Starting phenix.refine on Sun Dec 29 09:10:02 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=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 { 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" 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_6712476.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6712476.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.04, per 1000 atoms: 0.60 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: 0.54 Conformation dependent library (CDL) restraints added in 203.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.73 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 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_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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3614 r_free= 0.2015 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.470864 | | target function (ml) not normalized (work): 22041.357931 | | target function (ml) not normalized (free): 1149.970506 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3801 0.2230 4.854 4.9233| | 2: 3.78 - 3.00 1.00 2430 110 0.3386 0.1653 4.0767 4.0987| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.78 0.83 0.13 6610.10| | 2: 3.78 - 3.00 2430 110 0.94 11.22 1.48 0.26 448.48| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 377.56 max = 12055.57 mean = 3573.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.27| |phase err.(test): min = 0.00 max = 89.93 mean = 33.49| |-----------------------------------------------------------------------------| ----------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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3614 r_free= 0.2015 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.470864 | | target function (ml) not normalized (work): 22041.357931 | | target function (ml) not normalized (free): 1149.970506 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3569 0.3645 0.2096 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3569 0.3645 0.2096 n_refl.: 5182 remove outliers: r(all,work,free)=0.2516 0.2541 0.2096 n_refl.: 5178 overall B=-2.73 to atoms: r(all,work,free)=0.2413 0.2434 0.2050 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1566 0.1565 0.1585 n_refl.: 5178 remove outliers: r(all,work,free)=0.1562 0.1560 0.1585 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 0.3905 449.738 399.746 0.663 1.024 0.394 11.894-9.307 99.02 97 4 0.1837 714.445 689.127 0.943 1.024 0.382 9.237-7.194 100.00 213 7 0.2130 584.274 572.078 0.973 1.021 0.364 7.162-5.571 100.00 427 22 0.2332 438.426 420.841 0.931 1.017 0.326 5.546-4.326 100.00 867 58 0.1364 601.897 592.063 0.968 1.009 0.258 4.315-3.360 100.00 1859 96 0.1334 572.411 567.272 1.025 0.997 0.200 3.356-3.002 100.00 1373 60 0.1588 440.895 437.592 1.020 0.984 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.7468 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1560 r_free=0.1585 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=0.1565 r_free=0.1600 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.983674 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.895289 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 0.1161 0.1805 0.0644 0.010 1.0 1.9 0.5 0.0 0 9.492 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.61 18.05 6.44 3.013 16.125 1.895 0.018 10.25 18.12 7.86 4.928 16.405 1.895 0.015 Individual atomic B min max mean iso aniso Overall: 2.11 111.79 17.68 5.31 1785 0 Protein: 2.11 111.79 14.97 5.30 1519 0 Water: 4.13 111.57 33.46 N/A 258 0 Other: 17.22 37.62 24.31 N/A 8 0 