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_4596863.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_4596863.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4596863.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.03, per 1000 atoms: 0.60 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 230.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.79 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: 435 0.89 - 1.14: 1155 1.14 - 1.39: 580 1.39 - 1.64: 897 1.64 - 1.89: 86 Bond restraints: 3153 Sorted by residual: bond pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 1.330 1.053 0.277 1.31e-02 5.83e+03 4.48e+02 bond pdb=" CA LEU A 7 " pdb=" C LEU A 7 " ideal model delta sigma weight residual 1.524 1.264 0.260 1.23e-02 6.61e+03 4.47e+02 bond pdb=" N VAL A 23 " pdb=" CA VAL A 23 " ideal model delta sigma weight residual 1.461 1.249 0.212 1.19e-02 7.06e+03 3.17e+02 bond pdb=" N VAL A 71 " pdb=" CA VAL A 71 " ideal model delta sigma weight residual 1.459 1.664 -0.205 1.20e-02 6.94e+03 2.93e+02 bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.139 0.187 1.10e-02 8.26e+03 2.88e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 2914 4.23 - 8.45: 1849 8.45 - 12.67: 774 12.67 - 16.89: 199 16.89 - 21.11: 41 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.22 106.34 16.88 1.14e+00 7.69e-01 2.19e+02 angle pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " pdb=" CG ASP A 68 " ideal model delta sigma weight residual 112.60 98.68 13.92 1.00e+00 1.00e+00 1.94e+02 angle pdb=" O ACYS A 53 " pdb=" C ACYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.35 133.91 -12.56 9.20e-01 1.18e+00 1.86e+02 angle pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" O THR A 140 " ideal model delta sigma weight residual 120.36 134.87 -14.51 1.08e+00 8.57e-01 1.81e+02 angle pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" O SER A 155 " ideal model delta sigma weight residual 121.36 107.47 13.89 1.06e+00 8.90e-01 1.72e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1319 17.94 - 35.87: 110 35.87 - 53.81: 38 53.81 - 71.74: 12 71.74 - 89.68: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -142.62 20.02 0 2.50e+00 1.60e-01 6.41e+01 dihedral pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " ideal model delta harmonic sigma weight residual 122.80 141.29 -18.49 0 2.50e+00 1.60e-01 5.47e+01 dihedral pdb=" C ALA A 56 " pdb=" N ALA A 56 " pdb=" CA ALA A 56 " pdb=" CB ALA A 56 " ideal model delta harmonic sigma weight residual -122.60 -104.16 -18.44 0 2.50e+00 1.60e-01 5.44e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.188: 93 0.188 - 0.376: 68 0.376 - 0.564: 37 0.564 - 0.752: 33 0.752 - 0.940: 12 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ARG A 98 " pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CB ARG A 98 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CA ALYS A 132 " pdb=" N ALYS A 132 " pdb=" C ALYS A 132 " pdb=" CB ALYS A 132 " both_signs ideal model delta sigma weight residual False 2.51 3.41 -0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" CA ALEU A 153 " pdb=" N ALEU A 153 " pdb=" C ALEU A 153 " pdb=" CB ALEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.36 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.137 2.00e-02 2.50e+03 6.25e-02 1.17e+02 pdb=" CG PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.081 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.088 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.072 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.056 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.002 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 HIS A 126 " -0.007 2.00e-02 2.50e+03 6.44e-02 9.34e+01 