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_6446528.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=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" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6446528.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6446528.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.25, per 1000 atoms: 0.37 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: 0.32 Conformation dependent library (CDL) restraints added in 124.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.92: 547 0.92 - 1.19: 1123 1.19 - 1.46: 744 1.46 - 1.73: 724 1.73 - 1.99: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.232 0.227 1.19e-02 7.06e+03 3.64e+02 bond pdb=" C SER A 121 " pdb=" O SER A 121 " ideal model delta sigma weight residual 1.234 1.455 -0.221 1.27e-02 6.20e+03 3.04e+02 bond pdb=" C ILE A 105 " pdb=" N CYS A 106 " ideal model delta sigma weight residual 1.332 1.574 -0.242 1.40e-02 5.10e+03 2.98e+02 bond pdb=" CA ALYS A 99 " pdb=" C ALYS A 99 " ideal model delta sigma weight residual 1.527 1.309 0.218 1.27e-02 6.20e+03 2.94e+02 bond pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 1.520 1.320 0.200 1.21e-02 6.83e+03 2.73e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.95: 3315 4.95 - 9.90: 1822 9.90 - 14.85: 544 14.85 - 19.80: 87 19.80 - 24.75: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 141.59 -18.99 1.00e+00 1.00e+00 3.61e+02 angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 106.92 15.75 1.09e+00 8.42e-01 2.09e+02 angle pdb=" O VAL A 8 " pdb=" C VAL A 8 " pdb=" N ILE A 9 " ideal model delta sigma weight residual 123.20 137.66 -14.46 1.06e+00 8.90e-01 1.86e+02 angle pdb=" CA GLN A 95 " pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 120.55 134.58 -14.03 1.06e+00 8.90e-01 1.75e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.03 136.31 -13.28 1.11e+00 8.12e-01 1.43e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 18.03: 1330 18.03 - 36.04: 94 36.04 - 54.05: 44 54.05 - 72.06: 10 72.06 - 90.07: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -147.57 24.97 0 2.50e+00 1.60e-01 9.98e+01 dihedral pdb=" C VAL A 20 " pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" CB VAL A 20 " ideal model delta harmonic sigma weight residual -122.00 -143.79 21.79 0 2.50e+00 1.60e-01 7.60e+01 dihedral pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CA ALA A 183 " pdb=" CB ALA A 183 " ideal model delta harmonic sigma weight residual 122.90 144.59 -21.69 0 2.50e+00 1.60e-01 7.53e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.231: 96 0.231 - 0.460: 75 0.460 - 0.690: 53 0.690 - 0.919: 13 0.919 - 1.149: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.30e+01 chirality pdb=" CA PHE A 162 " pdb=" N PHE A 162 " pdb=" C PHE A 162 " pdb=" CB PHE A 162 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 1.37 1.12 2.00e-01 2.50e+01 3.14e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 45 " 0.010 2.00e-02 2.50e+03 8.86e-02 1.18e+02 pdb=" CD GLN A 45 " -0.167 2.00e-02 2.50e+03 pdb=" OE1 GLN A 45 " 0.095 2.00e-02 2.50e+03 pdb=" NE2 GLN A 45 " 0.062 2.00e-02 2.50e+03 pdb="HE21 GLN A 45 " 0.057 2.00e-02 2.50e+03 pdb="HE22 GLN A 45 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.062 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG PHE A 164 " 0.139 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.066 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.049 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.058 2.00e-02 2.50e+03 5.69e-02 9.71e+01 pdb=" CG PHE A 162 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.024 