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_8540717.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8540717.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8540717.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.18, per 1000 atoms: 0.64 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: 0.35 Conformation dependent library (CDL) restraints added in 124.9 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: 0.69 - 0.94: 683 0.94 - 1.19: 987 1.19 - 1.44: 673 1.44 - 1.69: 784 1.69 - 1.94: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " ideal model delta sigma weight residual 1.326 1.116 0.210 1.10e-02 8.26e+03 3.65e+02 bond pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 1.450 1.657 -0.207 1.16e-02 7.43e+03 3.19e+02 bond pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta sigma weight residual 1.540 1.335 0.205 1.17e-02 7.31e+03 3.06e+02 bond pdb=" C GLU A 147 " pdb=" N LYS A 148 " ideal model delta sigma weight residual 1.332 1.113 0.219 1.26e-02 6.30e+03 3.01e+02 bond pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 1.354 1.164 0.190 1.10e-02 8.26e+03 3.00e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 2885 4.09 - 8.18: 1796 8.18 - 12.26: 829 12.26 - 16.35: 224 16.35 - 20.44: 43 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N PRO A 54 " pdb=" CA PRO A 54 " pdb=" CB PRO A 54 " ideal model delta sigma weight residual 103.32 115.71 -12.39 8.40e-01 1.42e+00 2.18e+02 angle pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" O VAL A 177 " ideal model delta sigma weight residual 121.17 106.15 15.02 1.06e+00 8.90e-01 2.01e+02 angle pdb=" O AGLN A 80 " pdb=" C AGLN A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 122.12 107.19 14.93 1.06e+00 8.90e-01 1.99e+02 angle pdb=" CA ASP A 55 " pdb=" C ASP A 55 " pdb=" O ASP A 55 " ideal model delta sigma weight residual 119.97 136.10 -16.13 1.15e+00 7.56e-01 1.97e+02 angle pdb=" CA LYS A 32 " pdb=" C LYS A 32 " pdb=" O LYS A 32 " ideal model delta sigma weight residual 120.54 134.83 -14.29 1.04e+00 9.25e-01 1.89e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1325 17.47 - 34.93: 97 34.93 - 52.40: 43 52.40 - 69.87: 14 69.87 - 87.33: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N PRO A 54 " pdb=" C PRO A 54 " pdb=" CA PRO A 54 " pdb=" CB PRO A 54 " ideal model delta harmonic sigma weight residual 115.10 132.99 -17.89 0 2.50e+00 1.60e-01 5.12e+01 dihedral pdb=" C CYS A 106 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " pdb=" CB CYS A 106 " ideal model delta harmonic sigma weight residual -122.60 -139.73 17.13 0 2.50e+00 1.60e-01 4.69e+01 dihedral pdb=" N ASP A 131 " pdb=" C ASP A 131 " pdb=" CA ASP A 131 " pdb=" CB ASP A 131 " ideal model delta harmonic sigma weight residual 122.80 106.22 16.58 0 2.50e+00 1.60e-01 4.40e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 89 0.183 - 0.366: 76 0.366 - 0.549: 44 0.549 - 0.731: 25 0.731 - 0.914: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 1.64 0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -1.74 -0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -3.46 0.83 2.00e-01 2.50e+01 1.73e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.059 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.045 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.113 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.009 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.049 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.033 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.036 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG PHE A 162 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.073 