Starting phenix.refine on Sun Dec 29 09:24:42 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=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" } 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: 1.05, per 1000 atoms: 0.31 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 137.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.53 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 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2787 r_free= 0.1821 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.401291 | | target function (ml) not normalized (work): 71490.170096 | | target function (ml) not normalized (free): 3256.633915 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3190 0.2122 7.5064 5.0269| | 2: 3.63 - 2.88 1.00 2711 122 0.2644 0.1816 4.3333 4.3358| | 3: 2.88 - 2.52 1.00 2682 148 0.2601 0.1631 4.1862 4.1746| | 4: 2.52 - 2.29 1.00 2661 139 0.2522 0.1575 3.5071 3.6198| | 5: 2.29 - 2.13 1.00 2678 122 0.2625 0.1495 3.3928 3.4339| | 6: 2.13 - 2.00 1.00 2692 117 0.2745 0.1832 3.3196 3.3202| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.62 0.77 0.23 1310.38| | 2: 3.63 - 2.88 2711 122 0.83 23.93 1.31 0.23 1310.38| | 3: 2.88 - 2.52 2682 148 0.73 33.03 1.29 0.23 1310.38| | 4: 2.52 - 2.29 2661 139 0.94 11.09 1.29 0.26 129.20| | 5: 2.29 - 2.13 2678 122 0.92 13.21 1.31 0.26 129.20| | 6: 2.13 - 2.00 2692 117 0.90 15.96 1.33 0.26 129.20| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 129.20 max = 1310.38 mean = 726.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.95 mean = 19.15| |phase err.(test): min = 0.00 max = 89.88 mean = 19.69| |-----------------------------------------------------------------------------| ----------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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2787 r_free= 0.1821 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.401291 | | target function (ml) not normalized (work): 71490.170096 | | target function (ml) not normalized (free): 3256.633915 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3446 percent. r_work = 0.2921 r_free = 0.1964 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2868 0.2921 0.1964 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2868 0.2921 0.1964 n_refl.: 17050 remove outliers: r(all,work,free)=0.2160 0.2171 0.1964 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2134 0.2145 0.1943 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1624 0.1623 0.1641 n_refl.: 17045 remove outliers: r(all,work,free)=0.1623 0.1622 0.1641 n_refl.: 17044 ======================== 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 32.574-12.150 100.00 89 5 0.4050 394.807 364.635 0.650 1.011 0.397 11.894-9.307 99.02 97 4 0.1891 633.677 615.692 0.927 1.013 0.375 9.237-7.194 100.00 213 7 0.2181 518.284 508.931 0.957 1.012 0.371 7.162-5.571 100.00 427 22 0.2327 388.972 375.652 0.926 1.011 0.331 5.546-4.326 100.00 867 58 0.1385 533.997 528.130 0.958 1.010 0.220 4.315-3.360 100.00 1859 96 0.1291 507.836 504.050 1.015 1.006 0.191 3.356-2.611 100.00 3867 181 0.1664 333.619 329.008 1.013 1.000 0.034 2.608-2.000 99.99 8818 434 0.1666 217.463 213.527 1.027 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4077 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1622 r_free=0.1641 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=0.1625 r_free=0.1646 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.790950 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.798649 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1351 0.1635 0.0284 0.009 1.0 1.6 0.5 0.0 0 11.895 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.35 