Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1498316.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1498316.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1498316.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.36, per 1000 atoms: 0.40 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: 0.28 Conformation dependent library (CDL) restraints added in 121.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.90: 481 0.90 - 1.17: 1164 1.17 - 1.43: 688 1.43 - 1.70: 803 1.70 - 1.96: 17 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.339 1.158 0.181 7.50e-03 1.78e+04 5.81e+02 bond pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 1.526 1.292 0.234 1.01e-02 9.80e+03 5.37e+02 bond pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta sigma weight residual 1.458 1.227 0.230 1.14e-02 7.69e+03 4.08e+02 bond pdb=" CA MET A 133 " pdb=" C MET A 133 " ideal model delta sigma weight residual 1.524 1.752 -0.229 1.29e-02 6.01e+03 3.14e+02 bond pdb=" C PRO A 109 " pdb=" O PRO A 109 " ideal model delta sigma weight residual 1.237 1.006 0.231 1.32e-02 5.74e+03 3.06e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 3311 4.92 - 9.84: 1823 9.84 - 14.77: 555 14.77 - 19.69: 80 19.69 - 24.61: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 134.66 -13.43 8.10e-01 1.52e+00 2.75e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.29 109.32 9.97 6.50e-01 2.37e+00 2.35e+02 angle pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" C VAL A 20 " ideal model delta sigma weight residual 110.62 125.38 -14.76 1.02e+00 9.61e-01 2.09e+02 angle pdb=" O THR A 34 " pdb=" C THR A 34 " pdb=" N VAL A 35 " ideal model delta sigma weight residual 123.27 140.32 -17.05 1.18e+00 7.18e-01 2.09e+02 angle pdb=" CA ALYS A 93 " pdb=" C ALYS A 93 " pdb=" O ALYS A 93 " ideal model delta sigma weight residual 120.42 135.34 -14.92 1.06e+00 8.90e-01 1.98e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.32: 1323 17.32 - 34.64: 105 34.64 - 51.96: 37 51.96 - 69.28: 13 69.28 - 86.59: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALA A 183 " pdb=" N ALA A 183 " pdb=" CA ALA A 183 " pdb=" CB ALA A 183 " ideal model delta harmonic sigma weight residual -122.60 -141.70 19.10 0 2.50e+00 1.60e-01 5.84e+01 dihedral pdb=" C LEU A 185 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " pdb=" CB LEU A 185 " ideal model delta harmonic sigma weight residual -122.60 -140.35 17.75 0 2.50e+00 1.60e-01 5.04e+01 dihedral pdb=" N LEU A 128 " pdb=" C LEU A 128 " pdb=" CA LEU A 128 " pdb=" CB LEU A 128 " ideal model delta harmonic sigma weight residual 122.80 139.52 -16.72 0 2.50e+00 1.60e-01 4.47e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.171: 72 0.171 - 0.341: 69 0.341 - 0.511: 55 0.511 - 0.681: 33 0.681 - 0.851: 14 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB THR A 125 " pdb=" CA THR A 125 " pdb=" OG1 THR A 125 " pdb=" CG2 THR A 125 " both_signs ideal model delta sigma weight residual False 2.55 1.70 0.85 2.00e-01 2.50e+01 1.81e+01 chirality pdb=" CA LEU A 185 " pdb=" N LEU A 185 " pdb=" C LEU A 185 " pdb=" CB LEU A 185 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.79e+01 chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -1.83 -0.80 2.00e-01 2.50e+01 1.60e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.040 2.00e-02 2.50e+03 6.22e-02 1.16e+02 pdb=" CG PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.125 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.091 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.095 2.00e-02 2.50e+03 7.14e-02 1.15e+02 pdb=" CG HIS A 126 " -0.113 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " -0.050 