Chain A: 2.11 111.79 17.68 N/A 1785 0 Histogram: Values Number of atoms 2.11 - 13.07 896 13.07 - 24.04 496 24.04 - 35.01 196 35.01 - 45.98 111 45.98 - 56.95 56 56.95 - 67.91 12 67.91 - 78.88 9 78.88 - 89.85 5 89.85 - 100.82 1 100.82 - 111.79 3 =========================== Idealize ADP of riding H ========================== r_work=0.1025 r_free=0.1812 r_work=0.1020 r_free=0.1816 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1020 r_free = 0.1816 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 = 0.1013 r_free = 0.1811 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.18 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= 0.1013 r_free= 0.1811 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014068 | | target function (ls_wunit_k1) not normalized (work): 69.270425 | | target function (ls_wunit_k1) not normalized (free): 10.488727 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1053 0.1013 0.1811 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2118 0.2119 0.2225 n_refl.: 5176 remove outliers: r(all,work,free)=0.2118 0.2119 0.2225 n_refl.: 5176 overall B=-0.96 to atoms: r(all,work,free)=0.2077 0.2075 0.2213 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1049 0.1010 0.1799 n_refl.: 5176 remove outliers: r(all,work,free)=0.1049 0.1010 0.1799 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 0.3362 320.467 302.176 0.656 1.006 0.381 11.894-9.307 99.02 97 4 0.1477 509.088 502.125 0.957 1.007 0.361 9.237-7.194 100.00 213 7 0.1659 416.333 416.664 0.986 1.007 0.316 7.162-5.571 100.00 427 22 0.1634 312.407 308.708 0.946 1.005 0.312 5.546-4.326 100.00 867 58 0.0906 428.890 425.725 0.969 1.003 0.222 4.315-3.360 100.00 1859 96 0.0763 407.879 407.775 1.017 0.999 0.201 3.356-3.002 100.00 1373 60 0.0998 314.166 313.085 0.995 0.995 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.3361 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1010 r_free=0.1799 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 173 ASN Total number of N/Q/H flips: 2 r_work=0.1011 r_free=0.1796 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1011 r_free=0.1796 | n_water=258 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1035 r_free=0.1791 | n_water=249 | time (s): 19.390 (total time: 20.080) Filter (q & B) r_work=0.1035 r_free=0.1789 | n_water=246 | time (s): 1.390 (total time: 21.470) Compute maps r_work=0.1035 r_free=0.1789 | n_water=246 | time (s): 0.550 (total time: 22.020) Filter (map) r_work=0.1363 r_free=0.1860 | n_water=141 | time (s): 1.430 (total time: 23.450) Find peaks r_work=0.1363 r_free=0.1860 | n_water=141 | time (s): 0.390 (total time: 23.840) Add new water r_work=0.1733 r_free=0.2192 | n_water=232 | time (s): 1.390 (total time: 25.230) Refine new water occ: r_work=0.1166 r_free=0.1678 adp: r_work=0.1142 r_free=0.1675 occ: r_work=0.1140 r_free=0.1639 adp: r_work=0.1128 r_free=0.1648 occ: r_work=0.1127 r_free=0.1618 adp: r_work=0.1127 r_free=0.1618 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1618 r_work=0.1127 r_free=0.1618 | n_water=232 | time (s): 4.880 (total time: 30.110) Filter (q & B) r_work=0.1127 r_free=0.1622 | n_water=231 | time (s): 1.710 (total time: 31.820) Filter (dist only) r_work=0.1136 r_free=0.1598 | n_water=226 | time (s): 17.590 (total time: 49.