Starting phenix.refine on Sun Dec 29 09:24:41 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=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1498316.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1498316.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 1.97, per 1000 atoms: 0.58 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: 0.32 Conformation dependent library (CDL) restraints added in 198.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.46 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 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2791 r_free= 0.1814 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.414467 | | target function (ml) not normalized (work): 71704.183330 | | target function (ml) not normalized (free): 3253.388295 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3185 0.2113 7.6021 5.0345| | 2: 3.63 - 2.88 1.00 2711 122 0.2635 0.1759 4.3246 4.3176| | 3: 2.88 - 2.52 1.00 2682 148 0.2593 0.1687 4.1757 4.1628| | 4: 2.52 - 2.29 1.00 2661 139 0.2564 0.1580 3.5053 3.5798| | 5: 2.29 - 2.13 1.00 2678 122 0.2657 0.1438 3.4016 3.3963| | 6: 2.13 - 2.00 1.00 2692 117 0.2747 0.1869 3.311 3.4028| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.64 2819 159 0.88 17.39 0.77 0.23 1276.43| | 2: 3.63 - 2.88 2711 122 0.83 23.53 1.31 0.23 1276.43| | 3: 2.88 - 2.52 2682 148 0.73 32.61 1.29 0.23 1276.43| | 4: 2.52 - 2.29 2661 139 0.93 11.27 1.30 0.26 131.48| | 5: 2.29 - 2.13 2678 122 0.92 13.29 1.32 0.26 131.48| | 6: 2.13 - 2.00 2692 117 0.90 16.11 1.34 0.26 131.48| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 131.48 max = 1276.43 mean = 710.34| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.91 mean = 19.04| |phase err.(test): min = 0.00 max = 87.95 mean = 19.15| |-----------------------------------------------------------------------------| ----------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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2791 r_free= 0.1814 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.414467 | | target function (ml) not normalized (work): 71704.183330 | | target function (ml) not normalized (free): 3253.388295 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3019 percent. r_work = 0.2921 r_free = 0.1984 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2868 0.2921 0.1984 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2868 0.2921 0.1984 n_refl.: 17050 remove outliers: r(all,work,free)=0.2167 0.2178 0.1984 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2140 0.2151 0.1965 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1624 0.1622 0.1667 n_refl.: 17045 remove outliers: r(all,work,free)=0.1623 0.1621 0.1667 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4014 395.092 364.899 0.649 1.013 0.397 11.894-9.307 99.02 97 4 0.1863 634.134 614.313 0.930 1.013 0.380 9.237-7.194 100.00 213 7 0.2165 518.658 510.523 0.962 1.013 0.361 7.162-5.571 100.00 427 22 0.2339 389.253 376.914 0.926 1.012 0.279 5.546-4.326 100.00 867 58 0.1406 534.382 529.312 0.959 1.009 0.241 4.315-3.360 100.00 1859 96 0.1295 508.203 504.632 1.012 1.006 0.201 3.356-2.611 100.00 3867 181 0.1664 333.860 328.976 1.015 1.000 0.048 2.608-2.000 99.99 8818 434 0.1658 217.620 213.716 1.029 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4348 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1621 r_free=0.1667 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=0.1621 r_free=0.1671 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.763779 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.817101 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1353 0.1634 