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_6113322.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_6113322.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6113322.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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.22, per 1000 atoms: 0.36 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: 0.49 Conformation dependent library (CDL) restraints added in 181.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.96: 898 0.96 - 1.24: 861 1.24 - 1.52: 928 1.52 - 1.79: 458 1.79 - 2.07: 8 Bond restraints: 3153 Sorted by residual: bond pdb=" C ILE A 102 " pdb=" O ILE A 102 " ideal model delta sigma weight residual 1.237 1.020 0.217 1.09e-02 8.42e+03 3.96e+02 bond pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta sigma weight residual 1.458 1.233 0.226 1.23e-02 6.61e+03 3.37e+02 bond pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta sigma weight residual 1.459 1.226 0.233 1.27e-02 6.20e+03 3.36e+02 bond pdb=" C VAL A 25 " pdb=" O VAL A 25 " ideal model delta sigma weight residual 1.237 1.050 0.187 1.13e-02 7.83e+03 2.73e+02 bond pdb=" CA VAL A 33 " pdb=" CB VAL A 33 " ideal model delta sigma weight residual 1.539 1.728 -0.190 1.19e-02 7.06e+03 2.54e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3219 4.69 - 9.39: 1812 9.39 - 14.08: 621 14.08 - 18.77: 114 18.77 - 23.46: 11 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 70 " pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 120.57 103.80 16.77 1.07e+00 8.73e-01 2.46e+02 angle pdb=" OE1 GLN A 180 " pdb=" CD GLN A 180 " pdb=" NE2 GLN A 180 " ideal model delta sigma weight residual 122.60 108.26 14.34 1.00e+00 1.00e+00 2.06e+02 angle pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 119.20 131.65 -12.45 9.00e-01 1.23e+00 1.91e+02 angle pdb=" CA ILE A 102 " pdb=" C ILE A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 116.51 101.93 14.58 1.07e+00 8.73e-01 1.86e+02 angle pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" O VAL A 177 " ideal model delta sigma weight residual 120.85 106.64 14.21 1.06e+00 8.90e-01 1.80e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 1275 15.39 - 30.78: 138 30.78 - 46.17: 45 46.17 - 61.56: 17 61.56 - 76.95: 6 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 141.57 -18.77 0 2.50e+00 1.60e-01 5.64e+01 dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -140.93 18.33 0 2.50e+00 1.60e-01 5.38e+01 dihedral pdb=" C VAL A 70 " pdb=" N VAL A 70 " pdb=" CA VAL A 70 " pdb=" CB VAL A 70 " ideal model delta harmonic sigma weight residual -122.00 -139.39 17.39 0 2.50e+00 1.60e-01 4.84e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 99 0.214 - 0.428: 78 0.428 - 0.642: 38 0.642 - 0.856: 20 0.856 - 1.070: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB ILE A 117 " pdb=" CA ILE A 117 " pdb=" CG1 ILE A 117 " pdb=" CG2 ILE A 117 " both_signs ideal model delta sigma weight residual False 2.64 1.57 1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -3.63 1.00 2.00e-01 2.50e+01 2.52e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.63 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.111 2.00e-02 2.50e+03 9.57e-02 2.75e+02 pdb=" CG PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.148 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.126 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.173 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.103 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.160 2.00e-02 2.50e+03 7.58e-02 1.72e+02 pdb=" CG PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.053 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.159 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.108 9.50e-02 1.11e+02 8.40e-02 1.31e+02 pdb=" NE ARG A 48 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " 0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.073 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.076 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " 0.012 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.114 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.120 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.28: 811 2.28 - 2.86: 7922 2.86 - 3.44: 10498 3.44 - 4.02: 15339 4.02 - 4.60: 22072 Nonbonded interactions: 56642 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.705 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.829 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.843 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.845 2.450 x-y,-y,-z-4/3 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.846 2.450 ... (remaining 56637 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_6113322_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= 0.2786 r_free= 0.1806 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.391339 | | target function (ml) not normalized (work): 71328.526666 | | target function (ml) not normalized (free): 3248.335249 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3199 0.2196 7.5089 5.035| | 2: 3.63 - 2.88 1.00 2711 122 0.2656 0.1739 4.3337 4.3236| | 3: 2.88 - 2.52 1.00 2682 148 0.2570 0.1720 4.1848 4.1889| | 4: 2.52 - 2.29 1.00 2661 139 0.2537 0.1405 3.4835 3.4631| | 5: 2.29 - 2.13 1.00 2678 122 0.2628 0.1407 3.3813 3.4348| | 6: 2.13 - 2.00 1.00 2692 117 0.2715 0.1745 3.2927 3.4181| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.69 0.77 0.23 1314.14| | 2: 3.63 - 2.88 2711 122 0.83 23.97 1.32 0.23 1314.14| | 3: 2.88 - 2.52 2682 148 0.73 32.98 1.28 0.23 1314.14| | 4: 2.52 - 2.29 2661 139 0.94 10.47 1.30 0.26 119.54| | 5: 2.29 - 2.13 2678 122 0.93 12.61 1.31 0.26 119.54| | 6: 2.13 - 2.00 2692 117 0.91 15.09 1.33 0.26 119.54| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 119.54 max = 1314.14 mean = 723.50| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.94 mean = 18.81| |phase err.(test): min = 0.00 max = 88.63 mean = 19.04| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.276 1557 Z= 5.511 Angle : 5.139 16.891 2118 Z= 3.679 Chirality : 0.395 1.070 243 Planarity : 0.032 0.119 284 Dihedral : 13.647 76.946 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 3.11 % Favored : 94.41 % Cbeta Deviations : 25.95 % 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: -2.37 (0.49), residues: 224 helix: -2.22 (0.41), residues: 109 sheet: -0.66 (0.85), residues: 38 loop : -0.61 (0.59), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.026 ARG A 98 TYR 0.083 0.041 TYR A 139 PHE 0.190 0.055 PHE A 164 HIS 0.069 0.042 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= 0.2786 r_free= 0.1806 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.391339 | | target function (ml) not normalized (work): 71328.526666 | | target function (ml) not normalized (free): 3248.335249 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3235 percent. r_work = 0.2919 r_free = 0.1991 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2865 0.2919 0.1991 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2865 0.2919 0.1991 n_refl.: 17050 remove outliers: r(all,work,free)=0.2159 0.2170 0.1991 n_refl.: 17045 overall B=-0.38 to atoms: r(all,work,free)=0.2134 0.2145 0.1974 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1623 0.1623 0.1635 n_refl.: 17045 remove outliers: r(all,work,free)=0.1622 0.1622 0.1635 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 0.4161 394.810 357.328 0.646 1.013 0.393 11.894-9.307 99.02 97 4 0.1862 633.682 615.618 0.926 1.014 0.380 9.237-7.194 100.00 213 7 0.2153 518.288 510.254 0.951 1.013 0.350 7.162-5.571 100.00 427 22 0.2315 388.976 376.192 0.918 1.011 0.289 5.546-4.326 