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_6712476.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6712476.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6712476.pdb" 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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.13, per 1000 atoms: 0.33 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: 0.29 Conformation dependent library (CDL) restraints added in 114.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 595 0.92 - 1.18: 1069 1.18 - 1.43: 675 1.43 - 1.69: 783 1.69 - 1.95: 31 Bond restraints: 3153 Sorted by residual: bond pdb=" C HIS A 126 " pdb=" O HIS A 126 " ideal model delta sigma weight residual 1.235 1.007 0.228 1.28e-02 6.10e+03 3.18e+02 bond pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta sigma weight residual 1.457 1.674 -0.217 1.23e-02 6.61e+03 3.11e+02 bond pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 1.236 1.060 0.175 1.01e-02 9.80e+03 3.01e+02 bond pdb=" N SER A 155 " pdb=" CA SER A 155 " ideal model delta sigma weight residual 1.457 1.654 -0.197 1.20e-02 6.94e+03 2.70e+02 bond pdb=" CA GLU A 147 " pdb=" C GLU A 147 " ideal model delta sigma weight residual 1.520 1.329 0.191 1.21e-02 6.83e+03 2.50e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.82: 3221 4.82 - 9.65: 1857 9.65 - 14.47: 594 14.47 - 19.29: 94 19.29 - 24.11: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1 GLN A 45 " pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 122.60 107.69 14.91 1.00e+00 1.00e+00 2.22e+02 angle pdb=" O ALA A 167 " pdb=" C ALA A 167 " pdb=" N ILE A 168 " ideal model delta sigma weight residual 122.12 136.72 -14.60 1.06e+00 8.90e-01 1.90e+02 angle pdb=" CA HIS A 115 " pdb=" CB HIS A 115 " pdb=" CG HIS A 115 " ideal model delta sigma weight residual 113.80 100.71 13.09 1.00e+00 1.00e+00 1.71e+02 angle pdb=" CA VAL A 25 " pdb=" C VAL A 25 " pdb=" N MET A 26 " ideal model delta sigma weight residual 117.02 131.02 -14.00 1.11e+00 8.12e-01 1.59e+02 angle pdb=" O LEU A 166 " pdb=" C LEU A 166 " pdb=" N ALA A 167 " ideal model delta sigma weight residual 122.12 108.87 13.25 1.06e+00 8.90e-01 1.56e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 1303 17.49 - 34.97: 124 34.97 - 52.46: 37 52.46 - 69.94: 14 69.94 - 87.43: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 151 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual -122.60 -143.76 21.16 0 2.50e+00 1.60e-01 7.16e+01 dihedral pdb=" C VAL A 186 " pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta harmonic sigma weight residual -122.00 -142.94 20.94 0 2.50e+00 1.60e-01 7.02e+01 dihedral pdb=" N VAL A 186 " pdb=" C VAL A 186 " pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta harmonic sigma weight residual 123.40 143.24 -19.84 0 2.50e+00 1.60e-01 6.30e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.213: 100 0.213 - 0.421: 63 0.421 - 0.629: 50 0.629 - 0.838: 24 0.838 - 1.046: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA ALA A 11 " pdb=" N ALA A 11 " pdb=" C ALA A 11 " pdb=" CB ALA A 11 " both_signs ideal model delta sigma weight residual False 2.48 3.48 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CA LYS A 12 " pdb=" N LYS A 12 " pdb=" C LYS A 12 " pdb=" CB LYS A 12 " both_signs ideal model delta sigma weight residual False 2.51 3.49 -0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.047 2.00e-02 2.50e+03 5.85e-02 1.03e+02 pdb=" CG PHE A 162 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.049 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.091 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.089 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.122 2.00e-02 2.50e+03 5.38e-02 8.69e+01 pdb=" CG PHE A 119 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.042 