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.079 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.099 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 162 " 0.050 2.00e-02 2.50e+03 1.00e-01 1.00e+02 pdb=" C PHE A 162 " -0.173 2.00e-02 2.50e+03 pdb=" O PHE A 162 " 0.063 2.00e-02 2.50e+03 pdb=" N GLU A 163 " 0.060 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 641 2.26 - 2.84: 7707 2.84 - 3.43: 10608 3.43 - 4.01: 15403 4.01 - 4.60: 22229 Nonbonded interactions: 56588 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.671 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.797 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.799 2.450 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.844 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.851 2.450 ... (remaining 56583 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_8540717_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= 0.3621 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463901 | | target function (ml) not normalized (work): 22007.030062 | | target function (ml) not normalized (free): 1147.316170 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3802 0.2136 4.8513 4.8992| | 2: 3.78 - 3.00 1.00 2430 110 0.3400 0.1653 4.0653 4.1057| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.80 0.83 0.13 6606.59| | 2: 3.78 - 3.00 2430 110 0.94 11.32 1.48 0.26 440.81| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 371.19 max = 12065.13 mean = 3567.47| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.32| |phase err.(test): min = 0.00 max = 89.99 mean = 33.24| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.227 1557 Z= 5.298 Angle : 5.387 17.599 2118 Z= 3.799 Chirality : 0.356 0.914 243 Planarity : 0.031 0.138 284 Dihedral : 14.041 87.333 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.41 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 32.97 % 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: -3.30 (0.45), residues: 224 helix: -3.52 (0.31), residues: 103 sheet: -1.85 (0.65), residues: 40 loop : 0.05 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.020 ARG A 98 TYR 0.102 0.033 TYR A 139 PHE 0.077 0.036 PHE A 164 HIS 0.037 0.016 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3621 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463901 | | target function (ml) not normalized (work): 22007.030062 | | target function (ml) not normalized (free): 1147.316170 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3575 0.3653 0.2037 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3575 0.3653 0.2037 n_refl.: 5182 remove outliers: r(all,work,free)=0.2516 0.2544 0.2037 n_refl.: 5178 overall B=-2.83 to atoms: r(all,work,free)=0.2407 0.2432 0.1992 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1554 0.1555 0.1527 n_refl.: 5178 remove outliers: r(all,work,free)=0.1548 0.1549 0.1527 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 97.87 87 5 0.3727 453.404 409.769 0.671 1.060 0.404 11.894-9.307 99.02 97 4 0.1841 714.223 695.829 0.947 1.057 0.393 9.237-7.194 100.00 213 7 0.2135 584.092 577.402 0.976 1.051 0.364 7.162-5.571 100.00 427 22 0.2312 438.290 424.863 0.945 1.040 0.289 5.546-4.326 100.00 867 58 0.1376 601.711 594.985 0.983 1.022 0.258 4.315-3.360 100.00 1859 96 0.1309 572.233 565.961 1.050 0.991 0.168 3.356-3.002 100.00 1373 60 0.1585 440.758 431.907 1.061 0.961 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9559 b_overall=-3.5983 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1549 r_free=0.1527 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1549 r_free=0.1527 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.413185 