Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8230669.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_8230669.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8230669.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 =============================================================================== 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: 2.01, per 1000 atoms: 0.59 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: 0.47 Conformation dependent library (CDL) restraints added in 106.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 537 0.91 - 1.17: 1108 1.17 - 1.43: 657 1.43 - 1.68: 821 1.68 - 1.94: 30 Bond restraints: 3153 Sorted by residual: bond pdb=" CA VAL A 35 " pdb=" C VAL A 35 " ideal model delta sigma weight residual 1.526 1.763 -0.237 1.14e-02 7.69e+03 4.32e+02 bond pdb=" C ALA A 61 " pdb=" O ALA A 61 " ideal model delta sigma weight residual 1.236 1.494 -0.258 1.26e-02 6.30e+03 4.19e+02 bond pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta sigma weight residual 1.461 1.231 0.230 1.19e-02 7.06e+03 3.73e+02 bond pdb=" CD2 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.374 1.162 0.212 1.10e-02 8.26e+03 3.73e+02 bond pdb=" CA GLU A 116 " pdb=" C GLU A 116 " ideal model delta sigma weight residual 1.528 1.738 -0.210 1.25e-02 6.40e+03 2.83e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.01 - 4.10: 2787 4.10 - 8.19: 1926 8.19 - 12.29: 811 12.29 - 16.38: 221 16.38 - 20.47: 32 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH1 ARG A 145 " ideal model delta sigma weight residual 121.50 134.46 -12.96 1.00e+00 1.00e+00 1.68e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.36 108.72 10.64 8.40e-01 1.42e+00 1.60e+02 angle pdb=" CA SER A 161 " pdb=" C SER A 161 " pdb=" N PHE A 162 " ideal model delta sigma weight residual 117.07 131.07 -14.00 1.14e+00 7.69e-01 1.51e+02 angle pdb=" CA ILE A 91 " pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 120.83 108.26 12.57 1.07e+00 8.73e-01 1.38e+02 angle pdb=" O VAL A 186 " pdb=" C VAL A 186 " pdb=" N LEU A 187 " ideal model delta sigma weight residual 122.57 107.93 14.64 1.25e+00 6.40e-01 1.37e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 1262 15.63 - 31.26: 152 31.26 - 46.88: 46 46.88 - 62.51: 18 62.51 - 78.14: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALA A 29 " pdb=" N ALA A 29 " pdb=" CA ALA A 29 " pdb=" CB ALA A 29 " ideal model delta harmonic sigma weight residual -122.60 -147.83 25.23 0 2.50e+00 1.60e-01 1.02e+02 dihedral pdb=" N ALA A 29 " pdb=" C ALA A 29 " pdb=" CA ALA A 29 " pdb=" CB ALA A 29 " ideal model delta harmonic sigma weight residual 122.90 147.29 -24.39 0 2.50e+00 1.60e-01 9.52e+01 dihedral pdb=" N LYS A 12 " pdb=" C LYS A 12 " pdb=" CA LYS A 12 " pdb=" CB LYS A 12 " ideal model delta harmonic sigma weight residual 122.80 103.92 18.88 0 2.50e+00 1.60e-01 5.70e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.243: 116 0.243 - 0.486: 76 0.486 - 0.728: 34 0.728 - 0.970: 16 0.970 - 1.212: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 29 " pdb=" N ALA A 29 " pdb=" C ALA A 29 " pdb=" CB ALA A 29 " both_signs ideal model delta sigma weight residual False 2.48 1.27 1.21 2.00e-01 2.50e+01 3.68e+01 chirality pdb=" CA LEU A 166 " pdb=" N LEU A 166 " pdb=" C LEU A 166 " pdb=" CB LEU A 166 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.34e+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 -1.66 -0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.004 2.00e-02 2.50e+03 6.73e-02 1.36e+02 pdb=" CG PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.122 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.028 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.082 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.066 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.039 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG TYR A 141 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " -0.065 