Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7783516.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_7783516.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7783516.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" 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" } 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 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 2.06, per 1000 atoms: 0.61 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: 0.45 Conformation dependent library (CDL) restraints added in 190.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.58 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: 457 0.90 - 1.16: 1171 1.16 - 1.42: 639 1.42 - 1.68: 854 1.68 - 1.94: 32 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.539 1.409 0.130 5.40e-03 3.43e+04 5.79e+02 bond pdb=" C AGLU A 90 " pdb=" O AGLU A 90 " ideal model delta sigma weight residual 1.236 1.032 0.205 1.15e-02 7.56e+03 3.17e+02 bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.520 1.729 -0.209 1.23e-02 6.61e+03 2.88e+02 bond pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 1.331 1.545 -0.214 1.30e-02 5.92e+03 2.71e+02 bond pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 1.244 1.083 0.161 1.00e-02 1.00e+04 2.59e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 3022 4.36 - 8.71: 1846 8.71 - 13.07: 726 13.07 - 17.42: 159 17.42 - 21.78: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA HIS A 126 " pdb=" C HIS A 126 " pdb=" O HIS A 126 " ideal model delta sigma weight residual 120.70 138.95 -18.25 1.09e+00 8.42e-01 2.80e+02 angle pdb=" O GLY A 30 " pdb=" C GLY A 30 " pdb=" N ILE A 31 " ideal model delta sigma weight residual 122.30 140.94 -18.64 1.19e+00 7.06e-01 2.45e+02 angle pdb=" CA ALYS A 41 " pdb=" C ALYS A 41 " pdb=" O ALYS A 41 " ideal model delta sigma weight residual 119.49 138.25 -18.76 1.21e+00 6.83e-01 2.40e+02 angle pdb=" O ALYS A 41 " pdb=" C ALYS A 41 " pdb=" N ASP A 42 " ideal model delta sigma weight residual 122.39 102.59 19.80 1.30e+00 5.92e-01 2.32e+02 angle pdb=" O MET A 133 " pdb=" C MET A 133 " pdb=" N MET A 134 " ideal model delta sigma weight residual 122.15 105.06 17.09 1.14e+00 7.69e-01 2.25e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 1325 18.00 - 35.99: 107 35.99 - 53.98: 38 53.98 - 71.97: 8 71.97 - 89.96: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N PRO A 43 " pdb=" C PRO A 43 " pdb=" CA PRO A 43 " pdb=" CB PRO A 43 " ideal model delta harmonic sigma weight residual 115.10 136.12 -21.02 0 2.50e+00 1.60e-01 7.07e+01 dihedral pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CA GLU A 59 " pdb=" CB GLU A 59 " ideal model delta harmonic sigma weight residual 122.80 141.87 -19.07 0 2.50e+00 1.60e-01 5.82e+01 dihedral pdb=" C LEU A 151 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual -122.60 -140.83 18.23 0 2.50e+00 1.60e-01 5.32e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 101 0.208 - 0.416: 70 0.416 - 0.623: 48 0.623 - 0.831: 14 0.831 - 1.039: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 69 " pdb=" CA VAL A 69 " pdb=" CG1 VAL A 69 " pdb=" CG2 VAL A 69 " both_signs ideal model delta sigma weight residual False -2.63 -1.59 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.64 1.00 2.00e-01 2.50e+01 2.52e+01 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 1.51 1.00 2.00e-01 2.50e+01 2.48e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.093 9.50e-02 1.11e+02 7.14e-02 9.42e+01 pdb=" NE ARG A 145 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.159 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.051 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " -0.024 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " -0.068 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.079 2.00e-02 2.50e+03 