2.84 3.013 18.465 0.799 0.023 12.79 16.59 3.80 3.589 18.712 0.799 0.021 Individual atomic B min max mean iso aniso Overall: 6.24 113.90 19.96 4.03 1785 0 Protein: 6.24 112.30 17.21 4.03 1519 0 Water: 8.62 113.90 35.97 N/A 258 0 Other: 21.49 36.87 26.08 N/A 8 0 Chain A: 6.24 113.90 19.96 N/A 1785 0 Histogram: Values Number of atoms 6.24 - 17.01 1087 17.01 - 27.77 344 27.77 - 38.54 181 38.54 - 49.31 98 49.31 - 60.07 48 60.07 - 70.84 13 70.84 - 81.61 6 81.61 - 92.37 5 92.37 - 103.14 0 103.14 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1659 r_work=0.1283 r_free=0.1665 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1283 r_free = 0.1665 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1279 r_free = 0.1663 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1279 r_free= 0.1663 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.020060 | | target function (ls_wunit_k1) not normalized (work): 325.713543 | | target function (ls_wunit_k1) not normalized (free): 26.936587 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1297 0.1279 0.1663 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1915 0.1915 0.1980 n_refl.: 17044 remove outliers: r(all,work,free)=0.1915 0.1915 0.1980 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1887 0.1886 0.1964 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1296 0.1278 0.1654 n_refl.: 17044 remove outliers: r(all,work,free)=0.1294 0.1276 0.1654 n_refl.: 17042 ======================== 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 0.3603 302.768 280.355 0.621 1.008 0.370 11.894-9.307 99.02 97 4 0.1720 486.955 476.360 0.915 1.010 0.370 9.237-7.194 100.00 213 7 0.1839 398.280 395.041 0.959 1.009 0.351 7.162-5.571 100.00 427 22 0.1821 298.910 293.903 0.931 1.009 0.311 5.546-4.326 100.00 867 58 0.1041 410.355 408.184 0.957 1.007 0.205 4.315-3.360 100.00 1859 96 0.0925 390.252 389.908 1.019 1.005 0.191 3.356-2.611 100.00 3867 181 0.1302 256.373 255.136 1.016 1.000 0.081 2.608-2.000 99.99 8818 434 0.1352 167.111 165.647 1.023 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3937 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1654 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1654 | n_water=258 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1284 r_free=0.1642 | n_water=253 | time (s): 20.970 (total time: 21.690) Filter (q & B) r_work=0.1283 r_free=0.1640 | n_water=251 | time (s): 1.920 (total time: 23.610) Compute maps r_work=0.1283 r_free=0.1640 | n_water=251 | time (s): 0.840 (total time: 24.450) Filter (map) r_work=0.1323 r_free=0.1633 | n_water=210 | time (s): 1.990 (total time: 26.440) Find peaks r_work=0.1323 r_free=0.1633 | n_water=210 | time (s): 0.460 (total time: 26.900) Add new water r_work=0.1535 r_free=0.1816 | n_water=364 | time (s): 1.460 (total time: 28.360) Refine new water occ: r_work=0.1338 r_free=0.1561 adp: r_work=0.1281 r_free=0.1552 occ: r_work=0.1286 r_free=0.1536 adp: r_work=0.1253 r_free=0.1536 occ: r_work=0.1255 r_free=0.1526 adp: r_work=0.1244 r_free=0.1531 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1531 r_work=0.1244 r_free=0.1531 | n_water=364 | time (s): 18.120 (total time: 46.480) Filter (q & B) r_work=0.1247 r_free=0.1541 | n_water=356 | time (s): 2.220 (total time: 48.700) Filter (dist only) r_work=0.1247 r_free=0.1541 | n_water=355 | time (s): 28.740 (total time: 77.