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.059 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 95 " -0.036 2.00e-02 2.50e+03 7.41e-02 8.23e+01 pdb=" CD GLN A 95 " -0.068 2.00e-02 2.50e+03 pdb=" OE1 GLN A 95 " 0.072 2.00e-02 2.50e+03 pdb=" NE2 GLN A 95 " 0.085 2.00e-02 2.50e+03 pdb="HE21 GLN A 95 " 0.055 2.00e-02 2.50e+03 pdb="HE22 GLN A 95 " -0.107 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1115 2.33 - 2.90: 8135 2.90 - 3.46: 10501 3.46 - 4.03: 15194 4.03 - 4.60: 21730 Nonbonded interactions: 56675 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.760 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.813 2.450 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.826 2.270 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.849 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.852 2.100 ... (remaining 56670 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_6712476_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= 0.2789 r_free= 0.1838 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.416146 | | target function (ml) not normalized (work): 71731.455172 | | target function (ml) not normalized (free): 3267.485013 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3190 0.2161 7.6044 5.0383| | 2: 3.63 - 2.88 1.00 2711 122 0.2632 0.1723 4.3205 4.3073| | 3: 2.88 - 2.52 1.00 2682 148 0.2579 0.1731 4.1788 4.1851| | 4: 2.52 - 2.29 1.00 2661 139 0.2558 0.1490 3.4991 3.5199| | 5: 2.29 - 2.13 1.00 2678 122 0.2660 0.1578 3.3955 3.5123| | 6: 2.13 - 2.00 1.00 2692 117 0.2740 0.1923 3.3321 3.4509| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.37 0.77 0.23 1281.42| | 2: 3.63 - 2.88 2711 122 0.83 23.58 1.31 0.23 1281.42| | 3: 2.88 - 2.52 2682 148 0.74 32.50 1.29 0.23 1281.42| | 4: 2.52 - 2.29 2661 139 0.93 11.71 1.30 0.26 140.38| | 5: 2.29 - 2.13 2678 122 0.92 14.00 1.32 0.26 140.38| | 6: 2.13 - 2.00 2692 117 0.90 16.58 1.34 0.26 140.38| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 140.38 max = 1281.42 mean = 717.26| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.87 mean = 19.29| |phase err.(test): min = 0.00 max = 88.77 mean = 19.31| |-----------------------------------------------------------------------------| ----------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 0.237 1557 Z= 5.394 Angle : 5.266 18.400 2118 Z= 3.699 Chirality : 0.406 1.046 243 Planarity : 0.031 0.102 284 Dihedral : 14.221 87.429 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 28.11 % 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: -2.48 (0.50), residues: 224 helix: -2.80 (0.36), residues: 103 sheet: -1.52 (0.78), residues: 38 loop : 0.39 (0.66), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.115 0.035 ARG A 28 TYR 0.087 0.033 TYR A 141 PHE 0.091 0.041 PHE A 119 HIS 0.081 0.037 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= 0.2789 r_free= 0.1838 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.416146 | | target function (ml) not normalized (work): 71731.455172 | | target function (ml) not normalized (free): 3267.485013 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2721 percent. r_work = 0.2916 r_free = 0.1986 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2863 0.2916 0.1986 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2863 0.2916 0.1986 n_refl.: 17050 remove outliers: r(all,work,free)=0.2158 0.2170 0.1986 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2131 0.2142 0.1969 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1618 0.1615 0.1680 n_refl.: 17045 remove outliers: r(all,work,free)=0.1616 0.1613 0.1680 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 0.3937 399.015 357.175 0.652 1.012 0.393 11.894-9.307 99.02 97 4 0.1858 633.730 615.208 0.928 1.013 0.375 9.237-7.194 100.00 213 7 0.2125 518.327 511.270 0.959 1.012 0.345 7.162-5.571 100.00 427 