0.0281 0.009 1.0 1.0 0.5 0.0 0 11.382 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.34 2.81 3.013 18.457 0.817 0.023 12.77 16.57 3.79 3.583 18.726 0.817 0.020 Individual atomic B min max mean iso aniso Overall: 6.48 113.90 19.99 4.03 1785 0 Protein: 6.48 112.91 17.24 4.03 1519 0 Water: 8.88 113.90 35.99 N/A 258 0 Other: 21.82 36.86 26.31 N/A 8 0 Chain A: 6.48 113.90 19.99 N/A 1785 0 Histogram: Values Number of atoms 6.48 - 17.22 1102 17.22 - 27.96 325 27.96 - 38.70 186 38.70 - 49.45 100 49.45 - 60.19 46 60.19 - 70.93 12 70.93 - 81.67 6 81.67 - 92.41 4 92.41 - 103.16 1 103.16 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1657 r_work=0.1280 r_free=0.1663 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1663 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1275 r_free = 0.1655 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1275 r_free= 0.1655 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020012 | | target function (ls_wunit_k1) not normalized (work): 324.942198 | | target function (ls_wunit_k1) not normalized (free): 27.049238 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1655 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1917 0.1916 0.1983 n_refl.: 17044 remove outliers: r(all,work,free)=0.1917 0.1916 0.1983 n_refl.: 17044 overall B=-0.40 to atoms: r(all,work,free)=0.1887 0.1886 0.1966 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1276 0.1647 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1274 0.1647 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3537 302.648 278.870 0.626 1.011 0.370 11.894-9.307 99.02 97 4 0.1692 486.761 476.707 0.917 1.011 0.367 9.237-7.194 100.00 213 7 0.1813 398.121 395.660 0.960 1.010 0.351 7.162-5.571 100.00 427 22 0.1834 298.790 293.908 0.932 1.009 0.293 5.546-4.326 100.00 867 58 0.1050 410.191 407.747 0.957 1.008 0.215 4.315-3.360 100.00 1859 96 0.0932 390.096 389.766 1.016 1.005 0.201 3.356-2.611 100.00 3867 181 0.1294 256.271 255.026 1.016 1.000 0.111 2.608-2.000 99.99 8818 434 0.1348 167.045 165.572 1.024 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4140 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1647 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=0.1276 r_free=0.1650 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1650 | n_water=258 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1281 r_free=0.1636 | n_water=254 | time (s): 21.750 (total time: 22.650) Filter (q & B) r_work=0.1281 r_free=0.1636 | n_water=252 | time (s): 1.980 (total time: 24.630) Compute maps r_work=0.1281 r_free=0.1636 | n_water=252 | time (s): 0.770 (total time: 25.400) Filter (map) r_work=0.1314 r_free=0.1632 | n_water=213 | time (s): 1.920 (total time: 27.320) Find peaks r_work=0.1314 r_free=0.1632 | n_water=213 | time (s): 0.500 (total time: 27.820) Add new water r_work=0.1528 r_free=0.1860 | n_water=359 | time (s): 1.500 (total time: 29.320) Refine new water occ: r_work=0.1333 r_free=0.1613 adp: r_work=0.1275 r_free=0.1604 occ: r_work=0.1279 r_free=0.1579 adp: r_work=0.1248 r_free=0.1581 occ: r_work=0.1248 r_free=0.1573 adp: r_work=0.1238 r_free=0.1571 ADP+occupancy (water only), MIN, final r_work=0.1238 r_free=0.1571 r_work=0.1238 r_free=0.1571 | n_water=359 | time (s): 26.100 (total time: 55.420) Filter (q & B) r_work=0.1239 r_free=0.1581 | n_water=352 | time (s): 1.340 (total time: 56.760) Filter (dist only) r_work=0.1239 r_free=0.1582 | n_water=351 | time (s): 28.090 (total time: 84.