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.063 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.048 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.048 9.50e-02 1.11e+02 6.84e-02 9.97e+01 pdb=" NE ARG A 48 " 0.104 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.096 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.052 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.056 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.037 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.099 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 1368 2.36 - 2.92: 8316 2.92 - 3.48: 10404 3.48 - 4.04: 15058 4.04 - 4.60: 21501 Nonbonded interactions: 56647 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.804 2.450 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.808 2.450 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.821 2.450 nonbonded pdb=" O MET A 134 " pdb=" H GLY A 137 " model vdw 1.848 2.450 nonbonded pdb="HE21 GLN A 45 " pdb=" OD1 ASP A 49 " model vdw 1.864 2.450 ... (remaining 56642 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_1498316_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= 0.3608 r_free= 0.2009 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471243 | | target function (ml) not normalized (work): 22043.225540 | | target function (ml) not normalized (free): 1152.944761 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3793 0.2195 4.855 4.9195| | 2: 3.78 - 3.00 1.00 2430 110 0.3381 0.1693 4.0764 4.1307| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.90 0.83 0.13 6614.14| | 2: 3.78 - 3.00 2430 110 0.94 11.17 1.48 0.26 445.58| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 376.85 max = 12078.45 mean = 3573.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.30| |phase err.(test): min = 0.00 max = 89.96 mean = 33.19| |-----------------------------------------------------------------------------| ----------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 0.234 1557 Z= 5.492 Angle : 5.277 17.058 2118 Z= 3.714 Chirality : 0.374 0.851 243 Planarity : 0.031 0.102 284 Dihedral : 13.681 86.594 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.08 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 1.86 % Favored : 96.89 % Cbeta Deviations : 36.22 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.48), residues: 224 helix: -2.89 (0.33), residues: 103 sheet: -0.37 (0.95), residues: 28 loop : -0.02 (0.62), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.020 ARG A 98 TYR 0.106 0.042 TYR A 139 PHE 0.076 0.036 PHE A 164 HIS 0.047 0.022 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3608 r_free= 0.2009 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.471243 | | target function (ml) not normalized (work): 22043.225540 | | target function (ml) not normalized (free): 1152.944761 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3565 0.3642 0.2125 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3565 0.3642 0.2125 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2549 0.2125 n_refl.: 5178 overall B=-1.16 to atoms: r(all,work,free)=0.2480 0.2502 0.2102 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1564 0.1562 0.1604 n_refl.: 5178 remove outliers: r(all,work,free)=0.1560 0.1558 0.1604 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3839 450.088 409.359 0.606 1.113 0.397 11.894-9.307 99.02 97 4 0.1865 715.001 692.870 0.871 1.105 0.381 9.237-7.194 100.00 213 7 0.2163 584.729 575.861 0.909 1.093 0.362 7.162-5.571 100.00 427 22 0.2345 438.768 424.646 0.888 1.072 0.285 5.546-4.326 100.00 867 58 0.1397 602.366 595.698 0.944 1.039 0.253 4.315-3.360 100.00 1859 96 0.1299 572.857 567.276 1.044 0.983 0.156 