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.758881 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.992624 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1227 0.1616 0.0389 0.008 0.9 2.2 0.5 0.0 0 11.879 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 16.16 3.89 4.142 20.999 0.993 0.019 12.11 16.27 4.16 4.206 21.158 0.993 0.018 Individual atomic B min max mean iso aniso Overall: 6.67 106.91 21.05 4.21 1882 0 Protein: 6.67 106.91 17.55 4.21 1519 0 Water: 8.66 65.80 35.95 N/A 355 0 Other: 20.71 33.33 25.03 N/A 8 0 Chain A: 6.67 106.91 19.21 N/A 1737 0 Chain S: 17.85 63.36 43.11 N/A 145 0 Histogram: Values Number of atoms 6.67 - 16.70 1036 16.70 - 26.72 378 26.72 - 36.74 206 36.74 - 46.77 162 46.77 - 56.79 61 56.79 - 66.81 29 66.81 - 76.84 3 76.84 - 86.86 5 86.86 - 96.88 0 96.88 - 106.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1627 r_work=0.1212 r_free=0.1629 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1212 r_free = 0.1629 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1625 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1205 r_free= 0.1625 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017502 | | target function (ls_wunit_k1) not normalized (work): 284.144288 | | target function (ls_wunit_k1) not normalized (free): 25.083765 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1226 0.1205 0.1625 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1753 0.1745 0.1955 n_refl.: 17042 remove outliers: r(all,work,free)=0.1753 0.1745 0.1955 n_refl.: 17042 overall B=-0.50 to atoms: r(all,work,free)=0.1722 0.1713 0.1935 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1220 0.1200 0.1612 n_refl.: 17042 remove outliers: r(all,work,free)=0.1220 0.1200 0.1612 n_refl.: 17042 ======================== 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 0.3492 302.768 281.850 0.592 1.005 0.350 11.894-9.307 99.02 97 4 0.1587 486.955 482.593 0.911 1.005 0.340 9.237-7.194 100.00 213 7 0.1727 398.280 397.606 0.969 1.006 0.285 7.162-5.571 100.00 427 22 0.1564 298.910 295.002 0.936 1.005 0.271 5.546-4.326 100.00 867 58 0.0896 410.355 407.651 0.961 1.005 0.206 4.315-3.360 100.00 1859 96 0.0840 390.252 389.388 1.015 1.003 0.202 3.356-2.611 100.00 3867 181 0.1216 256.373 255.578 1.010 1.001 0.053 2.608-2.000 99.99 8818 434 0.1324 167.111 166.132 1.009 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1371 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1612 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1612 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1612 | n_water=355 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1200 r_free=0.1612 | n_water=355 | time (s): 24.140 (total time: 24.760) Filter (q & B) r_work=0.1200 r_free=0.1612 | n_water=355 | time (s): 0.870 (total time: 25.630) Compute maps r_work=0.1200 r_free=0.1612 | n_water=355 | time (s): 0.660 (total time: 26.290) Filter (map) r_work=0.1261 r_free=0.1617 | n_water=261 | time (s): 1.690 (total time: 27.980) Find peaks r_work=0.1261 r_free=0.1617 | n_water=261 | time (s): 0.420 (total time: 28.400) Add new water r_work=0.1446 r_free=0.1795 | n_water=415 | time (s): 1.460 (total time: 29.860) Refine new water occ: r_work=0.1247 r_free=0.1558 adp: r_work=0.1242 r_free=0.1566 occ: r_work=0.1221 r_free=0.1535 adp: r_work=0.1213 r_free=0.1538 occ: r_work=0.1202 r_free=0.1523 adp: r_work=0.1195 r_free=0.1524 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1524 r_work=0.1195 r_free=0.1524 | n_water=415 | time (s): 27.020 (total time: 56.880) Filter (q & B) r_work=0.1197 r_free=0.1541 | n_water=402 | time (s): 2.010 (total time: 58.890) Filter (dist only) r_work=0.1197 r_free=0.1539 | n_water=401 | time (s): 31.460 (total time: 90.