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.024196 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.861462 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 0.1014 0.1774 0.0761 0.009 1.0 4.8 0.5 0.6 0 11.512 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.14 17.74 7.61 4.682 16.974 2.861 0.014 9.38 17.93 8.55 5.668 17.454 2.861 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.99 16.86 6.71 1753 0 Protein: 0.00 107.99 15.40 6.69 1519 0 Water: 0.00 64.14 26.39 N/A 226 0 Other: 13.62 40.03 25.39 N/A 8 0 Chain A: 0.00 107.99 16.12 N/A 1664 0 Chain S: 2.60 60.42 30.76 N/A 89 0 Histogram: Values Number of atoms 0.00 - 10.80 640 10.80 - 21.60 702 21.60 - 32.40 214 32.40 - 43.19 122 43.19 - 53.99 36 53.99 - 64.79 25 64.79 - 75.59 6 75.59 - 86.39 4 86.39 - 97.19 3 97.19 - 107.99 1 =========================== Idealize ADP of riding H ========================== r_work=0.0938 r_free=0.1793 r_work=0.0934 r_free=0.1798 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0934 r_free = 0.1798 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0931 r_free = 0.1780 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= 0.0931 r_free= 0.1780 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ls_wunit_k1) (work): 0.011913 | | target function (ls_wunit_k1) not normalized (work): 58.660463 | | target function (ls_wunit_k1) not normalized (free): 9.401804 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0972 0.0931 0.1780 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2150 0.2155 0.2212 n_refl.: 5176 remove outliers: r(all,work,free)=0.2150 0.2155 0.2212 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2150 0.2155 0.2212 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0973 0.0930 0.1797 n_refl.: 5176 remove outliers: r(all,work,free)=0.0973 0.0930 0.1797 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 0.3209 320.467 306.530 0.705 1.010 0.393 11.894-9.307 99.02 97 4 0.1476 509.088 503.980 0.983 1.012 0.380 9.237-7.194 100.00 213 7 0.1454 416.333 418.624 1.012 1.011 0.309 7.162-5.571 100.00 427 22 0.1470 312.407 309.681 0.985 1.009 0.290 5.546-4.326 100.00 867 58 0.0790 428.890 426.216 1.012 1.005 0.260 4.315-3.360 100.00 1859 96 0.0697 407.879 407.706 1.064 0.998 0.200 3.356-3.002 100.00 1373 60 0.0972 314.166 313.345 1.047 0.992 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.6034 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0930 r_free=0.1797 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 76 ASN B A 80 GLN A Total number of N/Q/H flips: 4 r_work=0.0935 r_free=0.1793 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0935 r_free=0.1793 | n_water=226 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0956 r_free=0.1791 | n_water=223 | time (s): 17.950 (total time: 18.520) Filter (q & B) r_work=0.1021 r_free=0.1800 | n_water=221 | time (s): 1.320 (total time: 19.840) Compute maps r_work=0.1021 r_free=0.1800 | n_water=221 | time (s): 0.610 (total time: 20.450) Filter (map) r_work=0.1303 r_free=0.1855 | n_water=142 | time (s): 1.620 (total time: 22.070) Find peaks r_work=0.1303 r_free=0.1855 | n_water=142 | time (s): 0.460 (total time: 22.530) Add new water r_work=0.1717 r_free=0.2251 | n_water=233 | time (s): 1.240 (total time: 23.770) Refine new water occ: r_work=0.1071 r_free=0.1716 adp: r_work=0.1064 r_free=0.1729 occ: r_work=0.1052 r_free=0.1706 adp: r_work=0.1052 r_free=0.1717 occ: r_work=0.1041 r_free=0.1694 adp: r_work=0.1041 r_free=0.1705 ADP+occupancy (water only), MIN, final r_work=0.1041 r_free=0.1705 r_work=0.1041 r_free=0.1705 | n_water=233 | time (s): 10.980 (total time: 34.750) Filter (q & B) r_work=0.1041 r_free=0.1705 | n_water=233 | time (s): 1.170 (total time: 35.920) Filter (dist only) r_work=0.1056 r_free=0.1720 | n_water=230 | time (s): 18.250 (total time: 54.