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.444473 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.973921 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1213 0.1621 0.0409 0.008 0.9 1.9 0.5 0.0 0 12.222 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 16.21 4.09 4.147 21.007 0.974 0.018 11.98 16.54 4.56 4.225 21.268 0.974 0.018 Individual atomic B min max mean iso aniso Overall: 6.78 107.51 21.22 4.24 1878 0 Protein: 6.78 107.51 17.73 4.22 1519 0 Water: 8.64 65.78 36.01 N/A 351 0 Other: 25.50 44.94 35.08 N/A 8 0 Chain A: 6.78 107.51 19.49 N/A 1740 0 Chain S: 15.62 63.86 43.02 N/A 138 0 Histogram: Values Number of atoms 6.78 - 16.85 1043 16.85 - 26.92 364 26.92 - 37.00 213 37.00 - 47.07 158 47.07 - 57.14 64 57.14 - 67.22 26 67.22 - 77.29 3 77.29 - 87.37 4 87.37 - 97.44 1 97.44 - 107.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1654 r_work=0.1200 r_free=0.1655 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1655 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1646 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1198 r_free= 0.1646 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017102 | | target function (ls_wunit_k1) not normalized (work): 277.643205 | | target function (ls_wunit_k1) not normalized (free): 25.601337 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1198 0.1646 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1757 0.1748 0.1967 n_refl.: 17042 remove outliers: r(all,work,free)=0.1757 0.1748 0.1967 n_refl.: 17042 overall B=-0.40 to atoms: r(all,work,free)=0.1730 0.1721 0.1948 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1191 0.1634 n_refl.: 17042 remove outliers: r(all,work,free)=0.1212 0.1190 0.1634 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3258 299.493 282.377 0.603 1.002 0.350 11.894-9.307 99.02 97 4 0.1508 486.761 482.598 0.915 1.003 0.338 9.237-7.194 100.00 213 7 0.1668 398.121 398.248 0.978 1.003 0.310 7.162-5.571 100.00 427 22 0.1511 298.790 294.770 0.940 1.003 0.260 5.546-4.326 100.00 867 58 0.0875 410.191 407.268 0.961 1.003 0.211 4.315-3.360 100.00 1859 96 0.0840 390.096 388.811 1.017 1.002 0.201 3.356-2.611 100.00 3867 181 0.1200 256.271 255.519 1.015 1.001 0.121 2.608-2.000 99.99 8818 434 0.1331 167.045 166.458 1.019 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4458 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1634 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1634 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1634 | n_water=351 | time (s): 0.890 (total time: 0.890) Filter (dist) r_work=0.1190 r_free=0.1642 | n_water=349 | time (s): 28.470 (total time: 29.360) Filter (q & B) r_work=0.1190 r_free=0.1642 | n_water=349 | time (s): 1.100 (total time: 30.460) Compute maps r_work=0.1190 r_free=0.1642 | n_water=349 | time (s): 0.830 (total time: 31.290) Filter (map) r_work=0.1250 r_free=0.1644 | n_water=265 | time (s): 2.100 (total time: 33.390) Find peaks r_work=0.1250 r_free=0.1644 | n_water=265 | time (s): 0.560 (total time: 33.950) Add new water r_work=0.1424 r_free=0.1826 | n_water=409 | time (s): 1.510 (total time: 35.460) Refine new water occ: r_work=0.1240 r_free=0.1584 adp: r_work=0.1233 r_free=0.1591 occ: r_work=0.1216 r_free=0.1559 adp: r_work=0.1205 r_free=0.1566 occ: r_work=0.1199 r_free=0.1548 adp: r_work=0.1189 r_free=0.1548 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1548 r_work=0.1189 r_free=0.1548 | n_water=409 | time (s): 24.660 (total time: 60.120) Filter (q & B) r_work=0.1193 r_free=0.1557 | n_water=400 | time (s): 1.700 (total time: 61.820) Filter (dist only) r_work=0.1193 r_free=0.1557 | n_water=400 | time (s): 29.260 (total time: 91.