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.024 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.087 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.050 2.00e-02 2.50e+03 5.69e-02 9.72e+01 pdb=" CG PHE A 164 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.079 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.078 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.074 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.071 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 791 2.28 - 2.86: 7857 2.86 - 3.44: 10640 3.44 - 4.02: 15198 4.02 - 4.60: 22153 Nonbonded interactions: 56639 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.701 2.100 nonbonded pdb=" HB3 SER A 142 " pdb=" HG SER A 142 " model vdw 1.799 1.816 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.831 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.836 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.877 2.450 ... (remaining 56634 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_8230669_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= 0.2787 r_free= 0.1882 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.396415 | | target function (ml) not normalized (work): 71410.961748 | | target function (ml) not normalized (free): 3264.144358 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3202 0.2212 7.4962 5.0237| | 2: 3.63 - 2.88 1.00 2711 122 0.2644 0.1813 4.3332 4.3521| | 3: 2.88 - 2.52 1.00 2682 148 0.2541 0.1751 4.1876 4.1985| | 4: 2.52 - 2.29 1.00 2661 139 0.2554 0.1569 3.4823 3.544| | 5: 2.29 - 2.13 1.00 2678 122 0.2649 0.1555 3.3965 3.4339| | 6: 2.13 - 2.00 1.00 2692 117 0.2732 0.1907 3.3204 3.4314| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 1322.45| | 2: 3.63 - 2.88 2711 122 0.83 23.97 1.31 0.23 1322.45| | 3: 2.88 - 2.52 2682 148 0.73 32.98 1.28 0.23 1322.45| | 4: 2.52 - 2.29 2661 139 0.93 11.58 1.30 0.26 141.00| | 5: 2.29 - 2.13 2678 122 0.92 13.99 1.32 0.26 141.00| | 6: 2.13 - 2.00 2692 117 0.89 16.79 1.33 0.26 141.00| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 141.00 max = 1322.45 mean = 738.31| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 19.50| |phase err.(test): min = 0.00 max = 89.75 mean = 19.89| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.259 1557 Z= 5.417 Angle : 5.274 17.862 2118 Z= 3.651 Chirality : 0.388 1.212 243 Planarity : 0.030 0.083 284 Dihedral : 13.735 78.136 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.38 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 29.73 % 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: -3.11 (0.45), residues: 224 helix: -2.67 (0.35), residues: 108 sheet: -1.30 (0.77), residues: 40 loop : -1.07 (0.57), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.022 ARG A 28 TYR 0.072 0.025 TYR A 139 PHE 0.097 0.036 PHE A 119 HIS 0.079 0.024 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= 0.2787 r_free= 0.1882 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.396415 | | target function (ml) not normalized (work): 71410.961748 | | target function (ml) not normalized (free): 3264.144358 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2619 percent. r_work = 0.2913 r_free = 0.2031 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2861 0.2913 0.2031 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2861 0.2913 0.2031 n_refl.: 17050 remove outliers: r(all,work,free)=0.2151 0.2160 0.2031 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2125 0.2134 0.2015 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1618 0.1613 0.1710 n_refl.: 17045 remove outliers: r(all,work,free)=0.1616 0.1611 0.1710 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3835 398.952 362.766 0.647 1.017 0.400 11.894-9.307 99.02 97 4 0.1858 633.630 613.575 0.920 1.019 0.375 9.237-7.194 100.00 213 7 0.2165 518.246 510.955 0.956 1.018 0.371 7.162-5.571 100.00 427 22 0.2376 388.944 375.233 0.920 1.016 0.300 5.546-4.326 100.00 867 58 0.1428 533.958 528.408 0.955 1.013 0.231 4.315-3.360 