3.356-3.002 100.00 1373 60 0.1596 441.238 434.525 1.101 0.928 0.113 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-5.1814 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1558 r_free=0.1604 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1557 r_free=0.1608 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.815699 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.564393 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 0.1158 0.1775 0.0618 0.010 1.0 2.6 0.5 0.0 0 9.408 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 17.75 6.18 3.013 17.699 1.564 0.018 10.20 17.73 7.53 4.753 17.843 1.564 0.014 Individual atomic B min max mean iso aniso Overall: 3.52 113.28 19.00 5.14 1785 0 Protein: 3.52 113.28 16.30 5.14 1519 0 Water: 5.70 113.14 34.71 N/A 258 0 Other: 17.81 37.90 25.17 N/A 8 0 Chain A: 3.52 113.28 19.00 N/A 1785 0 Histogram: Values Number of atoms 3.52 - 14.50 906 14.50 - 25.48 494 25.48 - 36.45 190 36.45 - 47.43 108 47.43 - 58.40 57 58.40 - 69.38 13 69.38 - 80.36 8 80.36 - 91.33 5 91.33 - 102.31 1 102.31 - 113.28 3 =========================== Idealize ADP of riding H ========================== r_work=0.1020 r_free=0.1773 r_work=0.1013 r_free=0.1781 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1013 r_free = 0.1781 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 = 0.1007 r_free = 0.1791 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1007 r_free= 0.1791 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013823 | | target function (ls_wunit_k1) not normalized (work): 68.062872 | | target function (ls_wunit_k1) not normalized (free): 10.690282 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1048 0.1007 0.1791 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2160 0.2160 0.2259 n_refl.: 5176 remove outliers: r(all,work,free)=0.2160 0.2160 0.2259 n_refl.: 5176 overall B=-1.09 to atoms: r(all,work,free)=0.2111 0.2110 0.2243 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1055 0.1015 0.1789 n_refl.: 5176 remove outliers: r(all,work,free)=0.1055 0.1015 0.1789 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3288 316.533 301.783 0.651 1.013 0.381 11.894-9.307 99.02 97 4 0.1505 502.838 496.146 0.950 1.013 0.361 9.237-7.194 100.00 213 7 0.1635 411.222 411.988 0.988 1.011 0.331 7.162-5.571 100.00 427 22 0.1629 308.572 305.730 0.950 1.009 0.282 5.546-4.326 100.00 867 58 0.0910 423.626 420.756 0.972 1.005 0.223 4.315-3.360 100.00 1859 96 0.0773 402.873 402.800 1.025 0.998 0.163 3.356-3.002 100.00 1373 60 0.1010 310.309 308.426 1.016 0.991 0.089 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.8847 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1015 r_free=0.1789 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 180 GLN Total number of N/Q/H flips: 2 r_work=0.1019 r_free=0.1792 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1019 r_free=0.1792 | n_water=258 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.1059 r_free=0.1778 | n_water=246 | time (s): 21.370 (total time: 21.930) Filter (q & B) r_work=0.1060 r_free=0.1775 | n_water=243 | time (s): 1.700 (total time: 23.630) Compute maps r_work=0.1060 r_free=0.1775 | n_water=243 | time (s): 0.580 (total time: 24.210) Filter (map) r_work=0.1383 r_free=0.1806 | n_water=138 | time (s): 1.310 (total time: 25.520) Find peaks r_work=0.1383 r_free=0.1806 | n_water=138 | time (s): 0.410 (total time: 25.930) Add new water r_work=0.1730 r_free=0.2082 | n_water=227 | time (s): 1.290 (total time: 27.220) Refine new water occ: r_work=0.1176 r_free=0.1675 adp: r_work=0.1152 r_free=0.1678 occ: r_work=0.1150 r_free=0.1664 adp: r_work=0.1138 r_free=0.1665 occ: r_work=0.1136 r_free=0.1652 adp: r_work=0.1133 r_free=0.1654 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1654 r_work=0.1133 r_free=0.1654 | n_water=227 | time (s): 4.170 (total time: 31.390) Filter (q & B) r_work=0.1133 r_free=0.1654 | n_water=227 | time (s): 1.070 (total time: 32.460) Filter (dist only) r_work=0.1133 r_free=0.1647 | n_water=226 | time (s): 18.750 (total time: 51.