5.47e-02 8.99e+01 pdb=" CG PHE A 162 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.031 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.125 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.085 2.00e-02 2.50e+03 6.08e-02 8.32e+01 pdb=" CG HIS A 126 " -0.091 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.018 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.072 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.083 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.055 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.043 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.39: 1582 2.39 - 2.94: 8410 2.94 - 3.49: 10392 3.49 - 4.05: 15052 4.05 - 4.60: 21167 Nonbonded interactions: 56603 Sorted by model distance: nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.832 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.862 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.862 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.865 2.450 nonbonded pdb=" O ALA A 79 " pdb=" H SER A 83 " model vdw 1.878 2.450 ... (remaining 56598 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_7783516_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= 0.2789 r_free= 0.1830 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.409194 | | target function (ml) not normalized (work): 71618.540188 | | target function (ml) not normalized (free): 3268.657218 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2077 7.562 5.0265| | 2: 3.63 - 2.88 1.00 2711 122 0.2636 0.1728 4.3206 4.3204| | 3: 2.88 - 2.52 1.00 2682 148 0.2584 0.1796 4.1831 4.1889| | 4: 2.52 - 2.29 1.00 2661 139 0.2540 0.1642 3.4854 3.6075| | 5: 2.29 - 2.13 1.00 2678 122 0.2682 0.1476 3.4157 3.4579| | 6: 2.13 - 2.00 1.00 2692 117 0.2744 0.1907 3.3236 3.411| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.52 0.77 0.23 1289.71| | 2: 3.63 - 2.88 2711 122 0.83 23.82 1.31 0.23 1289.71| | 3: 2.88 - 2.52 2682 148 0.73 32.66 1.29 0.23 1289.71| | 4: 2.52 - 2.29 2661 139 0.93 11.74 1.30 0.26 139.40| | 5: 2.29 - 2.13 2678 122 0.92 13.76 1.32 0.26 139.40| | 6: 2.13 - 2.00 2692 117 0.90 16.64 1.33 0.26 139.40| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 139.40 max = 1289.71 mean = 720.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.86 mean = 19.36| |phase err.(test): min = 0.00 max = 89.99 mean = 19.57| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.217 1557 Z= 5.585 Angle : 5.378 19.804 2118 Z= 3.831 Chirality : 0.387 1.039 243 Planarity : 0.031 0.081 284 Dihedral : 14.039 89.962 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 1.62 % Allowed : 2.16 % Favored : 96.22 % Rotamer: Outliers : 0.62 % Allowed : 4.35 % Favored : 95.03 % Cbeta Deviations : 31.35 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.48), residues: 224 helix: -3.07 (0.36), residues: 109 sheet: 0.22 (0.97), residues: 28 loop : -1.10 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.021 ARG A 27 TYR 0.104 0.032 TYR A 139 PHE 0.055 0.027 PHE A 119 HIS 0.037 0.021 HIS A 115 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= 0.2789 r_free= 0.1830 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.409194 | | target function (ml) not normalized (work): 71618.540188 | | target function (ml) not normalized (free): 3268.657218 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3049 percent. r_work = 0.2920 r_free = 0.1964 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2920 0.1964 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2920 0.1964 n_refl.: 17050 remove outliers: r(all,work,free)=0.2158 0.2170 0.1964 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2131 0.2142 0.1943 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1619 0.1619 0.1636 n_refl.: 17045 remove outliers: r(all,work,free)=0.1618 0.1618 