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_6446528.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_6446528.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6446528.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: 1.19, per 1000 atoms: 0.35 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 119.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.92: 547 0.92 - 1.19: 1123 1.19 - 1.46: 744 1.46 - 1.73: 724 1.73 - 1.99: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.232 0.227 1.19e-02 7.06e+03 3.64e+02 bond pdb=" C SER A 121 " pdb=" O SER A 121 " ideal model delta sigma weight residual 1.234 1.455 -0.221 1.27e-02 6.20e+03 3.04e+02 bond pdb=" C ILE A 105 " pdb=" N CYS A 106 " ideal model delta sigma weight residual 1.332 1.574 -0.242 1.40e-02 5.10e+03 2.98e+02 bond pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " ideal model delta sigma weight residual 1.527 1.309 0.218 1.27e-02 6.20e+03 2.94e+02 bond pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 1.520 1.320 0.200 1.21e-02 6.83e+03 2.73e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 3315 4.95 - 9.90: 1822 9.90 - 14.85: 544 14.85 - 19.80: 87 19.80 - 24.75: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 141.59 -18.99 1.00e+00 1.00e+00 3.61e+02 angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 106.92 15.75 1.09e+00 8.42e-01 2.09e+02 angle pdb=" O VAL A 8 " pdb=" C VAL A 8 " pdb=" N ILE A 9 " ideal model delta sigma weight residual 123.20 137.66 -14.46 1.06e+00 8.90e-01 1.86e+02 angle pdb=" CA GLN A 95 " pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 120.55 134.58 -14.03 1.06e+00 8.90e-01 1.75e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.03 136.31 -13.28 1.11e+00 8.12e-01 1.43e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 18.03: 1330 18.03 - 36.04: 94 36.04 - 54.05: 44 54.05 - 72.06: 10 72.06 - 90.07: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -147.57 24.97 0 2.50e+00 1.60e-01 9.98e+01 dihedral pdb=" C VAL A 20 " pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta harmonic sigma weight residual -122.00 -143.79 21.79 0 2.50e+00 1.60e-01 7.60e+01 dihedral pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CA ALA A 183 " pdb=" CB ALA A 183 " ideal model delta harmonic sigma weight residual 122.90 144.59 -21.69 0 2.50e+00 1.60e-01 7.53e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.231: 96 0.231 - 0.460: 75 0.460 - 0.690: 53 0.690 - 0.919: 13 0.919 - 1.149: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.30e+01 chirality pdb=" CA PHE A 162 " pdb=" N PHE A 162 " pdb=" C PHE A 162 " pdb=" CB PHE A 162 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 1.37 1.12 2.00e-01 2.50e+01 3.14e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 45 " 0.010 2.00e-02 2.50e+03 8.86e-02 1.18e+02 pdb=" CD GLN A 45 " -0.167 2.00e-02 2.50e+03 pdb=" OE1 GLN A 45 " 0.095 2.00e-02 2.50e+03 pdb=" NE2 GLN A 45 " 0.062 2.00e-02 2.50e+03 pdb="HE21 GLN A 45 " 0.057 2.00e-02 2.50e+03 pdb="HE22 GLN A 45 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.062 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG PHE A 164 " 0.139 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.066 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.049 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.058 2.00e-02 2.50e+03 5.69e-02 9.71e+01 pdb=" CG PHE A 162 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.044 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.018 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1017 2.32 - 2.89: 8108 2.89 - 3.46: 10552 3.46 - 4.03: 15217 4.03 - 4.60: 21670 Nonbonded interactions: 56564 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.747 2.100 