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_3120282.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3120282.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3120282.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.98, per 1000 atoms: 0.59 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: 0.40 Conformation dependent library (CDL) restraints added in 203.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.89: 397 0.89 - 1.14: 1208 1.14 - 1.39: 565 1.39 - 1.64: 914 1.64 - 1.90: 69 Bond restraints: 3153 Sorted by residual: bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.506 -0.185 1.00e-02 1.00e+04 3.42e+02 bond pdb=" N BLYS A 93 " pdb=" CA BLYS A 93 " ideal model delta sigma weight residual 1.459 1.670 -0.211 1.17e-02 7.31e+03 3.26e+02 bond pdb=" N AGLU A 94 " pdb=" CA AGLU A 94 " ideal model delta sigma weight residual 1.459 1.244 0.215 1.21e-02 6.83e+03 3.17e+02 bond pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta sigma weight residual 1.454 1.229 0.225 1.27e-02 6.20e+03 3.14e+02 bond pdb=" C ASN A 144 " pdb=" O ASN A 144 " ideal model delta sigma weight residual 1.234 1.031 0.203 1.22e-02 6.72e+03 2.76e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.77: 3188 4.77 - 9.53: 1877 9.53 - 14.30: 618 14.30 - 19.07: 88 19.07 - 23.83: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 140.42 -17.75 1.02e+00 9.61e-01 3.03e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 136.53 -15.03 1.00e+00 1.00e+00 2.26e+02 angle pdb=" O HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 121.30 134.92 -13.62 1.03e+00 9.43e-01 1.75e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.55 134.31 -13.76 1.06e+00 8.90e-01 1.69e+02 angle pdb=" CA BGLU A 90 " pdb=" C BGLU A 90 " pdb=" O BGLU A 90 " ideal model delta sigma weight residual 120.55 134.06 -13.51 1.06e+00 8.90e-01 1.63e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1296 17.29 - 34.58: 130 34.58 - 51.88: 43 51.88 - 69.17: 9 69.17 - 86.46: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ILE A 21 " pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual -122.00 -143.71 21.71 0 2.50e+00 1.60e-01 7.54e+01 dihedral pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " ideal model delta harmonic sigma weight residual 122.80 141.92 -19.12 0 2.50e+00 1.60e-01 5.85e+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 -140.17 18.17 0 2.50e+00 1.60e-01 5.28e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.222: 98 0.222 - 0.441: 79 0.441 - 0.660: 48 0.660 - 0.879: 16 0.879 - 1.099: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.49 -1.10 2.00e-01 2.50e+01 3.02e+01 chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 1.57 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.86e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.023 2.00e-02 2.50e+03 6.81e-02 1.39e+02 pdb=" CG TYR A 139 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.135 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.064 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 27 " -0.145 9.50e-02 1.11e+02 7.50e-02 7.62e+01 pdb=" NE ARG A 27 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 27 " 0.126 2.00e-02 2.50e+03 pdb=" NH1 ARG A 27 " 0.037 2.00e-02 2.50e+03 pdb=" NH2 ARG A 27 " 0.048 2.00e-02 2.50e+03 pdb="HH11 ARG A 27 " -0.030 2.00e-02 2.50e+03 pdb="HH12 ARG A 27 " -0.032 2.00e-02 2.50e+03 pdb="HH21 ARG A 27 " -0.016 2.00e-02 2.50e+03 pdb="HH22 ARG A 27 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.010 2.00e-02 2.50e+03 4.87e-02 7.12e+01 pdb=" CG PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.075 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.066 