0.1096 0.1541 0.010 0.992 5.6 101.2 20.5 451 n/a 5_updatecdl: 0.1096 0.1541 0.010 0.992 5.6 101.2 20.5 451 n/a 5_setrh: 0.1098 0.1539 0.010 0.992 5.6 101.2 20.5 451 n/a 5_nqh: 0.1098 0.1539 0.010 0.992 5.6 101.2 20.5 451 n/a 5_sol: 0.1102 0.1485 0.010 0.992 5.6 101.2 20.6 466 n/a 5_weight: 0.1102 0.1485 0.010 0.992 5.6 101.2 20.6 466 n/a 5_xyzrec: 0.1121 0.1499 0.011 1.064 5.6 101.2 20.6 466 n/a 5_adp: 0.1112 0.1492 0.011 1.064 5.5 99.9 20.8 466 n/a 5_regHadp: 0.1112 0.1492 0.011 1.064 5.5 99.9 20.8 466 n/a 5_occ: 0.1102 0.1487 0.011 1.064 5.5 99.9 20.8 466 n/a end: 0.1103 0.1485 0.011 1.064 5.3 99.6 20.6 466 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4279219_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4279219_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.5800 Refinement macro-cycles (run) : 908.2000 Write final files (write_after_run_outputs) : 22.2800 Total : 934.0600 Total CPU time: 15.98 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:59 PST -0800 (1735494059.55 s) Start R-work = 0.1606, R-free = 0.1649 Final R-work = 0.1103, R-free = 0.1485 =============================================================================== Job complete usr+sys time: 983.63 seconds wall clock time: 16 minutes 46.17 seconds (1006.17 seconds total)