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 0.4059 395.279 363.408 0.654 1.010 0.397 11.894-9.307 99.02 97 4 0.1869 634.435 616.660 0.932 1.011 0.380 9.237-7.194 100.00 213 7 0.2192 518.904 510.943 0.957 1.011 0.355 7.162-5.571 100.00 427 22 0.2326 389.438 377.057 0.924 1.010 0.289 5.546-4.326 100.00 867 58 0.1395 534.636 528.608 0.958 1.009 0.251 4.315-3.360 100.00 1859 96 0.1288 508.444 505.083 1.016 1.005 0.181 3.356-2.611 100.00 3867 181 0.1661 334.019 328.843 1.015 1.000 0.039 2.608-2.000 99.99 8818 434 0.1655 217.723 213.668 1.028 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4575 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1618 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=0.1618 r_free=0.1636 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.628035 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.906538 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 0.1350 0.1626 0.0276 0.009 1.0 1.0 0.5 0.0 0 11.814 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.26 2.76 3.013 18.451 0.907 0.023 12.78 16.46 3.69 3.633 18.714 0.907 0.020 Individual atomic B min max mean iso aniso Overall: 6.13 113.89 19.98 4.11 1785 0 Protein: 6.13 112.89 17.20 4.11 1519 0 Water: 8.72 113.89 36.10 N/A 258 0 Other: 21.64 37.33 26.59 N/A 8 0 Chain A: 6.13 113.89 19.98 N/A 1785 0 Histogram: Values Number of atoms 6.13 - 16.91 1079 16.91 - 27.69 347 27.69 - 38.46 187 38.46 - 49.24 94 49.24 - 60.01 51 60.01 - 70.79 12 70.79 - 81.56 7 81.56 - 92.34 4 92.34 - 103.12 1 103.12 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1646 r_work=0.1281 r_free=0.1655 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1655 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 = 0.1649 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= 0.1275 r_free= 0.1649 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020006 | | target function (ls_wunit_k1) not normalized (work): 324.843982 | | target function (ls_wunit_k1) not normalized (free): 27.092722 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1649 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1915 0.1914 0.1987 n_refl.: 17044 remove outliers: r(all,work,free)=0.1915 0.1914 0.1987 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1887 0.1885 0.1971 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1294 0.1276 0.1645 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1275 0.1645 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 0.3514 303.322 279.792 0.626 1.011 0.370 11.894-9.307 99.02 97 4 0.1675 487.845 477.759 0.917 1.011 0.370 9.237-7.194 100.00 213 7 0.1811 399.008 396.576 0.959 1.010 0.351 7.162-5.571 100.00 427 22 0.1829 299.456 294.500 0.930 1.009 0.301 5.546-4.326 100.00 867 58 0.1044 411.105 408.835 0.958 1.008 0.231 4.315-3.360 100.00 1859 96 0.0931 390.965 390.627 1.016 1.005 0.181 3.356-2.611 100.00 3867 181 0.1295 256.842 255.531 1.015 1.000 0.101 2.608-2.000 99.99 8818 434 0.1353 167.417 165.942 1.023 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3813 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1645 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=0.1276 r_free=0.1644 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1644 | n_water=258 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1285 r_free=0.1637 | n_water=252 | time (s): 20.270 (total time: 21.070) Filter (q & B) r_work=0.1286 r_free=0.1637 | n_water=250 | time (s): 1.950 (total time: 23.020) Compute maps r_work=0.1286 r_free=0.1637 | n_water=250 | time (s): 0.860 (total time: 23.880) Filter (map) r_work=0.1321 r_free=0.1634 | n_water=213 | time (s): 2.020 (total time: 25.900) Find peaks r_work=0.1321 r_free=0.1634 | n_water=213 | time (s): 0.670 (total time: 26.570) Add new water r_work=0.1529 r_free=0.1876 | n_water=365 | time (s): 2.170 (total time: 28.740) Refine new water occ: r_work=0.1334 r_free=0.1589 adp: r_work=0.1276 r_free=0.1587 occ: r_work=0.1284 r_free=0.1559 adp: r_work=0.1250 r_free=0.1563 occ: r_work=0.1253 r_free=0.1555 adp: r_work=0.1242 r_free=0.1553 ADP+occupancy (water only), MIN, final r_work=0.1242 r_free=0.1553 r_work=0.1242 r_free=0.1553 | n_water=365 | time (s): 13.120 (total time: 41.860) Filter (q & B) r_work=0.1245 r_free=0.1562 | n_water=356 | time (s): 1.720 (total time: 43.580) Filter (dist only) r_work=0.1245 r_free=0.1564 | n_water=355 | time (s): 28.100 (total time: 71.