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_4912670.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4912670.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4912670.pdb" 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" 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 2 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: 1.28, per 1000 atoms: 0.38 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 132.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 731 0.94 - 1.21: 965 1.21 - 1.47: 787 1.47 - 1.74: 658 1.74 - 2.01: 12 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 107 " pdb=" N GLY A 108 " ideal model delta sigma weight residual 1.340 1.189 0.151 6.60e-03 2.30e+04 5.24e+02 bond pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 1.519 1.303 0.216 1.04e-02 9.25e+03 4.30e+02 bond pdb=" C ASP A 149 " pdb=" O ASP A 149 " ideal model delta sigma weight residual 1.235 1.020 0.215 1.14e-02 7.69e+03 3.55e+02 bond pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 1.234 1.026 0.209 1.11e-02 8.12e+03 3.53e+02 bond pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 1.330 1.087 0.243 1.30e-02 5.92e+03 3.49e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 3018 4.49 - 8.97: 1903 8.97 - 13.46: 684 13.46 - 17.95: 152 17.95 - 22.44: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 113.83 7.24 3.60e-01 7.72e+00 4.04e+02 angle pdb=" O VAL A 23 " pdb=" C VAL A 23 " pdb=" N ASP A 24 " ideal model delta sigma weight residual 121.94 106.42 15.52 1.00e+00 1.00e+00 2.41e+02 angle pdb=" CA VAL A 23 " pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 121.27 135.78 -14.51 1.04e+00 9.25e-01 1.95e+02 angle pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " pdb=" CG ASP A 49 " ideal model delta sigma weight residual 112.60 126.44 -13.84 1.00e+00 1.00e+00 1.91e+02 angle pdb=" O ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.20 108.37 14.83 1.08e+00 8.57e-01 1.88e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 1291 16.17 - 32.33: 125 32.33 - 48.50: 42 48.50 - 64.67: 19 64.67 - 80.83: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALYS A 99 " pdb=" N ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -141.59 18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" C ASP A 68 " pdb=" N ASP A 68 " pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " ideal model delta harmonic sigma weight residual -122.60 -140.95 18.35 0 2.50e+00 1.60e-01 5.39e+01 dihedral pdb=" C LEU A 77 " pdb=" N LEU A 77 " pdb=" CA LEU A 77 " pdb=" CB LEU A 77 " ideal model delta harmonic sigma weight residual -122.60 -139.94 17.34 0 2.50e+00 1.60e-01 4.81e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.207: 102 0.207 - 0.412: 72 0.412 - 0.616: 45 0.616 - 0.821: 22 0.821 - 1.026: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" CA VAL A 181 " pdb=" N VAL A 181 " pdb=" C VAL A 181 " pdb=" CB VAL A 181 " both_signs ideal model delta sigma weight residual False 2.44 3.26 -0.82 2.00e-01 2.50e+01 1.68e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.119 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG PHE A 119 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.052 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.071 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.081 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.021 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.132 9.50e-02 1.11e+02 8.48e-02 1.20e+02 pdb=" NE ARG A 5 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.106 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.105 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.069 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " -0.106 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.050 