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.084969 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.195715 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 0.0950 0.1825 0.0875 0.011 1.0 3.8 0.5 0.0 0 0.542 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.50 18.25 8.75 5.576 18.244 0.196 5.141 9.06 18.20 9.14 7.417 18.247 0.196 5.040 Individual atomic B min max mean iso aniso Overall: 0.00 108.93 16.79 9.08 1757 0 Protein: 0.00 108.93 15.54 9.06 1519 0 Water: 0.00 59.14 24.64 N/A 230 0 Other: 15.10 46.23 29.44 N/A 8 0 Chain A: 0.00 108.93 16.18 N/A 1649 0 Chain S: 0.00 56.49 26.18 N/A 108 0 Histogram: Values Number of atoms 0.00 - 10.89 656 10.89 - 21.79 681 21.79 - 32.68 232 32.68 - 43.57 115 43.57 - 54.46 35 54.46 - 65.36 21 65.36 - 76.25 10 76.25 - 87.14 2 87.14 - 98.04 4 98.04 - 108.93 1 =========================== Idealize ADP of riding H ========================== r_work=0.0906 r_free=0.1820 r_work=0.0911 r_free=0.1832 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0911 r_free = 0.1832 target_work(ml) = 5.044 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0896 r_free = 0.1812 target_work(ml) = 5.036 | | occupancies: max = 1.00 min = 0.27 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= 0.0896 r_free= 0.1812 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.036223 | | target function (ml) not normalized (work): 24798.361198 | | target function (ml) not normalized (free): 1803.365880 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0942 0.0896 0.1812 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2167 0.2175 0.2193 n_refl.: 5176 remove outliers: r(all,work,free)=0.2167 0.2175 0.2193 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2167 0.2175 0.2193 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0933 0.0888 0.1793 n_refl.: 5176 remove outliers: r(all,work,free)=0.0929 0.0884 0.1793 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 0.3617 319.882 289.725 0.602 0.994 0.340 11.894-9.307 99.02 97 4 0.1808 509.088 497.011 0.957 0.998 0.328 9.237-7.194 100.00 213 7 0.1861 416.333 413.246 0.996 1.000 0.301 7.162-5.571 100.00 427 22 0.1826 312.407 304.899 0.980 1.000 0.287 5.546-4.326 100.00 867 58 0.0919 428.890 424.231 1.010 1.001 0.250 4.315-3.360 100.00 1859 96 0.0587 407.879 407.366 1.069 1.001 0.207 3.356-3.002 100.00 1373 60 0.0603 314.166 313.893 1.050 1.002 0.059 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9176 b_overall=-6.9970 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0884 r_free=0.1793 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0884 r_free=0.1793 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0884 r_free=0.1793 | n_water=230 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0891 r_free=0.1784 | n_water=228 | time (s): 19.790 (total time: 20.370) Filter (q & B) r_work=0.0958 r_free=0.1812 | n_water=226 | time (s): 1.430 (total time: 21.800) Compute maps r_work=0.0958 r_free=0.1812 | n_water=226 | time (s): 0.600 (total time: 22.400) Filter (map) r_work=0.1219 r_free=0.1885 | n_water=156 | time (s): 1.940 (total time: 24.340) Find peaks r_work=0.1219 r_free=0.1885 | n_water=156 | time (s): 0.490 (total time: 24.830) Add new water r_work=0.1538 r_free=0.2173 | n_water=225 | time (s): 1.520 (total time: 26.350) Refine new water occ: r_work=0.1007 r_free=0.1760 adp: r_work=0.1003 r_free=0.1777 occ: r_work=0.0993 r_free=0.1750 adp: r_work=0.0993 r_free=0.1766 occ: r_work=0.0983 r_free=0.1738 adp: r_work=0.0983 r_free=0.1751 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1751 r_work=0.0983 r_free=0.1751 | n_water=225 | time (s): 10.430 (total time: 36.780) Filter (q & B) r_work=0.0983 r_free=0.1751 | n_water=225 | time (s): 0.830 (total time: 37.610) Filter (dist only) r_work=0.0985 r_free=0.1735 | n_water=222 | time (s): 17.320 (total time: 54.