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.670780 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.997678 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 0.1217 0.1607 0.0390 0.008 0.9 2.6 0.5 0.0 0 12.335 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.17 16.07 3.90 4.186 20.994 0.998 0.018 11.99 16.29 4.30 4.215 21.274 0.998 0.018 Individual atomic B min max mean iso aniso Overall: 6.53 107.50 21.26 4.26 1882 0 Protein: 6.53 107.50 17.73 4.25 1519 0 Water: 8.85 68.49 36.02 N/A 355 0 Other: 24.82 45.35 35.21 N/A 8 0 Chain A: 6.53 107.50 19.51 N/A 1740 0 Chain S: 20.13 68.49 42.64 N/A 142 0 Histogram: Values Number of atoms 6.53 - 16.63 1019 16.63 - 26.72 381 26.72 - 36.82 225 36.82 - 46.92 157 46.92 - 57.02 57 57.02 - 67.11 32 67.11 - 77.21 4 77.21 - 87.31 3 87.31 - 97.41 2 97.41 - 107.50 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1629 r_work=0.1201 r_free=0.1630 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1630 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1626 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 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= 0.1200 r_free= 0.1626 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017241 | | target function (ls_wunit_k1) not normalized (work): 279.903756 | | target function (ls_wunit_k1) not normalized (free): 25.063008 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1221 0.1200 0.1626 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1776 0.1769 0.1950 n_refl.: 17042 remove outliers: r(all,work,free)=0.1776 0.1769 0.1950 n_refl.: 17042 overall B=-0.37 to atoms: r(all,work,free)=0.1752 0.1745 0.1933 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1194 0.1611 n_refl.: 17042 remove outliers: r(all,work,free)=0.1213 0.1193 0.1611 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 0.3206 300.161 287.597 0.606 1.005 0.350 11.894-9.307 99.02 97 4 0.1575 487.845 484.010 0.912 1.006 0.337 9.237-7.194 100.00 213 7 0.1677 399.008 400.402 0.973 1.006 0.300 7.162-5.571 100.00 427 22 0.1590 299.456 295.715 0.934 1.005 0.281 5.546-4.326 100.00 867 58 0.0902 411.105 408.266 0.959 1.005 0.231 4.315-3.360 100.00 1859 96 0.0821 390.965 390.035 1.014 1.003 0.211 3.356-2.611 100.00 3867 181 0.1201 256.842 256.001 1.011 1.001 0.073 2.608-2.000 99.99 8818 434 0.1331 167.417 166.377 1.015 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3279 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1611 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1611 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1611 | n_water=355 | time (s): 0.750 (total time: 0.750) Filter (dist) r_work=0.1194 r_free=0.1612 | n_water=354 | time (s): 27.240 (total time: 27.990) Filter (q & B) r_work=0.1194 r_free=0.1611 | n_water=353 | time (s): 2.080 (total time: 30.070) Compute maps r_work=0.1194 r_free=0.1611 | n_water=353 | time (s): 0.860 (total time: 30.930) Filter (map) r_work=0.1259 r_free=0.1622 | n_water=264 | time (s): 1.930 (total time: 32.860) Find peaks r_work=0.1259 r_free=0.1622 | n_water=264 | time (s): 0.510 (total time: 33.370) Add new water r_work=0.1441 r_free=0.1769 | n_water=409 | time (s): 1.440 (total time: 34.810) Refine new water occ: r_work=0.1247 r_free=0.1568 adp: r_work=0.1237 r_free=0.1568 occ: r_work=0.1221 r_free=0.1550 adp: r_work=0.1208 r_free=0.1547 occ: r_work=0.1202 r_free=0.1548 adp: r_work=0.1191 r_free=0.1542 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1542 r_work=0.1191 r_free=0.1542 | n_water=409 | time (s): 33.610 (total time: 68.420) Filter (q & B) r_work=0.1193 r_free=0.1547 | n_water=401 | time (s): 2.040 (total time: 70.460) Filter (dist only) r_work=0.1192 r_free=0.1551 | n_water=400 | time (s): 33.980 (total time: 104.