pdb=" CG HIS A 126 " 0.081 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.114 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.052 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.094 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.024 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.043 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.003 2.00e-02 2.50e+03 5.12e-02 7.85e+01 pdb=" CG BTYR A 67 " 0.061 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.050 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.002 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.092 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.085 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.031 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.067 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.040 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.041 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 720 2.27 - 2.85: 7773 2.85 - 3.43: 10651 3.43 - 4.02: 15412 4.02 - 4.60: 22048 Nonbonded interactions: 56604 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.687 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.736 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O LEU A 185 " pdb=" H GLY A 159 " model vdw sym.op. 1.736 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.813 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.824 2.100 ... (remaining 56599 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_4596863_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3614 r_free= 0.2015 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468927 | | target function (ml) not normalized (work): 22031.809549 | | target function (ml) not normalized (free): 1149.926422 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3793 0.2216 4.8515 4.8997| | 2: 3.78 - 3.00 1.00 2430 110 0.3396 0.1674 4.0754 4.1288| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.82 0.83 0.13 6609.04| | 2: 3.78 - 3.00 2430 110 0.94 11.33 1.48 0.26 446.80| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 377.41 max = 12069.19 mean = 3571.67| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.34| |phase err.(test): min = 0.00 max = 89.92 mean = 33.22| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.277 1557 Z= 5.572 Angle : 5.344 17.887 2118 Z= 3.807 Chirality : 0.386 0.940 243 Planarity : 0.032 0.082 284 Dihedral : 13.763 89.679 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.48 % Allowed : 3.11 % Favored : 94.41 % Cbeta Deviations : 29.73 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.48), residues: 224 helix: -2.55 (0.37), residues: 108 sheet: 0.00 (1.01), residues: 24 loop : 0.45 (0.56), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.020 ARG A 98 TYR 0.098 0.047 TYR A 141 PHE 0.101 0.044 PHE A 164 HIS 0.106 0.032 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= 0.3614 r_free= 0.2015 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468927 | | target function (ml) not normalized (work): 22031.809549 | | target function (ml) not normalized (free): 1149.926422 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3570 0.3646 0.2133 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3570 0.3646 0.2133 n_refl.: 5182 remove outliers: r(all,work,free)=0.2524 0.2548 0.2133 n_refl.: 5178 overall B=-2.80 to atoms: r(all,work,free)=0.2417 0.2437 0.2086 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1569 0.1567 0.1616 n_refl.: 5178 remove outliers: r(all,work,free)=0.1565 0.1562 0.1616 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 0.3881 449.735 410.805 0.670 1.058 0.404 11.894-9.307 99.02 97 4 0.1902 714.441 694.748 0.943 1.057 0.377 9.237-7.194 100.00 213 7 