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.055 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.016 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.036 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.051 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1409 2.37 - 2.93: 8343 2.93 - 3.48: 10434 3.48 - 4.04: 15114 4.04 - 4.60: 21323 Nonbonded interactions: 56623 Sorted by model distance: nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.811 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.828 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.846 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.858 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.868 2.100 ... (remaining 56618 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_3120282_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= 0.3623 r_free= 0.2043 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.480364 | | target function (ml) not normalized (work): 22088.195115 | | target function (ml) not normalized (free): 1148.222763 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3807 0.2244 4.8585 4.9253| | 2: 3.78 - 3.00 1.00 2430 110 0.3399 0.1702 4.0914 4.0803| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 6615.07| | 2: 3.78 - 3.00 2430 110 0.93 11.58 1.48 0.26 464.89| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 396.22 max = 12059.89 mean = 3583.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.44| |phase err.(test): min = 0.00 max = 89.95 mean = 33.48| |-----------------------------------------------------------------------------| ----------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 0.291 1557 Z= 5.341 Angle : 5.232 17.755 2118 Z= 3.705 Chirality : 0.382 1.099 243 Planarity : 0.029 0.073 284 Dihedral : 13.950 86.460 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 4.97 % Favored : 94.41 % Cbeta Deviations : 31.89 % 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: -2.51 (0.47), residues: 224 helix: -2.60 (0.37), residues: 108 sheet: -0.34 (0.88), residues: 28 loop : -0.50 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.112 0.034 ARG A 48 TYR 0.100 0.043 TYR A 139 PHE 0.073 0.033 PHE A 162 HIS 0.060 0.029 HIS A 115 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= 0.3623 r_free= 0.2043 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.480364 | | target function (ml) not normalized (work): 22088.195115 | | target function (ml) not normalized (free): 1148.222763 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3581 0.3656 0.2133 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3581 0.3656 0.2133 n_refl.: 5182 remove outliers: r(all,work,free)=0.2549 0.2573 0.2133 n_refl.: 5178 overall B=-2.84 to atoms: r(all,work,free)=0.2441 0.2463 0.2083 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1599 0.1600 0.1588 n_refl.: 5178 remove outliers: r(all,work,free)=0.1595 0.1595 0.1588 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 0.3845 450.287 410.943 0.680 1.052 0.415 11.894-9.307 99.02 97 4 0.1835 715.316 695.018 0.955 1.051 0.389 9.237-7.194 100.00 213 7 0.2214 584.987 575.679 0.987 1.045 0.374 7.162-5.571 100.00 427 22 0.2421 438.961 421.833 0.944 1.035 0.336 5.546-4.326 100.00 867 58 0.1417 602.632 595.448 0.987 1.017 0.248 4.315-3.360 100.00 1859 96 0.1331 573.109 566.271 1.055 0.988 0.213 3.356-3.002 100.00 1373 60 0.1651 441.433 433.646 1.064 0.959 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.6361 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1595 r_free=0.1588 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1597 r_free=0.1587 