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.865109 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.159997 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 0.1179 0.1547 0.0367 0.009 1.0 2.9 0.5 0.0 0 0.933 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.79 15.47 3.67 4.335 21.565 0.160 4.991 11.57 15.53 3.96 4.890 21.493 0.160 4.970 Individual atomic B min max mean iso aniso Overall: 6.34 104.28 20.96 4.73 1927 0 Protein: 6.34 104.28 17.02 4.73 1519 0 Water: 8.70 62.55 35.67 N/A 400 0 Other: 26.37 45.66 34.04 N/A 8 0 Chain A: 6.34 104.28 18.86 N/A 1739 0 Chain S: 13.94 62.55 40.44 N/A 188 0 Histogram: Values Number of atoms 6.34 - 16.14 1065 16.14 - 25.93 340 25.93 - 35.72 218 35.72 - 45.52 178 45.52 - 55.31 78 55.31 - 65.11 35 65.11 - 74.90 4 74.90 - 84.69 4 84.69 - 94.49 3 94.49 - 104.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1553 r_work=0.1157 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1554 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1540 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.16 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= 0.1147 r_free= 0.1540 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.963653 | | target function (ml) not normalized (work): 80579.948563 | | target function (ml) not normalized (free): 4179.485349 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1166 0.1147 0.1540 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1686 0.1678 0.1861 n_refl.: 17041 remove outliers: r(all,work,free)=0.1686 0.1678 0.1861 n_refl.: 17041 overall B=-0.47 to atoms: r(all,work,free)=0.1654 0.1646 0.1847 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1145 0.1540 n_refl.: 17041 remove outliers: r(all,work,free)=0.1164 0.1145 0.1540 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 0.3546 300.161 279.925 0.569 1.005 0.340 11.894-9.307 99.02 97 4 0.1661 487.845 481.910 0.914 1.006 0.340 9.237-7.194 100.00 213 7 0.1747 399.008 398.626 0.983 1.007 0.275 7.162-5.571 100.00 427 22 0.1576 299.456 294.249 0.941 1.006 0.251 5.546-4.326 100.00 867 58 0.0950 411.105 407.793 0.963 1.005 0.221 4.315-3.360 100.00 1859 96 0.0883 390.965 388.405 1.012 1.004 0.222 3.356-2.611 100.00 3867 181 0.1281 256.842 254.719 1.010 1.001 0.142 2.608-2.000 99.99 8818 434 0.1099 167.417 166.000 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=-1.1700 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1145 r_free=0.1540 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1145 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1145 r_free=0.1540 | n_water=400 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1145 r_free=0.1540 | n_water=400 | time (s): 30.280 (total time: 30.920) Filter (q & B) r_work=0.1146 r_free=0.1540 | n_water=399 | time (s): 1.590 (total time: 32.510) Compute maps r_work=0.1146 r_free=0.1540 | n_water=399 | time (s): 0.560 (total time: 33.070) Filter (map) r_work=0.1207 r_free=0.1561 | n_water=307 | time (s): 1.830 (total time: 34.900) Find peaks r_work=0.1207 r_free=0.1561 | n_water=307 | time (s): 0.530 (total time: 35.430) Add new water r_work=0.1359 r_free=0.1670 | n_water=443 | time (s): 1.470 (total time: 36.900) Refine new water occ: r_work=0.1189 r_free=0.1511 adp: r_work=0.1180 r_free=0.1506 occ: r_work=0.1164 r_free=0.1502 adp: r_work=0.1154 r_free=0.1492 occ: r_work=0.1147 r_free=0.1497 adp: r_work=0.1139 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1491 r_work=0.1139 r_free=0.1491 | n_water=443 | time (s): 26.590 (total time: 63.490) Filter (q & B) r_work=0.1142 r_free=0.1501 | n_water=435 | time (s): 2.420 (total time: 65.910) Filter (dist only) r_work=0.1145 r_free=0.1505 | n_water=434 | time (s): 36.960 (total time: 102.