22 0.2326 389.005 375.743 0.922 1.011 0.321 5.546-4.326 100.00 867 58 0.1374 534.042 528.043 0.961 1.009 0.225 4.315-3.360 100.00 1859 96 0.1310 507.879 503.890 1.018 1.006 0.202 3.356-2.611 100.00 3867 181 0.1648 333.648 329.505 1.014 1.000 0.071 2.608-2.000 99.99 8818 434 0.1655 217.481 213.628 1.032 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4892 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1613 r_free=0.1680 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 173 ASN Total number of N/Q/H flips: 3 r_work=0.1618 r_free=0.1678 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.578486 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.936052 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 0.1352 0.1649 0.0297 0.008 1.0 1.0 0.5 0.0 0 11.289 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.49 2.97 3.013 18.441 0.936 0.023 12.80 16.72 3.92 3.673 18.718 0.936 0.020 Individual atomic B min max mean iso aniso Overall: 6.14 113.88 19.99 4.14 1785 0 Protein: 6.14 113.06 17.22 4.14 1519 0 Water: 9.13 113.88 36.09 N/A 258 0 Other: 21.84 38.11 26.51 N/A 8 0 Chain A: 6.14 113.88 19.99 N/A 1785 0 Histogram: Values Number of atoms 6.14 - 16.92 1080 16.92 - 27.69 344 27.69 - 38.46 186 38.46 - 49.24 99 49.24 - 60.01 49 60.01 - 70.79 13 70.79 - 81.56 6 81.56 - 92.33 4 92.33 - 103.11 1 103.11 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1280 r_free=0.1672 r_work=0.1284 r_free=0.1677 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1284 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 = 0.1277 r_free = 0.1682 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1277 r_free= 0.1682 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019951 | | target function (ls_wunit_k1) not normalized (work): 323.917118 | | target function (ls_wunit_k1) not normalized (free): 27.677320 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1297 0.1277 0.1682 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1904 0.1903 0.1991 n_refl.: 17043 remove outliers: r(all,work,free)=0.1904 0.1903 0.1991 n_refl.: 17043 overall B=-0.39 to atoms: r(all,work,free)=0.1876 0.1874 0.1975 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1296 0.1277 0.1678 n_refl.: 17043 remove outliers: r(all,work,free)=0.1296 0.1277 0.1678 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 0.3631 307.296 287.899 0.646 1.009 0.393 11.894-9.307 99.02 97 4 0.1697 488.058 477.140 0.915 1.010 0.365 9.237-7.194 100.00 213 7 0.1819 399.182 397.294 0.956 1.009 0.330 7.162-5.571 100.00 427 22 0.1850 299.587 294.373 0.929 1.009 0.311 5.546-4.326 100.00 867 58 0.1049 411.285 408.718 0.957 1.007 0.211 4.315-3.360 100.00 1859 96 0.0919 391.136 390.794 1.017 1.004 0.202 3.356-2.611 100.00 3867 181 0.1300 256.954 255.790 1.015 1.000 0.081 2.608-2.000 99.99 8818 434 0.1356 167.490 165.954 1.022 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3802 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1678 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 173 ASN Total number of N/Q/H flips: 2 r_work=0.1280 r_free=0.1680 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1280 r_free=0.1680 | n_water=258 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1285 r_free=0.1668 | n_water=254 | time (s): 20.810 (total time: 21.500) Filter (q & B) r_work=0.1284 r_free=0.1665 | n_water=252 | time (s): 1.650 (total time: 23.150) Compute maps r_work=0.1284 r_free=0.1665 | n_water=252 | time (s): 0.540 (total time: 23.690) Filter (map) r_work=0.1325 r_free=0.1657 | n_water=208 | time (s): 1.690 (total time: 25.380) Find peaks r_work=0.1325 r_free=0.1657 | n_water=208 | time (s): 0.590 (total time: 25.970) Add new water r_work=0.1558 r_free=0.1902 | n_water=369 | time (s): 2.070 (total time: 28.040) Refine new water occ: r_work=0.1342 r_free=0.1572 adp: r_work=0.1278 r_free=0.1580 occ: r_work=0.1284 r_free=0.1530 adp: r_work=0.1248 r_free=0.1549 occ: r_work=0.1249 r_free=0.1528 adp: r_work=0.1238 r_free=0.1537 ADP+occupancy (water only), MIN, final r_work=0.1238 r_free=0.1537 r_work=0.1238 r_free=0.1537 | n_water=369 | time (s): 24.230 (total time: 52.270) Filter (q & B) r_work=0.1239 r_free=0.1544 | n_water=363 | time (s): 1.650 (total time: 53.920) Filter (dist only) r_work=0.1240 r_free=0.1545 | n_water=362 | time (s): 28.940 (total time: 82.