Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4023827.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=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4023827.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4023827.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.74, per 1000 atoms: 0.51 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 134.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 502 0.91 - 1.16: 1128 1.16 - 1.41: 621 1.41 - 1.66: 847 1.66 - 1.91: 55 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 117 " pdb=" O ILE A 117 " ideal model delta sigma weight residual 1.237 1.452 -0.215 1.10e-02 8.26e+03 3.83e+02 bond pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 1.329 1.531 -0.201 1.13e-02 7.83e+03 3.18e+02 bond pdb=" C ALA A 179 " pdb=" O ALA A 179 " ideal model delta sigma weight residual 1.237 1.443 -0.207 1.16e-02 7.43e+03 3.17e+02 bond pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 1.446 1.598 -0.151 8.70e-03 1.32e+04 3.02e+02 bond pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta sigma weight residual 1.461 1.662 -0.201 1.17e-02 7.31e+03 2.94e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 3028 4.41 - 8.81: 1860 8.81 - 13.22: 705 13.22 - 17.62: 166 17.62 - 22.03: 18 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" C ARG A 156 " ideal model delta sigma weight residual 113.50 132.47 -18.97 1.23e+00 6.61e-01 2.38e+02 angle pdb=" O BGLU A 90 " pdb=" C BGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.12 136.84 -14.72 1.06e+00 8.90e-01 1.93e+02 angle pdb=" CA MET A 134 " pdb=" C MET A 134 " pdb=" O MET A 134 " ideal model delta sigma weight residual 119.28 134.81 -15.53 1.21e+00 6.83e-01 1.65e+02 angle pdb=" CA GLY A 108 " pdb=" C GLY A 108 " pdb=" O GLY A 108 " ideal model delta sigma weight residual 119.69 111.84 7.85 6.30e-01 2.52e+00 1.55e+02 angle pdb=" O ARG A 27 " pdb=" C ARG A 27 " pdb=" N ARG A 28 " ideal model delta sigma weight residual 122.15 136.24 -14.09 1.14e+00 7.69e-01 1.53e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 1305 17.43 - 34.85: 127 34.85 - 52.28: 30 52.28 - 69.71: 15 69.71 - 87.14: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 25 " pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual -122.00 -145.89 23.89 0 2.50e+00 1.60e-01 9.13e+01 dihedral pdb=" C THR A 160 " pdb=" N THR A 160 " pdb=" CA THR A 160 " pdb=" CB THR A 160 " ideal model delta harmonic sigma weight residual -122.00 -141.21 19.21 0 2.50e+00 1.60e-01 5.91e+01 dihedral pdb=" N BLYS A 41 " pdb=" C BLYS A 41 " pdb=" CA BLYS A 41 " pdb=" CB BLYS A 41 " ideal model delta harmonic sigma weight residual 122.80 141.35 -18.55 0 2.50e+00 1.60e-01 5.50e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.235: 122 0.235 - 0.465: 71 0.465 - 0.695: 36 0.695 - 0.925: 12 0.925 - 1.155: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.67 -1.15 2.00e-01 2.50e+01 3.33e+01 chirality pdb=" CA BLEU A 153 " pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CB BLEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.45 -0.94 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" CA THR A 160 " pdb=" N THR A 160 " pdb=" C THR A 160 " pdb=" CB THR A 160 " both_signs ideal model delta sigma weight residual False 2.53 1.62 0.91 2.00e-01 2.50e+01 2.06e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.012 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG BTYR A 67 " -0.037 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.071 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.117 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.034 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.069 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.094 