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.980540 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164563 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1171 0.1573 0.0403 0.009 1.0 3.8 0.5 0.0 0 0.990 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.71 15.73 4.03 4.319 21.463 0.165 4.997 11.52 15.75 4.23 4.822 21.424 0.165 4.975 Individual atomic B min max mean iso aniso Overall: 6.24 105.47 20.88 4.61 1927 0 Protein: 6.24 105.47 17.04 4.60 1519 0 Water: 9.02 61.04 35.21 N/A 400 0 Other: 25.96 45.82 34.14 N/A 8 0 Chain A: 6.24 105.47 18.85 N/A 1738 0 Chain S: 16.69 61.04 39.57 N/A 189 0 Histogram: Values Number of atoms 6.24 - 16.16 1059 16.16 - 26.09 351 26.09 - 36.01 234 36.01 - 45.93 172 45.93 - 55.86 73 55.86 - 65.78 26 65.78 - 75.70 4 75.70 - 85.63 3 85.63 - 95.55 3 95.55 - 105.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1152 r_free=0.1575 r_work=0.1152 r_free=0.1576 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1152 r_free = 0.1576 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1567 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1145 r_free= 0.1567 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.970372 | | target function (ml) not normalized (work): 80689.026133 | | target function (ml) not normalized (free): 4191.860166 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1165 0.1145 0.1567 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1673 0.1664 0.1881 n_refl.: 17041 remove outliers: r(all,work,free)=0.1673 0.1664 0.1881 n_refl.: 17041 overall B=-0.39 to atoms: r(all,work,free)=0.1646 0.1637 0.1866 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1163 0.1143 0.1566 n_refl.: 17041 remove outliers: r(all,work,free)=0.1162 0.1142 0.1566 n_refl.: 17040 ======================== 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 0.3525 295.937 277.708 0.558 1.005 0.334 11.894-9.307 99.02 97 4 0.1722 486.761 482.432 0.908 1.006 0.330 9.237-7.194 100.00 213 7 0.1811 398.121 397.482 0.982 1.006 0.259 7.162-5.571 100.00 427 22 0.1633 298.790 293.301 0.940 1.006 0.231 5.546-4.326 100.00 867 58 0.0943 410.191 406.623 0.963 1.005 0.211 4.315-3.360 100.00 1859 96 0.0878 390.096 387.820 1.013 1.003 0.201 3.356-2.611 100.00 3867 181 0.1271 256.271 254.198 1.014 1.001 0.142 2.608-2.000 99.99 8818 434 0.1092 167.045 165.663 1.020 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3878 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1566 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1142 r_free=0.1566 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1566 | n_water=400 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1142 r_free=0.1572 | n_water=399 | time (s): 32.330 (total time: 33.240) Filter (q & B) r_work=0.1142 r_free=0.1572 | n_water=399 | time (s): 1.040 (total time: 34.280) Compute maps r_work=0.1142 r_free=0.1572 | n_water=399 | time (s): 0.670 (total time: 34.950) Filter (map) r_work=0.1194 r_free=0.1628 | n_water=312 | time (s): 1.970 (total time: 36.920) Find peaks r_work=0.1194 r_free=0.1628 | n_water=312 | time (s): 0.470 (total time: 37.390) Add new water r_work=0.1337 r_free=0.1735 | n_water=448 | time (s): 1.820 (total time: 39.210) Refine new water occ: r_work=0.1175 r_free=0.1556 adp: r_work=0.1168 r_free=0.1558 occ: r_work=0.1152 r_free=0.1544 adp: r_work=0.1144 r_free=0.1541 occ: r_work=0.1136 r_free=0.1539 adp: r_work=0.1129 r_free=0.1534 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1534 r_work=0.1129 r_free=0.1534 | n_water=448 | time (s): 27.210 (total time: 66.420) Filter (q & B) r_work=0.1133 r_free=0.1543 | n_water=439 | time (s): 1.700 (total time: 68.120) Filter (dist only) r_work=0.1133 r_free=0.1543 | n_water=439 | time (s): 31.920 (total time: 100.