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.293380 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.984514 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 0.1211 0.1588 0.0377 0.008 0.9 2.9 0.5 0.0 0 12.147 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 15.88 3.77 4.205 21.113 0.985 0.018 11.98 16.03 4.04 4.201 21.374 0.985 0.018 Individual atomic B min max mean iso aniso Overall: 7.07 107.67 21.41 4.25 1889 0 Protein: 7.07 107.67 17.80 4.25 1519 0 Water: 8.53 74.86 36.40 N/A 362 0 Other: 23.20 38.30 28.98 N/A 8 0 Chain A: 7.07 107.67 19.43 N/A 1735 0 Chain S: 18.24 66.54 43.71 N/A 154 0 Histogram: Values Number of atoms 7.07 - 17.13 1047 17.13 - 27.19 363 27.19 - 37.25 221 37.25 - 47.31 147 47.31 - 57.37 76 57.37 - 67.43 24 67.43 - 77.49 4 77.49 - 87.55 3 87.55 - 97.61 2 97.61 - 107.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1603 r_work=0.1199 r_free=0.1604 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1604 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1599 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 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= 0.1195 r_free= 0.1599 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016891 | | target function (ls_wunit_k1) not normalized (work): 274.246383 | | target function (ls_wunit_k1) not normalized (free): 25.113270 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1195 0.1599 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1809 0.1806 0.1923 n_refl.: 17043 remove outliers: r(all,work,free)=0.1809 0.1806 0.1923 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1782 0.1779 0.1907 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1209 0.1189 0.1589 n_refl.: 17043 remove outliers: r(all,work,free)=0.1207 0.1188 0.1589 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 0.3323 306.733 285.337 0.623 1.007 0.380 11.894-9.307 99.02 97 4 0.1475 488.058 483.981 0.911 1.007 0.360 9.237-7.194 100.00 213 7 0.1605 399.182 400.977 0.974 1.006 0.290 7.162-5.571 100.00 427 22 0.1553 299.587 296.304 0.935 1.006 0.281 5.546-4.326 100.00 867 58 0.0861 411.285 408.090 0.957 1.005 0.210 4.315-3.360 100.00 1859 96 0.0837 391.136 390.576 1.013 1.004 0.201 3.356-2.611 100.00 3867 181 0.1199 256.954 256.207 1.011 1.001 0.111 2.608-2.000 99.99 8818 434 0.1328 167.490 166.447 1.016 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3378 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1589 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1589 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1589 | n_water=362 | time (s): 0.840 (total time: 0.840) Filter (dist) r_work=0.1187 r_free=0.1592 | n_water=361 | time (s): 29.720 (total time: 30.560) Filter (q & B) r_work=0.1187 r_free=0.1592 | n_water=361 | time (s): 1.000 (total time: 31.560) Compute maps r_work=0.1187 r_free=0.1592 | n_water=361 | time (s): 0.630 (total time: 32.190) Filter (map) r_work=0.1258 r_free=0.1618 | n_water=256 | time (s): 1.440 (total time: 33.630) Find peaks r_work=0.1258 r_free=0.1618 | n_water=256 | time (s): 0.440 (total time: 34.070) Add new water r_work=0.1453 r_free=0.1834 | n_water=405 | time (s): 1.750 (total time: 35.820) Refine new water occ: r_work=0.1246 r_free=0.1577 adp: r_work=0.1240 r_free=0.1591 occ: r_work=0.1218 r_free=0.1535 adp: r_work=0.1209 r_free=0.1550 occ: r_work=0.1198 r_free=0.1510 adp: r_work=0.1190 r_free=0.1520 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1520 r_work=0.1190 r_free=0.1520 | n_water=405 | time (s): 35.700 (total time: 71.520) Filter (q & B) r_work=0.1193 r_free=0.1524 | n_water=395 | time (s): 1.980 (total time: 73.500) Filter (dist only) r_work=0.1193 r_free=0.1524 | n_water=395 | time (s): 28.620 (total time: 102.