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.107 2.00e-02 2.50e+03 5.45e-02 8.92e+01 pdb=" CG ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.060 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.086 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.000 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.043 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.059 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.013 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 635 2.26 - 2.84: 7701 2.84 - 3.43: 10630 3.43 - 4.01: 15493 4.01 - 4.60: 22152 Nonbonded interactions: 56611 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.673 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.815 2.450 nonbonded pdb=" HG3BGLU A 90 " pdb=" O HOH A 373 " model vdw 1.848 2.620 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.851 2.450 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.855 2.450 ... (remaining 56606 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_4912670_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= 0.2794 r_free= 0.1770 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.417288 | | target function (ml) not normalized (work): 71750.004857 | | target function (ml) not normalized (free): 3256.242331 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3198 0.2105 7.6266 5.0244| | 2: 3.63 - 2.88 1.00 2711 122 0.2638 0.1642 4.3237 4.3136| | 3: 2.88 - 2.52 1.00 2682 148 0.2578 0.1682 4.173 4.1737| | 4: 2.52 - 2.29 1.00 2661 139 0.2551 0.1544 3.5104 3.607| | 5: 2.29 - 2.13 1.00 2678 122 0.2666 0.1387 3.3935 3.4034| | 6: 2.13 - 2.00 1.00 2692 117 0.2762 0.1763 3.3091 3.3915| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.20 0.77 0.23 1263.19| | 2: 3.63 - 2.88 2711 122 0.83 23.59 1.31 0.23 1263.19| | 3: 2.88 - 2.52 2682 148 0.74 32.50 1.29 0.23 1263.19| | 4: 2.52 - 2.29 2661 139 0.93 11.18 1.30 0.26 133.28| | 5: 2.29 - 2.13 2678 122 0.92 13.33 1.32 0.26 133.28| | 6: 2.13 - 2.00 2692 117 0.90 16.23 1.34 0.26 133.28| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 133.28 max = 1263.19 mean = 704.53| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.99 mean = 19.01| |phase err.(test): min = 0.00 max = 89.60 mean = 19.20| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.243 1557 Z= 5.444 Angle : 5.386 18.870 2118 Z= 3.769 Chirality : 0.364 1.026 243 Planarity : 0.031 0.082 284 Dihedral : 14.033 80.833 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 30.81 % 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: -2.70 (0.47), residues: 224 helix: -2.91 (0.33), residues: 102 sheet: -0.96 (0.72), residues: 38 loop : -0.27 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.013 ARG A 145 TYR 0.073 0.030 TYR A 139 PHE 0.111 0.049 PHE A 119 HIS 0.079 0.048 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2794 r_free= 0.1770 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.417288 | | target function (ml) not normalized (work): 71750.004857 | | target function (ml) not normalized (free): 3256.242331 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2747 percent. r_work = 0.2922 r_free = 0.1945 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2922 0.1945 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2922 0.1945 n_refl.: 17050 remove outliers: r(all,work,free)=0.2158 0.2172 0.1945 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2131 0.2144 0.1926 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1616 0.1615 0.1636 n_refl.: 17045 remove outliers: r(all,work,free)=0.1615 0.1614 0.1636 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 0.4073 394.649 359.756 0.655 1.011 0.393 11.894-9.307 99.02 97 4 0.1872 633.423 615.185 0.935 1.011 0.375 9.237-7.194 100.00 213 7 0.2210 518.076 508.121 0.962 1.011 0.350 7.162-5.571 