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.058 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.044 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.018 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1017 2.32 - 2.89: 8108 2.89 - 3.46: 10552 3.46 - 4.03: 15217 4.03 - 4.60: 21670 Nonbonded interactions: 56564 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.747 2.100 nonbonded pdb=" O LEU A 166 " pdb=" H GLU A 170 " model vdw 1.820 2.450 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.841 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.844 2.450 nonbonded pdb=" O GLU A 16 " pdb=" H VAL A 20 " model vdw 1.852 2.450 ... (remaining 56559 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 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_6446528_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3627 r_free= 0.2050 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474963 | | target function (ml) not normalized (work): 22061.567351 | | target function (ml) not normalized (free): 1151.427908 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2266 4.8565 4.9261| | 2: 3.78 - 3.00 1.00 2430 110 0.3414 0.1683 4.0825 4.1084| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.49 48.97 0.83 0.13 6618.02| | 2: 3.78 - 3.00 2430 110 0.94 11.42 1.48 0.26 457.16| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 388.57 max = 12075.96 mean = 3581.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.46| |phase err.(test): min = 0.00 max = 89.92 mean = 33.38| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.242 1557 Z= 5.374 Angle : 5.219 18.992 2118 Z= 3.663 Chirality : 0.412 1.149 243 Planarity : 0.032 0.167 284 Dihedral : 13.668 90.066 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.73 % Favored : 95.03 % Cbeta Deviations : 32.43 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.49), residues: 224 helix: -2.46 (0.40), residues: 109 sheet: -1.52 (0.69), residues: 30 loop : 0.37 (0.64), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.068 0.013 ARG A 145 TYR 0.134 0.039 TYR A 141 PHE 0.134 0.055 PHE A 164 HIS 0.055 0.031 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3627 r_free= 0.2050 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.474963 | | target function (ml) not normalized (work): 22061.567351 | | target function (ml) not normalized (free): 1151.427908 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3587 0.3660 0.2162 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3587 0.3660 0.2162 n_refl.: 5182 remove outliers: r(all,work,free)=0.2537 0.2558 0.2162 n_refl.: 5178 overall B=-2.89 to atoms: r(all,work,free)=0.2427 0.2444 0.2127 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1589 0.1587 0.1638 n_refl.: 5178 remove outliers: r(all,work,free)=0.1585 0.1582 0.1638 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 0.3908 449.576 406.781 0.685 1.036 0.397 11.894-9.307 99.02 97 4 0.1919 714.188 696.752 0.965 1.035 0.383 9.237-7.194 100.00 213 7 0.2225 584.064 575.992 1.002 1.032 0.348 7.162-5.571 100.00 427 22 0.2365 438.269 424.191 0.960 1.025 0.288 5.546-4.326 100.00 867 58 0.1359 601.681 594.319 0.991 1.014 0.215 4.315-3.360 100.00 1859 96 0.1355 572.205 565.191 1.048 0.995 0.190 3.356-3.002 100.00 1373 60 0.1602 440.737 432.001 1.046 0.976 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6919 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1582 r_free=0.1638 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1585 r_free=0.1636 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.853409 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.180647 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 