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.867990 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.134550 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 0.1173 0.1546 0.0373 0.009 1.0 4.2 0.5 0.0 0 0.934 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.73 15.46 3.73 4.333 21.520 0.135 4.994 11.55 15.59 4.03 4.849 21.410 0.135 4.969 Individual atomic B min max mean iso aniso Overall: 6.50 105.73 20.79 4.56 1922 0 Protein: 6.50 105.73 17.04 4.56 1519 0 Water: 9.18 66.88 35.05 N/A 395 0 Other: 22.24 39.29 28.59 N/A 8 0 Chain A: 6.50 105.73 18.68 N/A 1731 0 Chain S: 14.11 66.88 39.96 N/A 191 0 Histogram: Values Number of atoms 6.50 - 16.42 1067 16.42 - 26.35 356 26.35 - 36.27 232 36.27 - 46.19 156 46.19 - 56.11 73 56.11 - 66.04 25 66.04 - 75.96 5 75.96 - 85.88 3 85.88 - 95.80 3 95.80 - 105.73 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1559 r_work=0.1156 r_free=0.1559 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1559 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1538 target_work(ml) = 4.961 | | 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= 0.1147 r_free= 0.1538 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.961273 | | target function (ml) not normalized (work): 80541.303457 | | target function (ml) not normalized (free): 4180.746776 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1166 0.1147 0.1538 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1670 0.1666 0.1806 n_refl.: 17041 remove outliers: r(all,work,free)=0.1670 0.1666 0.1806 n_refl.: 17041 overall B=-0.39 to atoms: r(all,work,free)=0.1643 0.1638 0.1795 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1145 0.1529 n_refl.: 17041 remove outliers: r(all,work,free)=0.1163 0.1144 0.1529 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 0.3489 303.239 283.849 0.588 1.007 0.360 11.894-9.307 99.02 97 4 0.1771 488.058 481.050 0.907 1.007 0.337 9.237-7.194 100.00 213 7 0.1752 399.182 400.395 0.988 1.007 0.267 7.162-5.571 100.00 427 22 0.1608 299.587 294.041 0.934 1.007 0.256 5.546-4.326 100.00 867 58 0.0949 411.285 407.255 0.962 1.006 0.201 4.315-3.360 100.00 1859 96 0.0907 391.136 388.699 1.009 1.004 0.191 3.356-2.611 100.00 3867 181 0.1274 256.954 254.916 1.013 1.001 0.142 2.608-2.000 99.99 8818 434 0.1084 167.490 166.119 1.020 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3792 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1144 r_free=0.1529 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** Total number of N/Q/H flips: 1 r_work=0.1145 r_free=0.1526 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1526 | n_water=395 | time (s): 0.750 (total time: 0.750) Filter (dist) r_work=0.1145 r_free=0.1524 | n_water=394 | time (s): 30.800 (total time: 31.550) Filter (q & B) r_work=0.1145 r_free=0.1524 | n_water=393 | time (s): 1.630 (total time: 33.180) Compute maps r_work=0.1145 r_free=0.1524 | n_water=393 | time (s): 0.830 (total time: 34.010) Filter (map) r_work=0.1201 r_free=0.1573 | n_water=305 | time (s): 2.110 (total time: 36.120) Find peaks r_work=0.1201 r_free=0.1573 | n_water=305 | time (s): 0.630 (total time: 36.750) Add new water r_work=0.1342 r_free=0.1705 | n_water=451 | time (s): 2.150 (total time: 38.900) Refine new water occ: r_work=0.1174 r_free=0.1497 adp: r_work=0.1167 r_free=0.1509 occ: r_work=0.1151 r_free=0.1466 adp: r_work=0.1142 r_free=0.1475 occ: r_work=0.1136 r_free=0.1446 adp: r_work=0.1129 r_free=0.1452 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1452 r_work=0.1129 r_free=0.1452 | n_water=451 | time (s): 32.850 (total time: 71.750) Filter (q & B) r_work=0.1132 r_free=0.1460 | n_water=438 | time (s): 2.040 (total time: 73.790) Filter (dist only) r_work=0.1132 r_free=0.1460 | n_water=438 | time (s): 35.130 (total time: 108.