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.108 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.029 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.066 2.00e-02 2.50e+03 6.94e-02 1.09e+02 pdb=" CG HIS A 126 " -0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.098 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.097 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.020 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.109 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.044 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.022 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.139 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.038 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.040 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1259 2.35 - 2.91: 8260 2.91 - 3.48: 10522 3.48 - 4.04: 15154 4.04 - 4.60: 21363 Nonbonded interactions: 56558 Sorted by model distance: nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.791 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.812 2.270 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.820 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.825 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.845 2.450 ... (remaining 56553 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 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 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_4023827_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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3619 r_free= 0.2020 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474589 | | target function (ml) not normalized (work): 22059.725929 | | target function (ml) not normalized (free): 1151.584658 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3799 0.2210 4.854 4.9124| | 2: 3.78 - 3.00 1.00 2430 110 0.3400 0.1698 4.0843 4.1274| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2500 142 0.50 48.87 0.83 0.13 6615.76| | 2: 3.78 - 3.00 2430 110 0.94 11.30 1.48 0.26 454.40| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 386.18 max = 12080.23 mean = 3578.82| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.35| |phase err.(test): min = 0.00 max = 89.96 mean = 33.43| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.240 1557 Z= 5.502 Angle : 5.255 18.971 2118 Z= 3.703 Chirality : 0.369 1.155 243 Planarity : 0.033 0.120 284 Dihedral : 14.232 87.135 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 29.73 % 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: -2.63 (0.47), residues: 224 helix: -2.43 (0.40), residues: 108 sheet: -0.87 (0.81), residues: 38 loop : -0.73 (0.56), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.020 ARG A 28 TYR 0.121 0.038 TYR A 139 PHE 0.103 0.040 PHE A 162 HIS 0.071 0.039 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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3619 r_free= 0.2020 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474589 | | target function (ml) not normalized (work): 22059.725929 | | target function (ml) not normalized (free): 1151.584658 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3575 0.3652 0.2110 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3575 0.3652 0.2110 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2551 0.2110 n_refl.: 5178 overall B=-2.43 to atoms: r(all,work,free)=0.2431 0.2453 0.2075 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1572 0.1572 0.1575 n_refl.: 5178 remove outliers: r(all,work,free)=0.1568 0.1568 0.1575 n_refl.: 5176 ======================== 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 0.3862 449.507 405.966 0.627 1.075 0.398 11.894-9.307 99.02 97 4 0.1858 714.078 692.795 0.894 1.072 0.377 9.237-7.194 100.00 213 7 0.2199 