0.1163 0.1817 0.0654 0.010 1.0 2.2 0.5 0.0 0 9.427 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 18.17 6.54 3.013 15.972 2.181 0.018 10.17 17.89 7.73 5.100 16.148 2.181 0.014 Individual atomic B min max mean iso aniso Overall: 1.83 112.55 17.33 5.53 1785 0 Protein: 1.83 112.55 14.61 5.52 1519 0 Water: 3.98 111.41 33.12 N/A 258 0 Other: 17.30 36.89 24.37 N/A 8 0 Chain A: 1.83 112.55 17.33 N/A 1785 0 Histogram: Values Number of atoms 1.83 - 12.90 913 12.90 - 23.97 483 23.97 - 35.05 189 35.05 - 46.12 111 46.12 - 57.19 57 57.19 - 68.26 17 68.26 - 79.34 6 79.34 - 90.41 5 90.41 - 101.48 1 101.48 - 112.55 3 =========================== Idealize ADP of riding H ========================== r_work=0.1017 r_free=0.1789 r_work=0.1011 r_free=0.1796 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1011 r_free = 0.1796 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 = 0.1003 r_free = 0.1792 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 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= 0.1003 r_free= 0.1792 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013727 | | target function (ls_wunit_k1) not normalized (work): 67.590272 | | target function (ls_wunit_k1) not normalized (free): 10.613834 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1044 0.1003 0.1792 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2074 0.2071 0.2239 n_refl.: 5176 remove outliers: r(all,work,free)=0.2074 0.2071 0.2239 n_refl.: 5176 overall B=-0.96 to atoms: r(all,work,free)=0.2034 0.2030 0.2228 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1048 0.1007 0.1799 n_refl.: 5176 remove outliers: r(all,work,free)=0.1048 0.1007 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 0.3296 331.144 323.395 0.708 0.997 0.381 11.894-9.307 99.02 97 4 0.1501 526.049 518.765 0.996 1.000 0.361 9.237-7.194 100.00 213 7 0.1635 430.204 431.169 1.031 1.000 0.305 7.162-5.571 100.00 427 22 0.1607 322.816 318.848 0.986 1.000 0.282 5.546-4.326 100.00 867 58 0.0900 443.180 439.476 0.999 1.000 0.207 4.315-3.360 100.00 1859 96 0.0766 421.469 421.286 1.040 1.000 0.193 3.356-3.002 100.00 1373 60 0.0999 324.633 323.316 1.011 0.999 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4524 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1007 r_free=0.1799 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1007 r_free=0.1799 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1007 r_free=0.1799 | n_water=258 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.1034 r_free=0.1779 | n_water=248 | time (s): 21.440 (total time: 22.110) Filter (q & B) r_work=0.1034 r_free=0.1782 | n_water=245 | time (s): 1.570 (total time: 23.680) Compute maps r_work=0.1034 r_free=0.1782 | n_water=245 | time (s): 0.530 (total time: 24.210) Filter (map) r_work=0.1330 r_free=0.1859 | n_water=148 | time (s): 1.350 (total time: 25.560) Find peaks r_work=0.1330 r_free=0.1859 | n_water=148 | time (s): 0.390 (total time: 25.950) Add new water r_work=0.1691 r_free=0.2115 | n_water=238 | time (s): 1.670 (total time: 27.620) Refine new water occ: r_work=0.1154 r_free=0.1691 adp: r_work=0.1128 r_free=0.1693 occ: r_work=0.1126 r_free=0.1670 adp: r_work=0.1112 r_free=0.1681 occ: r_work=0.1113 r_free=0.1665 adp: r_work=0.1113 r_free=0.1665 ADP+occupancy (water only), MIN, final r_work=0.1113 r_free=0.1665 r_work=0.1113 r_free=0.1665 | n_water=238 | time (s): 3.720 (total time: 31.340) Filter (q & B) r_work=0.1113 r_free=0.1665 | n_water=238 | time (s): 0.900 (total time: 32.240) Filter (dist only) r_work=0.1118 r_free=0.1661 | n_water=236 | time (s): 19.080 (total time: 51.