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.915094 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.171174 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1120 0.1513 0.0394 0.010 1.0 4.5 0.5 0.0 0 0.958 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.20 15.13 3.94 4.429 21.033 0.171 4.955 11.07 15.14 4.07 4.651 21.046 0.171 4.947 Individual atomic B min max mean iso aniso Overall: 5.70 103.85 20.87 4.87 1965 0 Protein: 5.70 103.85 16.56 4.86 1519 0 Water: 8.62 67.01 35.62 N/A 438 0 Other: 23.12 42.25 30.18 N/A 8 0 Chain A: 5.70 103.85 18.17 N/A 1731 0 Chain S: 16.14 67.01 40.79 N/A 234 0 Histogram: Values Number of atoms 5.70 - 15.51 1044 15.51 - 25.33 372 25.33 - 35.14 224 35.14 - 44.96 182 44.96 - 54.77 102 54.77 - 64.59 26 64.59 - 74.40 6 74.40 - 84.22 4 84.22 - 94.03 3 94.03 - 103.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1514 r_work=0.1107 r_free=0.1515 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1107 r_free = 0.1515 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1098 r_free = 0.1507 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1098 r_free= 0.1507 coordinate error (max.-lik. estimate): 0.12 A | | | | normalized target function (ml) (work): 4.939151 | | target function (ml) not normalized (work): 80177.238288 | | target function (ml) not normalized (free): 4169.010607 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1118 0.1098 0.1507 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1590 0.1579 0.1829 n_refl.: 17040 remove outliers: r(all,work,free)=0.1590 0.1579 0.1829 n_refl.: 17040 overall B=-0.28 to atoms: r(all,work,free)=0.1572 0.1561 0.1820 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1117 0.1097 0.1504 n_refl.: 17040 remove outliers: r(all,work,free)=0.1117 0.1097 0.1504 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 0.3735 303.239 278.215 0.569 1.003 0.360 11.894-9.307 99.02 97 4 0.1734 488.058 482.318 0.920 1.004 0.340 9.237-7.194 100.00 213 7 0.1687 399.182 400.235 0.989 1.004 0.250 7.162-5.571 100.00 427 22 0.1518 299.587 294.986 0.939 1.004 0.250 5.546-4.326 100.00 867 58 0.0910 411.285 407.928 0.963 1.004 0.191 4.315-3.360 100.00 1859 96 0.0847 391.136 388.965 1.005 1.003 0.191 3.356-2.611 100.00 3867 181 0.1223 256.954 254.886 1.004 1.001 0.131 2.608-2.000 99.99 8818 434 0.1042 167.490 166.394 1.001 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9853 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1097 r_free=0.1504 After: r_work=0.1099 r_free=0.1503 ================================== NQH flips ================================== r_work=0.1099 r_free=0.1503 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1099 r_free=0.1503 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1099 r_free=0.1503 | n_water=438 | time (s): 0.880 (total time: 0.880) Filter (dist) r_work=0.1102 r_free=0.1502 | n_water=437 | time (s): 36.980 (total time: 37.860) Filter (q & B) r_work=0.1102 r_free=0.1502 | n_water=436 | time (s): 1.720 (total time: 39.580) Compute maps r_work=0.1102 r_free=0.1502 | n_water=436 | time (s): 0.690 (total time: 40.270) Filter (map) r_work=0.1177 r_free=0.1558 | n_water=326 | time (s): 1.540 (total time: 41.810) Find peaks r_work=0.1177 r_free=0.1558 | n_water=326 | time (s): 0.450 (total time: 42.260) Add new water r_work=0.1290 r_free=0.1660 | n_water=454 | time (s): 1.770 (total