100.00 867 58 0.1387 534.001 528.774 0.957 1.009 0.215 4.315-3.360 100.00 1859 96 0.1328 507.841 503.465 1.016 1.005 0.181 3.356-2.611 100.00 3867 181 0.1640 333.622 329.040 1.014 0.999 0.034 2.608-2.000 99.99 8818 434 0.1663 217.464 213.347 1.025 0.987 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3440 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1622 r_free=0.1635 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1622 r_free=0.1636 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.024102 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.903905 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 0.1355 0.1648 0.0293 0.008 1.0 1.0 0.5 0.0 0 11.012 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.55 16.48 2.93 3.013 18.482 0.904 0.023 12.80 16.64 3.83 3.632 18.700 0.904 0.021 Individual atomic B min max mean iso aniso Overall: 6.24 113.92 19.92 4.13 1785 0 Protein: 6.24 113.39 17.13 4.14 1519 0 Water: 8.50 113.92 36.18 N/A 258 0 Other: 21.91 37.58 26.44 N/A 8 0 Chain A: 6.24 113.92 19.92 N/A 1785 0 Histogram: Values Number of atoms 6.24 - 17.01 1088 17.01 - 27.78 342 27.78 - 38.55 180 38.55 - 49.32 99 49.32 - 60.08 49 60.08 - 70.85 13 70.85 - 81.62 6 81.62 - 92.39 4 92.39 - 103.15 1 103.15 - 113.92 3 =========================== Idealize ADP of riding H ========================== r_work=0.1280 r_free=0.1664 r_work=0.1283 r_free=0.1670 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1283 r_free = 0.1670 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 = 0.1277 r_free = 0.1662 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 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= 0.1277 r_free= 0.1662 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020065 | | target function (ls_wunit_k1) not normalized (work): 325.794345 | | target function (ls_wunit_k1) not normalized (free): 27.125002 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1277 0.1662 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1903 0.1901 0.1984 n_refl.: 17044 remove outliers: r(all,work,free)=0.1903 0.1901 0.1984 n_refl.: 17044 overall B=-0.46 to atoms: r(all,work,free)=0.1870 0.1868 0.1966 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1656 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1274 0.1656 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 0.3548 303.213 278.565 0.623 1.006 0.368 11.894-9.307 99.02 97 4 0.1707 487.671 476.781 0.917 1.007 0.367 9.237-7.194 100.00 213 7 0.1821 398.865 396.241 0.959 1.007 0.341 7.162-5.571 100.00 427 22 0.1819 299.349 294.406 0.933 1.006 0.301 5.546-4.326 100.00 867 58 0.1045 410.958 408.219 0.957 1.005 0.205 4.315-3.360 100.00 1859 96 0.0925 390.825 390.151 1.016 1.004 0.192 3.356-2.611 100.00 3867 181 0.1297 256.750 255.411 1.010 1.001 0.081 2.608-2.000 99.99 8818 434 0.1351 167.357 166.001 1.010 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1428 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1656 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1275 r_free=0.1659 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1659 | n_water=258 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1279 r_free=0.1649 | n_water=255 | time (s): 21.470 (total time: 22.110) Filter (q & B) r_work=0.1280 r_free=0.1649 | n_water=252 | time (s): 1.750 (total time: 23.860) Compute maps r_work=0.1280 r_free=0.1649 | n_water=252 | time (s): 0.690 (total time: 24.550) Filter (map) r_work=0.1314 r_free=0.1644 | n_water=214 | time (s): 1.800 (total time: 26.350) Find peaks r_work=0.1314 r_free=0.1644 | n_water=214 | time (s): 0.500 (total time: 26.850) Add new water r_work=0.1526 r_free=0.1884 | n_water=375 | time (s): 1.350 (total time: 28.200) Refine new water occ: r_work=0.1326 r_free=0.1616 adp: r_work=0.1268 r_free=0.1608 occ: r_work=0.1276 r_free=0.1590 adp: r_work=0.1242 r_free=0.1588 occ: r_work=0.1245 r_free=0.1583 adp: r_work=0.1235 r_free=0.1579 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1579 r_work=0.1235 r_free=0.1579 | n_water=375 | time (s): 12.140 (total time: 40.340) Filter (q & B) r_work=0.1235 r_free=0.1583 | n_water=368 | time (s): 2.020 (total time: 42.360) Filter (dist only) r_work=0.1235 r_free=0.1585 | n_water=367 | time (s): 31.200 (total time: 73.