nonbonded pdb=" O LEU A 166 " pdb=" H GLU A 170 " model vdw 1.820 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.841 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.844 2.450 nonbonded pdb=" O GLU A 16 " pdb=" H VAL A 20 " model vdw 1.852 2.450 ... (remaining 56559 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_6446528_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= 0.2793 r_free= 0.1821 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.401128 | | target function (ml) not normalized (work): 71487.519412 | | target function (ml) not normalized (free): 3260.082257 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3197 0.2160 7.5485 5.0351| | 2: 3.63 - 2.88 1.00 2711 122 0.2664 0.1721 4.3268 4.3357| | 3: 2.88 - 2.52 1.00 2682 148 0.2541 0.1687 4.1877 4.192| | 4: 2.52 - 2.29 1.00 2661 139 0.2550 0.1518 3.5066 3.5632| | 5: 2.29 - 2.13 1.00 2678 122 0.2661 0.1589 3.378 3.456| | 6: 2.13 - 2.00 1.00 2692 117 0.2760 0.1740 3.2948 3.3608| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.68 0.77 0.23 1319.92| | 2: 3.63 - 2.88 2711 122 0.83 23.97 1.32 0.23 1319.92| | 3: 2.88 - 2.52 2682 148 0.73 32.91 1.28 0.23 1319.92| | 4: 2.52 - 2.29 2661 139 0.94 10.67 1.30 0.26 125.52| | 5: 2.29 - 2.13 2678 122 0.92 12.89 1.32 0.26 125.52| | 6: 2.13 - 2.00 2692 117 0.91 15.58 1.34 0.26 125.52| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 125.52 max = 1319.92 mean = 729.38| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.98 mean = 18.96| |phase err.(test): min = 0.00 max = 87.22 mean = 19.10| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.242 1557 Z= 5.374 Angle : 5.219 18.992 2118 Z= 3.663 Chirality : 0.412 1.149 243 Planarity : 0.032 0.167 284 Dihedral : 13.668 90.066 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 32.43 % 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: -2.24 (0.49), residues: 224 helix: -2.46 (0.40), residues: 109 sheet: -1.52 (0.69), residues: 30 loop : 0.37 (0.64), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.013 ARG A 145 TYR 0.134 0.039 TYR A 141 PHE 0.134 0.055 PHE A 164 HIS 0.055 0.031 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2793 r_free= 0.1821 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.401128 | | target function (ml) not normalized (work): 71487.519412 | | target function (ml) not normalized (free): 3260.082257 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3252 percent. r_work = 0.2926 r_free = 0.1997 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2873 0.2926 0.1997 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2873 0.2926 0.1997 n_refl.: 17050 remove outliers: r(all,work,free)=0.2165 0.2176 0.1997 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2139 0.2149 0.1981 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1628 0.1625 0.1679 n_refl.: 17045 remove outliers: r(all,work,free)=0.1626 0.1623 0.1679 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 0.3935 398.922 358.650 0.648 1.018 0.397 11.894-9.307 99.02 97 4 0.1917 633.582 614.708 0.918 1.018 0.370 9.237-7.194 100.00 213 7 0.2213 518.206 508.758 0.956 1.017 0.340 7.162-5.571 100.00 427 22 0.2367 388.914 375.324 0.920 1.016 0.279 5.546-4.326 100.00 867 58 0.1366 533.917 527.926 0.956 1.013 0.220 4.315-3.360 100.00 1859 96 0.1338 507.760 503.024 1.013 1.007 0.201 3.356-2.611 100.00 3867 181 0.1669 333.569 328.875 1.013 0.999 0.091 2.608-2.000 99.99 8818 434 0.1644 217.430 213.528 1.035 0.984 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4325 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1623 r_free=0.1679 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1627 r_free=0.1686 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.090996 