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.924799 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.169301 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1172 0.1539 0.0367 0.009 1.0 3.2 0.5 0.0 0 0.962 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.72 15.39 3.67 4.271 21.121 0.169 4.986 11.56 15.60 4.04 4.809 21.107 0.169 4.970 Individual atomic B min max mean iso aniso Overall: 6.35 105.42 20.63 4.80 1928 0 Protein: 6.35 105.42 16.85 4.79 1519 0 Water: 8.96 64.39 34.90 N/A 401 0 Other: 17.40 36.44 23.70 N/A 8 0 Chain A: 6.35 105.42 18.51 N/A 1732 0 Chain S: 17.85 64.39 39.39 N/A 196 0 Histogram: Values Number of atoms 6.35 - 16.26 1068 16.26 - 26.16 363 26.16 - 36.07 214 36.07 - 45.98 171 45.98 - 55.88 74 55.88 - 65.79 24 65.79 - 75.70 6 75.70 - 85.60 4 85.60 - 95.51 2 95.51 - 105.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1156 r_free=0.1560 r_work=0.1156 r_free=0.1560 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1560 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1553 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1149 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.966931 | | target function (ml) not normalized (work): 80638.125459 | | target function (ml) not normalized (free): 4192.572177 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1168 0.1149 0.1553 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1662 0.1654 0.1851 n_refl.: 17042 remove outliers: r(all,work,free)=0.1662 0.1654 0.1851 n_refl.: 17042 overall B=-0.46 to atoms: r(all,work,free)=0.1631 0.1623 0.1835 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1166 0.1146 0.1552 n_refl.: 17042 remove outliers: r(all,work,free)=0.1165 0.1145 0.1552 n_refl.: 17041 ======================== 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 0.3745 299.285 276.308 0.552 1.005 0.330 11.894-9.307 99.02 97 4 0.1816 486.955 479.577 0.908 1.006 0.314 9.237-7.194 100.00 213 7 0.1818 398.280 398.768 0.982 1.007 0.255 7.162-5.571 100.00 427 22 0.1667 298.910 293.453 0.942 1.006 0.241 5.546-4.326 100.00 867 58 0.0964 410.355 407.019 0.967 1.005 0.201 4.315-3.360 100.00 1859 96 0.0891 390.252 387.934 1.013 1.004 0.192 3.356-2.611 100.00 3867 181 0.1281 256.373 254.247 1.010 1.001 0.142 2.608-2.000 99.99 8818 434 0.1071 167.111 165.764 1.011 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1477 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1552 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=0.1146 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1546 | n_water=401 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1146 r_free=0.1546 | n_water=401 | time (s): 30.810 (total time: 31.510) Filter (q & B) r_work=0.1146 r_free=0.1543 | n_water=400 | time (s): 1.660 (total time: 33.170) Compute maps r_work=0.1146 r_free=0.1543 | n_water=400 | time (s): 0.520 (total time: 33.690) Filter (map) r_work=0.1210 r_free=0.1573 | n_water=308 | time (s): 1.590 (total time: 35.280) Find peaks r_work=0.1210 r_free=0.1573 | n_water=308 | time (s): 0.500 (total time: 35.780) Add new water r_work=0.1347 r_free=0.1665 | n_water=449 | time (s): 1.910 (total time: 37.690) Refine new water occ: r_work=0.1179 r_free=0.1495 adp: r_work=0.1171 r_free=0.1498 occ: r_work=0.1157 r_free=0.1479 adp: r_work=0.1149 r_free=0.1479 occ: r_work=0.1142 r_free=0.1472 adp: r_work=0.1135 r_free=0.1473 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1473 r_work=0.1135 r_free=0.1473 | n_water=449 | time (s): 29.680 (total time: 67.370) Filter (q & B) r_work=0.1139 r_free=0.1484 | n_water=441 | time (s): 1.810 (total time: 69.180) Filter (dist only) r_work=0.1141 r_free=0.1486 | n_water=439 | time (s): 36.920 (total time: 106.