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.392272 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.499732 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 0.1013 0.1785 0.0773 0.009 1.0 6.1 0.5 0.6 0 11.196 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.13 17.85 7.73 4.690 18.373 2.500 0.014 9.43 18.13 8.70 5.447 18.636 2.500 0.012 Individual atomic B min max mean iso aniso Overall: 0.79 110.26 17.78 6.38 1753 0 Protein: 1.35 110.26 16.20 6.36 1519 0 Water: 0.79 64.51 28.11 N/A 226 0 Other: 12.55 39.12 24.32 N/A 8 0 Chain A: 0.79 110.26 16.96 N/A 1664 0 Chain S: 3.31 61.63 33.11 N/A 89 0 Histogram: Values Number of atoms 0.79 - 11.74 650 11.74 - 22.69 685 22.69 - 33.63 231 33.63 - 44.58 107 44.58 - 55.53 46 55.53 - 66.47 22 66.47 - 77.42 5 77.42 - 88.37 3 88.37 - 99.31 2 99.31 - 110.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.0943 r_free=0.1813 r_work=0.0940 r_free=0.1813 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0940 r_free = 0.1813 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0939 r_free = 0.1810 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0939 r_free= 0.1810 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011935 | | target function (ls_wunit_k1) not normalized (work): 58.765575 | | target function (ls_wunit_k1) not normalized (free): 9.903841 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0983 0.0939 0.1810 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2173 0.2182 0.2173 n_refl.: 5176 remove outliers: r(all,work,free)=0.2173 0.2182 0.2173 n_refl.: 5176 overall B=-0.79 to atoms: r(all,work,free)=0.2136 0.2144 0.2163 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0984 0.0940 0.1822 n_refl.: 5176 remove outliers: r(all,work,free)=0.0982 0.0938 0.1822 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3198 313.867 301.441 0.668 1.008 0.383 11.894-9.307 99.02 97 4 0.1420 502.838 496.608 0.951 1.010 0.371 9.237-7.194 100.00 213 7 0.1463 411.222 410.114 0.980 1.009 0.311 7.162-5.571 100.00 427 22 0.1397 308.572 305.023 0.954 1.007 0.292 5.546-4.326 100.00 867 58 0.0803 423.626 420.236 0.973 1.004 0.242 4.315-3.360 100.00 1859 96 0.0727 402.873 402.966 1.026 0.999 0.183 3.356-3.002 100.00 1373 60 0.0972 310.309 310.792 1.012 0.994 0.092 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.9297 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0938 r_free=0.1822 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=0.0939 r_free=0.1821 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0939 r_free=0.1821 | n_water=226 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0950 r_free=0.1783 | n_water=221 | time (s): 16.690 (total time: 17.350) Filter (q & B) r_work=0.1010 r_free=0.1801 | n_water=219 | time (s): 1.720 (total time: 19.070) Compute maps r_work=0.1010 r_free=0.1801 | n_water=219 | time (s): 0.650 (total time: 19.720) Filter (map) r_work=0.1267 r_free=0.1850 | n_water=147 | time (s): 1.530 (total time: 21.250) Find peaks r_work=0.1267 r_free=0.1850 | n_water=147 | time (s): 0.450 (total time: 21.700) Add new water r_work=0.1635 r_free=0.2196 | n_water=230 | time (s): 1.460 (total time: 23.160) Refine new water occ: r_work=0.1058 r_free=0.1788 adp: r_work=0.1051 r_free=0.1803 occ: r_work=0.1042 r_free=0.1780 adp: r_work=0.1041 r_free=0.1789 occ: r_work=0.1033 r_free=0.1768 adp: r_work=0.1031 r_free=0.1777 ADP+occupancy (water only), MIN, final r_work=0.1031 r_free=0.1777 r_work=0.1031 r_free=0.1777 | n_water=230 | time (s): 12.030 (total time: 35.190) Filter (q & B) r_work=0.1031 r_free=0.1777 | n_water=230 | time (s): 0.750 (total time: 35.940) Filter (dist only) r_work=0.1047 r_free=0.1789 | n_water=227 | time (s): 18.170 (total time: 54.