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.837235 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.819989 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 0.1165 0.1796 0.0631 0.010 1.0 3.5 0.5 0.0 0 9.419 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 17.96 6.31 3.013 16.016 1.820 0.018 10.31 17.90 7.58 4.779 16.143 1.820 0.015 Individual atomic B min max mean iso aniso Overall: 1.98 111.46 17.28 5.19 1785 0 Protein: 1.98 110.84 14.56 5.18 1519 0 Water: 4.02 111.46 33.09 N/A 258 0 Other: 17.21 38.51 23.78 N/A 8 0 Chain A: 1.98 111.46 17.28 N/A 1785 0 Histogram: Values Number of atoms 1.98 - 12.93 911 12.93 - 23.88 494 23.88 - 34.83 183 34.83 - 45.77 110 45.77 - 56.72 57 56.72 - 67.67 13 67.67 - 78.61 8 78.61 - 89.56 5 89.56 - 100.51 1 100.51 - 111.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.1031 r_free=0.1790 r_work=0.1026 r_free=0.1795 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1026 r_free = 0.1795 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1014 r_free = 0.1779 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.30 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= 0.1014 r_free= 0.1779 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013982 | | target function (ls_wunit_k1) not normalized (work): 68.847598 | | target function (ls_wunit_k1) not normalized (free): 10.539047 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1053 0.1014 0.1779 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2101 0.2102 0.2198 n_refl.: 5176 remove outliers: r(all,work,free)=0.2101 0.2102 0.2198 n_refl.: 5176 overall B=-0.93 to atoms: r(all,work,free)=0.2063 0.2061 0.2189 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1051 0.1012 0.1765 n_refl.: 5176 remove outliers: r(all,work,free)=0.1051 0.1012 0.1765 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 0.3305 330.404 323.246 0.709 0.998 0.391 11.894-9.307 99.02 97 4 0.1527 524.873 516.183 0.994 1.001 0.371 9.237-7.194 100.00 213 7 0.1660 429.242 429.558 1.029 1.002 0.330 7.162-5.571 100.00 427 22 0.1620 322.094 318.292 0.985 1.001 0.312 5.546-4.326 100.00 867 58 0.0908 442.189 438.687 0.997 1.001 0.212 4.315-3.360 100.00 1859 96 0.0767 420.527 420.610 1.038 1.000 0.203 3.356-3.002 100.00 1373 60 0.1004 323.907 322.545 1.009 0.999 0.031 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3353 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1012 r_free=0.1765 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1014 r_free=0.1769 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1014 r_free=0.1769 | n_water=258 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.1044 r_free=0.1766 | n_water=247 | time (s): 20.020 (total time: 20.510) Filter (q & B) r_work=0.1046 r_free=0.1770 | n_water=244 | time (s): 1.760 (total time: 22.270) Compute maps r_work=0.1046 r_free=0.1770 | n_water=244 | time (s): 0.510 (total time: 22.780) Filter (map) r_work=0.1365 r_free=0.1848 | n_water=139 | time (s): 1.500 (total time: 24.280) Find peaks r_work=0.1365 r_free=0.1848 | n_water=139 | time (s): 0.400 (total time: 24.680) Add new water r_work=0.1712 r_free=0.2068 | n_water=222 | time (s): 1.320 (total time: 26.000) Refine new water occ: r_work=0.1165 r_free=0.1706 adp: r_work=0.1143 r_free=0.1712 occ: r_work=0.1141 r_free=0.1699 adp: r_work=0.1131 r_free=0.1702 occ: r_work=0.1132 r_free=0.1702 adp: r_work=0.1129 r_free=0.1698 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1698 r_work=0.1129 r_free=0.1698 | n_water=222 | time (s): 3.040 (total time: 29.040) Filter (q & B) r_work=0.1129 r_free=0.1698 | n_water=222 | time (s): 0.750 (total time: 29.790) Filter (dist only) r_work=0.1131 r_free=0.1689 | n_water=218 | time (s): 17.120 (total time: 46.