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.002265 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.191824 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1130 0.1552 0.0422 0.010 1.0 4.8 0.5 0.0 0 1.001 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.52 4.22 4.536 20.747 0.192 4.958 11.18 15.52 4.33 4.615 20.785 0.192 4.949 Individual atomic B min max mean iso aniso Overall: 5.31 103.64 20.66 4.94 1966 0 Protein: 5.31 103.64 16.39 4.94 1519 0 Water: 8.62 63.94 35.36 N/A 439 0 Other: 17.16 35.06 23.80 N/A 8 0 Chain A: 5.31 103.64 17.96 N/A 1729 0 Chain S: 15.30 63.94 40.30 N/A 237 0 Histogram: Values Number of atoms 5.31 - 15.14 1024 15.14 - 24.98 384 24.98 - 34.81 223 34.81 - 44.64 193 44.64 - 54.48 100 54.48 - 64.31 27 64.31 - 74.14 7 74.14 - 83.98 3 83.98 - 93.81 3 93.81 - 103.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1118 r_free=0.1552 r_work=0.1118 r_free=0.1552 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1118 r_free = 0.1552 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1111 r_free = 0.1553 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1111 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.946798 | | target function (ml) not normalized (work): 80306.319862 | | target function (ml) not normalized (free): 4181.039032 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1111 0.1553 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1577 0.1566 0.1836 n_refl.: 17041 remove outliers: r(all,work,free)=0.1577 0.1566 0.1836 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1562 0.1549 0.1827 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1108 0.1548 n_refl.: 17041 remove outliers: r(all,work,free)=0.1129 0.1108 0.1548 n_refl.: 17041 ======================== 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 0.3838 299.285 275.611 0.534 1.004 0.320 11.894-9.307 99.02 97 4 0.1855 486.955 479.281 0.910 1.004 0.313 9.237-7.194 100.00 213 7 0.1839 398.280 398.593 0.981 1.004 0.230 7.162-5.571 100.00 427 22 0.1590 298.910 292.858 0.940 1.004 0.203 5.546-4.326 100.00 867 58 0.0926 410.355 406.933 0.965 1.004 0.185 4.315-3.360 100.00 1859 96 0.0855 390.252 387.914 1.007 1.003 0.174 3.356-2.611 100.00 3867 181 0.1230 256.373 254.133 1.004 1.001 0.141 2.608-2.000 99.99 8818 434 0.1037 167.111 165.848 0.997 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9076 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1108 r_free=0.1548 After: r_work=0.1110 r_free=0.1546 ================================== NQH flips ================================== r_work=0.1110 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1110 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1110 r_free=0.1546 | n_water=439 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1110 r_free=0.1546 | n_water=439 | time (s): 35.890 (total time: 36.790) Filter (q & B) r_work=0.1110 r_free=0.1546 | n_water=439 | time (s): 1.290 (total time: 38.080) Compute maps r_work=0.1110 r_free=0.1546 | n_water=439 | time (s): 0.830 (total time: 38.910) Filter (map) r_work=0.1173 r_free=0.1552 | n_water=337 | time (s): 2.070 (total time: 40.980) Find peaks r_work=0.1173 r_free=0.1552 | n_water=337 | time (s): 0.640 (total time: 41.620) Add new water r_work=0.1295 r_free=0.1620 | n_water=477 | time (s): 1.820 (total time: 43.440) Refine new water occ: r_work=0.1140 r_free=0.1485 adp: r_work=0.1134 r_free=0.1488 occ: r_work=0.1121 r_free=0.1478 adp: r_work=0.1114 r_free=0.1480 occ: r_work=0.1108 r_free=0.1479 adp: r_work=0.1102 r_free=0.1481 ADP+occupancy (water only), MIN, final r_work=0.1102 r_free=0.1481 r_work=0.1102 r_free=0.1481 | n_water=477 | time (s): 34.810 (total time: 78.250) Filter (q & B) r_work=0.1105 r_free=0.1490 | n_water=465 | time (s): 1.640 (total time: 79.890) Filter (dist only) r_work=0.1105 r_free=0.1489 | n_water=462 | time (s): 37.920 (total time: 117.