100.00 427 22 0.2352 388.817 373.850 0.923 1.010 0.289 5.546-4.326 100.00 867 58 0.1385 533.783 528.303 0.962 1.008 0.225 4.315-3.360 100.00 1859 96 0.1311 507.633 503.878 1.020 1.005 0.201 3.356-2.611 100.00 3867 181 0.1646 333.486 328.889 1.013 1.000 0.039 2.608-2.000 99.99 8818 434 0.1644 217.375 213.722 1.029 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4831 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1614 r_free=0.1636 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1616 r_free=0.1637 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.731456 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.854819 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1351 0.1621 0.0270 0.009 1.0 1.3 0.5 0.0 0 11.866 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.21 2.70 3.013 18.444 0.855 0.023 12.80 16.42 3.62 3.567 18.685 0.855 0.021 Individual atomic B min max mean iso aniso Overall: 6.19 113.88 19.93 4.06 1785 0 Protein: 6.19 112.77 17.16 4.06 1519 0 Water: 8.60 113.88 36.01 N/A 258 0 Other: 21.84 36.14 26.13 N/A 8 0 Chain A: 6.19 113.88 19.93 N/A 1785 0 Histogram: Values Number of atoms 6.19 - 16.96 1092 16.96 - 27.73 337 27.73 - 38.50 182 38.50 - 49.27 96 49.27 - 60.04 51 60.04 - 70.81 13 70.81 - 81.58 6 81.58 - 92.35 4 92.35 - 103.11 1 103.11 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1280 r_free=0.1642 r_work=0.1283 r_free=0.1648 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1283 r_free = 0.1648 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1278 r_free = 0.1642 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 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= 0.1278 r_free= 0.1642 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020167 | | target function (ls_wunit_k1) not normalized (work): 327.457059 | | target function (ls_wunit_k1) not normalized (free): 26.888988 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1278 0.1642 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1909 0.1909 0.1969 n_refl.: 17044 remove outliers: r(all,work,free)=0.1909 0.1909 0.1969 n_refl.: 17044 overall B=-0.37 to atoms: r(all,work,free)=0.1882 0.1881 0.1954 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1297 0.1280 0.1636 n_refl.: 17044 remove outliers: r(all,work,free)=0.1295 0.1278 0.1636 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 0.3539 304.071 280.230 0.633 1.000 0.368 11.894-9.307 99.02 97 4 0.1716 489.050 479.885 0.932 0.999 0.366 9.237-7.194 100.00 213 7 0.1832 399.994 397.270 0.971 0.998 0.351 7.162-5.571 100.00 427 22 0.1851 300.196 295.514 0.941 0.997 0.301 5.546-4.326 100.00 867 58 0.1047 412.120 410.212 0.969 0.995 0.205 4.315-3.360 100.00 1859 96 0.0938 391.930 391.833 1.030 0.991 0.191 3.356-2.611 100.00 3867 181 0.1303 257.476 255.997 1.028 0.986 0.101 2.608-2.000 99.99 8818 434 0.1347 167.830 166.112 1.036 0.976 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3340 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1636 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1280 r_free=0.1636 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1280 r_free=0.1636 | n_water=258 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1288 r_free=0.1627 | n_water=252 | time (s): 21.230 (total time: 21.960) Filter (q & B) r_work=0.1288 r_free=0.1628 | n_water=250 | time (s): 1.450 (total time: 23.410) Compute maps r_work=0.1288 r_free=0.1628 | n_water=250 | time (s): 0.610 (total time: 24.020) Filter (map) r_work=0.1318 r_free=0.1615 | n_water=215 | time (s): 1.610 (total time: 25.630) Find peaks r_work=0.1318 r_free=0.1615 | n_water=215 | time (s): 0.670 (total time: 26.300) Add new water r_work=0.1530 r_free=0.1858 | n_water=375 | time (s): 2.080 (total time: 28.380) Refine new water occ: r_work=0.1333 r_free=0.1581 adp: r_work=0.1276 r_free=0.1579 occ: r_work=0.1285 r_free=0.1554 adp: r_work=0.1250 r_free=0.1556 occ: r_work=0.1254 r_free=0.1553 adp: r_work=0.1241 r_free=0.1550 ADP+occupancy (water only), MIN, final r_work=0.1241 r_free=0.1550 r_work=0.1241 r_free=0.1550 | n_water=375 | time (s): 18.030 (total time: 46.410) Filter (q & B) r_work=0.1245 r_free=0.1562 | n_water=363 | time (s): 1.460 (total time: 47.870) Filter (dist only) r_work=0.1245 r_free=0.1564 | n_water=362 | time (s): 28.470 (total time: 76.