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.847831 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.772598 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 0.0991 0.1802 0.0811 0.009 1.0 3.8 0.5 0.6 0 11.424 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.91 18.02 8.11 4.807 16.704 2.773 0.013 9.32 18.12 8.81 5.344 17.061 2.773 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 111.26 16.42 6.38 1763 0 Protein: 0.00 111.26 14.81 6.37 1519 0 Water: 0.00 62.95 26.55 N/A 236 0 Other: 11.40 33.62 22.95 N/A 8 0 Chain A: 0.00 111.26 15.58 N/A 1673 0 Chain S: 7.16 61.26 31.95 N/A 90 0 Histogram: Values Number of atoms 0.00 - 11.13 743 11.13 - 22.25 625 22.25 - 33.38 217 33.38 - 44.50 109 44.50 - 55.63 37 55.63 - 66.75 21 66.75 - 77.88 5 77.88 - 89.00 3 89.00 - 100.13 2 100.13 - 111.26 1 =========================== Idealize ADP of riding H ========================== r_work=0.0932 r_free=0.1812 r_work=0.0929 r_free=0.1810 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0929 r_free = 0.1810 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0926 r_free = 0.1800 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.28 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= 0.0926 r_free= 0.1800 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011691 | | target function (ls_wunit_k1) not normalized (work): 57.567044 | | target function (ls_wunit_k1) not normalized (free): 9.951925 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0969 0.0926 0.1800 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2082 0.2085 0.2197 n_refl.: 5176 remove outliers: r(all,work,free)=0.2082 0.2085 0.2197 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2082 0.2085 0.2197 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0967 0.0923 0.1799 n_refl.: 5176 remove outliers: r(all,work,free)=0.0967 0.0923 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 0.3318 331.144 310.888 0.678 1.009 0.365 11.894-9.307 99.02 97 4 0.1425 526.049 522.999 0.981 1.010 0.340 9.237-7.194 100.00 213 7 0.1466 430.204 431.526 1.025 1.010 0.295 7.162-5.571 100.00 427 22 0.1372 322.816 320.876 0.988 1.008 0.290 5.546-4.326 100.00 867 58 0.0789 443.180 440.570 1.007 1.004 0.230 4.315-3.360 100.00 1859 96 0.0709 421.469 421.206 1.056 0.999 0.210 3.356-3.002 100.00 1373 60 0.0946 324.633 323.490 1.035 0.993 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.2111 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0923 r_free=0.1799 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 80 GLN A Total number of N/Q/H flips: 3 r_work=0.0927 r_free=0.1797 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0927 r_free=0.1797 | n_water=236 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.0945 r_free=0.1811 | n_water=232 | time (s): 17.990 (total time: 18.630) Filter (q & B) r_work=0.1005 r_free=0.1826 | n_water=230 | time (s): 1.270 (total time: 19.900) Compute maps r_work=0.1005 r_free=0.1826 | n_water=230 | time (s): 0.450 (total time: 20.350) Filter (map) r_work=0.1308 r_free=0.1867 | n_water=151 | time (s): 1.610 (total time: 21.960) Find peaks r_work=0.1308 r_free=0.1867 | n_water=151 | time (s): 0.400 (total time: 22.360) Add new water r_work=0.1709 r_free=0.2159 | n_water=240 | time (s): 1.350 (total time: 23.710) Refine new water occ: r_work=0.1051 r_free=0.1752 adp: r_work=0.1045 r_free=0.1762 occ: r_work=0.1035 r_free=0.1742 adp: r_work=0.1035 r_free=0.1751 occ: r_work=0.1026 r_free=0.1731 adp: r_work=0.1025 r_free=0.1739 ADP+occupancy (water only), MIN, final r_work=0.1025 r_free=0.1739 r_work=0.1025 r_free=0.1739 | n_water=240 | time (s): 8.590 (total time: 32.300) Filter (q & B) r_work=0.1025 r_free=0.1740 | n_water=239 | time (s): 1.600 (total time: 33.900) Filter (dist only) r_work=0.1043 r_free=0.1736 | n_water=235 | time (s): 20.650 (total time: 54.