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.196189 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.000301 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 0.1204 0.1603 0.0399 0.008 0.9 2.6 0.5 0.0 0 12.098 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 16.03 3.99 4.194 20.957 1.000 0.018 11.88 16.32 4.43 4.284 21.259 1.000 0.017 Individual atomic B min max mean iso aniso Overall: 6.70 107.93 21.37 4.38 1894 0 Protein: 6.70 107.93 17.67 4.37 1519 0 Water: 8.65 68.12 36.39 N/A 367 0 Other: 24.77 45.26 35.31 N/A 8 0 Chain A: 6.70 107.93 19.45 N/A 1741 0 Chain S: 16.25 68.12 43.28 N/A 153 0 Histogram: Values Number of atoms 6.70 - 16.82 1037 16.82 - 26.94 365 26.94 - 37.07 229 37.07 - 47.19 152 47.19 - 57.32 68 57.32 - 67.44 31 67.44 - 77.56 5 77.56 - 87.69 5 87.69 - 97.81 0 97.81 - 107.93 2 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1632 r_work=0.1190 r_free=0.1632 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1632 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1184 r_free = 0.1623 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1184 r_free= 0.1623 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016694 | | target function (ls_wunit_k1) not normalized (work): 271.028806 | | target function (ls_wunit_k1) not normalized (free): 24.761165 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1184 0.1623 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1749 0.1738 0.1980 n_refl.: 17042 remove outliers: r(all,work,free)=0.1749 0.1738 0.1980 n_refl.: 17042 overall B=-0.41 to atoms: r(all,work,free)=0.1723 0.1712 0.1962 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1180 0.1619 n_refl.: 17042 remove outliers: r(all,work,free)=0.1200 0.1179 0.1619 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 0.3158 300.053 288.403 0.604 1.006 0.350 11.894-9.307 99.02 97 4 0.1502 487.671 483.862 0.912 1.006 0.344 9.237-7.194 100.00 213 7 0.1647 398.865 398.937 0.975 1.006 0.295 7.162-5.571 100.00 427 22 0.1498 299.349 296.213 0.942 1.006 0.271 5.546-4.326 100.00 867 58 0.0848 410.958 408.686 0.958 1.005 0.206 4.315-3.360 100.00 1859 96 0.0810 390.825 389.809 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1190 256.750 255.912 1.009 1.000 0.101 2.608-2.000 99.99 8818 434 0.1333 167.357 166.233 1.011 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1432 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1179 r_free=0.1619 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=0.1180 r_free=0.1621 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1180 r_free=0.1621 | n_water=367 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1180 r_free=0.1621 | n_water=367 | time (s): 28.880 (total time: 29.570) Filter (q & B) r_work=0.1180 r_free=0.1621 | n_water=367 | time (s): 1.250 (total time: 30.820) Compute maps r_work=0.1180 r_free=0.1621 | n_water=367 | time (s): 0.810 (total time: 31.630) Filter (map) r_work=0.1249 r_free=0.1638 | n_water=269 | time (s): 2.100 (total time: 33.730) Find peaks r_work=0.1249 r_free=0.1638 | n_water=269 | time (s): 0.570 (total time: 34.300) Add new water r_work=0.1434 r_free=0.1793 | n_water=414 | time (s): 1.630 (total time: 35.930) Refine new water occ: r_work=0.1251 r_free=0.1584 adp: r_work=0.1241 r_free=0.1586 occ: r_work=0.1227 r_free=0.1562 adp: r_work=0.1214 r_free=0.1563 occ: r_work=0.1210 r_free=0.1554 adp: r_work=0.1199 r_free=0.1550 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1550 r_work=0.1199 r_free=0.1550 | n_water=414 | time (s): 41.910 (total time: 77.840) Filter (q & B) r_work=0.1202 r_free=0.1551 | n_water=407 | time (s): 1.560 (total time: 79.400) Filter (dist only) r_work=0.1203 r_free=0.1549 | n_water=406 | time (s): 33.060 (total time: 112.