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.001250 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1349 0.1636 0.0287 0.009 1.0 1.0 0.5 0.0 0 11.545 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.49 16.36 2.87 3.013 18.457 1.001 0.023 12.75 16.63 3.88 3.615 18.684 1.001 0.020 Individual atomic B min max mean iso aniso Overall: 5.94 113.90 19.91 4.14 1785 0 Protein: 5.94 113.89 17.13 4.14 1519 0 Water: 8.63 113.90 36.13 N/A 258 0 Other: 22.16 37.03 26.33 N/A 8 0 Chain A: 5.94 113.90 19.91 N/A 1785 0 Histogram: Values Number of atoms 5.94 - 16.74 1077 16.74 - 27.53 345 27.53 - 38.33 187 38.33 - 49.12 94 49.12 - 59.92 55 59.92 - 70.71 12 70.71 - 81.51 7 81.51 - 92.31 4 92.31 - 103.10 1 103.10 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1275 r_free=0.1663 r_work=0.1277 r_free=0.1669 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1277 r_free = 0.1669 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 = 0.1271 r_free = 0.1664 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.22 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= 0.1271 r_free= 0.1664 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019907 | | target function (ls_wunit_k1) not normalized (work): 323.208921 | | target function (ls_wunit_k1) not normalized (free): 27.212575 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1271 0.1664 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1894 0.1892 0.1985 n_refl.: 17043 remove outliers: r(all,work,free)=0.1894 0.1892 0.1985 n_refl.: 17043 overall B=-0.47 to atoms: r(all,work,free)=0.1861 0.1858 0.1966 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1289 0.1271 0.1657 n_refl.: 17043 remove outliers: r(all,work,free)=0.1289 0.1271 0.1657 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3612 307.557 284.606 0.646 1.007 0.387 11.894-9.307 99.02 97 4 0.1655 488.473 477.017 0.917 1.007 0.364 9.237-7.194 100.00 213 7 0.1855 399.521 395.310 0.958 1.007 0.351 7.162-5.571 100.00 427 22 0.1858 299.841 294.017 0.933 1.006 0.291 5.546-4.326 100.00 867 58 0.1046 411.634 408.854 0.957 1.005 0.206 4.315-3.360 100.00 1859 96 0.0929 391.468 390.769 1.015 1.004 0.192 3.356-2.611 100.00 3867 181 0.1290 257.172 255.811 1.010 1.001 0.101 2.608-2.000 99.99 8818 434 0.1340 167.632 166.301 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=-1.1733 ============================ 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 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1271 r_free=0.1658 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1271 r_free=0.1658 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1276 r_free=0.1647 | n_water=253 | time (s): 18.870 (total time: 19.530) Filter (q & B) r_work=0.1278 r_free=0.1649 | n_water=250 | time (s): 1.600 (total time: 21.130) Compute maps r_work=0.1278 r_free=0.1649 | n_water=250 | time (s): 0.500 (total time: 21.630) Filter (map) r_work=0.1319 r_free=0.1645 | n_water=207 | time (s): 1.460 (total time: 23.090) Find peaks r_work=0.1319 r_free=0.1645 | n_water=207 | time (s): 0.520 (total time: 23.610) Add new water r_work=0.1533 r_free=0.1852 | n_water=365 | time (s): 1.580 (total time: 25.190) Refine new water occ: r_work=0.1327 r_free=0.1580 adp: r_work=0.1272 r_free=0.1575 occ: r_work=0.1278 r_free=0.1552 adp: r_work=0.1247 r_free=0.1551 occ: r_work=0.1248 r_free=0.1546 adp: r_work=0.1236 r_free=0.1549 ADP+occupancy (water only), MIN, final r_work=0.1236 r_free=0.1549 r_work=0.1236 r_free=0.1549 | n_water=365 | time (s): 11.420 (total time: 36.610) Filter (q & B) r_work=0.1239 r_free=0.1558 | n_water=355 | time (s): 1.530 (total time: 38.140) Filter (dist only) r_work=0.1239 r_free=0.1560 | n_water=354 | time (s): 26.480 (total time: 64.