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.982980 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.252969 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 0.0908 0.1807 0.0899 0.011 1.0 4.8 0.5 0.0 0 0.491 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.08 18.07 8.99 7.066 18.287 0.253 5.011 8.86 18.24 9.38 8.593 18.453 0.253 4.947 Individual atomic B min max mean iso aniso Overall: 0.00 110.05 17.10 11.25 1749 0 Protein: 0.00 110.05 16.03 11.23 1519 0 Water: 0.00 59.38 23.83 N/A 222 0 Other: 18.97 45.14 32.06 N/A 8 0 Chain A: 0.00 110.05 16.53 N/A 1640 0 Chain S: 0.00 59.38 25.55 N/A 109 0 Histogram: Values Number of atoms 0.00 - 11.00 655 11.00 - 22.01 671 22.01 - 33.01 228 33.01 - 44.02 121 44.02 - 55.02 39 55.02 - 66.03 14 66.03 - 77.03 10 77.03 - 88.04 5 88.04 - 99.04 5 99.04 - 110.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.0886 r_free=0.1824 r_work=0.0891 r_free=0.1829 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0891 r_free = 0.1829 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1816 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.28 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= 0.0881 r_free= 0.1816 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.947657 | | target function (ml) not normalized (work): 24352.369139 | | target function (ml) not normalized (free): 2010.835261 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0928 0.0881 0.1816 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2124 0.2125 0.2233 n_refl.: 5174 remove outliers: r(all,work,free)=0.2124 0.2125 0.2233 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2124 0.2125 0.2233 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0927 0.0880 0.1820 n_refl.: 5174 remove outliers: r(all,work,free)=0.0927 0.0880 0.1820 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 0.3721 319.882 293.439 0.608 0.988 0.334 11.894-9.307 99.02 97 4 0.1907 509.088 494.037 0.960 0.993 0.330 9.237-7.194 100.00 213 7 0.2112 416.333 408.081 1.000 0.996 0.294 7.162-5.571 100.00 427 22 0.1976 312.407 303.857 0.987 0.997 0.280 5.546-4.326 100.00 867 58 0.0987 428.890 423.426 1.018 0.999 0.229 4.315-3.360 100.00 1859 96 0.0570 407.879 407.878 1.087 1.002 0.219 3.356-3.002 100.00 1373 60 0.0444 314.166 314.514 1.069 1.004 0.066 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8540 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0880 r_free=0.1820 After: r_work=0.0883 r_free=0.1819 ================================== NQH flips ================================== r_work=0.0883 r_free=0.1819 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=0.0883 r_free=0.1821 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0883 r_free=0.1821 | n_water=222 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0899 r_free=0.1836 | n_water=219 | time (s): 17.610 (total time: 18.270) Filter (q & B) r_work=0.0976 r_free=0.1873 | n_water=217 | time (s): 1.380 (total time: 19.650) Compute maps r_work=0.0976 r_free=0.1873 | n_water=217 | time (s): 0.450 (total time: 20.100) Filter (map) r_work=0.1198 r_free=0.1940 | n_water=164 | time (s): 1.230 (total time: 21.330) Find peaks r_work=0.1198 r_free=0.1940 | n_water=164 | time (s): 0.410 (total time: 21.740) Add new water r_work=0.1477 r_free=0.2198 | n_water=232 | time (s): 1.370 (total time: 