0.2197 584.271 575.515 0.976 1.051 0.364 7.162-5.571 100.00 427 22 0.2324 438.424 423.860 0.944 1.040 0.336 5.546-4.326 100.00 867 58 0.1380 601.894 594.627 0.982 1.022 0.258 4.315-3.360 100.00 1859 96 0.1305 572.408 566.566 1.052 0.991 0.189 3.356-3.002 100.00 1373 60 0.1614 440.893 432.975 1.060 0.960 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.5843 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1562 r_free=0.1616 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1565 r_free=0.1614 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.505345 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.626117 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 0.1772 0.0609 0.010 1.0 2.6 0.5 0.0 0 9.753 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.63 17.72 6.09 3.013 16.055 1.626 0.018 10.33 17.61 7.27 4.491 16.173 1.626 0.015 Individual atomic B min max mean iso aniso Overall: 2.39 111.50 17.31 4.93 1785 0 Protein: 2.39 111.35 14.61 4.92 1519 0 Water: 4.06 111.50 32.99 N/A 258 0 Other: 16.82 37.46 23.39 N/A 8 0 Chain A: 2.39 111.50 17.31 N/A 1785 0 Histogram: Values Number of atoms 2.39 - 13.30 949 13.30 - 24.21 462 24.21 - 35.12 181 35.12 - 46.03 111 46.03 - 56.94 52 56.94 - 67.85 13 67.85 - 78.76 8 78.76 - 89.67 5 89.67 - 100.58 1 100.58 - 111.50 3 =========================== Idealize ADP of riding H ========================== r_work=0.1033 r_free=0.1761 r_work=0.1026 r_free=0.1764 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1026 r_free = 0.1764 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 = 0.1022 r_free = 0.1771 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 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= 0.1022 r_free= 0.1771 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014225 | | target function (ls_wunit_k1) not normalized (work): 70.043700 | | target function (ls_wunit_k1) not normalized (free): 10.321926 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1060 0.1022 0.1771 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2098 0.2097 0.2214 n_refl.: 5176 remove outliers: r(all,work,free)=0.2098 0.2097 0.2214 n_refl.: 5176 overall B=-0.97 to atoms: r(all,work,free)=0.2057 0.2055 0.2204 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1057 0.1019 0.1752 n_refl.: 5176 remove outliers: r(all,work,free)=0.1057 0.1019 0.1752 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 0.3385 329.969 310.105 0.669 1.013 0.377 11.894-9.307 99.02 97 4 0.1509 524.182 515.550 0.976 1.015 0.351 9.237-7.194 100.00 213 7 0.1737 428.677 427.317 1.019 1.014 0.327 7.162-5.571 100.00 427 22 0.1639 321.670 318.015 0.977 1.011 0.314 5.546-4.326 100.00 867 58 0.0911 441.607 438.614 0.996 1.006 0.222 4.315-3.360 100.00 1859 96 0.0763 419.973 419.760 1.045 0.997 0.195 3.356-3.002 100.00 1373 60 0.1012 323.481 321.995 1.021 0.988 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4727 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1019 r_free=0.1752 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1019 r_free=0.1751 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1019 r_free=0.1751 | n_water=258 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.1042 r_free=0.1751 | n_water=250 | time (s): 20.310 (total time: 20.860) Filter (q & B) r_work=0.1041 r_free=0.1749 | n_water=247 | time (s): 1.340 (total time: 22.200) Compute maps r_work=0.1041 r_free=0.1749 | n_water=247 | time (s): 0.460 (total time: 22.660) Filter (map) r_work=0.1361 r_free=0.1838 | n_water=146 | time (s): 1.510 (total time: 24.170) Find peaks r_work=0.1361 r_free=0.1838 | n_water=146 | time (s): 0.490 (total time: 24.660) Add new water r_work=0.1713 r_free=0.2153 | n_water=234 | time (s): 1.760 (total