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.710794 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 0.1155 0.1776 0.0621 0.010 1.0 2.9 0.5 0.0 0 9.207 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.55 17.76 6.21 3.013 16.032 1.711 0.018 10.18 17.74 7.55 4.796 16.237 1.711 0.014 Individual atomic B min max mean iso aniso Overall: 2.26 111.47 17.45 5.14 1785 0 Protein: 2.26 111.44 14.76 5.14 1519 0 Water: 4.04 111.47 33.07 N/A 258 0 Other: 15.80 36.15 23.22 N/A 8 0 Chain A: 2.26 111.47 17.45 N/A 1785 0 Histogram: Values Number of atoms 2.26 - 13.18 918 13.18 - 24.10 483 24.10 - 35.03 188 35.03 - 45.95 109 45.95 - 56.87 56 56.87 - 67.79 14 67.79 - 78.71 8 78.71 - 89.63 5 89.63 - 100.55 1 100.55 - 111.47 3 =========================== Idealize ADP of riding H ========================== r_work=0.1018 r_free=0.1774 r_work=0.1012 r_free=0.1783 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1012 r_free = 0.1783 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1010 r_free = 0.1787 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1010 r_free= 0.1787 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013916 | | target function (ls_wunit_k1) not normalized (work): 68.506632 | | target function (ls_wunit_k1) not normalized (free): 10.499577 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1050 0.1010 0.1787 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2088 0.2086 0.2223 n_refl.: 5175 remove outliers: r(all,work,free)=0.2088 0.2086 0.2223 n_refl.: 5175 overall B=-0.99 to atoms: r(all,work,free)=0.2046 0.2043 0.2213 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1050 0.1010 0.1783 n_refl.: 5175 remove outliers: r(all,work,free)=0.1048 0.1008 0.1783 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 0.3306 329.323 311.346 0.650 1.033 0.370 11.894-9.307 99.02 97 4 0.1505 523.134 514.927 0.962 1.033 0.361 9.237-7.194 100.00 213 7 0.1678 427.819 427.198 0.999 1.029 0.310 7.162-5.571 100.00 427 22 0.1624 321.026 318.414 0.971 1.023 0.292 5.546-4.326 100.00 867 58 0.0910 440.724 437.725 0.991 1.012 0.232 4.315-3.360 100.00 1859 96 0.0760 419.133 419.076 1.047 0.994 0.183 3.356-3.002 100.00 1373 60 0.0998 322.834 321.448 1.036 0.977 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.5119 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1008 r_free=0.1783 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1008 r_free=0.1783 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1008 r_free=0.1783 | n_water=258 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1033 r_free=0.1761 | n_water=249 | time (s): 18.860 (total time: 19.460) Filter (q & B) r_work=0.1032 r_free=0.1760 | n_water=246 | time (s): 1.430 (total time: 20.890) Compute maps r_work=0.1032 r_free=0.1760 | n_water=246 | time (s): 0.540 (total time: 21.430) Filter (map) r_work=0.1323 r_free=0.1868 | n_water=148 | time (s): 1.320 (total time: 22.750) Find peaks r_work=0.1323 r_free=0.1868 | n_water=148 | time (s): 0.420 (total time: 23.170) Add new water r_work=0.1700 r_free=0.2208 | n_water=243 | time (s): 1.260 (total time: 24.430) Refine new water occ: r_work=0.1165 r_free=0.1714 adp: r_work=0.1136 r_free=0.1724 occ: r_work=0.1129 r_free=0.1681 adp: r_work=0.1116 r_free=0.1695 occ: r_work=0.1114 r_free=0.1674 adp: r_work=0.1111 r_free=0.1679 ADP+occupancy (water only), MIN, final r_work=0.1111 r_free=0.1679 r_work=0.1111 r_free=0.1679 | n_water=243 | time (s): 5.290 (total time: 29.720) Filter (q & B) r_work=0.1112 r_free=0.1682 | n_water=241 | time (s): 1.440 (total time: 31.160) Filter (dist only) r_work=0.1116 r_free=0.1670 | n_water=237 | time (s): 18.720 (total time: 49.