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.952154 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.166273 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 0.1126 0.1552 0.0426 0.009 1.0 3.5 0.5 0.0 0 0.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.52 4.26 4.524 20.984 0.166 4.957 11.14 15.56 4.42 4.664 21.022 0.166 4.951 Individual atomic B min max mean iso aniso Overall: 5.99 102.49 20.86 4.84 1961 0 Protein: 5.99 102.49 16.55 4.83 1519 0 Water: 8.84 64.63 35.82 N/A 434 0 Other: 20.90 41.38 28.86 N/A 8 0 Chain A: 5.99 102.49 18.27 N/A 1736 0 Chain S: 14.67 64.63 40.85 N/A 225 0 Histogram: Values Number of atoms 5.99 - 15.64 1052 15.64 - 25.29 363 25.29 - 34.94 200 34.94 - 44.59 194 44.59 - 54.24 105 54.24 - 63.89 31 63.89 - 73.54 8 73.54 - 83.19 3 83.19 - 92.84 3 92.84 - 102.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1114 r_free=0.1556 r_work=0.1114 r_free=0.1556 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1114 r_free = 0.1556 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1107 r_free = 0.1561 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.17 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= 0.1107 r_free= 0.1561 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.948624 | | target function (ml) not normalized (work): 80335.961248 | | target function (ml) not normalized (free): 4179.937803 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1107 0.1561 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1613 0.1604 0.1849 n_refl.: 17041 remove outliers: r(all,work,free)=0.1613 0.1604 0.1849 n_refl.: 17041 overall B=-0.27 to atoms: r(all,work,free)=0.1596 0.1586 0.1842 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1127 0.1106 0.1554 n_refl.: 17041 remove outliers: r(all,work,free)=0.1126 0.1105 0.1554 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 0.3561 296.597 280.755 0.569 1.002 0.340 11.894-9.307 99.02 97 4 0.1730 487.845 480.636 0.916 1.004 0.330 9.237-7.194 100.00 213 7 0.1664 399.008 399.172 0.987 1.004 0.245 7.162-5.571 100.00 427 22 0.1537 299.456 294.293 0.942 1.004 0.240 5.546-4.326 100.00 867 58 0.0918 411.105 407.569 0.961 1.004 0.208 4.315-3.360 100.00 1859 96 0.0857 390.965 388.611 1.006 1.003 0.194 3.356-2.611 100.00 3867 181 0.1231 256.842 254.795 1.003 1.001 0.151 2.608-2.000 99.99 8818 434 0.1055 167.417 166.242 0.998 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.9345 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1105 r_free=0.1554 After: r_work=0.1107 r_free=0.1553 ================================== NQH flips ================================== r_work=0.1107 r_free=0.1553 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1107 r_free=0.1553 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1107 r_free=0.1553 | n_water=434 | time (s): 0.760 (total time: 0.760) Filter (dist) r_work=0.1107 r_free=0.1553 | n_water=434 | time (s): 32.970 (total time: 33.730) Filter (q & B) r_work=0.1107 r_free=0.1554 | n_water=433 | time (s): 1.940 (total time: 35.670) Compute maps r_work=0.1107 r_free=0.1554 | n_water=433 | time (s): 0.580 (total time: 36.250) Filter (map) r_work=0.1180 r_free=0.1578 | n_water=327 | time (s): 1.930 (total time: 38.180) Find peaks r_work=0.1180 r_free=0.1578 | n_water=327 | time (s): 0.440 (total time: 38.620) Add new water r_work=0.1313 r_free=0.1679 | n_water=467 | time (s): 1.450 (total time: 40.070) Refine new water occ: r_work=0.1153 r_free=0.1522 adp: r_work=0.1145 r_free=0.1520 occ: r_work=0.1128 r_free=0.1507 adp: r_work=0.1119 r_free=0.1505 occ: r_work=0.1111 r_free=0.1503 adp: r_work=0.1104 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1104 r_free=0.1500 r_work=0.1104 r_free=0.1500 | n_water=467 | time (s): 34.130 (total time: 74.200) Filter (q & B) r_work=0.1106 r_free=0.1515 | n_water=458 | time (s): 1.680 (total time: 75.880) Filter (dist only) r_work=0.1106 r_free=0.1515 | n_water=457 | time (s): 37.190 (total time: 113.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.875660 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.152106 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 0.1143 0.1533 0.0389 0.009 1.0 7.0 0.5 0.0 0 0.938 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.43 15.33 3.89 4.541 20.814 0.152 4.963 11.31 15.07 3.76 4.644 20.863 0.152 4.949 Individual atomic B min max mean iso aniso Overall: 5.44 101.34 20.89 4.91 1984 0 Protein: 5.44 101.34 16.23 4.91 1519 0 Water: 8.65 66.17 36.30 N/A 457 0 Other: 19.66 37.20 25.76 N/A 8 0 Chain A: 5.44 101.34 17.92 N/A 1736 0 Chain S: 18.21 66.17 41.69 N/A 248 0 Histogram: Values Number of atoms 5.44 - 15.03 1026 15.03 - 24.62 388 24.62 - 34.21 194 34.21 - 43.80 195 43.80 - 53.39 128 53.39 - 62.98 36 62.98 - 72.57 8 72.57 - 82.16 2 82.16 - 91.75 3 91.75 - 101.34 4 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1507 r_work=0.1131 r_free=0.1508 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1508 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1124 r_free = 0.1527 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1124 r_free= 0.1527 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.947309 | | target function (ml) not normalized (work): 80309.668574 | | target function (ml) not normalized (free): 4170.659950 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1123 0.1382 5.4628 5.6462| | 2: 3.63 - 2.88 1.00 2711 122 0.1108 0.1599 5.2363 5.3914| | 3: 2.88 - 2.52 1.00 2681 148 0.1390 0.1684 5.1412 5.2169| | 4: 2.52 - 2.29 1.00 2661 139 0.0957 0.1523 4.6388 4.9502| | 5: 2.29 - 2.13 1.00 2678 122 0.0986 0.1496 4.5932 4.902| | 6: 2.13 - 2.00 1.00 2692 117 0.1136 0.1695 4.5823 4.7602| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.95 9.19 1.00 0.96 6566.42| | 2: 3.63 - 2.88 2711 122 0.92 12.95 1.01 0.96 6566.42| | 3: 2.88 - 2.52 2681 148 0.87 19.38 0.99 0.96 6566.42| | 4: 2.52 - 2.29 2661 139 0.93 12.35 1.01 0.97 2159.73| | 5: 2.29 - 2.13 2678 122 0.91 14.36 1.00 0.97 2159.73| | 6: 2.13 - 2.00 2692 117 0.89 17.03 0.99 0.97 2159.73| |alpha: min = 0.96 max = 0.97 mean = 0.97| |beta: min = 2159.73 max = 6566.42 mean = 4386.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.86 mean = 14.17| |phase err.(test): min = 0.00 max = 88.62 mean = 13.92| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1144 0.1124 0.1527 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1599 0.1588 0.1842 n_refl.: 17040 remove outliers: r(all,work,free)=0.1599 0.1588 0.1842 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1586 0.1575 0.1835 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1144 0.1125 0.1525 n_refl.: 17040 remove outliers: r(all,work,free)=0.1144 0.1125 0.1525 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 0.3581 296.597 276.400 0.552 1.006 0.340 11.894-9.307 99.02 97 4 0.1789 487.845 480.019 0.914 1.006 0.333 9.237-7.194 100.00 213 7 0.1722 399.008 400.378 0.990 1.006 0.240 7.162-5.571 100.00 427 22 0.1543 299.456 294.685 0.936 1.006 0.240 5.546-4.326 100.00 867 58 0.0958 411.105 407.582 0.960 1.005 0.191 4.315-3.360 100.00 1859 96 0.0877 390.965 388.798 1.002 1.003 0.174 3.356-2.611 100.00 3867 181 0.1265 256.842 254.570 0.999 1.001 0.131 2.608-2.000 99.99 8818 434 0.1058 167.417 