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.391607 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.002664 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 0.1219 0.1582 0.0363 0.008 0.9 2.2 0.5 0.0 0 11.696 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 15.82 3.63 4.155 21.045 1.003 0.018 12.02 16.13 4.12 4.301 21.340 1.003 0.018 Individual atomic B min max mean iso aniso Overall: 6.72 107.39 21.42 4.43 1889 0 Protein: 6.72 107.39 17.75 4.40 1519 0 Water: 8.69 68.34 36.44 N/A 362 0 Other: 25.63 49.56 38.22 N/A 8 0 Chain A: 6.72 107.39 19.57 N/A 1742 0 Chain S: 17.63 64.51 43.26 N/A 147 0 Histogram: Values Number of atoms 6.72 - 16.79 1020 16.79 - 26.86 378 26.86 - 36.92 221 36.92 - 46.99 158 46.99 - 57.06 71 57.06 - 67.12 29 67.12 - 77.19 5 77.19 - 87.26 4 87.26 - 97.33 1 97.33 - 107.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1613 r_work=0.1204 r_free=0.1616 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1616 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 = 0.1201 r_free = 0.1622 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1201 r_free= 0.1622 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017122 | | target function (ls_wunit_k1) not normalized (work): 277.981574 | | target function (ls_wunit_k1) not normalized (free): 25.352544 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1201 0.1622 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1758 0.1749 0.1960 n_refl.: 17042 remove outliers: r(all,work,free)=0.1758 0.1749 0.1960 n_refl.: 17042 overall B=-0.47 to atoms: r(all,work,free)=0.1728 0.1719 0.1939 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1196 0.1614 n_refl.: 17042 remove outliers: r(all,work,free)=0.1216 0.1196 0.1614 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 0.3308 304.071 286.611 0.609 1.005 0.350 11.894-9.307 99.02 97 4 0.1563 489.050 485.177 0.921 1.006 0.340 9.237-7.194 100.00 213 7 0.1694 399.994 400.576 0.975 1.005 0.300 7.162-5.571 100.00 427 22 0.1570 300.196 296.458 0.938 1.005 0.291 5.546-4.326 100.00 867 58 0.0880 412.120 409.550 0.961 1.004 0.211 4.315-3.360 100.00 1859 96 0.0826 391.930 391.201 1.015 1.003 0.202 3.356-2.611 100.00 3867 181 0.1200 257.476 256.548 1.010 1.000 0.122 2.608-2.000 99.99 8818 434 0.1340 167.830 166.719 1.012 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1789 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1614 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=0.1197 r_free=0.1614 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1614 | n_water=362 | time (s): 0.630 (total time: 0.630) Filter (dist) r_work=0.1197 r_free=0.1613 | n_water=361 | time (s): 30.420 (total time: 31.050) Filter (q & B) r_work=0.1197 r_free=0.1613 | n_water=361 | time (s): 1.030 (total time: 32.080) Compute maps r_work=0.1197 r_free=0.1613 | n_water=361 | time (s): 0.570 (total time: 32.650) Filter (map) r_work=0.1261 r_free=0.1633 | n_water=262 | time (s): 1.610 (total time: 34.260) Find peaks r_work=0.1261 r_free=0.1633 | n_water=262 | time (s): 0.520 (total time: 34.780) Add new water r_work=0.1452 r_free=0.1765 | n_water=412 | time (s): 1.560 (total time: 36.340) Refine new water occ: r_work=0.1251 r_free=0.1548 adp: r_work=0.1241 r_free=0.1562 occ: r_work=0.1225 r_free=0.1532 adp: r_work=0.1211 r_free=0.1540 occ: r_work=0.1205 r_free=0.1527 adp: r_work=0.1194 r_free=0.1529 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1529 r_work=0.1194 r_free=0.1529 | n_water=412 | time (s): 36.130 (total time: 72.470) Filter (q & B) r_work=0.1198 r_free=0.1538 | n_water=401 | time (s): 2.190 (total time: 74.660) Filter (dist only) r_work=0.1198 r_free=0.1538 | n_water=401 | time (s): 30.230 (total time: 104.