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.958740 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.153177 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 0.1544 0.0364 0.009 1.0 5.8 0.5 0.0 0 0.979 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 15.44 3.64 4.392 21.425 0.153 4.997 11.59 15.64 4.05 4.928 21.332 0.153 4.975 Individual atomic B min max mean iso aniso Overall: 6.37 105.16 20.77 4.67 1933 0 Protein: 6.37 105.16 16.87 4.67 1519 0 Water: 8.84 60.37 35.16 N/A 406 0 Other: 24.58 43.30 32.37 N/A 8 0 Chain A: 6.37 105.16 18.67 N/A 1739 0 Chain S: 18.26 60.37 39.61 N/A 194 0 Histogram: Values Number of atoms 6.37 - 16.25 1085 16.25 - 26.13 340 26.13 - 36.01 219 36.01 - 45.88 169 45.88 - 55.76 81 55.76 - 65.64 26 65.64 - 75.52 5 75.52 - 85.40 3 85.40 - 95.28 3 95.28 - 105.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1159 r_free=0.1564 r_work=0.1159 r_free=0.1565 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1159 r_free = 0.1565 target_work(ml) = 4.975 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1153 r_free = 0.1567 target_work(ml) = 4.970 | | 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= 0.1153 r_free= 0.1567 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.969676 | | target function (ml) not normalized (work): 80677.719304 | | target function (ml) not normalized (free): 4187.002654 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1173 0.1153 0.1567 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1671 0.1665 0.1845 n_refl.: 17041 remove outliers: r(all,work,free)=0.1671 0.1665 0.1845 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1646 0.1639 0.1833 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1171 0.1150 0.1570 n_refl.: 17041 remove outliers: r(all,work,free)=0.1171 0.1150 0.1570 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 0.3485 300.053 280.524 0.572 1.007 0.350 11.894-9.307 99.02 97 4 0.1699 487.671 480.626 0.902 1.008 0.344 9.237-7.194 100.00 213 7 0.1813 398.865 399.406 0.987 1.007 0.269 7.162-5.571 100.00 427 22 0.1583 299.349 294.708 0.945 1.007 0.229 5.546-4.326 100.00 867 58 0.0934 410.958 407.630 0.963 1.006 0.215 4.315-3.360 100.00 1859 96 0.0906 390.825 388.313 1.010 1.004 0.211 3.356-2.611 100.00 3867 181 0.1294 256.750 254.306 1.010 1.001 0.142 2.608-2.000 99.99 8818 434 0.1091 167.357 165.912 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1769 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1150 r_free=0.1570 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1150 r_free=0.1570 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1150 r_free=0.1570 | n_water=406 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1150 r_free=0.1570 | n_water=406 | time (s): 31.600 (total time: 32.250) Filter (q & B) r_work=0.1151 r_free=0.1570 | n_water=405 | time (s): 2.080 (total time: 34.330) Compute maps r_work=0.1151 r_free=0.1570 | n_water=405 | time (s): 0.600 (total time: 34.930) Filter (map) r_work=0.1206 r_free=0.1579 | n_water=305 | time (s): 1.850 (total time: 36.780) Find peaks r_work=0.1206 r_free=0.1579 | n_water=305 | time (s): 0.620 (total time: 37.400) Add new water r_work=0.1357 r_free=0.1704 | n_water=452 | time (s): 1.580 (total time: 38.980) Refine new water occ: r_work=0.1179 r_free=0.1535 adp: r_work=0.1170 r_free=0.1541 occ: r_work=0.1155 r_free=0.1517 adp: r_work=0.1145 r_free=0.1520 occ: r_work=0.1139 r_free=0.1511 adp: r_work=0.1130 r_free=0.1510 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1510 r_work=0.1130 r_free=0.1510 | n_water=452 | time (s): 24.700 (total time: 63.680) Filter (q & B) r_work=0.1133 r_free=0.1524 | n_water=444 | time (s): 1.700 (total time: 65.380) Filter (dist only) r_work=0.1133 r_free=0.1524 | n_water=444 | time (s): 34.210 (total time: 99.