time: 26.420) Refine new water occ: r_work=0.1159 r_free=0.1695 adp: r_work=0.1133 r_free=0.1698 occ: r_work=0.1130 r_free=0.1676 adp: r_work=0.1115 r_free=0.1687 occ: r_work=0.1114 r_free=0.1677 adp: r_work=0.1111 r_free=0.1678 ADP+occupancy (water only), MIN, final r_work=0.1111 r_free=0.1678 r_work=0.1111 r_free=0.1678 | n_water=234 | time (s): 5.050 (total time: 31.470) Filter (q & B) r_work=0.1111 r_free=0.1678 | n_water=234 | time (s): 0.810 (total time: 32.280) Filter (dist only) r_work=0.1118 r_free=0.1677 | n_water=231 | time (s): 18.220 (total time: 50.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.741165 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.660700 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 0.1036 0.1765 0.0729 0.009 1.0 4.8 0.5 0.6 0 11.371 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.36 17.65 7.29 4.435 16.663 2.661 0.014 9.67 17.97 8.30 5.309 16.928 2.661 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.66 16.30 6.25 1758 0 Protein: 0.00 107.66 14.61 6.24 1519 0 Water: 0.00 62.81 27.26 N/A 231 0 Other: 12.03 35.39 20.62 N/A 8 0 Chain A: 0.00 107.66 15.40 N/A 1670 0 Chain S: 0.00 60.70 33.50 N/A 88 0 Histogram: Values Number of atoms 0.00 - 10.77 707 10.77 - 21.53 656 21.53 - 32.30 204 32.30 - 43.06 110 43.06 - 53.83 45 53.83 - 64.59 26 64.59 - 75.36 3 75.36 - 86.12 3 86.12 - 96.89 2 96.89 - 107.66 2 =========================== Idealize ADP of riding H ========================== r_work=0.0967 r_free=0.1797 r_work=0.0963 r_free=0.1799 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0963 r_free = 0.1799 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0962 r_free = 0.1798 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.24 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= 0.0962 r_free= 0.1798 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012626 | | target function (ls_wunit_k1) not normalized (work): 62.168259 | | target function (ls_wunit_k1) not normalized (free): 9.741924 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1004 0.0962 0.1798 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2096 0.2098 0.2173 n_refl.: 5176 remove outliers: r(all,work,free)=0.2096 0.2098 0.2173 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2096 0.2098 0.2173 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1005 0.0962 0.1806 n_refl.: 5176 remove outliers: r(all,work,free)=0.1003 0.0960 0.1806 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 0.3247 327.190 316.962 0.681 1.011 0.377 11.894-9.307 99.02 97 4 0.1516 524.182 519.040 0.977 1.013 0.360 9.237-7.194 100.00 213 7 0.1554 428.677 429.514 1.019 1.013 0.295 7.162-5.571 100.00 427 22 0.1479 321.670 318.774 0.981 1.010 0.290 5.546-4.326 100.00 867 58 0.0805 441.607 438.951 1.003 1.006 0.230 4.315-3.360 100.00 1859 96 0.0740 419.973 419.846 1.054 0.998 0.200 3.356-3.002 100.00 1373 60 0.0986 323.481 322.470 1.031 0.990 0.056 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.9613 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0960 r_free=0.1806 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0960 r_free=0.1806 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0960 r_free=0.1806 | n_water=231 | time (s): 0.460 (total time: 0.460) Filter (dist) r_work=0.0979 r_free=0.1795 | n_water=226 | time (s): 17.120 (total time: 17.580) Filter (q & B) r_work=0.1048 r_free=0.1813 | n_water=223 | time (s): 1.410 (total time: 18.990) Compute maps r_work=0.1048 r_free=0.1813 | n_water=223 | time (s): 0.490 (total time: 19.480) Filter (map) r_work=0.1313 r_free=0.1821 | n_water=144 | time (s): 1.390 (total time: 20.870) Find peaks r_work=0.1313 r_free=0.1821 | n_water=144 | time (s): 0.420 (total