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.071131 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.228199 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 0.0935 0.1759 0.0825 0.011 1.0 3.8 0.5 0.0 0 0.536 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.35 17.59 8.25 5.344 17.584 0.228 5.152 8.88 17.91 9.02 7.174 17.637 0.228 5.050 Individual atomic B min max mean iso aniso Overall: 0.00 111.31 16.28 8.91 1762 0 Protein: 0.00 111.31 15.05 8.91 1519 0 Water: 0.00 57.95 23.96 N/A 235 0 Other: 10.64 34.45 23.64 N/A 8 0 Chain A: 0.00 111.31 15.73 N/A 1656 0 Chain S: 0.00 56.85 24.85 N/A 106 0 Histogram: Values Number of atoms 0.00 - 11.13 739 11.13 - 22.26 625 22.26 - 33.39 230 33.39 - 44.52 101 44.52 - 55.65 33 55.65 - 66.78 19 66.78 - 77.91 10 77.91 - 89.05 0 89.05 - 100.18 4 100.18 - 111.31 1 =========================== Idealize ADP of riding H ========================== r_work=0.0888 r_free=0.1791 r_work=0.0894 r_free=0.1799 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0894 r_free = 0.1799 target_work(ml) = 5.054 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0884 r_free = 0.1791 target_work(ml) = 5.048 | | occupancies: max = 1.00 min = 0.25 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= 0.0884 r_free= 0.1791 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.048458 | | target function (ml) not normalized (work): 24858.606339 | | target function (ml) not normalized (free): 1768.773542 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0930 0.0884 0.1791 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2136 0.2144 0.2132 n_refl.: 5176 remove outliers: r(all,work,free)=0.2136 0.2144 0.2132 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2136 0.2144 0.2132 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0923 0.0879 0.1785 n_refl.: 5176 remove outliers: r(all,work,free)=0.0919 0.0874 0.1785 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 0.3647 330.539 297.821 0.596 0.991 0.340 11.894-9.307 99.02 97 4 0.1780 526.049 512.578 0.950 0.995 0.338 9.237-7.194 100.00 213 7 0.1896 430.204 424.544 1.010 0.997 0.312 7.162-5.571 100.00 427 22 0.1840 322.816 313.822 0.981 0.998 0.310 5.546-4.326 100.00 867 58 0.0898 443.180 437.549 1.001 0.999 0.225 4.315-3.360 100.00 1859 96 0.0573 421.469 421.077 1.055 1.001 0.220 3.356-3.002 100.00 1373 60 0.0594 324.633 324.268 1.032 1.003 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9176 b_overall=-6.2651 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0874 r_free=0.1785 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0875 r_free=0.1784 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0875 r_free=0.1784 | n_water=235 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0887 r_free=0.1784 | n_water=233 | time (s): 17.180 (total time: 17.720) Filter (q & B) r_work=0.1001 r_free=0.1815 | n_water=229 | time (s): 1.370 (total time: 19.090) Compute maps r_work=0.1001 r_free=0.1815 | n_water=229 | time (s): 0.530 (total time: 19.620) Filter (map) r_work=0.1265 r_free=0.1883 | n_water=163 | time (s): 1.620 (total time: 21.240) Find peaks r_work=0.1265 r_free=0.1883 | n_water=163 | time (s): 0.390 (total time: 21.630) Add new water r_work=0.1581 r_free=0.2134 | n_water=240 | time (s): 1.230 (total time: 22.860) Refine new water occ: r_work=0.1007 r_free=0.1798 adp: r_work=0.0998 r_free=0.1811 occ: r_work=0.0991 r_free=0.1795 adp: r_work=0.0991 r_free=0.1804 occ: r_work=0.0984 r_free=0.1786 adp: r_work=0.0983 r_free=0.1795 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1795 r_work=0.0983 r_free=0.1795 | n_water=240 | time (s): 13.440 (total time: 36.300) Filter (q & B) r_work=0.0984 r_free=0.1796 | n_water=237 | time (s): 1.940 (total time: 38.240) Filter (dist only) r_work=0.0989 r_free=0.1802 | n_water=236 | time (s): 18.670 (total time: 56.