100.00 1859 96 0.1311 507.799 503.466 1.012 1.008 0.201 3.356-2.611 100.00 3867 181 0.1643 333.595 329.368 1.013 0.998 0.034 2.608-2.000 99.99 8818 434 0.1635 217.447 213.452 1.035 0.982 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4005 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1611 r_free=0.1710 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1611 r_free=0.1710 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.414135 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.865530 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 0.1348 0.1641 0.0292 0.009 1.0 0.6 0.5 0.0 0 11.707 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.48 16.41 2.92 3.013 18.466 0.866 0.022 12.74 16.61 3.86 3.601 18.715 0.866 0.020 Individual atomic B min max mean iso aniso Overall: 6.27 113.91 19.97 4.06 1785 0 Protein: 6.27 112.94 17.21 4.06 1519 0 Water: 8.74 113.91 36.00 N/A 258 0 Other: 21.79 37.11 26.42 N/A 8 0 Chain A: 6.27 113.91 19.97 N/A 1785 0 Histogram: Values Number of atoms 6.27 - 17.03 1087 17.03 - 27.80 343 27.80 - 38.56 183 38.56 - 49.32 98 49.32 - 60.09 48 60.09 - 70.85 12 70.85 - 81.62 6 81.62 - 92.38 4 92.38 - 103.14 1 103.14 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1274 r_free=0.1661 r_work=0.1277 r_free=0.1669 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1277 r_free = 0.1669 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 = 0.1272 r_free = 0.1661 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.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1272 r_free= 0.1661 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019793 | | target function (ls_wunit_k1) not normalized (work): 321.352668 | | target function (ls_wunit_k1) not normalized (free): 27.273083 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1272 0.1661 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1903 0.1901 0.1992 n_refl.: 17043 remove outliers: r(all,work,free)=0.1903 0.1901 0.1992 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1875 0.1873 0.1976 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1290 0.1272 0.1655 n_refl.: 17043 remove outliers: r(all,work,free)=0.1290 0.1272 0.1655 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3541 306.534 287.068 0.649 1.014 0.393 11.894-9.307 99.02 97 4 0.1654 486.849 476.358 0.913 1.014 0.380 9.237-7.194 100.00 213 7 0.1814 398.193 395.063 0.955 1.014 0.351 7.162-5.571 100.00 427 22 0.1818 298.844 294.001 0.928 1.012 0.301 5.546-4.326 100.00 867 58 0.1042 410.265 407.887 0.953 1.010 0.205 4.315-3.360 100.00 1859 96 0.0929 390.166 389.701 1.014 1.006 0.191 3.356-2.611 100.00 3867 181 0.1295 256.317 255.083 1.014 0.999 0.081 2.608-2.000 99.99 8818 434 0.1349 167.075 165.635 1.027 0.987 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3646 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1655 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1272 r_free=0.1655 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1655 | n_water=258 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1281 r_free=0.1646 | n_water=252 | time (s): 19.010 (total time: 19.700) Filter (q & B) r_work=0.1281 r_free=0.1645 | n_water=250 | time (s): 1.920 (total time: 21.620) Compute maps r_work=0.1281 r_free=0.1645 | n_water=250 | time (s): 0.820 (total time: 22.440) Filter (map) r_work=0.1318 r_free=0.1628 | n_water=208 | time (s): 2.060 (total time: 24.500) Find peaks r_work=0.1318 r_free=0.1628 | n_water=208 | time (s): 0.470 (total time: 24.970) Add new water r_work=0.1547 r_free=0.1885 | n_water=370 | time (s): 1.400 (total time: 26.370) Refine new water occ: r_work=0.1344 r_free=0.1578 adp: r_work=0.1281 r_free=0.1578 occ: r_work=0.1284 r_free=0.1537 adp: r_work=0.1249 r_free=0.1543 occ: r_work=0.1250 r_free=0.1531 adp: r_work=0.1239 r_free=0.1531 ADP+occupancy (water only), MIN, final r_work=0.1239 r_free=0.1531 r_work=0.1239 r_free=0.1531 | n_water=370 | time (s): 17.470 (total time: 43.840) Filter (q & B) r_work=0.1240 r_free=0.1537 | n_water=360 | time (s): 1.940 (total time: 45.780) Filter (dist only) r_work=0.1241 r_free=0.1538 | n_water=359 | time (s): 30.070 (total time: 75.