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.767654 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.136286 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 0.1180 0.1550 0.0370 0.009 0.9 3.5 0.5 0.0 0 0.884 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 15.50 3.70 4.432 21.518 0.136 5.002 11.60 15.61 4.00 4.931 21.408 0.136 4.977 Individual atomic B min max mean iso aniso Overall: 6.17 105.42 20.81 4.62 1928 0 Protein: 6.17 105.42 16.90 4.60 1519 0 Water: 8.49 64.25 35.33 N/A 401 0 Other: 26.83 47.92 35.91 N/A 8 0 Chain A: 6.17 105.42 18.69 N/A 1738 0 Chain S: 17.33 64.25 40.24 N/A 190 0 Histogram: Values Number of atoms 6.17 - 16.10 1065 16.10 - 26.02 351 26.02 - 35.95 221 35.95 - 45.87 181 45.87 - 55.79 69 55.79 - 65.72 28 65.72 - 75.64 5 75.64 - 85.57 4 85.57 - 95.49 2 95.49 - 105.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1561 r_work=0.1160 r_free=0.1561 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1561 target_work(ml) = 4.977 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1155 r_free = 0.1570 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1155 r_free= 0.1570 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.974369 | | target function (ml) not normalized (work): 80758.872835 | | target function (ml) not normalized (free): 4192.900331 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1175 0.1155 0.1570 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1673 0.1665 0.1862 n_refl.: 17042 remove outliers: r(all,work,free)=0.1673 0.1665 0.1862 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1647 0.1639 0.1849 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1172 0.1152 0.1568 n_refl.: 17042 remove outliers: r(all,work,free)=0.1171 0.1151 0.1568 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 0.3500 300.572 281.617 0.574 1.007 0.340 11.894-9.307 99.02 97 4 0.1762 489.050 482.405 0.915 1.008 0.324 9.237-7.194 100.00 213 7 0.1828 399.994 400.354 0.982 1.007 0.268 7.162-5.571 100.00 427 22 0.1604 300.196 295.550 0.937 1.007 0.257 5.546-4.326 100.00 867 58 0.0954 412.120 408.236 0.966 1.006 0.216 4.315-3.360 100.00 1859 96 0.0886 391.930 389.612 1.012 1.004 0.211 3.356-2.611 100.00 3867 181 0.1295 257.476 255.043 1.010 1.001 0.152 2.608-2.000 99.99 8818 434 0.1093 167.830 166.454 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1718 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1151 r_free=0.1568 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=0.1151 r_free=0.1563 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1151 r_free=0.1563 | n_water=401 | time (s): 0.940 (total time: 0.940) Filter (dist) r_work=0.1154 r_free=0.1567 | n_water=398 | time (s): 30.970 (total time: 31.910) Filter (q & B) r_work=0.1154 r_free=0.1567 | n_water=398 | time (s): 1.270 (total time: 33.180) Compute maps r_work=0.1154 r_free=0.1567 | n_water=398 | time (s): 0.800 (total time: 33.980) Filter (map) r_work=0.1207 r_free=0.1575 | n_water=310 | time (s): 2.120 (total time: 36.100) Find peaks r_work=0.1207 r_free=0.1575 | n_water=310 | time (s): 0.650 (total time: 36.750) Add new water r_work=0.1353 r_free=0.1689 | n_water=455 | time (s): 1.870 (total time: 38.620) Refine new water occ: r_work=0.1183 r_free=0.1524 adp: r_work=0.1173 r_free=0.1531 occ: r_work=0.1162 r_free=0.1511 adp: r_work=0.1150 r_free=0.1514 occ: r_work=0.1146 r_free=0.1507 adp: r_work=0.1137 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1137 r_free=0.1507 r_work=0.1137 r_free=0.1507 | n_water=455 | time (s): 32.930 (total time: 71.550) Filter (q & B) r_work=0.1140 r_free=0.1508 | n_water=447 | time (s): 1.500 (total time: 73.050) Filter (dist only) r_work=0.1140 r_free=0.1507 | n_water=446 | time (s): 36.470 (total time: 109.