23.110) Refine new water occ: r_work=0.0983 r_free=0.1851 adp: r_work=0.0976 r_free=0.1852 occ: r_work=0.0968 r_free=0.1835 adp: r_work=0.0968 r_free=0.1843 occ: r_work=0.0961 r_free=0.1826 adp: r_work=0.0960 r_free=0.1834 ADP+occupancy (water only), MIN, final r_work=0.0960 r_free=0.1834 r_work=0.0960 r_free=0.1834 | n_water=232 | time (s): 10.490 (total time: 33.600) Filter (q & B) r_work=0.0961 r_free=0.1834 | n_water=229 | time (s): 1.370 (total time: 34.970) Filter (dist only) r_work=0.0956 r_free=0.1833 | n_water=227 | time (s): 17.810 (total time: 52.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.931897 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.187878 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 0.0909 0.1826 0.0917 0.010 1.1 7.0 0.5 0.0 0 0.466 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.09 18.26 9.17 8.509 18.778 0.188 4.963 8.95 18.41 9.46 9.056 18.887 0.188 4.917 Individual atomic B min max mean iso aniso Overall: 0.00 112.61 17.44 12.03 1754 0 Protein: 0.00 112.61 16.40 12.01 1519 0 Water: 0.00 61.66 23.91 N/A 227 0 Other: 15.78 46.86 32.40 N/A 8 0 Chain A: 0.00 112.61 16.83 N/A 1636 0 Chain S: 0.00 61.66 25.90 N/A 118 0 Histogram: Values Number of atoms 0.00 - 11.26 660 11.26 - 22.52 659 22.52 - 33.78 240 33.78 - 45.04 126 45.04 - 56.30 35 56.30 - 67.56 15 67.56 - 78.82 9 78.82 - 90.09 5 90.09 - 101.35 3 101.35 - 112.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.0895 r_free=0.1841 r_work=0.0899 r_free=0.1841 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0899 r_free = 0.1841 target_work(ml) = 4.922 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0892 r_free = 0.1831 target_work(ml) = 4.918 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0892 r_free= 0.1831 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.918291 | | target function (ml) not normalized (work): 24207.826839 | | target function (ml) not normalized (free): 2110.331914 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1284 0.1881 5.5232 6.1986| | 2: 3.78 - 3.00 1.00 2430 110 0.0415 0.1746 4.2979 11.183| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.48 1.00 0.95 13110.74| | 2: 3.78 - 3.00 2430 110 0.99 1.69 1.00 0.97 812.02| |alpha: min = 0.93 max = 0.97 mean = 0.96| |beta: min = 510.51 max = 22098.37 mean = 7038.84| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.92 mean = 7.15| |phase err.(test): min = 0.00 max = 86.24 mean = 7.87| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0939 0.0892 0.1831 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2149 0.2149 0.2278 n_refl.: 5174 remove outliers: r(all,work,free)=0.2149 0.2149 0.2278 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2149 0.2149 0.2278 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0938 0.0891 0.1830 n_refl.: 5174 remove outliers: r(all,work,free)=0.0938 0.0891 0.1830 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 0.3782 319.882 284.993 0.602 0.986 0.320 11.894-9.307 99.02 97 4 0.2041 509.088 494.202 0.999 0.993 0.320 9.237-7.194 100.00 213 7 0.2233 416.333 409.842 1.054 0.996 0.290 7.162-5.571 100.00 427 22 0.2061 312.407 304.774 1.037 0.998 0.290 5.546-4.326 100.00 867 58 0.1029 428.890 422.895 1.071 1.000 0.230 4.315-3.360 100.00 1859 96 0.0561 407.879 408.059 1.155 1.003 0.220 3.356-3.002 100.00 1373 60 0.0399 314.166 313.951 1.136 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.8123 ================= 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 : 0.3614 0.2015 0.082 5.266 8.8 119.3 19.9 258 0.000 1_bss: 0.1560 0.1585 0.082 