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.040949 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.153373 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1121 0.1578 0.0457 0.010 1.0 4.2 0.5 0.0 0 1.020 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.21 15.78 4.57 4.454 21.117 0.153 4.960 11.11 15.82 4.71 4.620 21.128 0.153 4.954 Individual atomic B min max mean iso aniso Overall: 5.74 102.54 20.99 4.73 1966 0 Protein: 5.74 102.54 16.59 4.72 1519 0 Water: 8.93 66.13 36.02 N/A 439 0 Other: 23.94 42.31 31.12 N/A 8 0 Chain A: 5.74 102.54 18.34 N/A 1737 0 Chain S: 17.15 66.13 41.11 N/A 229 0 Histogram: Values Number of atoms 5.74 - 15.42 1023 15.42 - 25.10 387 25.10 - 34.78 205 34.78 - 44.46 208 44.46 - 54.14 91 54.14 - 63.82 36 63.82 - 73.50 7 73.50 - 83.18 4 83.18 - 92.86 3 92.86 - 102.54 2 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1582 r_work=0.1111 r_free=0.1582 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1582 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1588 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1101 r_free= 0.1588 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.951474 | | target function (ml) not normalized (work): 80377.271132 | | target function (ml) not normalized (free): 4191.057680 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1101 0.1588 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1606 0.1590 0.1927 n_refl.: 17040 remove outliers: r(all,work,free)=0.1606 0.1590 0.1927 n_refl.: 17040 overall B=-0.30 to atoms: r(all,work,free)=0.1586 0.1570 0.1915 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1124 0.1100 0.1587 n_refl.: 17040 remove outliers: r(all,work,free)=0.1124 0.1100 0.1587 n_refl.: 17040 ======================== 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 0.3498 295.937 274.811 0.549 1.002 0.324 11.894-9.307 99.02 97 4 0.1729 486.761 481.000 0.915 1.003 0.320 9.237-7.194 100.00 213 7 0.1707 398.121 399.068 0.986 1.004 0.240 7.162-5.571 100.00 427 22 0.1529 298.790 292.919 0.944 1.003 0.213 5.546-4.326 100.00 867 58 0.0897 410.191 406.991 0.965 1.003 0.203 4.315-3.360 100.00 1859 96 0.0843 390.096 388.055 1.009 1.002 0.201 3.356-2.611 100.00 3867 181 0.1237 256.271 254.028 1.006 1.001 0.151 2.608-2.000 99.99 8818 434 0.1050 167.045 165.769 1.005 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0558 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1587 After: r_work=0.1102 r_free=0.1585 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1585 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1585 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1585 | n_water=439 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1105 r_free=0.1579 | n_water=437 | time (s): 35.670 (total time: 36.360) Filter (q & B) r_work=0.1105 r_free=0.1579 | n_water=437 | time (s): 0.820 (total time: 37.180) Compute maps r_work=0.1105 r_free=0.1579 | n_water=437 | time (s): 0.590 (total time: 37.770) Filter (map) r_work=0.1176 r_free=0.1574 | n_water=337 | time (s): 1.910 (total time: 39.680) Find peaks r_work=0.1176 r_free=0.1574 | n_water=337 | time (s): 0.630 (total time: 40.310) Add new water r_work=0.1288 r_free=0.1681 | n_water=473 | time (s): 1.780 (total time: 42.090) Refine new water occ: r_work=0.1137 r_free=0.1558 adp: r_work=0.1131 r_free=0.1557 occ: r_work=0.1118 r_free=0.1546 adp: r_work=0.1110 r_free=0.1544 occ: r_work=0.1105 r_free=0.1539 adp: r_work=0.1099 r_free=0.1537 ADP+occupancy (water only), MIN, final r_work=0.1099 r_free=0.1537 r_work=0.1099 r_free=0.1537 | n_water=473 | time (s): 37.440 (total time: 79.530) Filter (q & B) r_work=0.1103 r_free=0.1538 | n_water=461 | time (s): 2.180 (total time: 81.710) Filter (dist only) r_work=0.1103 r_free=0.1538 | n_water=460 | time (s): 38.090 (total time: 119.