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.277294 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.987866 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 0.1216 0.1585 0.0368 0.008 0.9 2.2 0.5 0.0 0 12.139 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.16 15.85 3.68 4.162 21.090 0.988 0.018 12.03 15.99 3.96 4.251 21.353 0.988 0.018 Individual atomic B min max mean iso aniso Overall: 6.26 107.55 21.39 4.33 1886 0 Protein: 6.26 107.55 17.76 4.31 1519 0 Water: 8.28 68.19 36.43 N/A 359 0 Other: 24.78 45.20 34.62 N/A 8 0 Chain A: 6.26 107.55 19.43 N/A 1735 0 Chain S: 17.49 65.82 43.88 N/A 151 0 Histogram: Values Number of atoms 6.26 - 16.39 1009 16.39 - 26.52 388 26.52 - 36.65 213 36.65 - 46.78 167 46.78 - 56.91 71 56.91 - 67.04 25 67.04 - 77.17 6 77.17 - 87.30 4 87.30 - 97.43 1 97.43 - 107.55 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1599 r_work=0.1205 r_free=0.1598 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1598 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 = 0.1199 r_free = 0.1608 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1199 r_free= 0.1608 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017168 | | target function (ls_wunit_k1) not normalized (work): 278.741155 | | target function (ls_wunit_k1) not normalized (free): 25.433123 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1199 0.1608 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1810 0.1806 0.1938 n_refl.: 17043 remove outliers: r(all,work,free)=0.1810 0.1806 0.1938 n_refl.: 17043 overall B=-0.38 to atoms: r(all,work,free)=0.1783 0.1779 0.1919 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1193 0.1597 n_refl.: 17043 remove outliers: r(all,work,free)=0.1211 0.1192 0.1597 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 0.3502 308.562 276.980 0.612 1.006 0.364 11.894-9.307 99.02 97 4 0.1486 486.849 481.203 0.919 1.006 0.359 9.237-7.194 100.00 213 7 0.1696 398.193 397.914 0.968 1.006 0.285 7.162-5.571 100.00 427 22 0.1523 298.844 296.396 0.935 1.006 0.261 5.546-4.326 100.00 867 58 0.0862 410.265 407.688 0.958 1.005 0.206 4.315-3.360 100.00 1859 96 0.0846 390.166 389.267 1.014 1.004 0.201 3.356-2.611 100.00 3867 181 0.1207 256.317 255.440 1.011 1.001 0.121 2.608-2.000 99.99 8818 434 0.1322 167.075 166.002 1.017 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3426 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1597 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=0.1193 r_free=0.1599 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1599 | n_water=359 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1194 r_free=0.1599 | n_water=356 | time (s): 29.920 (total time: 30.520) Filter (q & B) r_work=0.1194 r_free=0.1599 | n_water=356 | time (s): 0.860 (total time: 31.380) Compute maps r_work=0.1194 r_free=0.1599 | n_water=356 | time (s): 0.630 (total time: 32.010) Filter (map) r_work=0.1265 r_free=0.1627 | n_water=259 | time (s): 1.950 (total time: 33.960) Find peaks r_work=0.1265 r_free=0.1627 | n_water=259 | time (s): 0.600 (total time: 34.560) Add new water r_work=0.1455 r_free=0.1829 | n_water=407 | time (s): 1.500 (total time: 36.060) Refine new water occ: r_work=0.1249 r_free=0.1586 adp: r_work=0.1243 r_free=0.1591 occ: r_work=0.1223 r_free=0.1554 adp: r_work=0.1213 r_free=0.1559 occ: r_work=0.1203 r_free=0.1535 adp: r_work=0.1194 r_free=0.1536 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1536 r_work=0.1194 r_free=0.1536 | n_water=407 | time (s): 33.030 (total time: 69.090) Filter (q & B) r_work=0.1198 r_free=0.1548 | n_water=396 | time (s): 1.600 (total time: 70.690) Filter (dist only) r_work=0.1198 r_free=0.1548 | n_water=396 | time (s): 28.390 (total time: 99.