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.961470 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.157594 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1130 0.1526 0.0397 0.010 1.0 7.7 0.5 0.0 0 0.981 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.26 3.97 4.589 20.640 0.158 4.952 11.21 15.22 4.00 4.663 20.666 0.158 4.943 Individual atomic B min max mean iso aniso Overall: 5.40 102.64 20.68 4.99 1989 0 Protein: 5.40 102.64 16.08 4.98 1519 0 Water: 8.24 66.26 35.75 N/A 462 0 Other: 18.13 34.28 24.45 N/A 8 0 Chain A: 5.40 102.64 17.64 N/A 1729 0 Chain S: 15.81 66.26 40.92 N/A 260 0 Histogram: Values Number of atoms 5.40 - 15.12 1043 15.12 - 24.85 376 24.85 - 34.57 217 34.57 - 44.30 194 44.30 - 54.02 109 54.02 - 63.75 29 63.75 - 73.47 12 73.47 - 83.19 4 83.19 - 92.92 1 92.92 - 102.64 4 =========================== Idealize ADP of riding H ========================== r_work=0.1121 r_free=0.1522 r_work=0.1121 r_free=0.1521 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1121 r_free = 0.1521 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1115 r_free = 0.1533 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1115 r_free= 0.1533 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.941560 | | target function (ml) not normalized (work): 80221.283264 | | target function (ml) not normalized (free): 4170.629778 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1140 0.1452 5.4813 5.6935| | 2: 3.63 - 2.88 1.00 2711 122 0.1098 0.1557 5.2377 5.3706| | 3: 2.88 - 2.52 1.00 2681 148 0.1366 0.1648 5.1485 5.2119| | 4: 2.52 - 2.29 1.00 2661 139 0.0934 0.1471 4.6149 4.9187| | 5: 2.29 - 2.13 1.00 2678 122 0.0961 0.1503 4.5716 4.8865| | 6: 2.13 - 2.00 1.00 2692 117 0.1117 0.1730 4.5645 4.7772| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2811 159 0.94 9.46 1.00 0.95 6770.09| | 2: 3.63 - 2.88 2711 122 0.92 13.41 1.01 0.95 6770.09| | 3: 2.88 - 2.52 2681 148 0.87 19.53 0.99 0.95 6770.09| | 4: 2.52 - 2.29 2661 139 0.93 12.04 1.01 0.97 2074.00| | 5: 2.29 - 2.13 2678 122 0.92 13.99 1.00 0.97 2074.00| | 6: 2.13 - 2.00 2692 117 0.89 16.73 0.99 0.97 2074.00| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2074.00 max = 6770.09 mean = 4446.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.93 mean = 14.16| |phase err.(test): min = 0.00 max = 88.13 mean = 13.91| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1115 0.1533 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1562 0.1552 0.1788 n_refl.: 17041 remove outliers: r(all,work,free)=0.1562 0.1552 0.1788 n_refl.: 17041 overall B=-0.21 to atoms: r(all,work,free)=0.1550 0.1540 0.1782 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1136 0.1116 0.1537 n_refl.: 17041 remove outliers: r(all,work,free)=0.1136 0.1116 0.1537 n_refl.: 17041 ======================== 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 0.3837 299.285 274.098 0.528 1.003 0.320 11.894-9.307 99.02 97 4 0.1815 486.955 480.166 0.916 1.003 0.320 9.237-7.194 100.00 213 7 0.1775 398.280 400.286 0.986 1.003 0.210 7.162-5.571 100.00 427 22 0.1586 298.910 292.977 0.936 1.003 0.200 5.546-4.326 100.00 867 58 0.0940 410.355 406.985 0.966 1.003 0.190 4.315-3.360 100.00 1859 96 0.0878 390.252 388.186 1.005 1.002 0.171 3.356-2.611 100.00 3867 181 0.1246 256.373 253.985 0.999 1.001 0.111 2.608-2.000 99.99 8818 434 0.1038 167.111 165.685 0.987 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7321 ================= 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 : 0.2787 0.1821 