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.997529 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.764752 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 0.1019 0.1803 0.0784 0.009 1.0 3.5 0.5 0.6 0 11.499 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.19 18.03 7.84 4.591 16.581 2.765 0.014 9.51 18.38 8.87 5.335 16.881 2.765 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 108.30 16.17 6.28 1745 0 Protein: 0.00 108.30 14.64 6.26 1519 0 Water: 0.00 62.81 26.51 N/A 218 0 Other: 13.50 40.22 25.72 N/A 8 0 Chain A: 0.00 108.30 15.41 N/A 1665 0 Chain S: 1.27 59.38 32.03 N/A 80 0 Histogram: Values Number of atoms 0.00 - 10.83 735 10.83 - 21.66 629 21.66 - 32.49 200 32.49 - 43.32 108 43.32 - 54.15 35 54.15 - 64.98 25 64.98 - 75.81 7 75.81 - 86.64 3 86.64 - 97.47 1 97.47 - 108.30 2 =========================== Idealize ADP of riding H ========================== r_work=0.0951 r_free=0.1838 r_work=0.0948 r_free=0.1837 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0948 r_free = 0.1837 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0946 r_free = 0.1837 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 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= 0.0946 r_free= 0.1837 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012213 | | target function (ls_wunit_k1) not normalized (work): 60.135332 | | target function (ls_wunit_k1) not normalized (free): 10.468968 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0991 0.0946 0.1837 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2142 0.2150 0.2170 n_refl.: 5176 remove outliers: r(all,work,free)=0.2142 0.2150 0.2170 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2142 0.2150 0.2170 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0993 0.0949 0.1836 n_refl.: 5176 remove outliers: r(all,work,free)=0.0991 0.0946 0.1836 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3269 327.621 309.900 0.674 1.000 0.360 11.894-9.307 99.02 97 4 0.1482 524.873 514.965 0.993 1.003 0.345 9.237-7.194 100.00 213 7 0.1473 429.242 428.252 1.033 1.004 0.320 7.162-5.571 100.00 427 22 0.1434 322.094 317.609 1.001 1.003 0.310 5.546-4.326 100.00 867 58 0.0813 442.189 438.757 1.014 1.002 0.230 4.315-3.360 100.00 1859 96 0.0732 420.527 421.010 1.063 1.001 0.215 3.356-3.002 100.00 1373 60 0.0967 323.907 324.577 1.040 0.999 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.6679 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0946 r_free=0.1836 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0947 r_free=0.1835 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0947 r_free=0.1835 | n_water=218 | time (s): 0.460 (total time: 0.460) Filter (dist) r_work=0.0971 r_free=0.1867 | n_water=213 | time (s): 17.130 (total time: 17.590) Filter (q & B) r_work=0.1059 r_free=0.1831 | n_water=210 | time (s): 1.490 (total time: 19.080) Compute maps r_work=0.1059 r_free=0.1831 | n_water=210 | time (s): 0.460 (total time: 19.540) Filter (map) r_work=0.1305 r_free=0.1918 | n_water=143 | time (s): 1.580 (total time: 21.120) Find peaks r_work=0.1305 r_free=0.1918 | n_water=143 | time (s): 0.410 (total time: 21.530) Add new water r_work=0.1690 r_free=0.2309 | n_water=228 | time (s): 1.260 (total time: 22.790) Refine new water occ: r_work=0.1088 r_free=0.1792 adp: r_work=0.1078 r_free=0.1819 occ: r_work=0.1067 r_free=0.1793 adp: r_work=0.1066 r_free=0.1805 occ: r_work=0.1057 r_free=0.1778 adp: r_work=0.1056 r_free=0.1789 ADP+occupancy (water only), MIN, final r_work=0.1056 r_free=0.1789 r_work=0.1056 r_free=0.1789 | n_water=228 | time (s): 11.070 (total time: 33.860) Filter (q & B) r_work=0.1057 r_free=0.1791 | n_water=227 | time (s): 1.330 (total time: 35.190) Filter (dist only) r_work=0.1064 r_free=0.1798 | n_water=224 | time (s): 18.270 (total time: 53.