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.914796 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.167084 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 0.1123 0.1537 0.0415 0.010 1.0 4.5 0.5 0.0 0 0.957 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 15.37 4.15 4.451 21.004 0.167 4.957 11.12 15.34 4.22 4.649 21.014 0.167 4.950 Individual atomic B min max mean iso aniso Overall: 5.68 103.63 20.90 4.84 1973 0 Protein: 5.68 103.63 16.43 4.83 1519 0 Water: 8.06 62.92 35.87 N/A 446 0 Other: 27.09 47.48 35.17 N/A 8 0 Chain A: 5.68 103.63 18.13 N/A 1735 0 Chain S: 17.32 62.92 41.14 N/A 238 0 Histogram: Values Number of atoms 5.68 - 15.48 1046 15.48 - 25.27 364 25.27 - 35.07 219 35.07 - 44.86 196 44.86 - 54.65 105 54.65 - 64.45 30 64.45 - 74.24 5 74.24 - 84.04 4 84.04 - 93.83 2 93.83 - 103.63 2 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1534 r_work=0.1112 r_free=0.1535 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1535 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1105 r_free = 0.1544 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1105 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.946798 | | target function (ml) not normalized (work): 80306.322470 | | target function (ml) not normalized (free): 4178.661392 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1105 0.1544 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1592 0.1577 0.1889 n_refl.: 17041 remove outliers: r(all,work,free)=0.1592 0.1577 0.1889 n_refl.: 17041 overall B=-0.26 to atoms: r(all,work,free)=0.1576 0.1561 0.1879 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1125 0.1103 0.1543 n_refl.: 17041 remove outliers: r(all,work,free)=0.1125 0.1103 0.1543 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 0.3683 300.572 276.081 0.547 1.001 0.330 11.894-9.307 99.02 97 4 0.1757 489.050 481.589 0.919 1.002 0.330 9.237-7.194 100.00 213 7 0.1744 399.994 401.781 0.987 1.002 0.250 7.162-5.571 100.00 427 22 0.1575 300.196 294.298 0.939 1.002 0.250 5.546-4.326 100.00 867 58 0.0910 412.120 408.609 0.969 1.002 0.221 4.315-3.360 100.00 1859 96 0.0835 391.930 389.932 1.007 1.002 0.191 3.356-2.611 100.00 3867 181 0.1238 257.476 255.201 1.002 1.001 0.161 2.608-2.000 99.99 8818 434 0.1046 167.830 166.553 0.995 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9032 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1103 r_free=0.1543 After: r_work=0.1105 r_free=0.1543 ================================== NQH flips ================================== r_work=0.1105 r_free=0.1543 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1105 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1105 r_free=0.1543 | n_water=446 | time (s): 0.760 (total time: 0.760) Filter (dist) r_work=0.1110 r_free=0.1541 | n_water=444 | time (s): 37.790 (total time: 38.550) Filter (q & B) r_work=0.1110 r_free=0.1541 | n_water=443 | time (s): 1.580 (total time: 40.130) Compute maps r_work=0.1110 r_free=0.1541 | n_water=443 | time (s): 0.550 (total time: 40.680) Filter (map) r_work=0.1185 r_free=0.1562 | n_water=336 | time (s): 1.580 (total time: 42.260) Find peaks r_work=0.1185 r_free=0.1562 | n_water=336 | time (s): 0.460 (total time: 42.720) Add new water r_work=0.1297 r_free=0.1649 | n_water=467 | time (s): 1.780 (total time: 44.500) Refine new water occ: r_work=0.1143 r_free=0.1522 adp: r_work=0.1135 r_free=0.1521 occ: r_work=0.1124 r_free=0.1509 adp: r_work=0.1116 r_free=0.1507 occ: r_work=0.1111 r_free=0.1499 adp: r_work=0.1105 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1105 r_free=0.1499 r_work=0.1105 r_free=0.1499 | n_water=467 | time (s): 19.150 (total time: 63.650) Filter (q & B) r_work=0.1106 r_free=0.1504 | n_water=460 | time (s): 2.070 (total time: 65.720) Filter (dist only) r_work=0.1106 r_free=0.1504 | n_water=460 | time (s): 36.030 (total time: 101.