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.033100 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.163257 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1122 0.1545 0.0423 0.010 1.1 6.4 0.5 0.0 0 1.017 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.22 15.45 4.23 4.478 20.852 0.163 4.948 11.09 15.33 4.24 4.597 20.914 0.163 4.938 Individual atomic B min max mean iso aniso Overall: 5.25 100.98 20.97 4.93 1987 0 Protein: 5.25 100.98 16.29 4.92 1519 0 Water: 8.36 65.51 36.26 N/A 460 0 Other: 23.28 38.99 29.91 N/A 8 0 Chain A: 5.25 100.98 17.99 N/A 1735 0 Chain S: 16.85 65.51 41.51 N/A 252 0 Histogram: Values Number of atoms 5.25 - 14.82 1002 14.82 - 24.40 397 24.40 - 33.97 207 33.97 - 43.54 205 43.54 - 53.11 120 53.11 - 62.69 34 62.69 - 72.26 12 72.26 - 81.83 3 81.83 - 91.41 4 91.41 - 100.98 3 =========================== Idealize ADP of riding H ========================== r_work=0.1109 r_free=0.1533 r_work=0.1108 r_free=0.1532 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1532 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1535 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1101 r_free= 0.1535 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.933317 | | target function (ml) not normalized (work): 80082.539378 | | target function (ml) not normalized (free): 4166.187352 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1096 0.1418 5.4381 5.6409| | 2: 3.63 - 2.88 1.00 2711 122 0.1088 0.1478 5.2164 5.3539| | 3: 2.88 - 2.52 1.00 2681 148 0.1357 0.1744 5.1265 5.2078| | 4: 2.52 - 2.29 1.00 2661 139 0.0939 0.1569 4.6302 4.969| | 5: 2.29 - 2.13 1.00 2678 122 0.0962 0.1472 4.5831 4.8829| | 6: 2.13 - 2.00 1.00 2692 117 0.1130 0.1754 4.5769 4.7774| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.94 9.09 1.00 0.95 6321.09| | 2: 3.63 - 2.88 2711 122 0.92 12.75 1.01 0.95 6321.09| | 3: 2.88 - 2.52 2681 148 0.88 18.90 0.99 0.95 6321.09| | 4: 2.52 - 2.29 2661 139 0.93 12.30 1.01 0.97 2146.03| | 5: 2.29 - 2.13 2678 122 0.91 14.31 1.00 0.97 2146.03| | 6: 2.13 - 2.00 2692 117 0.89 17.02 0.99 0.97 2146.03| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 2146.03 max = 6321.09 mean = 4255.55| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.78 mean = 14.02| |phase err.(test): min = 0.00 max = 87.02 mean = 13.66| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1122 0.1101 0.1535 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1579 0.1566 0.1844 n_refl.: 17040 remove outliers: r(all,work,free)=0.1579 0.1566 0.1844 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1565 0.1552 0.1836 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1102 0.1533 n_refl.: 17040 remove outliers: r(all,work,free)=0.1123 0.1102 0.1533 n_refl.: 17040 ======================== 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 0.3522 295.937 275.033 0.544 1.004 0.325 11.894-9.307 99.02 97 4 0.1686 486.761 483.274 0.918 1.005 0.321 9.237-7.194 100.00 213 7 0.1722 398.121 399.448 0.984 1.005 0.235 7.162-5.571 100.00 427 22 0.1534 298.790 293.064 0.942 1.005 0.218 5.546-4.326 100.00 867 58 0.0905 410.191 406.693 0.963 1.004 0.195 4.315-3.360 100.00 1859 96 0.0867 390.096 387.853 1.002 1.003 0.184 3.356-2.611 100.00 3867 181 0.1233 256.271 254.015 1.002 1.000 0.161 2.608-2.000 99.99 8818 434 0.1043 167.045 165.710 0.994 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8148 ================= 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 : 0.2791 0.1814 0.082 5.277 8.8 