time: 21.290) Add new water r_work=0.1715 r_free=0.2244 | n_water=241 | time (s): 1.370 (total time: 22.660) Refine new water occ: r_work=0.1075 r_free=0.1707 adp: r_work=0.1068 r_free=0.1725 occ: r_work=0.1057 r_free=0.1699 adp: r_work=0.1057 r_free=0.1709 occ: r_work=0.1047 r_free=0.1685 adp: r_work=0.1046 r_free=0.1695 ADP+occupancy (water only), MIN, final r_work=0.1046 r_free=0.1695 r_work=0.1046 r_free=0.1695 | n_water=241 | time (s): 7.240 (total time: 29.900) Filter (q & B) r_work=0.1047 r_free=0.1696 | n_water=240 | time (s): 1.440 (total time: 31.340) Filter (dist only) r_work=0.1059 r_free=0.1697 | n_water=238 | time (s): 17.750 (total time: 49.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.182360 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.228581 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 0.0952 0.1814 0.0863 0.011 1.1 6.1 0.5 0.6 0 0.591 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.52 18.14 8.63 5.232 17.345 0.229 5.164 9.04 18.47 9.43 7.102 17.380 0.229 5.065 Individual atomic B min max mean iso aniso Overall: 0.00 107.47 16.11 8.77 1765 0 Protein: 0.00 107.47 14.82 8.76 1519 0 Water: 0.00 61.71 24.18 N/A 238 0 Other: 11.97 37.12 21.34 N/A 8 0 Chain A: 0.00 107.47 15.47 N/A 1653 0 Chain S: 0.00 61.71 25.50 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.75 686 10.75 - 21.49 680 21.49 - 32.24 221 32.24 - 42.99 117 42.99 - 53.74 26 53.74 - 64.48 17 64.48 - 75.23 11 75.23 - 85.98 2 85.98 - 96.72 4 96.72 - 107.47 1 =========================== Idealize ADP of riding H ========================== r_work=0.0904 r_free=0.1847 r_work=0.0910 r_free=0.1856 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0910 r_free = 0.1856 target_work(ml) = 5.070 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0897 r_free = 0.1842 target_work(ml) = 5.060 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0897 r_free= 0.1842 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.060399 | | target function (ml) not normalized (work): 24912.343308 | | target function (ml) not normalized (free): 1827.694176 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0944 0.0897 0.1842 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2090 0.2095 0.2141 n_refl.: 5175 remove outliers: r(all,work,free)=0.2090 0.2095 0.2141 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2090 0.2095 0.2141 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0937 0.0891 0.1825 n_refl.: 5175 remove outliers: r(all,work,free)=0.0935 0.0889 0.1825 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 0.3683 329.366 296.861 0.590 0.994 0.332 11.894-9.307 99.02 97 4 0.1843 524.182 507.830 0.949 0.997 0.320 9.237-7.194 100.00 213 7 0.1946 428.677 422.953 1.002 0.999 0.300 7.162-5.571 100.00 427 22 0.1850 321.670 314.317 0.979 1.000 0.290 5.546-4.326 100.00 867 58 0.0914 441.607 436.521 0.999 1.001 0.227 4.315-3.360 100.00 1859 96 0.0579 419.973 419.539 1.053 1.002 0.210 3.356-3.002 100.00 1373 60 0.0608 323.481 322.918 1.028 1.002 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.1912 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0889 r_free=0.1825 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0893 r_free=0.1827 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0893 r_free=0.1827 | n_water=238 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0898 r_free=0.1823 | n_water=237 | time (s): 17.640 (total time: 18.230) Filter (q & B) r_work=0.0974 r_free=0.1828 | n_water=234 | time (s): 1.210 (total time: 19.440) Compute maps r_work=0.0974 r_free=0.1828 | n_water=234 | time (s): 0.500 (total time: 19.940) Filter (map) r_work=0.1257 r_free=0.1966 | n_water=162 | time (s): 1.450 (total time: 21.390) Find peaks