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.378463 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.404803 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 0.1002 0.1822 0.0820 0.009 1.0 4.5 0.5 0.6 0 11.189 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.02 18.22 8.20 4.579 16.909 2.405 0.014 9.40 18.20 8.79 5.257 17.237 2.405 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.26 16.70 6.10 1764 0 Protein: 1.00 106.26 14.93 6.09 1519 0 Water: 0.00 62.77 27.97 N/A 237 0 Other: 11.37 30.17 20.23 N/A 8 0 Chain A: 0.00 106.26 15.67 N/A 1673 0 Chain S: 1.05 59.92 35.63 N/A 91 0 Histogram: Values Number of atoms 0.00 - 10.63 667 10.63 - 21.25 671 21.25 - 31.88 223 31.88 - 42.50 111 42.50 - 53.13 45 53.13 - 63.75 32 63.75 - 74.38 8 74.38 - 85.00 2 85.00 - 95.63 3 95.63 - 106.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.0940 r_free=0.1820 r_work=0.0937 r_free=0.1816 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0937 r_free = 0.1816 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0932 r_free = 0.1797 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0932 r_free= 0.1797 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011920 | | target function (ls_wunit_k1) not normalized (work): 58.670504 | | target function (ls_wunit_k1) not normalized (free): 9.854199 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0976 0.0932 0.1797 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2103 0.2107 0.2163 n_refl.: 5174 remove outliers: r(all,work,free)=0.2103 0.2107 0.2163 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2103 0.2107 0.2163 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0977 0.0932 0.1807 n_refl.: 5174 remove outliers: r(all,work,free)=0.0975 0.0930 0.1807 n_refl.: 5173 ======================== 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 93.75 85 5 0.3193 331.550 309.885 0.654 1.007 0.354 11.894-9.307 99.02 97 4 0.1407 523.134 520.370 0.987 1.008 0.350 9.237-7.194 100.00 213 7 0.1429 427.819 429.729 1.026 1.008 0.300 7.162-5.571 100.00 427 22 0.1445 321.026 318.651 0.997 1.007 0.290 5.546-4.326 100.00 867 58 0.0767 440.724 438.177 1.012 1.004 0.250 4.315-3.360 100.00 1859 96 0.0710 419.133 418.924 1.057 0.999 0.190 3.356-3.002 100.00 1373 60 0.0995 322.834 321.408 1.038 0.995 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-4.3592 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0931 r_free=0.1807 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0931 r_free=0.1809 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0931 r_free=0.1809 | n_water=237 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0945 r_free=0.1784 | n_water=232 | time (s): 17.640 (total time: 18.180) Filter (q & B) r_work=0.0974 r_free=0.1812 | n_water=231 | time (s): 1.480 (total time: 19.660) Compute maps r_work=0.0974 r_free=0.1812 | n_water=231 | time (s): 0.550 (total time: 20.210) Filter (map) r_work=0.1257 r_free=0.1884 | n_water=150 | time (s): 1.340 (total time: 21.550) Find peaks r_work=0.1257 r_free=0.1884 | n_water=150 | time (s): 0.390 (total time: 21.940) Add new water r_work=0.1630 r_free=0.2213 | n_water=234 | time (s): 1.290 (total time: 23.230) Refine new water occ: r_work=0.1038 r_free=0.1783 adp: r_work=0.1035 r_free=0.1786 occ: r_work=0.1025 r_free=0.1771 adp: r_work=0.1025 r_free=0.1774 occ: r_work=0.1015 r_free=0.1758 adp: r_work=0.1015 r_free=0.1763 ADP+occupancy (water only), MIN, final r_work=0.1015 r_free=0.1763 r_work=0.1015 r_free=0.1763 | n_water=234 | time (s): 11.960 (total time: 35.190) Filter (q & B) r_work=0.1015 r_free=0.1763 | n_water=234 | time (s): 0.920 (total time: 36.110) Filter (dist only) r_work=0.1031 r_free=0.1774 | n_water=232 | time (s): 18.070 (total time: 54.