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.104456 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.226216 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 0.0962 0.1806 0.0844 0.011 1.1 4.8 0.5 1.2 0 0.552 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.62 18.06 8.44 5.266 17.409 0.226 5.185 9.14 18.22 9.08 7.248 17.478 0.226 5.083 Individual atomic B min max mean iso aniso Overall: 0.00 108.80 16.17 8.98 1751 0 Protein: 0.00 108.80 14.88 8.96 1519 0 Water: 0.00 58.12 24.47 N/A 224 0 Other: 13.71 45.43 28.67 N/A 8 0 Chain A: 0.00 108.80 15.65 N/A 1654 0 Chain S: 0.00 58.12 25.10 N/A 97 0 Histogram: Values Number of atoms 0.00 - 10.88 711 10.88 - 21.76 634 21.76 - 32.64 229 32.64 - 43.52 112 43.52 - 54.40 35 54.40 - 65.28 16 65.28 - 76.16 8 76.16 - 87.04 2 87.04 - 97.92 3 97.92 - 108.80 1 =========================== Idealize ADP of riding H ========================== r_work=0.0914 r_free=0.1822 r_work=0.0920 r_free=0.1831 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0920 r_free = 0.1831 target_work(ml) = 5.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0912 r_free = 0.1823 target_work(ml) = 5.083 | | 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.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0912 r_free= 0.1823 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.082833 | | target function (ml) not normalized (work): 25022.788747 | | target function (ml) not normalized (free): 1805.921764 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0959 0.0912 0.1823 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2148 0.2162 0.2093 n_refl.: 5175 remove outliers: r(all,work,free)=0.2148 0.2162 0.2093 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2148 0.2162 0.2093 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0951 0.0905 0.1813 n_refl.: 5175 remove outliers: r(all,work,free)=0.0948 0.0903 0.1813 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 0.3637 329.800 295.422 0.599 0.992 0.340 11.894-9.307 99.02 97 4 0.1951 524.873 505.472 0.942 0.996 0.336 9.237-7.194 100.00 213 7 0.1921 429.242 423.660 1.001 0.999 0.326 7.162-5.571 100.00 427 22 0.1865 322.094 312.656 0.982 1.000 0.320 5.546-4.326 100.00 867 58 0.0939 442.189 436.905 1.001 1.001 0.230 4.315-3.360 100.00 1859 96 0.0595 420.527 420.492 1.058 1.004 0.220 3.356-3.002 100.00 1373 60 0.0610 323.907 323.764 1.034 1.005 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.5202 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0903 r_free=0.1813 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0903 r_free=0.1813 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0903 r_free=0.1813 | n_water=224 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.0922 r_free=0.1833 | n_water=218 | time (s): 17.790 (total time: 18.290) Filter (q & B) r_work=0.0991 r_free=0.1818 | n_water=215 | time (s): 1.650 (total time: 19.940) Compute maps r_work=0.0991 r_free=0.1818 | n_water=215 | time (s): 0.640 (total time: 20.580) Filter (map) r_work=0.1249 r_free=0.1907 | n_water=154 | time (s): 1.740 (total time: 22.320) Find peaks r_work=0.1249 r_free=0.1907 | n_water=154 | time (s): 0.450 (total time: 22.770) Add new water r_work=0.1575 r_free=0.2169 | n_water=231 | time (s): 1.180 (total time: 23.950) Refine new water occ: r_work=0.1022 r_free=0.1815 adp: r_work=0.1015 r_free=0.1837 occ: r_work=0.1007 r_free=0.1813 adp: r_work=0.1006 r_free=0.1825 occ: r_work=0.0999 r_free=0.1801 adp: r_work=0.0998 r_free=0.1812 ADP+occupancy (water only), MIN, final r_work=0.0998 r_free=0.1812 r_work=0.0998 r_free=0.1812 | n_water=231 | time (s): 12.500 (total time: 36.450) Filter (q & B) r_work=0.0998 r_free=0.1812 | n_water=231 | time (s): 0.770 (total time: 37.220) Filter (dist only) r_work=0.0999 r_free=0.1808 | n_water=229 | time (s): 18.070 (total time: 55.