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.982573 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.267762 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 0.0892 0.1841 0.0949 0.010 1.0 3.8 0.5 0.6 0 0.491 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.92 18.41 9.49 6.954 17.864 0.268 5.021 8.71 18.59 9.88 8.107 17.948 0.268 4.960 Individual atomic B min max mean iso aniso Overall: 0.00 112.88 16.53 10.57 1763 0 Protein: 0.00 112.88 15.41 10.58 1519 0 Water: 0.00 56.20 23.52 N/A 236 0 Other: 8.18 35.37 23.00 N/A 8 0 Chain A: 0.00 112.88 15.92 N/A 1641 0 Chain S: 0.00 56.20 24.78 N/A 122 0 Histogram: Values Number of atoms 0.00 - 11.29 732 11.29 - 22.58 626 22.58 - 33.86 238 33.86 - 45.15 106 45.15 - 56.44 31 56.44 - 67.73 14 67.73 - 79.02 10 79.02 - 90.30 1 90.30 - 101.59 4 101.59 - 112.88 1 =========================== Idealize ADP of riding H ========================== r_work=0.0871 r_free=0.1859 r_work=0.0875 r_free=0.1862 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0875 r_free = 0.1862 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0866 r_free = 0.1856 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.24 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= 0.0866 r_free= 0.1856 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.956527 | | target function (ml) not normalized (work): 24396.025120 | | target function (ml) not normalized (free): 2065.166770 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0916 0.0866 0.1856 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2055 0.2054 0.2203 n_refl.: 5174 remove outliers: r(all,work,free)=0.2055 0.2054 0.2203 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2055 0.2054 0.2203 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0914 0.0865 0.1847 n_refl.: 5174 remove outliers: r(all,work,free)=0.0914 0.0865 0.1847 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 0.3850 330.539 298.051 0.577 0.987 0.319 11.894-9.307 99.02 97 4 0.1842 526.049 511.588 0.955 0.992 0.316 9.237-7.194 100.00 213 7 0.2060 430.204 422.410 1.007 0.995 0.307 7.162-5.571 100.00 427 22 0.2027 322.816 312.214 0.993 0.996 0.300 5.546-4.326 100.00 867 58 0.0955 443.180 437.149 1.014 0.999 0.225 4.315-3.360 100.00 1859 96 0.0546 421.469 421.325 1.075 1.002 0.220 3.356-3.002 100.00 1373 60 0.0442 324.633 324.629 1.053 1.005 0.071 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.3147 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0865 r_free=0.1848 After: r_work=0.0868 r_free=0.1846 ================================== NQH flips ================================== r_work=0.0868 r_free=0.1846 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=0.0870 r_free=0.1841 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0870 r_free=0.1841 | n_water=236 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.0887 r_free=0.1840 | n_water=234 | time (s): 18.980 (total time: 19.630) Filter (q & B) r_work=0.1012 r_free=0.1853 | n_water=231 | time (s): 1.440 (total time: 21.070) Compute maps r_work=0.1012 r_free=0.1853 | n_water=231 | time (s): 0.450 (total time: 21.520) Filter (map) r_work=0.1248 r_free=0.1936 | n_water=165 | time (s): 1.320 (total time: 22.840) Find peaks r_work=0.1248 r_free=0.1936 | n_water=165 | time (s): 0.390 (total time: 23.230) Add new water r_work=0.1530 r_free=0.2130 | n_water=231 | time (s): 1.400 (total time: 24.630) Refine new water occ: r_work=0.1007 r_free=0.1843 adp: r_work=0.0994 r_free=0.1856 occ: r_work=0.0988 r_free=0.1843 adp: r_work=0.0987 r_free=0.1849 occ: r_work=0.0981 r_free=0.1835 adp: r_work=0.0981 r_free=0.1835 ADP+occupancy (water only), MIN, final r_work=0.0981 r_free=0.1835 r_work=0.0981 r_free=0.1835 | n_water=231 | time (s): 11.300 (total time: 35.930) Filter (q & B) r_work=0.0982 r_free=0.1840 | n_water=230 | time (s): 1.350 (total time: 37.280) Filter (dist only) r_work=0.0982 r_free=0.1840 | n_water=230 | time (s): 15.970 (total time: 53.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.000208 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.232665 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 0.1819 0.0911 0.011 1.1 7.0 0.5 0.6 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.08 18.19 9.11 8.047 18.063 0.233 5.012 8.92 18.57 9.64 9.013 18.263 0.233 4.955 Individual atomic B min max mean iso aniso Overall: 0.00 114.98 16.86 11.91 1757 0 Protein: 0.00 114.98 15.98 11.91 1519 0 Water: 0.00 55.04 22.52 N/A 230 0 Other: 5.89 35.68 21.99 N/A 8 0 Chain A: 0.00 114.98 16.39 N/A 1635 0 Chain S: 0.00 52.04 23.17 N/A 122 0 Histogram: Values Number of atoms 0.00 - 11.50 709 11.50 - 23.00 651 23.00 - 34.49 238 34.49 - 45.99 93 45.99 - 57.49 33 57.49 - 68.99 17 68.99 - 80.49 8 80.49 - 91.98 3 91.98 - 103.48 3 103.48 - 114.98 2 =========================== Idealize ADP of riding H ========================== r_work=0.0892 r_free=0.1857 r_work=0.0896 r_free=0.1862 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0896 r_free = 0.1862 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0893 r_free = 0.1858 target_work(ml) = 4.957 | | 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= 0.0893 r_free= 0.1858 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.957134 | | target function (ml) not normalized (work): 24399.014000 | | target function (ml) not normalized (free): 2107.175671 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1274 0.1893 5.5397 6.3237| | 2: 3.78 - 3.00 1.00 2430 110 0.0428 0.1800 4.3597 10.993| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.92 12.11 1.00 0.98 13394.79| | 2: 3.78 - 3.00 2430 110 0.99 1.96 1.00 1.00 925.47| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 591.04 max = 22425.90 mean = 7238.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.90 mean = 7.10| |phase err.(test): min = 0.00 max = 77.16 mean = 7.18| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0940 0.0893 0.1858 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2112 0.2107 0.2307 n_refl.: 5174 remove outliers: r(all,work,free)=0.2112 0.2107 0.2307 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2112 0.2107 0.2307 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0939 0.0891 0.1858 n_refl.: 5174 remove outliers: r(all,work,free)=0.0939 0.0891 0.1858 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 0.3872 330.539 297.618 0.583 0.984 0.320 11.894-9.307 99.02 97 4 0.1918 526.049 512.599 0.958 0.991 0.320 9.237-7.194 100.00 213 7 0.2125 430.204 420.951 1.003 0.995 0.300 7.162-5.571 100.00 427 22 0.2111 322.816 312.223 0.993 0.997 0.280 5.546-4.326 100.00 867 58 0.1019 443.180 437.521 1.022 0.999 0.230 4.315-3.360 100.00 1859 96 0.0568 421.469 421.665 1.091 1.003 0.230 3.356-3.002 100.00 1373 60 0.0413 324.633 324.431 1.070 1.006 0.066 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.0256 ================= 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 : 0.3627 