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.125302 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.213530 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 0.0931 0.1913 0.0981 0.011 1.1 4.5 0.5 0.6 0 0.563 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.31 19.13 9.81 5.171 17.642 0.214 5.158 8.88 19.18 10.30 7.108 17.683 0.214 5.061 Individual atomic B min max mean iso aniso Overall: 0.00 106.20 16.34 8.73 1759 0 Protein: 0.00 106.20 15.15 8.73 1519 0 Water: 0.00 58.21 24.08 N/A 232 0 Other: 7.21 30.40 18.71 N/A 8 0 Chain A: 0.00 106.20 15.83 N/A 1661 0 Chain S: 0.00 58.21 25.07 N/A 98 0 Histogram: Values Number of atoms 0.00 - 10.62 656 10.62 - 21.24 673 21.24 - 31.86 242 31.86 - 42.48 115 42.48 - 53.10 36 53.10 - 63.72 19 63.72 - 74.34 9 74.34 - 84.96 4 84.96 - 95.58 3 95.58 - 106.20 2 =========================== Idealize ADP of riding H ========================== r_work=0.0888 r_free=0.1918 r_work=0.0892 r_free=0.1932 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0892 r_free = 0.1932 target_work(ml) = 5.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0884 r_free = 0.1912 target_work(ml) = 5.059 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0884 r_free= 0.1912 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.059094 | | target function (ml) not normalized (work): 24895.799246 | | target function (ml) not normalized (free): 1882.316690 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0936 0.0884 0.1912 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2054 0.2054 0.2191 n_refl.: 5173 remove outliers: r(all,work,free)=0.2054 0.2054 0.2191 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2054 0.2054 0.2191 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0933 0.0881 0.1911 n_refl.: 5173 remove outliers: r(all,work,free)=0.0933 0.0881 0.1911 n_refl.: 5173 ======================== 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 93.75 85 5 0.3659 331.550 301.413 0.597 0.991 0.330 11.894-9.307 99.02 97 4 0.1777 523.134 509.747 0.956 0.996 0.330 9.237-7.194 100.00 213 7 0.1834 427.819 421.661 1.005 0.998 0.295 7.162-5.571 100.00 427 22 0.1803 321.026 312.371 0.977 0.999 0.290 5.546-4.326 100.00 867 58 0.0892 440.724 435.504 1.003 1.000 0.240 4.315-3.360 100.00 1859 96 0.0592 419.133 418.580 1.052 1.002 0.200 3.356-3.002 100.00 1373 60 0.0619 322.834 322.303 1.035 1.003 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.3860 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0881 r_free=0.1911 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0881 r_free=0.1911 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0881 r_free=0.1911 | n_water=232 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0896 r_free=0.1920 | n_water=228 | time (s): 19.500 (total time: 20.010) Filter (q & B) r_work=0.1014 r_free=0.1946 | n_water=223 | time (s): 1.590 (total time: 21.600) Compute maps r_work=0.1014 r_free=0.1946 | n_water=223 | time (s): 0.670 (total time: 22.270) Filter (map) r_work=0.1273 r_free=0.1995 | n_water=158 | time (s): 1.960 (total time: 24.230) Find peaks r_work=0.1273 r_free=0.1995 | n_water=158 | time (s): 0.440 (total time: 24.670) Add new water r_work=0.1568 r_free=0.2314 | n_water=229 | time (s): 1.490 (total time: 26.160) Refine new water occ: r_work=0.1017 r_free=0.1908 adp: r_work=0.1007 r_free=0.1923 occ: r_work=0.0999 r_free=0.1900 adp: r_work=0.0998 r_free=0.1914 occ: r_work=0.0990 r_free=0.1892 adp: r_work=0.0989 r_free=0.1904 ADP+occupancy (water only), MIN, final r_work=0.0989 r_free=0.1904 r_work=0.0989 r_free=0.1904 | n_water=229 | time (s): 9.710 (total time: 35.870) Filter (q & B) r_work=0.0989 r_free=0.1904 | n_water=229 | time (s): 0.820 (total time: 36.690) Filter (dist only) r_work=0.0998 r_free=0.1896 | n_water=227 | time (s): 16.820 (total time: 53.