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.038544 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.256276 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 0.0918 0.1873 0.0955 0.011 1.1 5.8 0.5 1.2 0 0.519 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.18 18.73 9.55 6.977 17.746 0.256 5.041 8.90 19.13 10.23 8.398 17.859 0.256 4.973 Individual atomic B min max mean iso aniso Overall: 0.00 109.55 16.53 10.97 1756 0 Protein: 0.00 109.55 15.28 10.96 1519 0 Water: 0.00 63.74 24.36 N/A 229 0 Other: 13.03 43.22 29.25 N/A 8 0 Chain A: 0.00 109.55 15.90 N/A 1641 0 Chain S: 0.00 56.92 25.57 N/A 115 0 Histogram: Values Number of atoms 0.00 - 10.96 698 10.96 - 21.91 612 21.91 - 32.87 259 32.87 - 43.82 113 43.82 - 54.78 44 54.78 - 65.73 11 65.73 - 76.69 11 76.69 - 87.64 4 87.64 - 98.60 3 98.60 - 109.55 1 =========================== Idealize ADP of riding H ========================== r_work=0.0890 r_free=0.1913 r_work=0.0894 r_free=0.1921 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0894 r_free = 0.1921 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0884 r_free = 0.1906 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.25 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= 0.0884 r_free= 0.1906 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.971488 | | target function (ml) not normalized (work): 24469.663275 | | target function (ml) not normalized (free): 2150.925088 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0884 0.1906 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2103 0.2103 0.2241 n_refl.: 5174 remove outliers: r(all,work,free)=0.2103 0.2103 0.2241 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2103 0.2103 0.2241 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0932 0.0882 0.1894 n_refl.: 5174 remove outliers: r(all,work,free)=0.0932 0.0882 0.1894 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 0.3804 329.800 301.835 0.584 0.984 0.317 11.894-9.307 99.02 97 4 0.1931 524.873 507.031 0.951 0.991 0.314 9.237-7.194 100.00 213 7 0.2078 429.242 421.743 1.010 0.994 0.290 7.162-5.571 100.00 427 22 0.2022 322.094 309.685 0.989 0.997 0.280 5.546-4.326 100.00 867 58 0.0974 442.189 436.107 1.018 0.999 0.235 4.315-3.360 100.00 1859 96 0.0574 420.527 420.450 1.083 1.003 0.230 3.356-3.002 100.00 1373 60 0.0441 323.907 324.025 1.059 1.006 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6502 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0882 r_free=0.1894 After: r_work=0.0885 r_free=0.1892 ================================== NQH flips ================================== r_work=0.0885 r_free=0.1892 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0885 r_free=0.1892 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0885 r_free=0.1892 | n_water=229 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.0895 r_free=0.1910 | n_water=226 | time (s): 18.150 (total time: 18.750) Filter (q & B) r_work=0.0935 r_free=0.1927 | n_water=225 | time (s): 1.570 (total time: 20.320) Compute maps r_work=0.0935 r_free=0.1927 | n_water=225 | time (s): 0.630 (total time: 20.950) Filter (map) r_work=0.1237 r_free=0.1974 | n_water=157 | time (s): 1.910 (total time: 22.860) Find peaks r_work=0.1237 r_free=0.1974 | n_water=157 | time (s): 0.450 (total time: 23.310) Add new water r_work=0.1512 r_free=0.2213 | n_water=225 | time (s): 1.390 (total time: 24.700) Refine new water occ: r_work=0.0997 r_free=0.1889 adp: r_work=0.0993 r_free=0.1889 occ: r_work=0.0985 r_free=0.1884 adp: r_work=0.0985 r_free=0.1885 occ: r_work=0.0978 r_free=0.1879 adp: r_work=0.0977 r_free=0.1880 ADP+occupancy (water only), MIN, final r_work=0.0977 r_free=0.1880 r_work=0.0977 r_free=0.1880 | n_water=225 | time (s): 11.720 (total time: 36.420) Filter (q & B) r_work=0.0980 r_free=0.1878 | n_water=224 | time (s): 1.570 (total time: 37.990) Filter (dist only) r_work=0.0980 r_free=0.1870 | n_water=222 | time (s): 16.260 (total time: 54.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.932983 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.248864 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 0.0916 0.1858 0.0943 0.010 1.1 7.0 0.5 0.6 0 0.466 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.16 18.58 9.43 8.302 18.092 0.249 5.010 9.00 18.54 9.54 9.179 18.232 0.249 4.961 Individual atomic B min max mean iso aniso Overall: 0.00 111.17 16.81 12.23 1749 0 Protein: 0.00 111.17 15.74 12.22 1519 0 Water: 0.00 58.74 23.66 N/A 222 0 Other: 14.01 41.92 30.92 N/A 8 0 Chain A: 0.00 111.17 16.25 N/A 1634 0 Chain S: 0.00 56.81 24.87 N/A 115 0 Histogram: Values Number of atoms 0.00 - 11.12 678 11.12 - 22.23 622 22.23 - 33.35 261 33.35 - 44.47 111 44.47 - 55.59 47 55.59 - 66.70 12 66.70 - 77.82 9 77.82 - 88.94 4 88.94 - 100.06 3 100.06 - 111.17 2 =========================== Idealize ADP of riding H ========================== r_work=0.0900 r_free=0.1854 r_work=0.0904 r_free=0.1856 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0904 r_free = 0.1856 target_work(ml) = 4.969 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0895 r_free = 0.1841 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0895 r_free= 0.1841 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.961657 | | target function (ml) not normalized (work): 24421.274365 | | target function (ml) not normalized (free): 2113.804636 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1278 0.1823 5.5507 6.2341| | 2: 3.78 - 3.00 1.00 2430 110 0.0429 0.1872 4.3576 11.169| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.29 1.00 0.97 13389.40| | 2: 3.78 - 3.00 2430 110 0.99 1.85 1.00 0.99 912.83| |alpha: min = 0.97 max = 0.99 mean = 0.98| |beta: min = 574.57 max = 22246.70 mean = 7229.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.99 mean = 7.14| |phase err.(test): min = 0.00 max = 81.54 mean = 7.14| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0943 0.0895 0.1841 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2153 0.2153 0.2291 n_refl.: 5174 remove outliers: r(all,work,free)=0.2153 0.2153 0.2291 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2153 0.2153 0.2291 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0943 0.0895 0.1857 n_refl.: 5174 remove outliers: r(all,work,free)=0.0943 0.0895 0.1857 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 0.3897 329.800 298.651 0.631 0.982 0.330 11.894-9.307 99.02 97 4 0.1936 524.873 508.907 1.011 0.990 0.330 9.237-7.194 100.00 213 7 0.2040 429.242 418.871 1.055 0.994 0.330 7.162-5.571 100.00 427 22 0.2133 322.094 308.126 1.023 0.997 0.264 5.546-4.326 100.00 867 58 0.1025 442.189 436.340 1.067 1.000 0.250 4.315-3.360 100.00 1859 96 0.0578 420.527 421.002 1.145 1.003 0.230 3.356-3.002 100.00 1373 60 0.0414 323.907 324.275 1.125 1.006 0.030 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.3876 ================= 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 : 