0.2050 0.081 5.219 8.8 119.3 19.9 258 0.000 1_bss: 0.1582 0.1638 0.081 5.219 6.0 116.4 17.0 258 0.000 1_settarget: 0.1582 0.1638 0.081 5.219 6.0 116.4 17.0 258 0.000 1_nqh: 0.1585 0.1636 0.081 5.219 6.0 116.4 17.0 258 0.006 1_weight: 0.1585 0.1636 0.081 5.219 6.0 116.4 17.0 258 0.006 1_xyzrec: 0.1163 0.1817 0.010 0.976 6.0 116.4 17.0 258 0.212 1_adp: 0.1017 0.1789 0.010 0.976 1.8 112.6 17.3 258 0.212 1_regHadp: 0.1011 0.1796 0.010 0.976 1.8 112.6 17.3 258 0.212 1_occ: 0.1003 0.1792 0.010 0.976 1.8 112.6 17.3 258 0.212 2_bss: 0.1007 0.1799 0.010 0.976 0.9 111.6 16.4 258 0.212 2_settarget: 0.1007 0.1799 0.010 0.976 0.9 111.6 16.4 258 0.212 2_updatecdl: 0.1007 0.1799 0.010 0.990 0.9 111.6 16.4 258 0.212 2_nqh: 0.1007 0.1799 0.010 0.990 0.9 111.6 16.4 258 0.212 2_sol: 0.1118 0.1661 0.010 0.990 0.9 111.6 15.7 236 n/a 2_weight: 0.1118 0.1661 0.010 0.990 0.9 111.6 15.7 236 n/a 2_xyzrec: 0.0991 0.1802 0.009 0.961 0.9 111.6 15.7 236 n/a 2_adp: 0.0932 0.1812 0.009 0.961 0.0 111.3 16.4 236 n/a 2_regHadp: 0.0929 0.1810 0.009 0.961 0.0 111.3 16.4 236 n/a 2_occ: 0.0926 0.1800 0.009 0.961 0.0 111.3 16.4 236 n/a 3_bss: 0.0923 0.1799 0.009 0.961 0.0 111.3 16.4 236 n/a 3_settarget: 0.0923 0.1799 0.009 0.961 0.0 111.3 16.4 236 n/a 3_updatecdl: 0.0923 0.1799 0.009 0.964 0.0 111.3 16.4 236 n/a 3_nqh: 0.0927 0.1797 0.009 0.964 0.0 111.3 16.4 236 n/a 3_sol: 0.1043 0.1736 0.009 0.964 0.0 111.3 16.2 235 n/a 3_weight: 0.1043 0.1736 0.009 0.964 0.0 111.3 16.2 235 n/a 3_xyzrec: 0.0935 0.1759 0.011 1.041 0.0 111.3 16.2 235 n/a 3_adp: 0.0888 0.1791 0.011 1.041 0.0 111.3 16.3 235 n/a 3_regHadp: 0.0894 0.1799 0.011 1.041 0.0 111.3 16.3 235 n/a 3_occ: 0.0884 0.1791 0.011 1.041 0.0 111.3 16.3 235 n/a 4_bss: 0.0874 0.1785 0.011 1.041 0.0 111.3 16.3 235 n/a 4_settarget: 0.0874 0.1785 0.011 1.041 0.0 111.3 16.3 235 n/a 4_updatecdl: 0.0874 0.1785 0.011 1.066 0.0 111.3 16.3 235 n/a 4_nqh: 0.0875 0.1784 0.011 1.066 0.0 111.3 16.3 235 n/a 4_sol: 0.0989 0.1802 0.011 1.066 0.0 111.3 16.4 236 n/a 4_weight: 0.0989 0.1802 0.011 1.066 0.0 111.3 16.4 236 n/a 4_xyzrec: 0.0892 0.1841 0.010 1.040 0.0 111.3 16.4 236 n/a 4_adp: 0.0871 0.1859 0.010 1.040 0.0 112.9 16.5 236 n/a 4_regHadp: 0.0875 0.1862 0.010 1.040 0.0 112.9 16.5 236 n/a 4_occ: 0.0866 0.1856 0.010 1.040 0.0 112.9 16.5 236 n/a 5_bss: 0.0865 0.1848 0.010 1.040 0.0 112.9 16.5 236 n/a 5_settarget: 0.0865 0.1848 0.010 1.040 0.0 112.9 16.5 236 n/a 5_updatecdl: 0.0865 0.1848 0.010 1.045 0.0 112.9 16.5 236 n/a 5_setrh: 0.0868 0.1846 0.010 1.045 0.0 112.9 16.5 236 n/a 5_nqh: 0.0870 0.1841 0.010 1.045 0.0 112.9 16.5 236 n/a 5_sol: 0.0982 0.1840 0.010 1.045 0.0 112.9 16.5 230 n/a 5_weight: 0.0982 0.1840 0.010 1.045 0.0 112.9 16.5 230 n/a 5_xyzrec: 0.0908 0.1819 0.011 1.128 0.0 112.9 16.5 230 n/a 5_adp: 0.0892 0.1857 0.011 1.128 0.0 115.0 16.9 230 n/a 5_regHadp: 0.0896 0.1862 0.011 1.128 0.0 115.0 16.9 230 n/a 5_occ: 0.0893 0.1858 0.011 1.128 0.0 115.0 16.9 230 n/a end: 0.0891 0.1858 0.011 1.128 0.0 115.0 16.9 230 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6446528_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6446528_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7900 Refinement macro-cycles (run) : 491.4200 Write final files (write_after_run_outputs) : 9.1700 Total : 504.3800 Total CPU time: 8.77 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:08 PST -0800 (1735492748.10 s) Start R-work = 0.1582, R-free = 0.1638 Final R-work = 0.0891, R-free = 0.1858 =============================================================================== Job complete usr+sys time: 534.50 seconds wall clock time: 9 minutes 16.92 seconds (556.92 seconds total)