0.084 5.344 8.8 119.3 19.9 258 0.000 1_bss: 0.1622 0.1641 0.084 5.344 8.5 118.9 19.5 258 0.000 1_settarget: 0.1622 0.1641 0.084 5.344 8.5 118.9 19.5 258 0.000 1_nqh: 0.1625 0.1646 0.084 5.344 8.5 118.9 19.5 258 0.003 1_weight: 0.1625 0.1646 0.084 5.344 8.5 118.9 19.5 258 0.003 1_xyzrec: 0.1351 0.1635 0.009 0.992 8.5 118.9 19.5 258 0.154 1_adp: 0.1279 0.1659 0.009 0.992 6.2 113.9 20.0 258 0.154 1_regHadp: 0.1283 0.1665 0.009 0.992 6.2 113.9 20.0 258 0.154 1_occ: 0.1279 0.1663 0.009 0.992 6.2 113.9 20.0 258 0.154 2_bss: 0.1276 0.1654 0.009 0.992 5.8 113.5 19.6 258 0.154 2_settarget: 0.1276 0.1654 0.009 0.992 5.8 113.5 19.6 258 0.154 2_updatecdl: 0.1276 0.1654 0.009 1.003 5.8 113.5 19.6 258 0.154 2_nqh: 0.1276 0.1654 0.009 1.003 5.8 113.5 19.6 258 0.154 2_sol: 0.1247 0.1541 0.009 1.003 5.8 111.9 20.8 355 n/a 2_weight: 0.1247 0.1541 0.009 1.003 5.8 111.9 20.8 355 n/a 2_xyzrec: 0.1227 0.1616 0.008 0.929 5.8 111.9 20.8 355 n/a 2_adp: 0.1211 0.1627 0.008 0.929 6.7 106.9 21.1 355 n/a 2_regHadp: 0.1212 0.1629 0.008 0.929 6.7 106.9 21.1 355 n/a 2_occ: 0.1205 0.1625 0.008 0.929 6.7 106.9 21.1 355 n/a 3_bss: 0.1200 0.1612 0.008 0.929 6.2 106.4 20.6 355 n/a 3_settarget: 0.1200 0.1612 0.008 0.929 6.2 106.4 20.6 355 n/a 3_updatecdl: 0.1200 0.1612 0.008 0.930 6.2 106.4 20.6 355 n/a 3_nqh: 0.1200 0.1612 0.008 0.930 6.2 106.4 20.6 355 n/a 3_sol: 0.1197 0.1539 0.008 0.930 6.2 106.4 20.7 401 n/a 3_weight: 0.1197 0.1539 0.008 0.930 6.2 106.4 20.7 401 n/a 3_xyzrec: 0.1172 0.1539 0.009 0.968 6.2 106.4 20.7 401 n/a 3_adp: 0.1156 0.1560 0.009 0.968 6.3 105.4 20.6 401 n/a 3_regHadp: 0.1156 0.1560 0.009 0.968 6.3 105.4 20.6 401 n/a 3_occ: 0.1149 0.1553 0.009 0.968 6.3 105.4 20.6 401 n/a 4_bss: 0.1145 0.1552 0.009 0.968 5.9 105.0 20.2 401 n/a 4_settarget: 0.1145 0.1552 0.009 0.968 5.9 105.0 20.2 401 n/a 4_updatecdl: 0.1145 0.1552 0.009 0.968 5.9 105.0 20.2 401 n/a 4_nqh: 0.1146 0.1546 0.009 0.968 5.9 105.0 20.2 401 n/a 4_sol: 0.1141 0.1486 0.009 0.968 5.9 105.0 20.6 439 n/a 4_weight: 0.1141 0.1486 0.009 0.968 5.9 105.0 20.6 439 n/a 4_xyzrec: 0.1130 0.1552 0.010 0.991 5.9 105.0 20.6 439 n/a 4_adp: 0.1118 0.1552 0.010 0.991 5.3 103.6 20.7 439 n/a 4_regHadp: 0.1118 0.1552 0.010 0.991 5.3 103.6 20.7 439 n/a 4_occ: 0.1111 0.1553 0.010 0.991 5.3 103.6 20.7 439 n/a 5_bss: 0.1108 0.1548 0.010 0.991 5.0 103.4 20.4 439 n/a 5_settarget: 0.1108 0.1548 0.010 0.991 5.0 103.4 20.4 439 n/a 5_updatecdl: 0.1108 0.1548 0.010 0.991 5.0 103.4 20.4 439 n/a 5_setrh: 0.1110 0.1546 0.010 0.991 5.0 103.4 20.4 439 n/a 5_nqh: 0.1110 0.1546 0.010 0.991 5.0 103.4 20.4 439 n/a 5_sol: 0.1105 0.1489 0.010 0.991 5.0 103.4 20.6 462 n/a 5_weight: 0.1105 0.1489 0.010 0.991 5.0 103.4 20.6 462 n/a 5_xyzrec: 0.1130 0.1526 0.010 1.027 5.0 103.4 20.6 462 n/a 5_adp: 0.1121 0.1522 0.010 1.027 5.4 102.6 20.7 462 n/a 5_regHadp: 0.1121 0.1521 0.010 1.027 5.4 102.6 20.7 462 n/a 5_occ: 0.1115 0.1533 0.010 1.027 5.4 102.6 20.7 462 n/a end: 0.1116 0.1537 0.010 1.027 5.2 102.4 20.5 462 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4596863_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4596863_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1000 Refinement macro-cycles (run) : 918.1400 Write final files (write_after_run_outputs) : 20.3300 Total : 942.5700 Total CPU time: 16.09 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:07 PST -0800 (1735494068.00 s) Start R-work = 0.1622, R-free = 0.1641 Final R-work = 0.1116, R-free = 0.1537 =============================================================================== Job complete usr+sys time: 988.53 seconds wall clock time: 16 minutes 52.67 seconds (1012.67 seconds total)