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.601824 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.994304 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 0.1598 0.0384 0.009 0.9 2.2 0.5 0.0 0 12.801 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 15.98 3.84 4.199 20.857 0.994 0.018 12.00 16.14 4.14 4.272 21.101 0.994 0.018 Individual atomic B min max mean iso aniso Overall: 6.91 108.43 21.07 4.31 1881 0 Protein: 6.91 108.43 17.58 4.31 1519 0 Water: 8.28 65.71 35.82 N/A 354 0 Other: 23.65 40.88 31.49 N/A 8 0 Chain A: 6.91 108.43 19.21 N/A 1734 0 Chain S: 18.39 63.08 43.07 N/A 147 0 Histogram: Values Number of atoms 6.91 - 17.06 1064 17.06 - 27.21 353 27.21 - 37.37 210 37.37 - 47.52 152 47.52 - 57.67 72 57.67 - 67.82 20 67.82 - 77.97 3 77.97 - 88.12 5 88.12 - 98.27 0 98.27 - 108.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1614 r_work=0.1202 r_free=0.1614 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1614 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1603 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1197 r_free= 0.1603 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017113 | | target function (ls_wunit_k1) not normalized (work): 277.853108 | | target function (ls_wunit_k1) not normalized (free): 25.114886 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1197 0.1603 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1801 0.1797 0.1948 n_refl.: 17043 remove outliers: r(all,work,free)=0.1801 0.1797 0.1948 n_refl.: 17043 overall B=-0.41 to atoms: r(all,work,free)=0.1773 0.1768 0.1932 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1194 0.1602 n_refl.: 17043 remove outliers: r(all,work,free)=0.1213 0.1193 0.1602 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 0.3370 309.591 282.800 0.623 1.008 0.368 11.894-9.307 99.02 97 4 0.1529 488.473 485.104 0.914 1.008 0.335 9.237-7.194 100.00 213 7 0.1648 399.521 400.789 0.966 1.008 0.311 7.162-5.571 100.00 427 22 0.1557 299.841 296.121 0.937 1.007 0.269 5.546-4.326 100.00 867 58 0.0904 411.634 409.156 0.957 1.006 0.211 4.315-3.360 100.00 1859 96 0.0831 391.468 390.519 1.013 1.004 0.201 3.356-2.611 100.00 3867 181 0.1209 257.172 256.393 1.009 1.001 0.132 2.608-2.000 99.99 8818 434 0.1322 167.632 166.601 1.011 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1425 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1602 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=0.1607 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1607 | n_water=354 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1196 r_free=0.1609 | n_water=353 | time (s): 29.700 (total time: 30.610) Filter (q & B) r_work=0.1196 r_free=0.1609 | n_water=353 | time (s): 0.750 (total time: 31.360) Compute maps r_work=0.1196 r_free=0.1609 | n_water=353 | time (s): 0.680 (total time: 32.040) Filter (map) r_work=0.1265 r_free=0.1619 | n_water=257 | time (s): 1.620 (total time: 33.660) Find peaks r_work=0.1265 r_free=0.1619 | n_water=257 | time (s): 0.480 (total time: 34.140) Add new water r_work=0.1467 r_free=0.1861 | n_water=418 | time (s): 1.810 (total time: 35.950) Refine new water occ: r_work=0.1254 r_free=0.1619 adp: r_work=0.1248 r_free=0.1617 occ: r_work=0.1228 r_free=0.1596 adp: r_work=0.1218 r_free=0.1592 occ: r_work=0.1211 r_free=0.1577 adp: r_work=0.1199 r_free=0.1573 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1573 r_work=0.1199 r_free=0.1573 | n_water=418 | time (s): 28.520 (total time: 64.470) Filter (q & B) r_work=0.1201 r_free=0.1578 | n_water=408 | time (s): 1.930 (total time: 66.400) Filter (dist only) r_work=0.1200 r_free=0.1580 | n_water=406 | time (s): 32.660 (total time: 99.