r_work=0.1257 r_free=0.1966 | n_water=162 | time (s): 0.410 (total time: 21.800) Add new water r_work=0.1570 r_free=0.2197 | n_water=239 | time (s): 1.210 (total time: 23.010) Refine new water occ: r_work=0.1013 r_free=0.1843 adp: r_work=0.1004 r_free=0.1855 occ: r_work=0.0995 r_free=0.1843 adp: r_work=0.0995 r_free=0.1850 occ: r_work=0.0986 r_free=0.1836 adp: r_work=0.0986 r_free=0.1843 ADP+occupancy (water only), MIN, final r_work=0.0986 r_free=0.1843 r_work=0.0986 r_free=0.1843 | n_water=239 | time (s): 10.150 (total time: 33.160) Filter (q & B) r_work=0.0987 r_free=0.1845 | n_water=238 | time (s): 1.890 (total time: 35.050) Filter (dist only) r_work=0.0986 r_free=0.1848 | n_water=237 | time (s): 18.790 (total time: 53.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.004121 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.256964 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 0.0900 0.1833 0.0933 0.011 1.1 5.1 0.5 0.6 0 0.502 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.00 18.33 9.33 6.827 17.588 0.257 5.013 8.79 18.50 9.72 8.236 17.716 0.257 4.947 Individual atomic B min max mean iso aniso Overall: 0.00 107.49 16.44 10.78 1764 0 Protein: 0.00 107.49 15.25 10.77 1519 0 Water: 0.00 56.71 23.85 N/A 237 0 Other: 10.00 40.14 22.77 N/A 8 0 Chain A: 0.00 107.49 15.83 N/A 1645 0 Chain S: 0.00 56.71 24.87 N/A 119 0 Histogram: Values Number of atoms 0.00 - 10.75 693 10.75 - 21.50 638 21.50 - 32.25 229 32.25 - 43.00 129 43.00 - 53.75 39 53.75 - 64.49 18 64.49 - 75.24 10 75.24 - 85.99 4 85.99 - 96.74 3 96.74 - 107.49 1 =========================== Idealize ADP of riding H ========================== r_work=0.0879 r_free=0.1850 r_work=0.0883 r_free=0.1858 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0883 r_free = 0.1858 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0874 r_free = 0.1846 target_work(ml) = 4.946 | | 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= 0.0874 r_free= 0.1846 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.945984 | | target function (ml) not normalized (work): 24344.131129 | | target function (ml) not normalized (free): 2171.300039 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0923 0.0874 0.1846 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2044 0.2043 0.2189 n_refl.: 5174 remove outliers: r(all,work,free)=0.2044 0.2043 0.2189 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2044 0.2043 0.2189 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0921 0.0872 0.1838 n_refl.: 5174 remove outliers: r(all,work,free)=0.0921 0.0872 0.1838 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 0.3900 329.366 298.939 0.571 0.988 0.314 11.894-9.307 99.02 97 4 0.1962 524.182 506.243 0.946 0.993 0.310 9.237-7.194 100.00 213 7 0.2159 428.677 419.589 1.006 0.996 0.280 7.162-5.571 100.00 427 22 0.2050 321.670 311.888 0.989 0.998 0.270 5.546-4.326 100.00 867 58 0.0968 441.607 436.033 1.017 1.000 0.220 4.315-3.360 100.00 1859 96 0.0537 419.973 419.651 1.077 1.003 0.210 3.356-3.002 100.00 1373 60 0.0434 323.481 323.318 1.055 1.005 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4037 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0872 r_free=0.1838 After: r_work=0.0876 r_free=0.1836 ================================== NQH flips ================================== r_work=0.0876 r_free=0.1836 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0876 r_free=0.1836 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0876 r_free=0.1836 | n_water=237 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.0890 r_free=0.1833 | n_water=232 | time (s): 18.540 (total time: 19.030) Filter (q & B) r_work=0.1033 r_free=0.1868 | n_water=228 | time (s): 1.620 (total time: 