5.266 6.1 116.6 17.2 258 0.000 1_settarget: 0.1560 0.1585 0.082 5.266 6.1 116.6 17.2 258 0.000 1_nqh: 0.1565 0.1600 0.082 5.266 6.1 116.6 17.2 258 0.009 1_weight: 0.1565 0.1600 0.082 5.266 6.1 116.6 17.2 258 0.009 1_xyzrec: 0.1161 0.1805 0.010 0.967 6.1 116.6 17.2 258 0.217 1_adp: 0.1025 0.1812 0.010 0.967 2.1 111.8 17.7 258 0.217 1_regHadp: 0.1020 0.1816 0.010 0.967 2.1 111.8 17.7 258 0.217 1_occ: 0.1013 0.1811 0.010 0.967 2.1 111.8 17.7 258 0.217 2_bss: 0.1010 0.1799 0.010 0.967 1.1 110.8 16.7 258 0.217 2_settarget: 0.1010 0.1799 0.010 0.967 1.1 110.8 16.7 258 0.217 2_updatecdl: 0.1010 0.1799 0.010 0.982 1.1 110.8 16.7 258 0.217 2_nqh: 0.1011 0.1796 0.010 0.982 1.1 110.8 16.7 258 0.216 2_sol: 0.1136 0.1598 0.010 0.982 1.1 110.8 15.9 226 n/a 2_weight: 0.1136 0.1598 0.010 0.982 1.1 110.8 15.9 226 n/a 2_xyzrec: 0.1014 0.1774 0.009 0.964 1.1 110.8 15.9 226 n/a 2_adp: 0.0938 0.1793 0.009 0.964 0.0 108.0 16.9 226 n/a 2_regHadp: 0.0934 0.1798 0.009 0.964 0.0 108.0 16.9 226 n/a 2_occ: 0.0931 0.1780 0.009 0.964 0.0 108.0 16.9 226 n/a 3_bss: 0.0930 0.1797 0.009 0.964 0.0 108.0 16.9 226 n/a 3_settarget: 0.0930 0.1797 0.009 0.964 0.0 108.0 16.9 226 n/a 3_updatecdl: 0.0930 0.1797 0.009 0.972 0.0 108.0 16.9 226 n/a 3_nqh: 0.0935 0.1793 0.009 0.972 0.0 108.0 16.9 226 n/a 3_sol: 0.1056 0.1720 0.009 0.972 0.0 108.0 16.8 230 n/a 3_weight: 0.1056 0.1720 0.009 0.972 0.0 108.0 16.8 230 n/a 3_xyzrec: 0.0950 0.1825 0.011 1.029 0.0 108.0 16.8 230 n/a 3_adp: 0.0906 0.1820 0.011 1.029 0.0 108.9 16.8 230 n/a 3_regHadp: 0.0911 0.1832 0.011 1.029 0.0 108.9 16.8 230 n/a 3_occ: 0.0896 0.1812 0.011 1.029 0.0 108.9 16.8 230 n/a 4_bss: 0.0884 0.1793 0.011 1.029 0.0 108.9 16.8 230 n/a 4_settarget: 0.0884 0.1793 0.011 1.029 0.0 108.9 16.8 230 n/a 4_updatecdl: 0.0884 0.1793 0.011 1.029 0.0 108.9 16.8 230 n/a 4_nqh: 0.0884 0.1793 0.011 1.029 0.0 108.9 16.8 230 n/a 4_sol: 0.0985 0.1735 0.011 1.029 0.0 108.9 16.8 222 n/a 4_weight: 0.0985 0.1735 0.011 1.029 0.0 108.9 16.8 222 n/a 4_xyzrec: 0.0908 0.1807 0.011 1.026 0.0 108.9 16.8 222 n/a 4_adp: 0.0886 0.1824 0.011 1.026 0.0 110.0 17.1 222 n/a 4_regHadp: 0.0891 0.1829 0.011 1.026 0.0 110.0 17.1 222 n/a 4_occ: 0.0881 0.1816 0.011 1.026 0.0 110.0 17.1 222 n/a 5_bss: 0.0880 0.1820 0.011 1.026 0.0 110.0 17.1 222 n/a 5_settarget: 0.0880 0.1820 0.011 1.026 0.0 110.0 17.1 222 n/a 5_updatecdl: 0.0880 0.1820 0.011 1.044 0.0 110.0 17.1 222 n/a 5_setrh: 0.0883 0.1819 0.011 1.044 0.0 110.0 17.1 222 n/a 5_nqh: 0.0883 0.1821 0.011 1.044 0.0 110.0 17.1 222 n/a 5_sol: 0.0956 0.1833 0.011 1.044 0.0 110.0 17.2 227 n/a 5_weight: 0.0956 0.1833 0.011 1.044 0.0 110.0 17.2 227 n/a 5_xyzrec: 0.0909 0.1826 0.010 1.079 0.0 110.0 17.2 227 n/a 5_adp: 0.0895 0.1841 0.010 1.079 0.0 112.6 17.4 227 n/a 5_regHadp: 0.0899 0.1841 0.010 1.079 0.0 112.6 17.4 227 n/a 5_occ: 0.0892 0.1831 0.010 1.079 0.0 112.6 17.4 227 n/a end: 0.0891 0.1830 0.010 1.079 0.0 112.6 17.4 227 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6712476_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6712476_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3200 Refinement macro-cycles (run) : 484.7000 Write final files (write_after_run_outputs) : 9.7600 Total : 497.7800 Total CPU time: 8.70 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:03 PST -0800 (1735492743.37 s) Start R-work = 0.1560, R-free = 0.1585 Final R-work = 0.0891, R-free = 0.1830 =============================================================================== Job complete usr+sys time: 529.65 seconds wall clock time: 9 minutes 11.53 seconds (551.53 seconds total)