165.962 0.991 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7533 ================= 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 : 0.2789 0.1830 0.083 5.378 8.8 119.3 19.9 258 0.000 1_bss: 0.1618 0.1636 0.083 5.378 8.4 118.9 19.5 258 0.000 1_settarget: 0.1618 0.1636 0.083 5.378 8.4 118.9 19.5 258 0.000 1_nqh: 0.1618 0.1636 0.083 5.378 8.4 118.9 19.5 258 0.003 1_weight: 0.1618 0.1636 0.083 5.378 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1350 0.1626 0.009 0.976 8.4 118.9 19.5 258 0.145 1_adp: 0.1278 0.1646 0.009 0.976 6.1 113.9 20.0 258 0.145 1_regHadp: 0.1281 0.1655 0.009 0.976 6.1 113.9 20.0 258 0.145 1_occ: 0.1275 0.1649 0.009 0.976 6.1 113.9 20.0 258 0.145 2_bss: 0.1275 0.1645 0.009 0.976 5.7 113.5 19.6 258 0.145 2_settarget: 0.1275 0.1645 0.009 0.976 5.7 113.5 19.6 258 0.145 2_updatecdl: 0.1275 0.1645 0.009 0.987 5.7 113.5 19.6 258 0.145 2_nqh: 0.1276 0.1644 0.009 0.987 5.7 113.5 19.6 258 0.142 2_sol: 0.1245 0.1564 0.009 0.987 5.7 112.5 20.7 355 n/a 2_weight: 0.1245 0.1564 0.009 0.987 5.7 112.5 20.7 355 n/a 2_xyzrec: 0.1217 0.1607 0.008 0.924 5.7 112.5 20.7 355 n/a 2_adp: 0.1199 0.1629 0.008 0.924 6.5 107.5 21.3 355 n/a 2_regHadp: 0.1201 0.1630 0.008 0.924 6.5 107.5 21.3 355 n/a 2_occ: 0.1200 0.1626 0.008 0.924 6.5 107.5 21.3 355 n/a 3_bss: 0.1193 0.1611 0.008 0.924 6.2 107.1 20.9 355 n/a 3_settarget: 0.1193 0.1611 0.008 0.924 6.2 107.1 20.9 355 n/a 3_updatecdl: 0.1193 0.1611 0.008 0.924 6.2 107.1 20.9 355 n/a 3_nqh: 0.1193 0.1611 0.008 0.924 6.2 107.1 20.9 355 n/a 3_sol: 0.1192 0.1551 0.008 0.924 6.2 107.1 21.1 400 n/a 3_weight: 0.1192 0.1551 0.008 0.924 6.2 107.1 21.1 400 n/a 3_xyzrec: 0.1179 0.1547 0.009 0.963 6.2 107.1 21.1 400 n/a 3_adp: 0.1157 0.1553 0.009 0.963 6.3 104.3 21.0 400 n/a 3_regHadp: 0.1157 0.1554 0.009 0.963 6.3 104.3 21.0 400 n/a 3_occ: 0.1147 0.1540 0.009 0.963 6.3 104.3 21.0 400 n/a 4_bss: 0.1145 0.1540 0.009 0.963 5.9 103.8 20.5 400 n/a 4_settarget: 0.1145 0.1540 0.009 0.963 5.9 103.8 20.5 400 n/a 4_updatecdl: 0.1145 0.1540 0.009 0.963 5.9 103.8 20.5 400 n/a 4_nqh: 0.1145 0.1540 0.009 0.963 5.9 103.8 20.5 400 n/a 4_sol: 0.1145 0.1505 0.009 0.963 5.9 103.8 20.8 434 n/a 4_weight: 0.1145 0.1505 0.009 0.963 5.9 103.8 20.8 434 n/a 4_xyzrec: 0.1126 0.1552 0.009 0.973 5.9 103.8 20.8 434 n/a 4_adp: 0.1114 0.1556 0.009 0.973 6.0 102.5 20.9 434 n/a 4_regHadp: 0.1114 0.1556 0.009 0.973 6.0 102.5 20.9 434 n/a 4_occ: 0.1107 0.1561 0.009 0.973 6.0 102.5 20.9 434 n/a 5_bss: 0.1105 0.1554 0.009 0.973 5.7 102.2 20.6 434 n/a 5_settarget: 0.1105 0.1554 0.009 0.973 5.7 102.2 20.6 434 n/a 5_updatecdl: 0.1105 0.1554 0.009 0.974 5.7 102.2 20.6 434 n/a 5_setrh: 0.1107 0.1553 0.009 0.974 5.7 102.2 20.6 434 n/a 5_nqh: 0.1107 0.1553 0.009 0.974 5.7 102.2 20.6 434 n/a 5_sol: 0.1106 0.1515 0.009 0.974 5.7 102.2 20.8 457 n/a 5_weight: 0.1106 0.1515 0.009 0.974 5.7 102.2 20.8 457 n/a 5_xyzrec: 0.1143 0.1533 0.009 1.011 5.7 102.2 20.8 457 n/a 5_adp: 0.1131 0.1507 0.009 1.011 5.4 101.3 20.9 457 n/a 5_regHadp: 0.1131 0.1508 0.009 1.011 5.4 101.3 20.9 457 n/a 5_occ: 0.1124 0.1527 0.009 1.011 5.4 101.3 20.9 457 n/a end: 0.1125 0.1525 0.009 1.011 5.2 101.1 20.7 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7783516_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7783516_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.4900 Refinement macro-cycles (run) : 919.6100 Write final files (write_after_run_outputs) : 20.4400 Total : 944.5400 Total CPU time: 16.13 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:09 PST -0800 (1735494069.88 s) Start R-work = 0.1618, R-free = 0.1636 Final R-work = 0.1125, R-free = 0.1525 =============================================================================== Job complete usr+sys time: 992.25 seconds wall clock time: 16 minutes 55.58 seconds (1015.58 seconds total)