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.009975 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.158854 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 0.1117 0.1568 0.0450 0.010 1.0 4.5 0.5 0.0 0 1.005 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.68 4.50 4.474 20.958 0.159 4.957 11.06 15.68 4.62 4.602 21.004 0.159 4.949 Individual atomic B min max mean iso aniso Overall: 5.75 102.61 20.95 4.75 1971 0 Protein: 5.75 102.61 16.47 4.74 1519 0 Water: 8.35 63.02 36.10 N/A 444 0 Other: 24.65 42.17 31.84 N/A 8 0 Chain A: 5.75 102.61 18.24 N/A 1739 0 Chain S: 15.39 63.02 41.33 N/A 232 0 Histogram: Values Number of atoms 5.75 - 15.44 1046 15.44 - 25.13 366 25.13 - 34.81 216 34.81 - 44.50 185 44.50 - 54.18 106 54.18 - 63.87 38 63.87 - 73.56 6 73.56 - 83.24 3 83.24 - 92.93 3 92.93 - 102.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1568 r_work=0.1106 r_free=0.1569 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1569 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1097 r_free = 0.1576 target_work(ml) = 4.947 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1097 r_free= 0.1576 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.947038 | | target function (ml) not normalized (work): 80310.208707 | | target function (ml) not normalized (free): 4187.900003 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1120 0.1097 0.1576 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1598 0.1587 0.1856 n_refl.: 17041 remove outliers: r(all,work,free)=0.1598 0.1587 0.1856 n_refl.: 17041 overall B=-0.27 to atoms: r(all,work,free)=0.1582 0.1570 0.1847 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1118 0.1095 0.1570 n_refl.: 17041 remove outliers: r(all,work,free)=0.1118 0.1095 0.1570 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 0.3632 300.053 278.450 0.564 1.003 0.340 11.894-9.307 99.02 97 4 0.1734 487.671 480.410 0.912 1.004 0.337 9.237-7.194 100.00 213 7 0.1672 398.865 400.627 0.993 1.004 0.230 7.162-5.571 100.00 427 22 0.1511 299.349 295.083 0.943 1.004 0.225 5.546-4.326 100.00 867 58 0.0914 410.958 407.499 0.963 1.004 0.210 4.315-3.360 100.00 1859 96 0.0843 390.825 388.525 1.005 1.003 0.201 3.356-2.611 100.00 3867 181 0.1227 256.750 254.551 1.001 1.001 0.141 2.608-2.000 99.99 8818 434 0.1039 167.357 166.124 0.998 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9241 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1095 r_free=0.1570 After: r_work=0.1097 r_free=0.1569 ================================== NQH flips ================================== r_work=0.1097 r_free=0.1569 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=0.1098 r_free=0.1564 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1098 r_free=0.1564 | n_water=444 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1105 r_free=0.1564 | n_water=442 | time (s): 36.650 (total time: 37.270) Filter (q & B) r_work=0.1105 r_free=0.1564 | n_water=441 | time (s): 1.720 (total time: 38.990) Compute maps r_work=0.1105 r_free=0.1564 | n_water=441 | time (s): 0.570 (total time: 39.560) Filter (map) r_work=0.1182 r_free=0.1583 | n_water=342 | time (s): 1.490 (total time: 41.050) Find peaks r_work=0.1182 r_free=0.1583 | n_water=342 | time (s): 0.590 (total time: 41.640) Add new water r_work=0.1310 r_free=0.1694 | n_water=481 | time (s): 2.000 (total time: 43.640) Refine new water occ: r_work=0.1148 r_free=0.1533 adp: r_work=0.1142 r_free=0.1541 occ: r_work=0.1124 r_free=0.1506 adp: r_work=0.1116 r_free=0.1514 occ: r_work=0.1107 r_free=0.1491 adp: r_work=0.1100 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1100 r_free=0.1496 r_work=0.1100 r_free=0.1496 | n_water=481 | time (s): 41.100 (total time: 84.740) Filter (q & B) r_work=0.1101 r_free=0.1502 | n_water=474 | time (s): 1.740 (total time: 86.480) Filter (dist only) r_work=0.1101 r_free=0.1502 | n_water=474 | time (s): 35.120 (total time: 121.