0.3623 0.2043 0.081 5.232 8.8 119.3 19.9 258 0.000 1_bss: 0.1595 0.1588 0.081 5.232 6.0 116.5 17.0 258 0.000 1_settarget: 0.1595 0.1588 0.081 5.232 6.0 116.5 17.0 258 0.000 1_nqh: 0.1597 0.1587 0.081 5.232 6.0 116.5 17.0 258 0.003 1_weight: 0.1597 0.1587 0.081 5.232 6.0 116.5 17.0 258 0.003 1_xyzrec: 0.1165 0.1796 0.010 0.961 6.0 116.5 17.0 258 0.217 1_adp: 0.1031 0.1790 0.010 0.961 2.0 111.5 17.3 258 0.217 1_regHadp: 0.1026 0.1795 0.010 0.961 2.0 111.5 17.3 258 0.217 1_occ: 0.1014 0.1779 0.010 0.961 2.0 111.5 17.3 258 0.217 2_bss: 0.1012 0.1765 0.010 0.961 1.1 110.5 16.4 258 0.217 2_settarget: 0.1012 0.1765 0.010 0.961 1.1 110.5 16.4 258 0.217 2_updatecdl: 0.1012 0.1765 0.010 0.984 1.1 110.5 16.4 258 0.217 2_nqh: 0.1014 0.1769 0.010 0.984 1.1 110.5 16.4 258 0.214 2_sol: 0.1131 0.1689 0.010 0.984 1.1 109.9 15.6 218 n/a 2_weight: 0.1131 0.1689 0.010 0.984 1.1 109.9 15.6 218 n/a 2_xyzrec: 0.1019 0.1803 0.009 0.999 1.1 109.9 15.6 218 n/a 2_adp: 0.0951 0.1838 0.009 0.999 0.0 108.3 16.2 218 n/a 2_regHadp: 0.0948 0.1837 0.009 0.999 0.0 108.3 16.2 218 n/a 2_occ: 0.0946 0.1837 0.009 0.999 0.0 108.3 16.2 218 n/a 3_bss: 0.0946 0.1836 0.009 0.999 0.0 108.3 16.2 218 n/a 3_settarget: 0.0946 0.1836 0.009 0.999 0.0 108.3 16.2 218 n/a 3_updatecdl: 0.0946 0.1836 0.009 1.004 0.0 108.3 16.2 218 n/a 3_nqh: 0.0947 0.1835 0.009 1.004 0.0 108.3 16.2 218 n/a 3_sol: 0.1064 0.1798 0.009 1.004 0.0 108.3 16.0 224 n/a 3_weight: 0.1064 0.1798 0.009 1.004 0.0 108.3 16.0 224 n/a 3_xyzrec: 0.0962 0.1806 0.011 1.055 0.0 108.3 16.0 224 n/a 3_adp: 0.0914 0.1822 0.011 1.055 0.0 108.8 16.2 224 n/a 3_regHadp: 0.0920 0.1831 0.011 1.055 0.0 108.8 16.2 224 n/a 3_occ: 0.0912 0.1823 0.011 1.055 0.0 108.8 16.2 224 n/a 4_bss: 0.0903 0.1813 0.011 1.055 0.0 108.8 16.2 224 n/a 4_settarget: 0.0903 0.1813 0.011 1.055 0.0 108.8 16.2 224 n/a 4_updatecdl: 0.0903 0.1813 0.011 1.061 0.0 108.8 16.2 224 n/a 4_nqh: 0.0903 0.1813 0.011 1.061 0.0 108.8 16.2 224 n/a 4_sol: 0.0999 0.1808 0.011 1.061 0.0 108.8 16.3 229 n/a 4_weight: 0.0999 0.1808 0.011 1.061 0.0 108.8 16.3 229 n/a 4_xyzrec: 0.0918 0.1873 0.011 1.062 0.0 108.8 16.3 229 n/a 4_adp: 0.0890 0.1913 0.011 1.062 0.0 109.6 16.5 229 n/a 4_regHadp: 0.0894 0.1921 0.011 1.062 0.0 109.6 16.5 229 n/a 4_occ: 0.0884 0.1906 0.011 1.062 0.0 109.6 16.5 229 n/a 5_bss: 0.0882 0.1894 0.011 1.062 0.0 109.6 16.5 229 n/a 5_settarget: 0.0882 0.1894 0.011 1.062 0.0 109.6 16.5 229 n/a 5_updatecdl: 0.0882 0.1894 0.011 1.070 0.0 109.6 16.5 229 n/a 5_setrh: 0.0885 0.1892 0.011 1.070 0.0 109.6 16.5 229 n/a 5_nqh: 0.0885 0.1892 0.011 1.070 0.0 109.6 16.5 229 n/a 5_sol: 0.0980 0.1870 0.011 1.070 0.0 109.6 16.5 222 n/a 5_weight: 0.0980 0.1870 0.011 1.070 0.0 109.6 16.5 222 n/a 5_xyzrec: 0.0916 0.1858 0.010 1.125 0.0 109.6 16.5 222 n/a 5_adp: 0.0900 0.1854 0.010 1.125 0.0 111.2 16.8 222 n/a 5_regHadp: 0.0904 0.1856 0.010 1.125 0.0 111.2 16.8 222 n/a 5_occ: 0.0895 0.1841 0.010 1.125 0.0 111.2 16.8 222 n/a end: 0.0895 0.1857 0.010 1.125 0.0 111.2 16.8 222 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3120282_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3120282_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0800 Refinement macro-cycles (run) : 482.3600 Write final files (write_after_run_outputs) : 10.1800 Total : 496.6200 Total CPU time: 8.63 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:59 PST -0800 (1735492739.47 s) Start R-work = 0.1595, R-free = 0.1588 Final R-work = 0.0895, R-free = 0.1857 =============================================================================== Job complete usr+sys time: 525.95 seconds wall clock time: 9 minutes 8.14 seconds (548.14 seconds total)