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.948941 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.179789 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 0.1183 0.1541 0.0358 0.009 1.0 4.5 0.5 0.0 0 0.974 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.83 15.41 3.58 4.348 21.273 0.180 5.005 11.63 15.56 3.93 4.900 21.178 0.180 4.980 Individual atomic B min max mean iso aniso Overall: 5.84 105.61 20.62 4.69 1933 0 Protein: 5.84 105.61 16.78 4.69 1519 0 Water: 8.70 61.36 34.77 N/A 406 0 Other: 22.91 40.06 30.03 N/A 8 0 Chain A: 5.84 105.61 18.45 N/A 1731 0 Chain S: 16.92 61.36 39.16 N/A 202 0 Histogram: Values Number of atoms 5.84 - 15.82 1055 15.82 - 25.80 360 25.80 - 35.77 229 35.77 - 45.75 172 45.75 - 55.73 78 55.73 - 65.70 25 65.70 - 75.68 6 75.68 - 85.66 3 85.66 - 95.64 3 95.64 - 105.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1163 r_free=0.1556 r_work=0.1164 r_free=0.1557 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1164 r_free = 0.1557 target_work(ml) = 4.980 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1152 r_free = 0.1546 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1152 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.972307 | | target function (ml) not normalized (work): 80725.408570 | | target function (ml) not normalized (free): 4198.040760 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1171 0.1152 0.1546 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1669 0.1662 0.1863 n_refl.: 17042 remove outliers: r(all,work,free)=0.1669 0.1662 0.1863 n_refl.: 17042 overall B=-0.34 to atoms: r(all,work,free)=0.1647 0.1639 0.1853 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1168 0.1149 0.1543 n_refl.: 17042 remove outliers: r(all,work,free)=0.1166 0.1147 0.1543 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 0.3591 303.497 284.941 0.567 1.006 0.334 11.894-9.307 99.02 97 4 0.1825 488.473 479.423 0.907 1.008 0.330 9.237-7.194 100.00 213 7 0.1812 399.521 401.341 0.979 1.008 0.255 7.162-5.571 100.00 427 22 0.1656 299.841 294.663 0.944 1.007 0.241 5.546-4.326 100.00 867 58 0.0941 411.634 407.983 0.962 1.006 0.201 4.315-3.360 100.00 1859 96 0.0891 391.468 389.239 1.012 1.004 0.201 3.356-2.611 100.00 3867 181 0.1293 257.172 254.834 1.010 1.001 0.058 2.608-2.000 99.99 8818 434 0.1078 167.632 166.160 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1608 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1147 r_free=0.1543 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=0.1147 r_free=0.1539 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1147 r_free=0.1539 | n_water=406 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1147 r_free=0.1543 | n_water=405 | time (s): 30.580 (total time: 31.480) Filter (q & B) r_work=0.1148 r_free=0.1543 | n_water=404 | time (s): 1.440 (total time: 32.920) Compute maps r_work=0.1148 r_free=0.1543 | n_water=404 | time (s): 0.530 (total time: 33.450) Filter (map) r_work=0.1209 r_free=0.1550 | n_water=315 | time (s): 1.600 (total time: 35.050) Find peaks r_work=0.1209 r_free=0.1550 | n_water=315 | time (s): 0.640 (total time: 35.690) Add new water r_work=0.1336 r_free=0.1677 | n_water=452 | time (s): 1.990 (total time: 37.680) Refine new water occ: r_work=0.1180 r_free=0.1505 adp: r_work=0.1174 r_free=0.1511 occ: r_work=0.1160 r_free=0.1485 adp: r_work=0.1152 r_free=0.1486 occ: r_work=0.1147 r_free=0.1474 adp: r_work=0.1140 r_free=0.1474 ADP+occupancy (water only), MIN, final r_work=0.1140 r_free=0.1474 r_work=0.1140 r_free=0.1474 | n_water=452 | time (s): 22.840 (total time: 60.520) Filter (q & B) r_work=0.1144 r_free=0.1487 | n_water=438 | time (s): 1.830 (total time: 62.350) Filter (dist only) r_work=0.1148 r_free=0.1486 | n_water=436 | time (s): 34.120 (total time: 96.