119.3 19.9 258 0.000 1_bss: 0.1621 0.1667 0.082 5.277 8.4 118.9 19.5 258 0.000 1_settarget: 0.1621 0.1667 0.082 5.277 8.4 118.9 19.5 258 0.000 1_nqh: 0.1621 0.1671 0.082 5.277 8.4 118.9 19.5 258 0.003 1_weight: 0.1621 0.1671 0.082 5.277 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1353 0.1634 0.009 0.967 8.4 118.9 19.5 258 0.148 1_adp: 0.1277 0.1657 0.009 0.967 6.5 113.9 20.0 258 0.148 1_regHadp: 0.1280 0.1663 0.009 0.967 6.5 113.9 20.0 258 0.148 1_occ: 0.1275 0.1655 0.009 0.967 6.5 113.9 20.0 258 0.148 2_bss: 0.1274 0.1647 0.009 0.967 6.1 113.5 19.6 258 0.148 2_settarget: 0.1274 0.1647 0.009 0.967 6.1 113.5 19.6 258 0.148 2_updatecdl: 0.1274 0.1647 0.009 0.980 6.1 113.5 19.6 258 0.148 2_nqh: 0.1276 0.1650 0.009 0.980 6.1 113.5 19.6 258 0.145 2_sol: 0.1239 0.1582 0.009 0.980 6.1 112.5 20.7 351 n/a 2_weight: 0.1239 0.1582 0.009 0.980 6.1 112.5 20.7 351 n/a 2_xyzrec: 0.1213 0.1621 0.008 0.928 6.1 112.5 20.7 351 n/a 2_adp: 0.1198 0.1654 0.008 0.928 6.8 107.5 21.2 351 n/a 2_regHadp: 0.1200 0.1655 0.008 0.928 6.8 107.5 21.2 351 n/a 2_occ: 0.1198 0.1646 0.008 0.928 6.8 107.5 21.2 351 n/a 3_bss: 0.1190 0.1634 0.008 0.928 6.4 107.1 20.8 351 n/a 3_settarget: 0.1190 0.1634 0.008 0.928 6.4 107.1 20.8 351 n/a 3_updatecdl: 0.1190 0.1634 0.008 0.928 6.4 107.1 20.8 351 n/a 3_nqh: 0.1190 0.1634 0.008 0.928 6.4 107.1 20.8 351 n/a 3_sol: 0.1193 0.1557 0.008 0.928 6.4 107.1 21.0 400 n/a 3_weight: 0.1193 0.1557 0.008 0.928 6.4 107.1 21.0 400 n/a 3_xyzrec: 0.1171 0.1573 0.009 0.971 6.4 107.1 21.0 400 n/a 3_adp: 0.1152 0.1575 0.009 0.971 6.2 105.5 20.9 400 n/a 3_regHadp: 0.1152 0.1576 0.009 0.971 6.2 105.5 20.9 400 n/a 3_occ: 0.1145 0.1567 0.009 0.971 6.2 105.5 20.9 400 n/a 4_bss: 0.1142 0.1566 0.009 0.971 5.9 105.1 20.5 400 n/a 4_settarget: 0.1142 0.1566 0.009 0.971 5.9 105.1 20.5 400 n/a 4_updatecdl: 0.1142 0.1566 0.009 0.971 5.9 105.1 20.5 400 n/a 4_nqh: 0.1142 0.1566 0.009 0.971 5.9 105.1 20.5 400 n/a 4_sol: 0.1133 0.1543 0.009 0.971 5.9 105.1 21.0 439 n/a 4_weight: 0.1133 0.1543 0.009 0.971 5.9 105.1 21.0 439 n/a 4_xyzrec: 0.1121 0.1578 0.010 0.991 5.9 105.1 21.0 439 n/a 4_adp: 0.1111 0.1582 0.010 0.991 5.7 102.5 21.0 439 n/a 4_regHadp: 0.1111 0.1582 0.010 0.991 5.7 102.5 21.0 439 n/a 4_occ: 0.1101 0.1588 0.010 0.991 5.7 102.5 21.0 439 n/a 5_bss: 0.1100 0.1587 0.010 0.991 5.4 102.2 20.7 439 n/a 5_settarget: 0.1100 0.1587 0.010 0.991 5.4 102.2 20.7 439 n/a 5_updatecdl: 0.1100 0.1587 0.010 0.991 5.4 102.2 20.7 439 n/a 5_setrh: 0.1102 0.1585 0.010 0.991 5.4 102.2 20.7 439 n/a 5_nqh: 0.1102 0.1585 0.010 0.991 5.4 102.2 20.7 439 n/a 5_sol: 0.1103 0.1538 0.010 0.991 5.4 102.2 20.9 460 n/a 5_weight: 0.1103 0.1538 0.010 0.991 5.4 102.2 20.9 460 n/a 5_xyzrec: 0.1122 0.1545 0.010 1.111 5.4 102.2 20.9 460 n/a 5_adp: 0.1109 0.1533 0.010 1.111 5.3 101.0 21.0 460 n/a 5_regHadp: 0.1108 0.1532 0.010 1.111 5.3 101.0 21.0 460 n/a 5_occ: 0.1101 0.1535 0.010 1.111 5.3 101.0 21.0 460 n/a end: 0.1102 0.1533 0.010 1.111 5.0 100.7 20.7 460 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1498316_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1498316_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1200 Refinement macro-cycles (run) : 914.5500 Write final files (write_after_run_outputs) : 20.1600 Total : 937.8300 Total CPU time: 16.02 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:02 PST -0800 (1735494062.37 s) Start R-work = 0.1621, R-free = 0.1667 Final R-work = 0.1102, R-free = 0.1533 =============================================================================== Job complete usr+sys time: 986.21 seconds wall clock time: 16 minutes 49.24 seconds (1009.24 seconds total)