20.650) Compute maps r_work=0.1033 r_free=0.1868 | n_water=228 | time (s): 0.480 (total time: 21.130) Filter (map) r_work=0.1280 r_free=0.1983 | n_water=165 | time (s): 1.500 (total time: 22.630) Find peaks r_work=0.1280 r_free=0.1983 | n_water=165 | time (s): 0.420 (total time: 23.050) Add new water r_work=0.1515 r_free=0.2227 | n_water=227 | time (s): 1.840 (total time: 24.890) Refine new water occ: r_work=0.0988 r_free=0.1860 adp: r_work=0.0976 r_free=0.1865 occ: r_work=0.0972 r_free=0.1859 adp: r_work=0.0971 r_free=0.1862 occ: r_work=0.0968 r_free=0.1856 adp: r_work=0.0968 r_free=0.1859 ADP+occupancy (water only), MIN, final r_work=0.0968 r_free=0.1859 r_work=0.0968 r_free=0.1859 | n_water=227 | time (s): 9.460 (total time: 34.350) Filter (q & B) r_work=0.0968 r_free=0.1863 | n_water=226 | time (s): 1.930 (total time: 36.280) Filter (dist only) r_work=0.0973 r_free=0.1870 | n_water=225 | time (s): 18.430 (total time: 54.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.930990 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.236217 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 0.0923 0.1882 0.0959 0.011 1.1 7.7 0.5 0.6 0 0.465 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.23 18.82 9.59 8.173 17.940 0.236 5.022 9.02 18.96 9.94 9.157 18.104 0.236 4.961 Individual atomic B min max mean iso aniso Overall: 0.00 106.54 16.72 12.16 1752 0 Protein: 0.00 106.54 15.75 12.16 1519 0 Water: 0.00 56.30 23.01 N/A 225 0 Other: 11.42 45.03 23.96 N/A 8 0 Chain A: 0.00 106.54 16.26 N/A 1640 0 Chain S: 0.00 56.30 23.39 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.65 671 10.65 - 21.31 614 21.31 - 31.96 274 31.96 - 42.61 108 42.61 - 53.27 46 53.27 - 63.92 18 63.92 - 74.58 11 74.58 - 85.23 6 85.23 - 95.88 1 95.88 - 106.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.0902 r_free=0.1896 r_work=0.0906 r_free=0.1899 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0906 r_free = 0.1899 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0902 r_free = 0.1891 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0902 r_free= 0.1891 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.963727 | | target function (ml) not normalized (work): 24431.463647 | | target function (ml) not normalized (free): 2284.064784 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1289 0.1872 5.5527 6.2485| | 2: 3.78 - 3.00 1.00 2430 110 0.0431 0.1925 4.3597 12.698| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.38 1.00 0.97 13727.96| | 2: 3.78 - 3.00 2430 110 0.99 1.84 1.00 0.99 903.36| |alpha: min = 0.96 max = 0.99 mean = 0.98| |beta: min = 571.26 max = 23012.00 mean = 7396.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.92 mean = 7.18| |phase err.(test): min = 0.00 max = 89.67 mean = 7.13| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0952 0.0902 0.1891 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2104 0.2102 0.2231 n_refl.: 5174 remove outliers: r(all,work,free)=0.2104 0.2102 0.2231 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2104 0.2102 0.2231 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0951 0.0900 0.1909 n_refl.: 5174 remove outliers: r(all,work,free)=0.0951 0.0900 0.1909 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 0.3947 329.366 291.609 0.568 0.986 0.320 11.894-9.307 99.02 97 4 0.1888 524.182 510.627 0.967 0.993 0.340 9.237-7.194 100.00 213 7 0.2161 428.677 420.920 1.002 0.996 0.324 7.162-5.571 100.00 427 22 0.2080 321.670 311.761 0.996 0.998 0.310 5.546-4.326 100.00 867 58 0.1048 441.607 435.653 1.019 1.000 0.230 4.315-3.360 100.00 1859 96 0.0575 419.973 420.083 1.088 1.002 0.220 3.356-3.002 100.00 1373 60 0.0414 323.481 323.114 1.068 1.004 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8828 