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.000480 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.165281 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 0.1131 0.1521 0.0389 0.010 1.0 2.9 0.5 0.0 0 1.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 15.21 3.89 4.484 20.812 0.165 4.954 11.22 15.22 4.00 4.652 20.837 0.165 4.948 Individual atomic B min max mean iso aniso Overall: 5.67 103.08 20.67 4.83 1963 0 Protein: 5.67 103.08 16.38 4.83 1519 0 Water: 8.54 65.73 35.45 N/A 436 0 Other: 22.66 39.03 29.50 N/A 8 0 Chain A: 5.67 103.08 17.99 N/A 1729 0 Chain S: 16.24 65.73 40.49 N/A 234 0 Histogram: Values Number of atoms 5.67 - 15.41 1053 15.41 - 25.15 361 25.15 - 34.89 219 34.89 - 44.63 196 44.63 - 54.37 82 54.37 - 64.11 35 64.11 - 73.85 8 73.85 - 83.59 4 83.59 - 93.34 3 93.34 - 103.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1122 r_free=0.1522 r_work=0.1122 r_free=0.1523 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1122 r_free = 0.1523 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1115 r_free = 0.1524 target_work(ml) = 4.944 | | 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.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1115 r_free= 0.1524 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.943803 | | target function (ml) not normalized (work): 80252.749982 | | target function (ml) not normalized (free): 4175.615545 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1115 0.1524 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1569 0.1558 0.1819 n_refl.: 17040 remove outliers: r(all,work,free)=0.1569 0.1558 0.1819 n_refl.: 17040 overall B=-0.27 to atoms: r(all,work,free)=0.1553 0.1541 0.1811 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1132 0.1113 0.1517 n_refl.: 17040 remove outliers: r(all,work,free)=0.1132 0.1113 0.1517 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 0.3721 303.497 276.172 0.537 1.001 0.318 11.894-9.307 99.02 97 4 0.1916 488.473 477.860 0.912 1.003 0.310 9.237-7.194 100.00 213 7 0.1857 399.521 400.683 0.981 1.004 0.231 7.162-5.571 100.00 427 22 0.1643 299.841 293.487 0.939 1.004 0.212 5.546-4.326 100.00 867 58 0.0936 411.634 408.213 0.964 1.004 0.191 4.315-3.360 100.00 1859 96 0.0877 391.468 388.944 1.009 1.003 0.191 3.356-2.611 100.00 3867 181 0.1237 257.172 255.050 1.004 1.001 0.091 2.608-2.000 99.99 8818 434 0.1027 167.632 166.473 0.998 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9312 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1113 r_free=0.1517 After: r_work=0.1115 r_free=0.1515 ================================== NQH flips ================================== r_work=0.1115 r_free=0.1515 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1115 r_free=0.1515 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1115 r_free=0.1515 | n_water=436 | time (s): 0.850 (total time: 0.850) Filter (dist) r_work=0.1117 r_free=0.1521 | n_water=434 | time (s): 37.810 (total time: 38.660) Filter (q & B) r_work=0.1117 r_free=0.1521 | n_water=434 | time (s): 1.220 (total time: 39.880) Compute maps r_work=0.1117 r_free=0.1521 | n_water=434 | time (s): 0.710 (total time: 40.590) Filter (map) r_work=0.1171 r_free=0.1524 | n_water=348 | time (s): 2.210 (total time: 42.800) Find peaks r_work=0.1171 r_free=0.1524 | n_water=348 | time (s): 0.640 (total time: 43.440) Add new water r_work=0.1280 r_free=0.1614 | n_water=487 | time (s): 1.780 (total time: 45.220) Refine new water occ: r_work=0.1138 r_free=0.1498 adp: r_work=0.1131 r_free=0.1499 occ: r_work=0.1121 r_free=0.1488 adp: r_work=0.1113 r_free=0.1488 occ: r_work=0.1108 r_free=0.1480 adp: r_work=0.1102 r_free=0.1481 ADP+occupancy (water only), MIN, final r_work=0.1102 r_free=0.1481 r_work=0.1102 r_free=0.1481 | n_water=487 | time (s): 43.600 (total time: 88.820) Filter (q & B) r_work=0.1105 r_free=0.1490 | n_water=478 | time (s): 1.930 (total time: 90.750) Filter (dist only) r_work=0.1105 r_free=0.1491 | n_water=477 | time (s): 39.440 (total time: 130.