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.224815 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.196661 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 0.0950 0.1883 0.0933 0.012 1.1 5.1 0.5 0.6 0 0.612 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.50 18.83 9.33 5.422 18.239 0.197 5.129 9.05 18.96 9.90 7.208 18.286 0.197 5.033 Individual atomic B min max mean iso aniso Overall: 0.00 109.97 16.79 8.76 1754 0 Protein: 0.00 109.97 15.64 8.75 1519 0 Water: 0.00 58.72 24.24 N/A 227 0 Other: 10.13 38.02 22.90 N/A 8 0 Chain A: 0.00 109.97 16.23 N/A 1647 0 Chain S: 0.00 58.03 25.33 N/A 107 0 Histogram: Values Number of atoms 0.00 - 11.00 664 11.00 - 21.99 678 21.99 - 32.99 238 32.99 - 43.99 106 43.99 - 54.99 30 54.99 - 65.98 23 65.98 - 76.98 8 76.98 - 87.98 2 87.98 - 98.97 4 98.97 - 109.97 1 =========================== Idealize ADP of riding H ========================== r_work=0.0905 r_free=0.1896 r_work=0.0911 r_free=0.1907 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0911 r_free = 0.1907 target_work(ml) = 5.036 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0902 r_free = 0.1891 target_work(ml) = 5.030 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0902 r_free= 0.1891 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.029562 | | target function (ml) not normalized (work): 24760.534090 | | target function (ml) not normalized (free): 1847.283858 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0952 0.0902 0.1891 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2164 0.2175 0.2181 n_refl.: 5175 remove outliers: r(all,work,free)=0.2164 0.2175 0.2181 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2164 0.2175 0.2181 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0947 0.0898 0.1883 n_refl.: 5175 remove outliers: r(all,work,free)=0.0945 0.0896 0.1883 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 0.3675 315.955 285.909 0.609 0.997 0.350 11.894-9.307 99.02 97 4 0.1768 502.838 492.057 0.960 1.000 0.350 9.237-7.194 100.00 213 7 0.1879 411.222 406.020 0.994 1.001 0.310 7.162-5.571 100.00 427 22 0.1859 308.572 300.641 0.976 1.001 0.299 5.546-4.326 100.00 867 58 0.0923 423.626 419.289 1.002 1.002 0.240 4.315-3.360 100.00 1859 96 0.0604 402.873 402.249 1.060 1.002 0.200 3.356-3.002 100.00 1373 60 0.0607 310.309 309.727 1.041 1.002 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.6237 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0896 r_free=0.1883 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0896 r_free=0.1883 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0896 r_free=0.1883 | n_water=227 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0896 r_free=0.1882 | n_water=226 | time (s): 18.000 (total time: 18.530) Filter (q & B) r_work=0.0943 r_free=0.1881 | n_water=224 | time (s): 1.380 (total time: 19.910) Compute maps r_work=0.0943 r_free=0.1881 | n_water=224 | time (s): 0.630 (total time: 20.540) Filter (map) r_work=0.1194 r_free=0.1901 | n_water=158 | time (s): 1.900 (total time: 22.440) Find peaks r_work=0.1194 r_free=0.1901 | n_water=158 | time (s): 0.400 (total time: 22.840) Add new water r_work=0.1529 r_free=0.2161 | n_water=230 | time (s): 1.360 (total time: 24.200) Refine new water occ: r_work=0.1013 r_free=0.1858 adp: r_work=0.1009 r_free=0.1875 occ: r_work=0.1000 r_free=0.1852 adp: r_work=0.0999 r_free=0.1866 occ: r_work=0.0991 r_free=0.1841 adp: r_work=0.0990 r_free=0.1853 ADP+occupancy (water only), MIN, final r_work=0.0990 r_free=0.1853 r_work=0.0990 r_free=0.1853 | n_water=230 | time (s): 12.680 (total time: 36.880) Filter (q & B) r_work=0.0991 r_free=0.1850 | n_water=229 | time (s): 1.280 (total time: 38.160) Filter (dist only) r_work=0.0998 r_free=0.1841 | n_water=227 | time (s): 17.600 (total time: 55.