583.974 575.225 0.927 1.064 0.374 7.162-5.571 100.00 427 22 0.2366 438.201 421.934 0.897 1.050 0.298 5.546-4.326 100.00 867 58 0.1389 601.588 595.357 0.946 1.027 0.224 4.315-3.360 100.00 1859 96 0.1310 572.117 566.124 1.026 0.988 0.188 3.356-3.002 100.00 1373 60 0.1611 440.669 433.620 1.044 0.949 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.2096 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1568 r_free=0.1575 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 A 180 GLN Total number of N/Q/H flips: 3 r_work=0.1571 r_free=0.1574 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.107791 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.923865 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1154 0.1758 0.0604 0.010 1.0 2.2 0.5 0.0 0 9.554 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.54 17.58 6.04 3.012 16.432 1.924 0.018 10.10 17.49 7.40 4.929 16.630 1.924 0.014 Individual atomic B min max mean iso aniso Overall: 2.48 111.96 17.83 5.32 1785 0 Protein: 2.48 111.96 15.12 5.31 1519 0 Water: 4.44 111.87 33.61 N/A 258 0 Other: 16.59 38.40 24.51 N/A 8 0 Chain A: 2.48 111.96 17.83 N/A 1785 0 Histogram: Values Number of atoms 2.48 - 13.42 911 13.42 - 24.37 482 24.37 - 35.32 191 35.32 - 46.27 115 46.27 - 57.22 55 57.22 - 68.16 14 68.16 - 79.11 8 79.11 - 90.06 5 90.06 - 101.01 1 101.01 - 111.96 3 =========================== Idealize ADP of riding H ========================== r_work=0.1010 r_free=0.1749 r_work=0.1003 r_free=0.1754 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1003 r_free = 0.1754 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0998 r_free = 0.1767 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0998 r_free= 0.1767 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013543 | | target function (ls_wunit_k1) not normalized (work): 66.684550 | | target function (ls_wunit_k1) not normalized (free): 10.380111 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1037 0.0998 0.1767 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2107 0.2107 0.2222 n_refl.: 5176 remove outliers: r(all,work,free)=0.2107 0.2107 0.2222 n_refl.: 5176 overall B=-1.06 to atoms: r(all,work,free)=0.2062 0.2060 0.2212 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1040 0.1001 0.1772 n_refl.: 5176 remove outliers: r(all,work,free)=0.1040 0.1001 0.1772 n_refl.: 5176 ======================== 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 0.3307 317.841 301.981 0.663 1.038 0.387 11.894-9.307 99.02 97 4 0.1502 504.916 497.357 0.960 1.037 0.356 9.237-7.194 100.00 213 7 0.1631 412.921 413.444 0.995 1.033 0.315 7.162-5.571 100.00 427 22 0.1608 309.847 306.802 0.965 1.025 0.292 5.546-4.326 100.00 867 58 0.0897 425.376 422.788 0.991 1.013 0.197 4.315-3.360 100.00 1859 96 0.0755 404.537 404.524 1.056 0.993 0.183 3.356-3.002 100.00 1373 60 0.0997 311.592 310.229 1.048 0.972 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.7858 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1001 r_free=0.1772 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1003 r_free=0.1775 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1003 r_free=0.1775 | n_water=258 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1039 r_free=0.1773 | n_water=247 | time (s): 20.000 (total time: 20.710) Filter (q & B) r_work=0.1039 r_free=0.1776 | n_water=244 | time (s): 1.740 (total time: 22.450) Compute maps r_work=0.1039 r_free=0.1776 | n_water=244 | time (s): 0.480 (total time: 22.930) Filter (map) r_work=0.1374 r_free=0.1800 | n_water=139 | time (s): 1.410 (total time: 24.340) Find peaks r_work=0.1374 r_free=0.1800 | n_water=139 | time (s): 0.490 (total time: 24.830) Add new water r_work=0.1706 r_free=0.2054 | n_water=219 | time (s): 1.690 (total time: 26.520) Refine new water occ: r_work=0.1167 r_free=0.1672 adp: r_work=0.1147 r_free=0.1676 occ: r_work=0.1145 r_free=0.1653 adp: r_work=0.1135 r_free=0.1664 occ: r_work=0.1135 r_free=0.1653 adp: r_work=0.1132 r_free=0.1653 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1653 r_work=0.1132 r_free=0.1653 | n_water=219 | time (s): 3.970 (total time: 30.490) Filter (q & B) r_work=0.1132 r_free=0.1653 | n_water=219 | time (s): 0.700 (total time: 31.190) Filter (dist only) r_work=0.1133 r_free=0.1647 | n_water=218 | time (s): 15.470 (total time: 46.