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.018002 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.249831 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 0.0911 0.1899 0.0989 0.011 1.0 6.4 0.5 0.6 0 0.509 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.11 18.99 9.89 6.821 17.890 0.250 5.050 8.88 19.11 10.22 8.096 17.978 0.250 4.989 Individual atomic B min max mean iso aniso Overall: 0.00 106.91 16.62 10.48 1754 0 Protein: 0.00 106.91 15.50 10.47 1519 0 Water: 0.00 59.24 24.01 N/A 227 0 Other: 5.67 35.09 19.47 N/A 8 0 Chain A: 0.00 106.91 16.07 N/A 1646 0 Chain S: 0.00 59.24 25.06 N/A 108 0 Histogram: Values Number of atoms 0.00 - 10.69 651 10.69 - 21.38 656 21.38 - 32.07 262 32.07 - 42.76 108 42.76 - 53.46 38 53.46 - 64.15 21 64.15 - 74.84 6 74.84 - 85.53 7 85.53 - 96.22 3 96.22 - 106.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.0888 r_free=0.1911 r_work=0.0893 r_free=0.1914 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0893 r_free = 0.1914 target_work(ml) = 4.995 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0884 r_free = 0.1888 target_work(ml) = 4.988 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0884 r_free= 0.1888 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.988272 | | target function (ml) not normalized (work): 24547.284454 | | target function (ml) not normalized (free): 2096.897850 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0935 0.0884 0.1888 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2093 0.2094 0.2194 n_refl.: 5173 remove outliers: r(all,work,free)=0.2093 0.2094 0.2194 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2093 0.2094 0.2194 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0933 0.0882 0.1900 n_refl.: 5173 remove outliers: r(all,work,free)=0.0933 0.0882 0.1900 n_refl.: 5173 ======================== 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 93.75 85 5 0.3800 331.550 292.266 0.573 0.986 0.318 11.894-9.307 99.02 97 4 0.1886 523.134 513.579 0.966 0.993 0.308 9.237-7.194 100.00 213 7 0.2067 427.819 419.885 1.010 0.996 0.300 7.162-5.571 100.00 427 22 0.2004 321.026 312.572 0.992 0.998 0.300 5.546-4.326 100.00 867 58 0.0970 440.724 434.015 1.017 1.000 0.250 4.315-3.360 100.00 1859 96 0.0562 419.133 418.980 1.081 1.003 0.210 3.356-3.002 100.00 1373 60 0.0478 322.834 322.658 1.065 1.005 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6976 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0882 r_free=0.1900 After: r_work=0.0884 r_free=0.1899 ================================== NQH flips ================================== r_work=0.0884 r_free=0.1899 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN Total number of N/Q/H flips: 1 r_work=0.0896 r_free=0.1903 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0896 r_free=0.1903 | n_water=227 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0904 r_free=0.1899 | n_water=225 | time (s): 18.770 (total time: 19.340) Filter (q & B) r_work=0.1029 r_free=0.1941 | n_water=221 | time (s): 1.750 (total time: 21.090) Compute maps r_work=0.1029 r_free=0.1941 | n_water=221 | time (s): 0.470 (total time: 21.560) Filter (map) r_work=0.1286 r_free=0.1996 | n_water=149 | time (s): 1.400 (total time: 22.960) Find peaks r_work=0.1286 r_free=0.1996 | n_water=149 | time (s): 0.520 (total time: 23.480) Add new water r_work=0.1580 r_free=0.2317 | n_water=220 | time (s): 1.660 (total time: 25.140) Refine new water occ: r_work=0.1014 r_free=0.1918 adp: r_work=0.1003 r_free=0.1929 occ: r_work=0.0997 r_free=0.1910 adp: r_work=0.0995 r_free=0.1923 occ: r_work=0.0990 r_free=0.1902 adp: r_work=0.0988 r_free=0.1913 ADP+occupancy (water only), MIN, final r_work=0.0988 r_free=0.1913 r_work=0.0988 r_free=0.1913 | n_water=220 | time (s): 12.810 (total time: 37.950) Filter (q & B) r_work=0.0987 r_free=0.1917 | n_water=219 | time (s): 1.380 (total time: 39.330) Filter (dist only) r_work=0.0993 r_free=0.1916 | n_water=218 | time (s): 17.860 (total time: 57.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.976629 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.215936 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 0.0925 0.1902 0.0977 0.010 1.1 8.0 0.5 1.2 0 0.488 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.25 19.02 9.77 7.970 18.107 0.216 5.046 9.01 19.19 10.18 8.695 18.243 0.216 4.988 Individual atomic B min max mean iso aniso Overall: 0.00 108.59 16.86 11.48 1745 0 Protein: 0.00 108.59 15.97 11.46 1519 0 Water: 0.40 55.51 22.94 N/A 218 0 Other: 3.72 33.20 19.52 N/A 8 0 Chain A: 0.00 108.59 16.39 N/A 1633 0 Chain S: 0.40 55.51 23.74 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.86 636 10.86 - 21.72 653 21.72 - 32.58 273 32.58 - 43.44 108 43.44 - 54.29 39 54.29 - 65.15 18 65.15 - 76.01 6 76.01 - 86.87 4 86.87 - 97.73 5 97.73 - 108.59 3 =========================== Idealize ADP of riding H ========================== r_work=0.0901 r_free=0.1919 r_work=0.0904 r_free=0.1919 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0904 r_free = 0.1919 target_work(ml) = 4.992 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0899 r_free = 0.1911 target_work(ml) = 4.988 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5173 (all), 4.87 % free)-------------| | | | r_work= 0.0899 r_free= 0.1911 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.988435 | | target function (ml) not normalized (work): 24548.090004 | | target function (ml) not normalized (free): 2185.390079 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2491 142 0.1263 0.1865 5.5375 6.2068| | 2: 3.78 - 3.00 1.00 2430 110 0.0455 0.1989 4.4256 11.855| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2491 142 0.92 12.14 1.00 0.98 13000.02| | 2: 3.78 - 3.00 2430 110 0.99 2.12 1.00 1.00 1018.75| |alpha: min = 0.96 max = 1.00 mean = 0.99| |beta: min = 661.05 max = 21548.95 mean = 7083.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.87 mean = 7.19| |phase err.(test): min = 0.00 max = 89.87 mean = 7.55| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0949 0.0899 0.1911 n_refl.: 5173 re-set all scales: r(all,work,free)=0.2154 0.2157 0.2248 n_refl.: 5173 remove outliers: r(all,work,free)=0.2154 0.2157 0.2248 n_refl.: 5173 overall B=-0.00 to atoms: r(all,work,free)=0.2154 0.2157 0.2248 n_refl.: 5173 bulk-solvent and scaling: r(all,work,free)=0.0950 0.0900 0.1910 n_refl.: 5173 remove outliers: r(all,work,free)=0.0950 0.0900 0.1910 n_refl.: 5173 ======================== 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 93.75 85 5 0.3917 331.550 297.954 0.617 0.981 0.320 11.894-9.307 99.02 97 4 0.1899 523.134 509.352 1.010 0.990 0.318 9.237-7.194 100.00 213 7 0.2125 427.819 416.527 1.050 0.994 0.296 7.162-5.571 100.00 427 22 0.2042 321.026 311.773 1.032 0.996 0.277 5.546-4.326 100.00 867 58 0.1028 440.724 434.510 1.071 0.999 0.250 4.315-3.360 100.00 1859 96 0.0583 419.133 419.200 1.145 1.003 0.230 3.356-3.002 100.00 1373 60 0.0438 322.834 323.116 1.128 1.006 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.4922 ================= 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 : 0.3621 0.1957 0.082 5.387 8.8 119.3 19.9 258 0.000 1_bss: 0.1549 0.1527 0.082 5.387 6.0 116.5 17.1 258 0.000 1_settarget: 0.1549 0.1527 0.082 5.387 6.0 116.5 17.1 258 0.000 1_nqh: 0.1549 0.1527 0.082 5.387 6.0 116.5 17.1 258 0.000 1_weight: 0.1549 0.1527 0.082 5.387 6.0 116.5 17.1 258 0.000 1_xyzrec: 0.1155 0.1776 0.010 0.954 6.0 116.5 17.1 258 0.206 1_adp: 0.1018 0.1774 0.010 0.954 2.3 111.5 17.4 258 0.206 1_regHadp: 0.1012 0.1783 0.010 0.954 2.3 111.5 17.4 258 0.206 1_occ: 0.1010 0.1787 0.010 0.954 2.3 111.5 17.4 258 0.206 2_bss: 0.1008 0.1783 0.010 0.954 1.3 110.5 16.5 258 0.206 2_settarget: 0.1008 0.1783 0.010 0.954 1.3 110.5 16.5 258 0.206 2_updatecdl: 0.1008 0.1783 0.010 0.981 1.3 110.5 16.5 258 0.206 2_nqh: 0.1008 0.1783 0.010 0.981 1.3 110.5 16.5 258 0.206 2_sol: 0.1116 0.1670 0.010 0.981 1.0 110.5 16.1 237 n/a 2_weight: 0.1116 0.1670 0.010 0.981 1.0 110.5 16.1 237 n/a 2_xyzrec: 0.1002 0.1822 0.009 0.976 1.0 110.5 16.1 237 n/a 2_adp: 0.0940 0.1820 0.009 0.976 0.0 106.3 16.7 237 n/a 2_regHadp: 0.0937 0.1816 0.009 0.976 0.0 106.3 16.7 237 n/a 2_occ: 0.0932 0.1797 0.009 0.976 0.0 106.3 16.7 237 n/a 3_bss: 0.0931 0.1807 0.009 0.976 0.0 106.3 16.7 237 n/a 3_settarget: 0.0931 0.1807 0.009 0.976 0.0 106.3 16.7 237 n/a 3_updatecdl: 0.0931 0.1807 0.009 0.983 0.0 106.3 16.7 237 n/a 3_nqh: 0.0931 0.1809 0.009 0.983 0.0 106.3 16.7 237 n/a 3_sol: 0.1031 0.1774 0.009 0.983 1.0 106.3 16.3 232 n/a 3_weight: 0.1031 0.1774 0.009 0.983 1.0 106.3 16.3 232 n/a 3_xyzrec: 0.0931 0.1913 0.011 1.066 1.0 106.3 16.3 232 n/a 3_adp: 0.0888 0.1918 0.011 1.066 0.0 106.2 16.3 232 n/a 3_regHadp: 0.0892 0.1932 0.011 1.066 0.0 106.2 16.3 232 n/a 3_occ: 0.0884 0.1912 0.011 1.066 0.0 106.2 16.3 232 n/a 4_bss: 0.0881 0.1911 0.011 1.066 0.0 106.2 16.3 232 n/a 4_settarget: 0.0881 0.1911 0.011 1.066 0.0 106.2 16.3 232 n/a 4_updatecdl: 0.0881 0.1911 0.011 1.075 0.0 106.2 16.3 232 n/a 4_nqh: 0.0881 0.1911 0.011 1.075 0.0 106.2 16.3 232 n/a 4_sol: 0.0998 0.1896 0.011 1.075 0.0 106.2 16.5 227 n/a 4_weight: 0.0998 0.1896 0.011 1.075 0.0 106.2 16.5 227 n/a 4_xyzrec: 0.0911 0.1899 0.011 1.048 0.0 106.2 16.5 227 n/a 4_adp: 0.0888 0.1911 0.011 1.048 0.0 106.9 16.6 227 n/a 4_regHadp: 0.0893 0.1914 0.011 1.048 0.0 106.9 16.6 227 n/a 4_occ: 0.0884 0.1888 0.011 1.048 0.0 106.9 16.6 227 n/a 5_bss: 0.0882 0.1900 0.011 1.048 0.0 106.9 16.6 227 n/a 5_settarget: 0.0882 0.1900 0.011 1.048 0.0 106.9 16.6 227 n/a 5_updatecdl: 0.0882 0.1900 0.011 1.046 0.0 106.9 16.6 227 n/a 5_setrh: 0.0884 0.1899 0.011 1.046 0.0 106.9 16.6 227 n/a 5_nqh: 0.0896 0.1903 0.011 1.046 0.0 106.9 16.6 227 n/a 5_sol: 0.0993 0.1916 0.011 1.046 0.0 106.9 16.6 218 n/a 5_weight: 0.0993 0.1916 0.011 1.046 0.0 106.9 16.6 218 n/a 5_xyzrec: 0.0925 0.1902 0.010 1.113 0.0 106.9 16.6 218 n/a 5_adp: 0.0901 0.1919 0.010 1.113 0.0 108.6 16.9 218 n/a 5_regHadp: 0.0904 0.1919 0.010 1.113 0.0 108.6 16.9 218 n/a 5_occ: 0.0899 0.1911 0.010 1.113 0.0 108.6 16.9 218 n/a end: 0.0900 0.1910 0.010 1.113 0.0 108.6 16.9 218 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8540717_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8540717_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9600 Refinement macro-cycles (run) : 491.7500 Write final files (write_after_run_outputs) : 9.6700 Total : 505.3800 Total CPU time: 8.79 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:08 PST -0800 (1735492748.42 s) Start R-work = 0.1549, R-free = 0.1527 Final R-work = 0.0900, R-free = 0.1910 =============================================================================== Job complete usr+sys time: 534.66 seconds wall clock time: 9 minutes 16.39 seconds (556.39 seconds total)