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.986922 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.245579 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0916 0.1897 0.0981 0.011 1.0 4.5 0.5 0.6 0 0.493 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.16 18.97 9.81 6.867 18.418 0.246 5.004 8.92 19.30 10.39 8.158 18.544 0.246 4.937 Individual atomic B min max mean iso aniso Overall: 0.00 110.08 17.17 10.68 1754 0 Protein: 0.00 110.08 16.10 10.66 1519 0 Water: 0.00 56.23 24.11 N/A 227 0 Other: 10.43 39.73 22.21 N/A 8 0 Chain A: 0.00 110.08 16.63 N/A 1642 0 Chain S: 0.00 56.23 25.01 N/A 112 0 Histogram: Values Number of atoms 0.00 - 11.01 650 11.01 - 22.02 649 22.02 - 33.02 265 33.02 - 44.03 115 44.03 - 55.04 42 55.04 - 66.05 13 66.05 - 77.06 11 77.06 - 88.07 4 88.07 - 99.07 4 99.07 - 110.08 1 =========================== Idealize ADP of riding H ========================== r_work=0.0892 r_free=0.1930 r_work=0.0896 r_free=0.1936 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0896 r_free = 0.1936 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0884 r_free = 0.1914 target_work(ml) = 4.934 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0884 r_free= 0.1914 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.934079 | | target function (ml) not normalized (work): 24285.534893 | | target function (ml) not normalized (free): 2145.814876 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0936 0.0884 0.1914 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2129 0.2126 0.2308 n_refl.: 5174 remove outliers: r(all,work,free)=0.2129 0.2126 0.2308 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2129 0.2126 0.2308 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0882 0.1914 n_refl.: 5174 remove outliers: r(all,work,free)=0.0934 0.0882 0.1914 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 0.3763 315.955 288.152 0.608 0.990 0.334 11.894-9.307 99.02 97 4 0.1859 502.838 488.815 0.953 0.995 0.320 9.237-7.194 100.00 213 7 0.2074 411.222 403.013 0.995 0.998 0.310 7.162-5.571 100.00 427 22 0.2018 308.572 299.435 0.986 0.999 0.290 5.546-4.326 100.00 867 58 0.0988 423.626 418.262 1.012 1.000 0.240 4.315-3.360 100.00 1859 96 0.0571 402.873 402.500 1.077 1.002 0.210 3.356-3.002 100.00 1373 60 0.0447 310.309 309.693 1.059 1.003 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4131 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0882 r_free=0.1914 After: r_work=0.0885 r_free=0.1912 ================================== NQH flips ================================== r_work=0.0885 r_free=0.1912 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0887 r_free=0.1916 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0887 r_free=0.1916 | n_water=227 | time (s): 0.460 (total time: 0.460) Filter (dist) r_work=0.0902 r_free=0.1916 | n_water=223 | time (s): 16.550 (total time: 17.010) Filter (q & B) r_work=0.1000 r_free=0.1917 | n_water=220 | time (s): 1.450 (total time: 18.460) Compute maps r_work=0.1000 r_free=0.1917 | n_water=220 | time (s): 0.590 (total time: 19.050) Filter (map) r_work=0.1281 r_free=0.1944 | n_water=156 | time (s): 1.870 (total time: 