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.466949 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.659280 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1011 0.1822 0.0811 0.009 1.0 3.8 0.5 0.6 0 11.733 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.11 18.22 8.11 4.709 17.048 2.659 0.014 9.47 18.40 8.94 5.377 17.392 2.659 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.33 16.67 6.36 1745 0 Protein: 0.00 108.33 15.22 6.34 1519 0 Water: 0.00 63.10 26.53 N/A 218 0 Other: 11.22 38.86 22.72 N/A 8 0 Chain A: 0.00 108.33 15.91 N/A 1665 0 Chain S: 5.10 60.36 32.42 N/A 80 0 Histogram: Values Number of atoms 0.00 - 10.83 655 10.83 - 21.67 685 21.67 - 32.50 218 32.50 - 43.33 109 43.33 - 54.17 36 54.17 - 65.00 28 65.00 - 75.83 8 75.83 - 86.67 2 86.67 - 97.50 2 97.50 - 108.33 2 =========================== Idealize ADP of riding H ========================== r_work=0.0947 r_free=0.1840 r_work=0.0944 r_free=0.1840 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0944 r_free = 0.1840 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0940 r_free = 0.1829 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0940 r_free= 0.1829 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011912 | | target function (ls_wunit_k1) not normalized (work): 58.656526 | | target function (ls_wunit_k1) not normalized (free): 10.229015 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0984 0.0940 0.1829 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2134 0.2140 0.2200 n_refl.: 5176 remove outliers: r(all,work,free)=0.2134 0.2140 0.2200 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2134 0.2140 0.2200 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0988 0.0943 0.1849 n_refl.: 5176 remove outliers: r(all,work,free)=0.0988 0.0943 0.1849 n_refl.: 5176 ======================== 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 0.3225 317.841 303.238 0.702 1.006 0.381 11.894-9.307 99.02 97 4 0.1396 504.916 501.210 0.990 1.008 0.360 9.237-7.194 100.00 213 7 0.1458 412.921 414.918 1.019 1.008 0.310 7.162-5.571 100.00 427 22 0.1408 309.847 307.842 0.989 1.007 0.300 5.546-4.326 100.00 867 58 0.0812 425.376 422.988 1.007 1.004 0.230 4.315-3.360 100.00 1859 96 0.0727 404.537 404.292 1.059 0.998 0.194 3.356-3.002 100.00 1373 60 0.0984 311.592 310.083 1.037 0.993 0.083 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.3143 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0943 r_free=0.1849 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0948 r_free=0.1849 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0948 r_free=0.1849 | n_water=218 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0980 r_free=0.1877 | n_water=212 | time (s): 16.860 (total time: 17.440) Filter (q & B) r_work=0.1061 r_free=0.1847 | n_water=209 | time (s): 1.910 (total time: 19.350) Compute maps r_work=0.1061 r_free=0.1847 | n_water=209 | time (s): 0.630 (total time: 19.980) Filter (map) r_work=0.1293 r_free=0.1916 | n_water=143 | time (s): 1.830 (total time: 21.810) Find peaks r_work=0.1293 r_free=0.1916 | n_water=143 | time (s): 0.610 (total time: 22.420) Add new water r_work=0.1702 r_free=0.2269 | n_water=231 | time (s): 1.840 (total time: 24.260) Refine new water occ: r_work=0.1083 r_free=0.1757 adp: r_work=0.1078 r_free=0.1784 occ: r_work=0.1062 r_free=0.1755 adp: r_work=0.1063 r_free=0.1769 occ: r_work=0.1050 r_free=0.1742 adp: r_work=0.1051 r_free=0.1754 ADP+occupancy (water only), MIN, final r_work=0.1051 r_free=0.1754 r_work=0.1051 r_free=0.1754 | n_water=231 | time (s): 11.220 (total time: 35.480) Filter (q & B) r_work=0.1051 r_free=0.1753 | n_water=229 | time (s): 1.650 (total time: 37.130) Filter (dist only) r_work=0.1062 r_free=0.1770 | n_water=228 | time (s): 18.060 (total time: 55.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.155883 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.221352 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0960 0.1865 0.0904 0.011 1.1 3.8 0.5 0.0 0 0.578 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.60 18.65 9.04 5.349 17.981 0.221 5.134 9.12 18.58 9.47 7.414 17.979 0.221 5.030 Individual atomic B min max mean iso aniso Overall: 0.00 107.97 16.56 9.12 1755 0 Protein: 0.00 107.97 15.34 9.10 1519 0 Water: 0.00 58.81 24.47 N/A 228 0 Other: 11.75 42.48 23.19 N/A 8 0 Chain A: 0.00 107.97 16.01 N/A 1651 0 Chain S: 0.00 58.81 25.33 N/A 104 0 Histogram: Values Number of atoms 0.00 - 10.80 676 10.80 - 21.60 656 21.60 - 32.39 237 32.39 - 43.19 116 43.19 - 53.99 31 53.99 - 64.78 20 64.78 - 75.58 11 75.58 - 86.38 3 86.38 - 97.18 4 97.18 - 107.97 1 =========================== Idealize ADP of riding H ========================== r_work=0.0912 r_free=0.1858 r_work=0.0917 r_free=0.1871 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0917 r_free = 0.1871 target_work(ml) = 5.034 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0903 r_free = 0.1848 target_work(ml) = 5.024 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0903 r_free= 0.1848 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.024104 | | target function (ml) not normalized (work): 24738.686757 | | target function (ml) not normalized (free): 1863.506752 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0951 0.0903 0.1848 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2157 0.2170 0.2111 n_refl.: 5176 remove outliers: r(all,work,free)=0.2157 0.2170 0.2111 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2157 0.2170 0.2111 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0941 0.0894 0.1831 n_refl.: 5176 remove outliers: r(all,work,free)=0.0937 0.0889 0.1831 n_refl.: 5174 ======================== 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 0.3595 317.260 287.029 0.604 0.995 0.340 11.894-9.307 99.02 97 4 0.1772 504.916 489.438 0.952 0.999 0.340 9.237-7.194 100.00 213 7 0.1898 412.921 408.906 1.002 1.000 0.320 7.162-5.571 100.00 427 22 0.1902 309.847 300.780 0.974 1.001 0.259 5.546-4.326 100.00 867 58 0.0928 425.376 421.079 1.007 1.002 0.240 4.315-3.360 100.00 1859 96 0.0590 404.537 404.111 1.067 1.002 0.200 3.356-3.002 100.00 1373 60 0.0588 311.592 310.805 1.044 1.003 0.066 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9175 b_overall=-6.8558 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0889 r_free=0.1831 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0891 r_free=0.1828 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0891 r_free=0.1828 | n_water=228 | time (s): 0.460 (total time: 0.460) Filter (dist) r_work=0.0912 r_free=0.1848 | n_water=222 | time (s): 19.090 (total time: 19.550) Filter (q & B) r_work=0.0966 r_free=0.1883 | n_water=220 | time (s): 1.500 (total time: 21.050) Compute maps r_work=0.0966 r_free=0.1883 | n_water=220 | time (s): 0.560 (total time: 21.610) Filter (map) r_work=0.1219 r_free=0.1954 | n_water=153 | time (s): 1.460 (total time: 23.070) Find peaks r_work=0.1219 r_free=0.1954 | n_water=153 | time (s): 0.450 (total time: 23.520) Add new water r_work=0.1532 r_free=0.2291 | n_water=227 | time (s): 1.280 (total time: 24.800) Refine new water occ: r_work=0.1014 r_free=0.1889 adp: r_work=0.1009 r_free=0.1900 occ: r_work=0.1000 r_free=0.1880 adp: r_work=0.0999 r_free=0.1888 occ: r_work=0.0991 r_free=0.1870 adp: r_work=0.0990 r_free=0.1878 ADP+occupancy (water only), MIN, final r_work=0.0990 r_free=0.1878 r_work=0.0990 r_free=0.1878 | n_water=227 | time (s): 12.790 (total time: 37.590) Filter (q & B) r_work=0.0991 r_free=0.1879 | n_water=225 | time (s): 1.930 (total time: 39.520) Filter (dist only) r_work=0.0991 r_free=0.1879 | n_water=225 | time (s): 16.680 (total time: 56.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.979845 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.201653 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0910 0.1912 0.1001 0.011 1.1 3.8 0.5 0.6 0 0.490 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.10 19.12 10.01 7.088 18.124 0.202 5.001 8.93 19.43 10.49 8.342 18.229 0.202 4.938 Individual atomic B min max mean iso aniso Overall: 0.00 107.13 16.80 10.85 1752 0 Protein: 0.00 107.13 15.73 10.84 1519 0 Water: 0.00 53.66 23.83 N/A 225 0 Other: 11.83 42.29 23.88 N/A 8 0 Chain A: 0.00 107.13 16.24 N/A 1640 0 Chain S: 0.00 53.66 25.07 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.71 634 10.71 - 21.43 667 21.43 - 32.14 261 32.14 - 42.85 107 42.85 - 53.56 46 53.56 - 64.28 16 64.28 - 74.99 9 74.99 - 85.70 6 85.70 - 96.42 5 96.42 - 107.13 1 =========================== Idealize ADP of riding H ========================== r_work=0.0893 r_free=0.1943 r_work=0.0897 r_free=0.1950 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0897 r_free = 0.1950 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0885 r_free = 0.1924 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0885 r_free= 0.1924 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.932661 | | target function (ml) not normalized (work): 24278.557959 | | target function (ml) not normalized (free): 2227.293490 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0938 0.0885 0.1924 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2100 0.2099 0.2268 n_refl.: 5174 remove outliers: r(all,work,free)=0.2100 0.2099 0.2268 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2100 0.2099 0.2268 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0936 0.0884 0.1912 n_refl.: 5174 remove outliers: r(all,work,free)=0.0936 0.0884 0.1912 n_refl.: 5174 ======================== 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 0.3706 317.260 289.086 0.586 0.987 0.320 11.894-9.307 99.02 97 4 0.1924 504.916 487.987 0.955 0.992 0.320 9.237-7.194 100.00 213 7 0.2140 412.921 404.986 1.010 0.995 0.320 7.162-5.571 100.00 427 22 0.2082 309.847 299.804 0.983 0.997 0.250 5.546-4.326 100.00 867 58 0.0993 425.376 419.492 1.024 0.999 0.224 4.315-3.360 100.00 1859 96 0.0563 404.537 404.227 1.091 1.003 0.210 3.356-3.002 100.00 1373 60 0.0430 311.592 311.549 1.069 1.006 0.045 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.0384 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0884 r_free=0.1912 After: r_work=0.0887 r_free=0.1910 ================================== NQH flips ================================== r_work=0.0887 r_free=0.1910 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0887 r_free=0.1910 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0887 r_free=0.1910 | n_water=225 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.0909 r_free=0.1881 | n_water=219 | time (s): 17.830 (total time: 18.430) Filter (q & B) r_work=0.0964 r_free=0.1903 | n_water=217 | time (s): 1.250 (total time: 19.680) Compute maps r_work=0.0964 r_free=0.1903 | n_water=217 | time (s): 0.460 (total time: 20.140) Filter (map) r_work=0.1255 r_free=0.1976 | n_water=155 | time (s): 1.380 (total time: 21.520) Find peaks r_work=0.1255 r_free=0.1976 | n_water=155 | time (s): 0.450 (total time: 21.970) Add new water r_work=0.1501 r_free=0.2215 | n_water=218 | time (s): 1.390 (total time: 23.360) Refine new water occ: r_work=0.1001 r_free=0.1883 adp: r_work=0.0996 r_free=0.1897 occ: r_work=0.0990 r_free=0.1883 adp: r_work=0.0990 r_free=0.1888 occ: r_work=0.0985 r_free=0.1875 adp: r_work=0.0985 r_free=0.1880 ADP+occupancy (water only), MIN, final r_work=0.0985 r_free=0.1880 r_work=0.0985 r_free=0.1880 | n_water=218 | time (s): 13.000 (total time: 36.360) Filter (q & B) r_work=0.0984 r_free=0.1883 | n_water=215 | time (s): 1.780 (total time: 38.140) Filter (dist only) r_work=0.0990 r_free=0.1893 | n_water=214 | time (s): 16.740 (total time: 54.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.956481 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.203431 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0938 0.1861 0.0923 0.010 1.1 6.1 0.5 0.0 0 0.478 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.38 18.61 9.23 8.236 18.368 0.203 4.999 9.19 18.86 9.67 9.057 18.477 0.203 4.945 Individual atomic B min max mean iso aniso Overall: 0.00 106.26 17.00 11.97 1741 0 Protein: 0.00 106.26 16.06 11.96 1519 0 Water: 0.00 51.71 23.46 N/A 214 0 Other: 10.54 43.58 23.34 N/A 8 0 Chain A: 0.00 106.26 16.52 N/A 1634 0 Chain S: 0.00 49.77 24.31 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.63 610 10.63 - 21.25 673 21.25 - 31.88 260 31.88 - 42.50 103 42.50 - 53.13 55 53.13 - 63.75 15 63.75 - 74.38 10 74.38 - 85.01 8 85.01 - 95.63 4 95.63 - 106.26 3 =========================== Idealize ADP of riding H ========================== r_work=0.0919 r_free=0.1886 r_work=0.0922 r_free=0.1889 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0922 r_free = 0.1889 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0917 r_free = 0.1887 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0917 r_free= 0.1887 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.944927 | | target function (ml) not normalized (work): 24338.928998 | | target function (ml) not normalized (free): 2210.258558 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1309 0.1848 5.5306 6.1965| | 2: 3.78 - 3.00 1.00 2430 110 0.0438 0.1953 4.3443 12.094| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2492 142 0.91 12.43 1.00 0.93 12646.46| | 2: 3.78 - 3.00 2430 110 0.99 1.91 1.01 0.95 883.82| |alpha: min = 0.92 max = 0.96 mean = 0.94| |beta: min = 559.25 max = 21024.35 mean = 6839.22| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.19 mean = 7.24| |phase err.(test): min = 0.00 max = 85.77 mean = 7.03| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0966 0.0917 0.1887 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2158 0.2159 0.2259 n_refl.: 5174 remove outliers: r(all,work,free)=0.2158 0.2159 0.2259 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2158 0.2159 0.2259 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0965 0.0916 0.1898 n_refl.: 5174 remove outliers: r(all,work,free)=0.0965 0.0916 0.1898 n_refl.: 5174 ======================== 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 0.3771 317.260 289.757 0.618 0.987 0.320 11.894-9.307 99.02 97 4 0.1975 504.916 489.414 1.003 0.994 0.320 9.237-7.194 100.00 213 7 0.2178 412.921 404.812 1.051 0.997 0.299 7.162-5.571 100.00 427 22 0.2159 309.847 299.621 1.022 0.999 0.280 5.546-4.326 100.00 867 58 0.1067 425.376 419.249 1.074 1.001 0.250 4.315-3.360 100.00 1859 96 0.0588 404.537 404.576 1.156 1.002 0.210 3.356-3.002 100.00 1373 60 0.0417 311.592 311.519 1.138 1.004 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.8230 ================= 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 : 0.3619 0.2020 0.083 5.255 8.8 119.3 19.9 258 0.000 1_bss: 0.1568 0.1575 0.083 5.255 6.4 116.9 17.5 258 0.000 1_settarget: 0.1568 0.1575 0.083 5.255 6.4 116.9 17.5 258 0.000 1_nqh: 0.1571 0.1574 0.083 5.255 6.4 116.9 17.5 258 0.010 1_weight: 0.1571 0.1574 0.083 5.255 6.4 116.9 17.5 258 0.010 1_xyzrec: 0.1154 0.1758 0.010 0.974 6.4 116.9 17.5 258 0.217 1_adp: 0.1010 0.1749 0.010 0.974 2.5 112.0 17.8 258 0.217 1_regHadp: 0.1003 0.1754 0.010 0.974 2.5 112.0 17.8 258 0.217 1_occ: 0.0998 0.1767 0.010 0.974 2.5 112.0 17.8 258 0.217 2_bss: 0.1001 0.1772 0.010 0.974 1.4 110.9 16.8 258 0.217 2_settarget: 0.1001 0.1772 0.010 0.974 1.4 110.9 16.8 258 0.217 2_updatecdl: 0.1001 0.1772 0.010 1.002 1.4 110.9 16.8 258 0.217 2_nqh: 0.1003 0.1775 0.010 1.002 1.4 110.9 16.8 258 0.212 2_sol: 0.1133 0.1647 0.010 1.002 1.0 110.9 16.0 218 n/a 2_weight: 0.1133 0.1647 0.010 1.002 1.0 110.9 16.0 218 n/a 2_xyzrec: 0.1011 0.1822 0.009 0.995 1.0 110.9 16.0 218 n/a 2_adp: 0.0947 0.1840 0.009 0.995 0.0 108.3 16.7 218 n/a 2_regHadp: 0.0944 0.1840 0.009 0.995 0.0 108.3 16.7 218 n/a 2_occ: 0.0940 0.1829 0.009 0.995 0.0 108.3 16.7 218 n/a 3_bss: 0.0943 0.1849 0.009 0.995 0.0 108.3 16.7 218 n/a 3_settarget: 0.0943 0.1849 0.009 0.995 0.0 108.3 16.7 218 n/a 3_updatecdl: 0.0943 0.1849 0.009 1.007 0.0 108.3 16.7 218 n/a 3_nqh: 0.0948 0.1849 0.009 1.007 0.0 108.3 16.7 218 n/a 3_sol: 0.1062 0.1770 0.009 1.007 0.0 108.3 16.6 228 n/a 3_weight: 0.1062 0.1770 0.009 1.007 0.0 108.3 16.6 228 n/a 3_xyzrec: 0.0960 0.1865 0.011 1.082 0.0 108.3 16.6 228 n/a 3_adp: 0.0912 0.1858 0.011 1.082 0.0 108.0 16.6 228 n/a 3_regHadp: 0.0917 0.1871 0.011 1.082 0.0 108.0 16.6 228 n/a 3_occ: 0.0903 0.1848 0.011 1.082 0.0 108.0 16.6 228 n/a 4_bss: 0.0889 0.1831 0.011 1.082 0.0 108.0 16.6 228 n/a 4_settarget: 0.0889 0.1831 0.011 1.082 0.0 108.0 16.6 228 n/a 4_updatecdl: 0.0889 0.1831 0.011 1.093 0.0 108.0 16.6 228 n/a 4_nqh: 0.0891 0.1828 0.011 1.093 0.0 108.0 16.6 228 n/a 4_sol: 0.0991 0.1879 0.011 1.093 0.0 108.0 16.6 225 n/a 4_weight: 0.0991 0.1879 0.011 1.093 0.0 108.0 16.6 225 n/a 4_xyzrec: 0.0910 0.1912 0.011 1.052 0.0 108.0 16.6 225 n/a 4_adp: 0.0893 0.1943 0.011 1.052 0.0 107.1 16.8 225 n/a 4_regHadp: 0.0897 0.1950 0.011 1.052 0.0 107.1 16.8 225 n/a 4_occ: 0.0885 0.1924 0.011 1.052 0.0 107.1 16.8 225 n/a 5_bss: 0.0884 0.1912 0.011 1.052 0.0 107.1 16.8 225 n/a 5_settarget: 0.0884 0.1912 0.011 1.052 0.0 107.1 16.8 225 n/a 5_updatecdl: 0.0884 0.1912 0.011 1.054 0.0 107.1 16.8 225 n/a 5_setrh: 0.0887 0.1910 0.011 1.054 0.0 107.1 16.8 225 n/a 5_nqh: 0.0887 0.1910 0.011 1.054 0.0 107.1 16.8 225 n/a 5_sol: 0.0990 0.1893 0.011 1.054 0.0 107.1 16.8 214 n/a 5_weight: 0.0990 0.1893 0.011 1.054 0.0 107.1 16.8 214 n/a 5_xyzrec: 0.0938 0.1861 0.010 1.129 0.0 107.1 16.8 214 n/a 5_adp: 0.0919 0.1886 0.010 1.129 0.0 106.3 17.0 214 n/a 5_regHadp: 0.0922 0.1889 0.010 1.129 0.0 106.3 17.0 214 n/a 5_occ: 0.0917 0.1887 0.010 1.129 0.0 106.3 17.0 214 n/a end: 0.0916 0.1898 0.010 1.129 0.0 106.3 17.0 214 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4023827_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4023827_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.2000 Refinement macro-cycles (run) : 493.3400 Write final files (write_after_run_outputs) : 9.1300 Total : 506.6700 Total CPU time: 8.81 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:10 PST -0800 (1735492750.34 s) Start R-work = 0.1568, R-free = 0.1575 Final R-work = 0.0916, R-free = 0.1898 =============================================================================== Job complete usr+sys time: 535.24 seconds wall clock time: 9 minutes 17.97 seconds (557.97 seconds total)