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.886791 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.177874 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1130 0.1526 0.0395 0.010 1.1 5.4 0.5 0.0 0 0.943 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.26 3.95 4.533 20.757 0.178 4.948 11.19 15.17 3.98 4.675 20.798 0.178 4.940 Individual atomic B min max mean iso aniso Overall: 5.17 102.78 20.85 5.01 1987 0 Protein: 5.17 102.78 16.13 4.99 1519 0 Water: 7.87 62.84 36.20 N/A 460 0 Other: 25.40 46.34 34.26 N/A 8 0 Chain A: 5.17 102.78 17.80 N/A 1734 0 Chain S: 16.61 62.84 41.78 N/A 253 0 Histogram: Values Number of atoms 5.17 - 14.93 1031 14.93 - 24.69 369 24.69 - 34.45 227 34.45 - 44.21 191 44.21 - 53.97 123 53.97 - 63.73 31 63.73 - 73.49 7 73.49 - 83.25 4 83.25 - 93.01 1 93.01 - 102.78 3 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1517 r_work=0.1119 r_free=0.1516 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1119 r_free = 0.1516 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1114 r_free = 0.1512 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1114 r_free= 0.1512 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.935217 | | target function (ml) not normalized (work): 80118.315037 | | target function (ml) not normalized (free): 4163.342108 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1135 0.1414 5.4684 5.6704| | 2: 3.63 - 2.88 1.00 2711 122 0.1094 0.1456 5.2241 5.3402| | 3: 2.88 - 2.52 1.00 2681 148 0.1370 0.1682 5.1352 5.2046| | 4: 2.52 - 2.29 1.00 2661 139 0.0933 0.1483 4.6179 4.9193| | 5: 2.29 - 2.13 1.00 2678 122 0.0960 0.1522 4.5716 4.8791| | 6: 2.13 - 2.00 1.00 2692 117 0.1120 0.1730 4.5638 4.7942| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2811 159 0.94 9.14 1.00 0.96 6423.97| | 2: 3.63 - 2.88 2711 122 0.92 12.92 1.01 0.96 6423.97| | 3: 2.88 - 2.52 2681 148 0.87 19.00 0.99 0.96 6423.97| | 4: 2.52 - 2.29 2661 139 0.93 11.98 1.01 0.97 2063.20| | 5: 2.29 - 2.13 2678 122 0.92 13.91 1.00 0.97 2063.20| | 6: 2.13 - 2.00 2692 117 0.90 16.54 0.99 0.97 2063.20| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2063.20 max = 6423.97 mean = 4266.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.95 mean = 13.88| |phase err.(test): min = 0.00 max = 88.61 mean = 13.33| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1114 0.1512 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1587 0.1573 0.1873 n_refl.: 17041 remove outliers: r(all,work,free)=0.1587 0.1573 0.1873 n_refl.: 17041 overall B=-0.20 to atoms: r(all,work,free)=0.1576 0.1561 0.1865 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1114 0.1512 n_refl.: 17041 remove outliers: r(all,work,free)=0.1134 0.1114 0.1512 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 0.3581 300.572 281.433 0.556 1.004 0.340 11.894-9.307 99.02 97 4 0.1753 489.050 482.816 0.922 1.005 0.330 9.237-7.194 100.00 213 7 0.1750 399.994 400.567 0.981 1.005 0.251 7.162-5.571 100.00 427 22 0.1616 300.196 293.582 0.936 1.005 0.232 5.546-4.326 100.00 867 58 0.0921 412.120 408.521 0.962 1.004 0.209 4.315-3.360 100.00 1859 96 0.0890 391.930 389.579 1.001 1.003 0.181 3.356-2.611 100.00 3867 181 0.1248 257.476 255.068 0.998 1.000 0.072 2.608-2.000 99.99 8818 434 0.1037 167.830 166.464 0.988 