20.920) Find peaks r_work=0.1281 r_free=0.1944 | n_water=156 | time (s): 0.550 (total time: 21.470) Add new water r_work=0.1546 r_free=0.2193 | n_water=218 | time (s): 1.540 (total time: 23.010) Refine new water occ: r_work=0.1026 r_free=0.1881 adp: r_work=0.1018 r_free=0.1897 occ: r_work=0.1010 r_free=0.1886 adp: r_work=0.1010 r_free=0.1894 occ: r_work=0.1003 r_free=0.1883 adp: r_work=0.1003 r_free=0.1889 ADP+occupancy (water only), MIN, final r_work=0.1003 r_free=0.1889 r_work=0.1003 r_free=0.1889 | n_water=218 | time (s): 10.940 (total time: 33.950) Filter (q & B) r_work=0.1003 r_free=0.1895 | n_water=216 | time (s): 1.720 (total time: 35.670) Filter (dist only) r_work=0.1003 r_free=0.1895 | n_water=216 | time (s): 14.970 (total time: 50.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.036096 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.230803 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 0.0942 0.1898 0.0957 0.011 1.1 6.4 0.5 0.6 0 0.518 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.42 18.98 9.57 8.138 18.839 0.231 5.017 9.13 19.09 9.96 9.082 18.918 0.231 4.952 Individual atomic B min max mean iso aniso Overall: 0.00 112.89 17.35 11.94 1743 0 Protein: 0.00 112.89 16.45 11.93 1519 0 Water: 0.00 59.42 23.52 N/A 216 0 Other: 7.10 39.22 20.89 N/A 8 0 Chain A: 0.00 112.89 16.88 N/A 1630 0 Chain S: 0.00 59.42 24.09 N/A 113 0 Histogram: Values Number of atoms 0.00 - 11.29 661 11.29 - 22.58 634 22.58 - 33.87 273 33.87 - 45.16 105 45.16 - 56.45 36 56.45 - 67.74 14 67.74 - 79.02 10 79.02 - 90.31 3 90.31 - 101.60 6 101.60 - 112.89 1 =========================== Idealize ADP of riding H ========================== r_work=0.0913 r_free=0.1909 r_work=0.0917 r_free=0.1913 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0917 r_free = 0.1913 target_work(ml) = 4.958 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0910 r_free = 0.1907 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0910 r_free= 0.1907 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.953858 | | target function (ml) not normalized (work): 24382.889374 | | target function (ml) not normalized (free): 2154.152989 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1287 0.1909 5.5233 6.2377| | 2: 3.78 - 3.00 1.00 2430 110 0.0452 0.1904 4.3699 11.531| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.92 12.24 1.00 0.95 12130.79| | 2: 3.78 - 3.00 2430 110 0.99 2.03 1.00 0.97 931.23| |alpha: min = 0.94 max = 0.97 mean = 0.96| |beta: min = 591.75 max = 19883.51 mean = 6601.55| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 88.82 mean = 7.20| |phase err.(test): min = 0.00 max = 75.03 mean = 7.14| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0960 0.0910 0.1907 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2186 0.2184 0.2336 n_refl.: 5174 remove outliers: r(all,work,free)=0.2186 0.2184 0.2336 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2186 0.2184 0.2336 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0959 0.0909 0.1906 n_refl.: 5174 remove outliers: r(all,work,free)=0.0959 0.0909 0.1906 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 0.3909 315.955 288.440 0.608 0.984 0.328 11.894-9.307 99.02 97 4 0.1843 502.838 489.404 0.970 0.991 0.323 9.237-7.194 100.00 213 7 0.2136 411.222 401.612 0.998 0.995 0.303 7.162-5.571 100.00 427 22 0.2064 308.572 299.164 0.990 0.997 0.287 5.546-4.326 100.00 867 58 0.1043 423.626 417.956 1.021 0.999 0.250 4.315-3.360 100.00 1859 96 0.0603 402.873 402.645 1.094 1.002 0.220 3.356-3.002 100.00 1373 60 0.0428 310.309 310.153 1.077 1.004 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.1813 ================= 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 : 0.3608 0.2009 0.082 5.277 8.8 119.3 19.9 258 0.000 1_bss: 0.1558 0.1604 0.082 5.277 7.7 118.1 18.7 258 0.000 1_settarget: 0.1558 0.1604 0.082 5.277 7.7 118.1 18.7 258 0.000 1_nqh: 0.1557 0.1608 0.082 5.277 7.7 118.1 18.7 258 0.003 1_weight: 0.1557 0.1608 0.082 5.277 7.7 118.1 18.7 258 0.003 1_xyzrec: 0.1158 0.1775 0.010 0.961 7.7 118.1 18.7 258 0.206 1_adp: 0.1020 0.1773 0.010 0.961 3.5 113.3 19.0 258 0.206 1_regHadp: 0.1013 0.1781 0.010 0.961 3.5 113.3 19.0 258 0.206 1_occ: 0.1007 0.1791 0.010 0.961 3.5 113.3 19.0 258 0.206 2_bss: 0.1015 0.1789 0.010 0.961 2.4 112.2 17.9 258 0.206 2_settarget: 0.1015 0.1789 0.010 0.961 2.4 112.2 17.9 258 0.206 2_updatecdl: 0.1015 0.1789 0.010 0.985 2.4 112.2 17.9 258 0.206 2_nqh: 0.1019 0.1792 0.010 0.985 2.4 112.2 17.9 258 0.206 2_sol: 0.1133 0.1647 0.010 0.985 1.0 112.2 17.3 226 n/a 2_weight: 0.1133 0.1647 0.010 0.985 1.0 112.2 17.3 226 n/a 2_xyzrec: 0.1013 0.1785 0.009 0.969 1.0 112.2 17.3 226 n/a 2_adp: 0.0943 0.1813 0.009 0.969 0.8 110.3 17.8 226 n/a 2_regHadp: 0.0940 0.1813 0.009 0.969 0.8 110.3 17.8 226 n/a 2_occ: 0.0939 0.1810 0.009 0.969 0.8 110.3 17.8 226 n/a 3_bss: 0.0938 0.1822 0.009 0.969 0.0 109.5 17.0 226 n/a 3_settarget: 0.0938 0.1822 0.009 0.969 0.0 109.5 17.0 226 n/a 3_updatecdl: 0.0938 0.1822 0.009 0.973 0.0 109.5 17.0 226 n/a 3_nqh: 0.0939 0.1821 0.009 0.973 0.0 109.5 17.0 226 n/a 3_sol: 0.1047 0.1789 0.009 0.973 0.6 109.5 16.7 227 n/a 3_weight: 0.1047 0.1789 0.009 0.973 0.6 109.5 16.7 227 n/a 3_xyzrec: 0.0950 0.1883 0.012 1.089 0.6 109.5 16.7 227 n/a 3_adp: 0.0905 0.1896 0.012 1.089 0.0 110.0 16.8 227 n/a 3_regHadp: 0.0911 0.1907 0.012 1.089 0.0 110.0 16.8 227 n/a 3_occ: 0.0902 0.1891 0.012 1.089 0.0 110.0 16.8 227 n/a 4_bss: 0.0896 0.1883 0.012 1.089 0.0 110.0 16.8 227 n/a 4_settarget: 0.0896 0.1883 0.012 1.089 0.0 110.0 16.8 227 n/a 4_updatecdl: 0.0896 0.1883 0.012 1.092 0.0 110.0 16.8 227 n/a 4_nqh: 0.0896 0.1883 0.012 1.092 0.0 110.0 16.8 227 n/a 4_sol: 0.0998 0.1841 0.012 1.092 0.0 110.0 16.9 227 n/a 4_weight: 0.0998 0.1841 0.012 1.092 0.0 110.0 16.9 227 n/a 4_xyzrec: 0.0916 0.1897 0.011 1.028 0.0 110.0 16.9 227 n/a 4_adp: 0.0892 0.1930 0.011 1.028 0.0 110.1 17.2 227 n/a 4_regHadp: 0.0896 0.1936 0.011 1.028 0.0 110.1 17.2 227 n/a 4_occ: 0.0884 0.1914 0.011 1.028 0.0 110.1 17.2 227 n/a 5_bss: 0.0882 0.1914 0.011 1.028 0.0 110.1 17.2 227 n/a 5_settarget: 0.0882 0.1914 0.011 1.028 0.0 110.1 17.2 227 n/a 5_updatecdl: 0.0882 0.1914 0.011 1.034 0.0 110.1 17.2 227 n/a 5_setrh: 0.0885 0.1912 0.011 1.034 0.0 110.1 17.2 227 n/a 5_nqh: 0.0887 0.1916 0.011 1.034 0.0 110.1 17.2 227 n/a 5_sol: 0.1003 0.1895 0.011 1.034 0.0 110.1 17.2 216 n/a 5_weight: 0.1003 0.1895 0.011 1.034 0.0 110.1 17.2 216 n/a 5_xyzrec: 0.0942 0.1898 0.011 1.146 0.0 110.1 17.2 216 n/a 5_adp: 0.0913 0.1909 0.011 1.146 0.0 112.9 17.3 216 n/a 5_regHadp: 0.0917 0.1913 0.011 1.146 0.0 112.9 17.3 216 n/a 5_occ: 0.0910 0.1907 0.011 1.146 0.0 112.9 17.3 216 n/a end: 0.0909 0.1906 0.011 1.146 0.0 112.9 17.3 216 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1498316_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1498316_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.2100 Refinement macro-cycles (run) : 474.1700 Write final files (write_after_run_outputs) : 10.6700 Total : 489.0500 Total CPU time: 8.50 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:51 PST -0800 (1735492731.70 s) Start R-work = 0.1558, R-free = 0.1604 Final R-work = 0.0909, R-free = 0.1906 =============================================================================== Job complete usr+sys time: 518.86 seconds wall clock time: 9 minutes 1.24 seconds (541.24 seconds total)