time: 44.030) Refine new water occ: r_work=0.1142 r_free=0.1484 adp: r_work=0.1135 r_free=0.1491 occ: r_work=0.1123 r_free=0.1461 adp: r_work=0.1114 r_free=0.1468 occ: r_work=0.1111 r_free=0.1449 adp: r_work=0.1103 r_free=0.1454 ADP+occupancy (water only), MIN, final r_work=0.1103 r_free=0.1454 r_work=0.1103 r_free=0.1454 | n_water=454 | time (s): 21.440 (total time: 65.470) Filter (q & B) r_work=0.1105 r_free=0.1467 | n_water=445 | time (s): 1.950 (total time: 67.420) Filter (dist only) r_work=0.1105 r_free=0.1467 | n_water=445 | time (s): 34.550 (total time: 101.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.019337 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160183 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 0.1118 0.1485 0.0367 0.010 1.0 5.8 0.5 0.0 0 1.010 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 14.85 3.67 4.559 20.751 0.160 4.943 11.11 14.84 3.73 4.656 20.770 0.160 4.937 Individual atomic B min max mean iso aniso Overall: 5.50 103.34 20.72 4.98 1972 0 Protein: 5.50 103.34 16.23 4.98 1519 0 Water: 8.38 65.74 35.87 N/A 445 0 Other: 23.83 39.96 29.90 N/A 8 0 Chain A: 5.50 103.34 17.81 N/A 1730 0 Chain S: 16.76 65.74 41.52 N/A 242 0 Histogram: Values Number of atoms 5.50 - 15.28 1056 15.28 - 25.07 350 25.07 - 34.85 229 34.85 - 44.64 181 44.64 - 54.42 113 54.42 - 64.20 26 64.20 - 73.99 8 73.99 - 83.77 3 83.77 - 93.56 3 93.56 - 103.34 3 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1484 r_work=0.1111 r_free=0.1484 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1484 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1106 r_free = 0.1482 target_work(ml) = 4.932 | | 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= 0.1106 r_free= 0.1482 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.931907 | | target function (ml) not normalized (work): 80059.653331 | | target function (ml) not normalized (free): 4157.264087 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1124 0.1418 5.463 5.6807| | 2: 3.63 - 2.88 1.00 2711 122 0.1079 0.1372 5.2069 5.3102| | 3: 2.88 - 2.52 1.00 2681 148 0.1373 0.1642 5.1242 5.1853| | 4: 2.52 - 2.29 1.00 2661 139 0.0931 0.1502 4.6262 4.9539| | 5: 2.29 - 2.13 1.00 2678 122 0.0959 0.1422 4.5763 4.8575| | 6: 2.13 - 2.00 1.00 2692 117 0.1108 0.1726 4.5651 4.7654| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.74 1.00 0.96 6209.20| | 2: 3.63 - 2.88 2711 122 0.92 12.64 1.01 0.96 6209.20| | 3: 2.88 - 2.52 2681 148 0.88 18.73 0.99 0.96 6209.20| | 4: 2.52 - 2.29 2661 139 0.93 12.01 1.01 0.97 2098.69| | 5: 2.29 - 2.13 2678 122 0.91 14.16 1.00 0.97 2098.69| | 6: 2.13 - 2.00 2692 117 0.89 16.78 0.99 0.97 2098.69| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2098.69 max = 6209.20 mean = 4175.59| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.97 mean = 13.80| |phase err.(test): min = 0.00 max = 89.38 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1106 0.1482 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1574 0.1568 0.1735 n_refl.: 17040 remove outliers: r(all,work,free)=0.1574 0.1568 0.1735 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1561 0.1554 0.1727 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1108 0.1484 n_refl.: 17040 remove outliers: r(all,work,free)=0.1126 0.1108 0.1484 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 0.3718 303.239 275.935 0.569 1.002 0.360 11.894-9.307 99.02 97 4 0.1754 488.058 480.311 0.916 1.003 0.340 9.237-7.194 100.00 213 7 0.1749 399.182 402.209 0.991 1.003 0.250 7.162-5.571 100.00 427 22 0.1571 299.587 294.180 0.934 1.003 0.240 5.546-4.326 100.00 867 58 0.0937 411.285 408.547 0.964 1.003 0.190 4.315-3.360 100.00 1859 96 0.0867 391.136 389.007 1.003 1.002 0.191 3.356-2.611 100.00 3867 181 0.1241 256.954 254.655 0.999 1.001 0.091 2.608-2.000 99.99 8818 434 0.1034 