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.977852 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.150069 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 0.1128 0.1550 0.0422 0.010 1.1 10.6 0.5 0.0 0 0.989 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.28 15.50 4.22 4.478 20.893 0.150 4.962 11.17 15.31 4.14 4.599 20.931 0.150 4.951 Individual atomic B min max mean iso aniso Overall: 5.52 101.54 21.10 4.84 2001 0 Protein: 5.52 101.54 16.15 4.83 1519 0 Water: 8.00 63.64 36.81 N/A 474 0 Other: 23.64 40.36 30.62 N/A 8 0 Chain A: 5.52 101.54 17.87 N/A 1738 0 Chain S: 17.92 63.64 42.45 N/A 263 0 Histogram: Values Number of atoms 5.52 - 15.12 1044 15.12 - 24.73 366 24.73 - 34.33 209 34.33 - 43.93 186 43.93 - 53.53 139 53.53 - 63.13 39 63.13 - 72.73 9 72.73 - 82.33 3 82.33 - 91.94 2 91.94 - 101.54 4 =========================== Idealize ADP of riding H ========================== r_work=0.1117 r_free=0.1531 r_work=0.1117 r_free=0.1531 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1117 r_free = 0.1531 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1109 r_free = 0.1524 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1109 r_free= 0.1524 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.944876 | | target function (ml) not normalized (work): 80275.124569 | | target function (ml) not normalized (free): 4179.048204 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1110 0.1441 5.4529 5.6835| | 2: 3.63 - 2.88 1.00 2711 122 0.1097 0.1527 5.2297 5.3822| | 3: 2.88 - 2.52 1.00 2681 148 0.1364 0.1559 5.1423 5.1858| | 4: 2.52 - 2.29 1.00 2661 139 0.0935 0.1552 4.6373 4.9715| | 5: 2.29 - 2.13 1.00 2678 122 0.0968 0.1559 4.5942 4.9313| | 6: 2.13 - 2.00 1.00 2692 117 0.1130 0.1685 4.5838 4.7743| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.95 9.18 1.00 0.96 6575.55| | 2: 3.63 - 2.88 2711 122 0.92 13.08 1.01 0.96 6575.55| | 3: 2.88 - 2.52 2681 148 0.87 19.24 0.99 0.96 6575.55| | 4: 2.52 - 2.29 2661 139 0.93 12.34 1.01 0.97 2198.43| | 5: 2.29 - 2.13 2678 122 0.91 14.42 1.00 0.97 2198.43| | 6: 2.13 - 2.00 2692 117 0.89 17.18 0.99 0.97 2198.43| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2198.43 max = 6575.55 mean = 4410.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 90.00 mean = 14.20| |phase err.(test): min = 0.00 max = 87.21 mean = 13.87| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1109 0.1524 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1569 0.1557 0.1831 n_refl.: 17041 remove outliers: r(all,work,free)=0.1569 0.1557 0.1831 n_refl.: 17041 overall B=-0.22 to atoms: r(all,work,free)=0.1557 0.1544 0.1823 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1109 0.1523 n_refl.: 17041 remove outliers: r(all,work,free)=0.1129 0.1109 0.1523 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 0.3589 300.053 282.177 0.557 1.004 0.334 11.894-9.307 99.02 97 4 0.1727 487.671 480.879 0.913 1.005 0.330 9.237-7.194 100.00 213 7 0.1675 398.865 401.169 0.992 1.005 0.230 7.162-5.571 100.00 427 22 0.1532 299.349 294.413 0.943 1.005 0.230 5.546-4.326 100.00 867 58 0.0930 410.958 407.418 0.961 1.004 0.200 4.315-3.360 100.00 1859 96 0.0877 390.825 388.296 1.002 1.003 0.201 3.356-2.611 100.00 3867 181 0.1248 256.750 254.484 0.998 1.000 0.131 2.608-2.000 99.99 8818 434 0.1039 167.357 