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.979184 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.179621 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1115 0.1502 0.0387 0.010 1.0 6.4 0.5 0.0 0 0.990 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.15 15.02 3.87 4.525 20.708 0.180 4.940 11.06 14.96 3.91 4.592 20.789 0.180 4.934 Individual atomic B min max mean iso aniso Overall: 5.35 101.54 20.93 5.01 2004 0 Protein: 5.35 101.54 16.15 5.01 1519 0 Water: 8.30 66.58 36.01 N/A 477 0 Other: 22.18 38.10 28.80 N/A 8 0 Chain A: 5.35 101.54 17.72 N/A 1728 0 Chain S: 15.76 66.58 41.02 N/A 276 0 Histogram: Values Number of atoms 5.35 - 14.97 1047 14.97 - 24.59 359 24.59 - 34.21 224 34.21 - 43.83 197 43.83 - 53.45 121 53.45 - 63.07 32 63.07 - 72.68 15 72.68 - 82.30 2 82.30 - 91.92 3 91.92 - 101.54 4 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1496 r_work=0.1106 r_free=0.1497 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1497 target_work(ml) = 4.934 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1493 target_work(ml) = 4.929 | | occupancies: max = 1.00 min = 0.19 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= 0.1493 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.929228 | | target function (ml) not normalized (work): 80016.157553 | | target function (ml) not normalized (free): 4162.759746 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1130 0.1456 5.4638 5.7137| | 2: 3.63 - 2.88 1.00 2711 122 0.1092 0.1407 5.2221 5.3313| | 3: 2.88 - 2.52 1.00 2681 148 0.1337 0.1593 5.1304 5.1865| | 4: 2.52 - 2.29 1.00 2661 139 0.0912 0.1406 4.6092 4.8842| | 5: 2.29 - 2.13 1.00 2678 122 0.0940 0.1483 4.5625 4.8839| | 6: 2.13 - 2.00 1.00 2692 117 0.1109 0.1792 4.5571 4.7993| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.94 9.17 1.00 0.96 6480.48| | 2: 3.63 - 2.88 2711 122 0.92 12.91 1.01 0.96 6480.48| | 3: 2.88 - 2.52 2681 148 0.87 19.04 0.99 0.96 6480.48| | 4: 2.52 - 2.29 2661 139 0.93 11.88 1.01 0.97 2048.81| | 5: 2.29 - 2.13 2678 122 0.92 13.81 1.00 0.97 2048.81| | 6: 2.13 - 2.00 2692 117 0.90 16.54 0.99 0.97 2048.81| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2048.81 max = 6480.48 mean = 4287.99| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.97 mean = 13.86| |phase err.(test): min = 0.00 max = 89.20 mean = 13.62| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1120 0.1101 0.1493 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1533 0.1522 0.1772 n_refl.: 17040 remove outliers: r(all,work,free)=0.1533 0.1522 0.1772 n_refl.: 17040 overall B=-0.20 to atoms: r(all,work,free)=0.1522 0.1511 0.1766 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1119 0.1100 0.1491 n_refl.: 17040 remove outliers: r(all,work,free)=0.1119 0.1100 0.1491 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 0.3627 303.497 280.243 0.543 1.003 0.330 11.894-9.307 99.02 97 4 0.1753 488.473 480.303 0.903 1.005 0.330 9.237-7.194 100.00 213 7 0.1772 399.521 401.032 0.983 1.005 0.193 7.162-5.571 100.00 427 22 0.1659 299.841 294.000 0.933 1.005 0.192 5.546-4.326 100.00 867 58 0.0917 411.634 408.666 0.963 1.004 0.187 4.315-3.360 100.00 1859 96 0.0873 391.468 388.890 1.003 1.003 0.181 3.356-2.611 100.00 3867 181 0.1232 257.172 255.039 0.999 1.000 0.091 2.608-2.000 99.99 8818 434 0.1015 167.632 166.377 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.6954 ================= 