167.490 166.218 0.989 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7786 ================= 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 : 0.2789 0.1838 0.082 5.266 8.8 119.3 19.9 258 0.000 1_bss: 0.1613 0.1680 0.082 5.266 8.4 118.9 19.5 258 0.000 1_settarget: 0.1613 0.1680 0.082 5.266 8.4 118.9 19.5 258 0.000 1_nqh: 0.1618 0.1678 0.082 5.266 8.4 118.9 19.5 258 0.009 1_weight: 0.1618 0.1678 0.082 5.266 8.4 118.9 19.5 258 0.009 1_xyzrec: 0.1352 0.1649 0.008 0.970 8.4 118.9 19.5 258 0.163 1_adp: 0.1280 0.1672 0.008 0.970 6.1 113.9 20.0 258 0.163 1_regHadp: 0.1284 0.1677 0.008 0.970 6.1 113.9 20.0 258 0.163 1_occ: 0.1277 0.1682 0.008 0.970 6.1 113.9 20.0 258 0.163 2_bss: 0.1277 0.1678 0.008 0.970 5.8 113.5 19.6 258 0.163 2_settarget: 0.1277 0.1678 0.008 0.970 5.8 113.5 19.6 258 0.163 2_updatecdl: 0.1277 0.1678 0.009 0.980 5.8 113.5 19.6 258 0.163 2_nqh: 0.1280 0.1680 0.009 0.980 5.8 113.5 19.6 258 0.157 2_sol: 0.1240 0.1545 0.009 0.980 5.8 112.7 20.9 362 n/a 2_weight: 0.1240 0.1545 0.009 0.980 5.8 112.7 20.9 362 n/a 2_xyzrec: 0.1211 0.1588 0.008 0.914 5.8 112.7 20.9 362 n/a 2_adp: 0.1198 0.1603 0.008 0.914 7.1 107.7 21.4 362 n/a 2_regHadp: 0.1199 0.1604 0.008 0.914 7.1 107.7 21.4 362 n/a 2_occ: 0.1195 0.1599 0.008 0.914 7.1 107.7 21.4 362 n/a 3_bss: 0.1188 0.1589 0.008 0.914 6.7 107.3 21.0 362 n/a 3_settarget: 0.1188 0.1589 0.008 0.914 6.7 107.3 21.0 362 n/a 3_updatecdl: 0.1188 0.1589 0.008 0.914 6.7 107.3 21.0 362 n/a 3_nqh: 0.1188 0.1589 0.008 0.914 6.7 107.3 21.0 362 n/a 3_sol: 0.1193 0.1524 0.008 0.914 6.7 107.3 21.0 395 n/a 3_weight: 0.1193 0.1524 0.008 0.914 6.7 107.3 21.0 395 n/a 3_xyzrec: 0.1173 0.1546 0.009 0.968 6.7 107.3 21.0 395 n/a 3_adp: 0.1155 0.1559 0.009 0.968 6.5 105.7 20.8 395 n/a 3_regHadp: 0.1156 0.1559 0.009 0.968 6.5 105.7 20.8 395 n/a 3_occ: 0.1147 0.1538 0.009 0.968 6.5 105.7 20.8 395 n/a 4_bss: 0.1144 0.1529 0.009 0.968 6.1 105.3 20.4 395 n/a 4_settarget: 0.1144 0.1529 0.009 0.968 6.1 105.3 20.4 395 n/a 4_updatecdl: 0.1144 0.1529 0.009 0.966 6.1 105.3 20.4 395 n/a 4_nqh: 0.1145 0.1526 0.009 0.966 6.1 105.3 20.4 395 n/a 4_sol: 0.1132 0.1460 0.009 0.966 6.1 105.3 20.8 438 n/a 4_weight: 0.1132 0.1460 0.009 0.966 6.1 105.3 20.8 438 n/a 4_xyzrec: 0.1120 0.1513 0.010 1.001 6.1 105.3 20.8 438 n/a 4_adp: 0.1107 0.1514 0.010 1.001 5.7 103.8 20.9 438 n/a 4_regHadp: 0.1107 0.1515 0.010 1.001 5.7 103.8 20.9 438 n/a 4_occ: 0.1098 0.1507 0.010 1.001 5.7 103.8 20.9 438 n/a 5_bss: 0.1097 0.1504 0.010 1.001 5.4 103.6 20.6 438 n/a 5_settarget: 0.1097 0.1504 0.010 1.001 5.4 103.6 20.6 438 n/a 5_updatecdl: 0.1097 0.1504 0.010 1.002 5.4 103.6 20.6 438 n/a 5_setrh: 0.1099 0.1503 0.010 1.002 5.4 103.6 20.6 438 n/a 5_nqh: 0.1099 0.1503 0.010 1.002 5.4 103.6 20.6 438 n/a 5_sol: 0.1105 0.1467 0.010 1.002 5.4 103.6 20.7 445 n/a 5_weight: 0.1105 0.1467 0.010 1.002 5.4 103.6 20.7 445 n/a 5_xyzrec: 0.1118 0.1485 0.010 1.035 5.4 103.6 20.7 445 n/a 5_adp: 0.1111 0.1484 0.010 1.035 5.5 103.3 20.7 445 n/a 5_regHadp: 0.1111 0.1484 0.010 1.035 5.5 103.3 20.7 445 n/a 5_occ: 0.1106 0.1482 0.010 1.035 5.5 103.3 20.7 445 n/a end: 0.1108 0.1484 0.010 1.035 5.3 103.1 20.5 445 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6712476_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6712476_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1800 Refinement macro-cycles (run) : 932.4000 Write final files (write_after_run_outputs) : 21.4900 Total : 957.0700 Total CPU time: 16.28 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:18 PST -0800 (1735494078.83 s) Start R-work = 0.1613, R-free = 0.1680 Final R-work = 0.1108, R-free = 0.1484 =============================================================================== Job complete usr+sys time: 1000.89 seconds wall clock time: 17 minutes 4.36 seconds (1024.36 seconds total)