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3614 0.2015 0.084 5.344 8.8 119.3 19.9 258 0.000 1_bss: 0.1562 0.1616 0.084 5.344 6.0 116.5 17.1 258 0.000 1_settarget: 0.1562 0.1616 0.084 5.344 6.0 116.5 17.1 258 0.000 1_nqh: 0.1565 0.1614 0.084 5.344 6.0 116.5 17.1 258 0.003 1_weight: 0.1565 0.1614 0.084 5.344 6.0 116.5 17.1 258 0.003 1_xyzrec: 0.1163 0.1772 0.010 0.995 6.0 116.5 17.1 258 0.216 1_adp: 0.1033 0.1761 0.010 0.995 2.4 111.5 17.3 258 0.216 1_regHadp: 0.1026 0.1764 0.010 0.995 2.4 111.5 17.3 258 0.216 1_occ: 0.1022 0.1771 0.010 0.995 2.4 111.5 17.3 258 0.216 2_bss: 0.1019 0.1752 0.010 0.995 1.4 110.5 16.3 258 0.216 2_settarget: 0.1019 0.1752 0.010 0.995 1.4 110.5 16.3 258 0.216 2_updatecdl: 0.1019 0.1752 0.010 1.009 1.4 110.5 16.3 258 0.216 2_nqh: 0.1019 0.1751 0.010 1.009 1.4 110.5 16.3 258 0.219 2_sol: 0.1118 0.1677 0.010 1.009 1.0 110.4 15.8 231 n/a 2_weight: 0.1118 0.1677 0.010 1.009 1.0 110.4 15.8 231 n/a 2_xyzrec: 0.1036 0.1765 0.009 0.998 1.0 110.4 15.8 231 n/a 2_adp: 0.0967 0.1797 0.009 0.998 0.0 107.7 16.3 231 n/a 2_regHadp: 0.0963 0.1799 0.009 0.998 0.0 107.7 16.3 231 n/a 2_occ: 0.0962 0.1798 0.009 0.998 0.0 107.7 16.3 231 n/a 3_bss: 0.0960 0.1806 0.009 0.998 0.0 107.7 16.3 231 n/a 3_settarget: 0.0960 0.1806 0.009 0.998 0.0 107.7 16.3 231 n/a 3_updatecdl: 0.0960 0.1806 0.009 1.003 0.0 107.7 16.3 231 n/a 3_nqh: 0.0960 0.1806 0.009 1.003 0.0 107.7 16.3 231 n/a 3_sol: 0.1059 0.1697 0.009 1.003 0.0 107.7 16.0 238 n/a 3_weight: 0.1059 0.1697 0.009 1.003 0.0 107.7 16.0 238 n/a 3_xyzrec: 0.0952 0.1814 0.011 1.080 0.0 107.7 16.0 238 n/a 3_adp: 0.0904 0.1847 0.011 1.080 0.0 107.5 16.1 238 n/a 3_regHadp: 0.0910 0.1856 0.011 1.080 0.0 107.5 16.1 238 n/a 3_occ: 0.0897 0.1842 0.011 1.080 0.0 107.5 16.1 238 n/a 4_bss: 0.0889 0.1825 0.011 1.080 0.0 107.5 16.1 238 n/a 4_settarget: 0.0889 0.1825 0.011 1.080 0.0 107.5 16.1 238 n/a 4_updatecdl: 0.0889 0.1825 0.011 1.098 0.0 107.5 16.1 238 n/a 4_nqh: 0.0893 0.1827 0.011 1.098 0.0 107.5 16.1 238 n/a 4_sol: 0.0986 0.1848 0.011 1.098 0.0 107.5 16.2 237 n/a 4_weight: 0.0986 0.1848 0.011 1.098 0.0 107.5 16.2 237 n/a 4_xyzrec: 0.0900 0.1833 0.011 1.066 0.0 107.5 16.2 237 n/a 4_adp: 0.0879 0.1850 0.011 1.066 0.0 107.5 16.4 237 n/a 4_regHadp: 0.0883 0.1858 0.011 1.066 0.0 107.5 16.4 237 n/a 4_occ: 0.0874 0.1846 0.011 1.066 0.0 107.5 16.4 237 n/a 5_bss: 0.0872 0.1838 0.011 1.066 0.0 107.5 16.4 237 n/a 5_settarget: 0.0872 0.1838 0.011 1.066 0.0 107.5 16.4 237 n/a 5_updatecdl: 0.0872 0.1838 0.011 1.066 0.0 107.5 16.4 237 n/a 5_setrh: 0.0876 0.1836 0.011 1.066 0.0 107.5 16.4 237 n/a 5_nqh: 0.0876 0.1836 0.011 1.066 0.0 107.5 16.4 237 n/a 5_sol: 0.0973 0.1870 0.011 1.066 0.0 107.5 16.4 225 n/a 5_weight: 0.0973 0.1870 0.011 1.066 0.0 107.5 16.4 225 n/a 5_xyzrec: 0.0923 0.1882 0.011 1.132 0.0 107.5 16.4 225 n/a 5_adp: 0.0902 0.1896 0.011 1.132 0.0 106.5 16.7 225 n/a 5_regHadp: 0.0906 0.1899 0.011 1.132 0.0 106.5 16.7 225 n/a 5_occ: 0.0902 0.1891 0.011 1.132 0.0 106.5 16.7 225 n/a end: 0.0900 0.1909 0.011 1.132 0.0 106.5 16.7 225 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4596863_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4596863_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9100 Refinement macro-cycles (run) : 475.0100 Write final files (write_after_run_outputs) : 11.2500 Total : 490.1700 Total CPU time: 8.57 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:55 PST -0800 (1735492735.83 s) Start R-work = 0.1562, R-free = 0.1616 Final R-work = 0.0900, R-free = 0.1909 =============================================================================== Job complete usr+sys time: 522.49 seconds wall clock time: 9 minutes 4.91 seconds (544.91 seconds total)