166.100 0.992 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7548 ================= 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 : 0.2786 0.1806 0.084 5.139 8.8 119.3 19.9 258 0.000 1_bss: 0.1622 0.1635 0.084 5.139 8.5 118.9 19.5 258 0.000 1_settarget: 0.1622 0.1635 0.084 5.139 8.5 118.9 19.5 258 0.000 1_nqh: 0.1622 0.1636 0.084 5.139 8.5 118.9 19.5 258 0.003 1_weight: 0.1622 0.1636 0.084 5.139 8.5 118.9 19.5 258 0.003 1_xyzrec: 0.1355 0.1648 0.008 0.959 8.5 118.9 19.5 258 0.155 1_adp: 0.1280 0.1664 0.008 0.959 6.2 113.9 19.9 258 0.155 1_regHadp: 0.1283 0.1670 0.008 0.959 6.2 113.9 19.9 258 0.155 1_occ: 0.1277 0.1662 0.008 0.959 6.2 113.9 19.9 258 0.155 2_bss: 0.1274 0.1656 0.008 0.959 5.8 113.5 19.5 258 0.155 2_settarget: 0.1274 0.1656 0.008 0.959 5.8 113.5 19.5 258 0.155 2_updatecdl: 0.1274 0.1656 0.008 0.969 5.8 113.5 19.5 258 0.155 2_nqh: 0.1275 0.1659 0.008 0.969 5.8 113.5 19.5 258 0.152 2_sol: 0.1235 0.1585 0.008 0.969 5.8 112.9 20.8 367 n/a 2_weight: 0.1235 0.1585 0.008 0.969 5.8 112.9 20.8 367 n/a 2_xyzrec: 0.1204 0.1603 0.008 0.919 5.8 112.9 20.8 367 n/a 2_adp: 0.1188 0.1632 0.008 0.919 6.7 107.9 21.4 367 n/a 2_regHadp: 0.1190 0.1632 0.008 0.919 6.7 107.9 21.4 367 n/a 2_occ: 0.1184 0.1623 0.008 0.919 6.7 107.9 21.4 367 n/a 3_bss: 0.1179 0.1619 0.008 0.919 6.3 107.5 21.0 367 n/a 3_settarget: 0.1179 0.1619 0.008 0.919 6.3 107.5 21.0 367 n/a 3_updatecdl: 0.1179 0.1619 0.008 0.918 6.3 107.5 21.0 367 n/a 3_nqh: 0.1180 0.1621 0.008 0.918 6.3 107.5 21.0 367 n/a 3_sol: 0.1203 0.1549 0.008 0.918 6.3 107.5 20.9 406 n/a 3_weight: 0.1203 0.1549 0.008 0.918 6.3 107.5 20.9 406 n/a 3_xyzrec: 0.1180 0.1544 0.009 0.966 6.3 107.5 20.9 406 n/a 3_adp: 0.1159 0.1564 0.009 0.966 6.4 105.2 20.8 406 n/a 3_regHadp: 0.1159 0.1565 0.009 0.966 6.4 105.2 20.8 406 n/a 3_occ: 0.1153 0.1567 0.009 0.966 6.4 105.2 20.8 406 n/a 4_bss: 0.1150 0.1570 0.009 0.966 6.0 104.8 20.4 406 n/a 4_settarget: 0.1150 0.1570 0.009 0.966 6.0 104.8 20.4 406 n/a 4_updatecdl: 0.1150 0.1570 0.009 0.967 6.0 104.8 20.4 406 n/a 4_nqh: 0.1150 0.1570 0.009 0.967 6.0 104.8 20.4 406 n/a 4_sol: 0.1133 0.1524 0.009 0.967 6.0 104.8 20.9 444 n/a 4_weight: 0.1133 0.1524 0.009 0.967 6.0 104.8 20.9 444 n/a 4_xyzrec: 0.1117 0.1568 0.010 0.982 6.0 104.8 20.9 444 n/a 4_adp: 0.1106 0.1568 0.010 0.982 5.8 102.6 21.0 444 n/a 4_regHadp: 0.1106 0.1569 0.010 0.982 5.8 102.6 21.0 444 n/a 4_occ: 0.1097 0.1576 0.010 0.982 5.8 102.6 21.0 444 n/a 5_bss: 0.1095 0.1570 0.010 0.982 5.5 102.3 20.7 444 n/a 5_settarget: 0.1095 0.1570 0.010 0.982 5.5 102.3 20.7 444 n/a 5_updatecdl: 0.1095 0.1570 0.010 0.982 5.5 102.3 20.7 444 n/a 5_setrh: 0.1097 0.1569 0.010 0.982 5.5 102.3 20.7 444 n/a 5_nqh: 0.1098 0.1564 0.010 0.982 5.5 102.3 20.7 444 n/a 5_sol: 0.1101 0.1502 0.010 0.982 5.5 102.3 21.0 474 n/a 5_weight: 0.1101 0.1502 0.010 0.982 5.5 102.3 21.0 474 n/a 5_xyzrec: 0.1128 0.1550 0.010 1.094 5.5 102.3 21.0 474 n/a 5_adp: 0.1117 0.1531 0.010 1.094 5.5 101.5 21.1 474 n/a 5_regHadp: 0.1117 0.1531 0.010 1.094 5.5 101.5 21.1 474 n/a 5_occ: 0.1109 0.1524 0.010 1.094 5.5 101.5 21.1 474 n/a end: 0.1109 0.1523 0.010 1.094 5.3 101.3 20.9 474 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6113322_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6113322_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9100 Refinement macro-cycles (run) : 930.8100 Write final files (write_after_run_outputs) : 20.2500 Total : 953.9700 Total CPU time: 16.27 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:17 PST -0800 (1735494077.35 s) Start R-work = 0.1622, R-free = 0.1635 Final R-work = 0.1109, R-free = 0.1523 =============================================================================== Job complete usr+sys time: 996.10 seconds wall clock time: 16 minutes 58.71 seconds (1018.71 seconds total)