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 : 0.2793 0.1821 0.081 5.219 8.8 119.3 19.9 258 0.000 1_bss: 0.1623 0.1679 0.081 5.219 8.4 118.9 19.5 258 0.000 1_settarget: 0.1623 0.1679 0.081 5.219 8.4 118.9 19.5 258 0.000 1_nqh: 0.1627 0.1686 0.081 5.219 8.4 118.9 19.5 258 0.006 1_weight: 0.1627 0.1686 0.081 5.219 8.4 118.9 19.5 258 0.006 1_xyzrec: 0.1349 0.1636 0.009 0.982 8.4 118.9 19.5 258 0.150 1_adp: 0.1275 0.1663 0.009 0.982 5.9 113.9 19.9 258 0.150 1_regHadp: 0.1277 0.1669 0.009 0.982 5.9 113.9 19.9 258 0.150 1_occ: 0.1271 0.1664 0.009 0.982 5.9 113.9 19.9 258 0.150 2_bss: 0.1271 0.1657 0.009 0.982 5.5 113.4 19.4 258 0.150 2_settarget: 0.1271 0.1657 0.009 0.982 5.5 113.4 19.4 258 0.150 2_updatecdl: 0.1271 0.1657 0.009 0.990 5.5 113.4 19.4 258 0.150 2_nqh: 0.1271 0.1658 0.009 0.990 5.5 113.4 19.4 258 0.144 2_sol: 0.1239 0.1560 0.009 0.990 5.5 113.4 20.6 354 n/a 2_weight: 0.1239 0.1560 0.009 0.990 5.5 113.4 20.6 354 n/a 2_xyzrec: 0.1214 0.1598 0.009 0.938 5.5 113.4 20.6 354 n/a 2_adp: 0.1200 0.1614 0.009 0.938 6.9 108.4 21.1 354 n/a 2_regHadp: 0.1202 0.1614 0.009 0.938 6.9 108.4 21.1 354 n/a 2_occ: 0.1197 0.1603 0.009 0.938 6.9 108.4 21.1 354 n/a 3_bss: 0.1193 0.1602 0.009 0.938 6.5 108.0 20.7 354 n/a 3_settarget: 0.1193 0.1602 0.009 0.938 6.5 108.0 20.7 354 n/a 3_updatecdl: 0.1193 0.1602 0.009 0.938 6.5 108.0 20.7 354 n/a 3_nqh: 0.1195 0.1607 0.009 0.938 6.5 108.0 20.7 354 n/a 3_sol: 0.1200 0.1580 0.009 0.938 6.5 108.0 20.8 406 n/a 3_weight: 0.1200 0.1580 0.009 0.938 6.5 108.0 20.8 406 n/a 3_xyzrec: 0.1183 0.1541 0.009 0.953 6.5 108.0 20.8 406 n/a 3_adp: 0.1163 0.1556 0.009 0.953 5.8 105.6 20.6 406 n/a 3_regHadp: 0.1164 0.1557 0.009 0.953 5.8 105.6 20.6 406 n/a 3_occ: 0.1152 0.1546 0.009 0.953 5.8 105.6 20.6 406 n/a 4_bss: 0.1147 0.1543 0.009 0.953 5.5 105.3 20.3 406 n/a 4_settarget: 0.1147 0.1543 0.009 0.953 5.5 105.3 20.3 406 n/a 4_updatecdl: 0.1147 0.1543 0.009 0.951 5.5 105.3 20.3 406 n/a 4_nqh: 0.1147 0.1539 0.009 0.951 5.5 105.3 20.3 406 n/a 4_sol: 0.1148 0.1486 0.009 0.951 5.5 105.3 20.6 436 n/a 4_weight: 0.1148 0.1486 0.009 0.951 5.5 105.3 20.6 436 n/a 4_xyzrec: 0.1131 0.1521 0.010 0.974 5.5 105.3 20.6 436 n/a 4_adp: 0.1122 0.1522 0.010 0.974 5.7 103.1 20.7 436 n/a 4_regHadp: 0.1122 0.1523 0.010 0.974 5.7 103.1 20.7 436 n/a 4_occ: 0.1115 0.1524 0.010 0.974 5.7 103.1 20.7 436 n/a 5_bss: 0.1113 0.1517 0.010 0.974 5.4 102.8 20.4 436 n/a 5_settarget: 0.1113 0.1517 0.010 0.974 5.4 102.8 20.4 436 n/a 5_updatecdl: 0.1113 0.1517 0.010 0.977 5.4 102.8 20.4 436 n/a 5_setrh: 0.1115 0.1515 0.010 0.977 5.4 102.8 20.4 436 n/a 5_nqh: 0.1115 0.1515 0.010 0.977 5.4 102.8 20.4 436 n/a 5_sol: 0.1105 0.1491 0.010 0.977 5.4 102.8 20.8 477 n/a 5_weight: 0.1105 0.1491 0.010 0.977 5.4 102.8 20.8 477 n/a 5_xyzrec: 0.1115 0.1502 0.010 1.024 5.4 102.8 20.8 477 n/a 5_adp: 0.1106 0.1496 0.010 1.024 5.3 101.5 20.9 477 n/a 5_regHadp: 0.1106 0.1497 0.010 1.024 5.3 101.5 20.9 477 n/a 5_occ: 0.1101 0.1493 0.010 1.024 5.3 101.5 20.9 477 n/a end: 0.1100 0.1491 0.010 1.024 5.1 101.3 20.7 477 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6446528_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6446528_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1000 Refinement macro-cycles (run) : 920.7000 Write final files (write_after_run_outputs) : 19.9700 Total : 943.7700 Total CPU time: 16.08 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:06 PST -0800 (1735494066.75 s) Start R-work = 0.1623, R-free = 0.1679 Final R-work = 0.1100, R-free = 0.1491 =============================================================================== Job complete usr+sys time: 989.17 seconds wall clock time: 16 minutes 52.66 seconds (1012.66 seconds total)