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.6934 ================= 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 : 0.2794 0.1770 0.081 5.386 8.8 119.3 19.9 258 0.000 1_bss: 0.1614 0.1636 0.081 5.386 8.4 118.9 19.5 258 0.000 1_settarget: 0.1614 0.1636 0.081 5.386 8.4 118.9 19.5 258 0.000 1_nqh: 0.1616 0.1637 0.081 5.386 8.4 118.9 19.5 258 0.003 1_weight: 0.1616 0.1637 0.081 5.386 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1351 0.1621 0.009 0.984 8.4 118.9 19.5 258 0.139 1_adp: 0.1280 0.1642 0.009 0.984 6.2 113.9 19.9 258 0.139 1_regHadp: 0.1283 0.1648 0.009 0.984 6.2 113.9 19.9 258 0.139 1_occ: 0.1278 0.1642 0.009 0.984 6.2 113.9 19.9 258 0.139 2_bss: 0.1278 0.1636 0.009 0.984 5.8 113.5 19.6 258 0.139 2_settarget: 0.1278 0.1636 0.009 0.984 5.8 113.5 19.6 258 0.139 2_updatecdl: 0.1278 0.1636 0.009 1.006 5.8 113.5 19.6 258 0.139 2_nqh: 0.1280 0.1636 0.009 1.006 5.8 113.5 19.6 258 0.136 2_sol: 0.1245 0.1564 0.009 1.006 5.8 112.4 20.9 362 n/a 2_weight: 0.1245 0.1564 0.009 1.006 5.8 112.4 20.9 362 n/a 2_xyzrec: 0.1219 0.1582 0.008 0.926 5.8 112.4 20.9 362 n/a 2_adp: 0.1202 0.1613 0.008 0.926 6.7 107.4 21.4 362 n/a 2_regHadp: 0.1204 0.1616 0.008 0.926 6.7 107.4 21.4 362 n/a 2_occ: 0.1201 0.1622 0.008 0.926 6.7 107.4 21.4 362 n/a 3_bss: 0.1196 0.1614 0.008 0.926 6.3 106.9 20.9 362 n/a 3_settarget: 0.1196 0.1614 0.008 0.926 6.3 106.9 20.9 362 n/a 3_updatecdl: 0.1196 0.1614 0.008 0.923 6.3 106.9 20.9 362 n/a 3_nqh: 0.1197 0.1614 0.008 0.923 6.3 106.9 20.9 362 n/a 3_sol: 0.1198 0.1538 0.008 0.923 6.3 106.9 21.0 401 n/a 3_weight: 0.1198 0.1538 0.008 0.923 6.3 106.9 21.0 401 n/a 3_xyzrec: 0.1180 0.1550 0.009 0.943 6.3 106.9 21.0 401 n/a 3_adp: 0.1160 0.1561 0.009 0.943 6.2 105.4 20.8 401 n/a 3_regHadp: 0.1160 0.1561 0.009 0.943 6.2 105.4 20.8 401 n/a 3_occ: 0.1155 0.1570 0.009 0.943 6.2 105.4 20.8 401 n/a 4_bss: 0.1151 0.1568 0.009 0.943 5.8 105.0 20.4 401 n/a 4_settarget: 0.1151 0.1568 0.009 0.943 5.8 105.0 20.4 401 n/a 4_updatecdl: 0.1151 0.1568 0.009 0.945 5.8 105.0 20.4 401 n/a 4_nqh: 0.1151 0.1563 0.009 0.945 5.8 105.0 20.4 401 n/a 4_sol: 0.1140 0.1507 0.009 0.945 5.8 105.0 20.9 446 n/a 4_weight: 0.1140 0.1507 0.009 0.945 5.8 105.0 20.9 446 n/a 4_xyzrec: 0.1123 0.1537 0.010 0.992 5.8 105.0 20.9 446 n/a 4_adp: 0.1112 0.1534 0.010 0.992 5.7 103.6 20.9 446 n/a 4_regHadp: 0.1112 0.1535 0.010 0.992 5.7 103.6 20.9 446 n/a 4_occ: 0.1105 0.1544 0.010 0.992 5.7 103.6 20.9 446 n/a 5_bss: 0.1103 0.1543 0.010 0.992 5.4 103.4 20.6 446 n/a 5_settarget: 0.1103 0.1543 0.010 0.992 5.4 103.4 20.6 446 n/a 5_updatecdl: 0.1103 0.1543 0.010 0.992 5.4 103.4 20.6 446 n/a 5_setrh: 0.1105 0.1543 0.010 0.992 5.4 103.4 20.6 446 n/a 5_nqh: 0.1105 0.1543 0.010 0.992 5.4 103.4 20.6 446 n/a 5_sol: 0.1106 0.1504 0.010 0.992 5.4 103.4 20.8 460 n/a 5_weight: 0.1106 0.1504 0.010 0.992 5.4 103.4 20.8 460 n/a 5_xyzrec: 0.1130 0.1526 0.010 1.075 5.4 103.4 20.8 460 n/a 5_adp: 0.1119 0.1517 0.010 1.075 5.2 102.8 20.8 460 n/a 5_regHadp: 0.1119 0.1516 0.010 1.075 5.2 102.8 20.8 460 n/a 5_occ: 0.1114 0.1512 0.010 1.075 5.2 102.8 20.8 460 n/a end: 0.1114 0.1512 0.010 1.075 5.0 102.6 20.6 460 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4912670_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_4912670_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9400 Refinement macro-cycles (run) : 929.6800 Write final files (write_after_run_outputs) : 18.8100 Total : 952.4300 Total CPU time: 16.26 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:16 PST -0800 (1735494076.83 s) Start R-work = 0.1614, R-free = 0.1636 Final R-work = 0.1114, R-free = 0.1512 =============================================================================== Job complete usr+sys time: 997.73 seconds wall clock time: 17 minutes 0.44 seconds (1020.44 seconds total)