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.002850 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.162837 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 0.1173 0.1528 0.0355 0.009 1.0 3.2 0.5 0.0 0 1.001 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.73 15.28 3.55 4.370 21.510 0.163 4.985 11.55 15.47 3.91 4.900 21.435 0.163 4.966 Individual atomic B min max mean iso aniso Overall: 6.42 106.49 20.84 4.72 1923 0 Protein: 6.42 106.49 17.08 4.71 1519 0 Water: 9.03 62.94 34.98 N/A 396 0 Other: 25.97 45.68 34.01 N/A 8 0 Chain A: 6.42 106.49 18.74 N/A 1731 0 Chain S: 17.89 62.94 39.73 N/A 192 0 Histogram: Values Number of atoms 6.42 - 16.42 1080 16.42 - 26.43 347 26.43 - 36.44 229 36.44 - 46.44 156 46.44 - 56.45 79 56.45 - 66.46 19 66.46 - 76.47 5 76.47 - 86.47 4 86.47 - 96.48 2 96.48 - 106.49 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1547 r_work=0.1156 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1548 target_work(ml) = 4.966 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1532 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1149 r_free= 0.1532 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.959393 | | target function (ml) not normalized (work): 80515.739194 | | target function (ml) not normalized (free): 4181.626336 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1168 0.1149 0.1532 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1672 0.1666 0.1834 n_refl.: 17042 remove outliers: r(all,work,free)=0.1672 0.1666 0.1834 n_refl.: 17042 overall B=-0.40 to atoms: r(all,work,free)=0.1644 0.1638 0.1817 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1162 0.1144 0.1528 n_refl.: 17042 remove outliers: r(all,work,free)=0.1161 0.1142 0.1528 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 0.3612 302.488 281.381 0.567 1.006 0.340 11.894-9.307 99.02 97 4 0.1860 486.849 480.171 0.913 1.007 0.333 9.237-7.194 100.00 213 7 0.1902 398.193 397.634 0.977 1.007 0.236 7.162-5.571 100.00 427 22 0.1638 298.844 293.700 0.938 1.006 0.220 5.546-4.326 100.00 867 58 0.0945 410.265 406.870 0.964 1.006 0.211 4.315-3.360 100.00 1859 96 0.0888 390.166 388.192 1.012 1.004 0.191 3.356-2.611 100.00 3867 181 0.1282 256.317 254.089 1.014 1.001 0.152 2.608-2.000 99.99 8818 434 0.1068 167.075 165.663 1.022 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.4207 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1528 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=0.1143 r_free=0.1525 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1525 | n_water=396 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1142 r_free=0.1522 | n_water=395 | time (s): 33.760 (total time: 34.670) Filter (q & B) r_work=0.1142 r_free=0.1522 | n_water=395 | time (s): 1.120 (total time: 35.790) Compute maps r_work=0.1142 r_free=0.1522 | n_water=395 | time (s): 0.630 (total time: 36.420) Filter (map) r_work=0.1203 r_free=0.1542 | n_water=308 | time (s): 1.660 (total time: 38.080) Find peaks r_work=0.1203 r_free=0.1542 | n_water=308 | time (s): 0.480 (total time: 38.560) Add new water r_work=0.1333 r_free=0.1650 | n_water=430 | time (s): 2.000 (total time: 40.560) Refine new water occ: r_work=0.1178 r_free=0.1517 adp: r_work=0.1172 r_free=0.1519 occ: r_work=0.1156 r_free=0.1498 adp: r_work=0.1149 r_free=0.1498 occ: r_work=0.1142 r_free=0.1484 adp: r_work=0.1136 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1487 r_work=0.1136 r_free=0.1487 | n_water=430 | time (s): 36.140 (total time: 76.700) Filter (q & B) r_work=0.1140 r_free=0.1490 | n_water=421 | time (s): 1.760 (total time: 78.460) Filter (dist only) r_work=0.1143 r_free=0.1493 | n_water=419 | time (s): 33.010 (total time: 111.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.983705 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.166475 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 0.1540 0.0412 0.010 1.0 3.2 0.5 0.0 0 0.992 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.28 15.40 4.12 4.517 20.979 0.166 4.945 11.20 15.42 4.22 4.646 21.010 0.166 4.941 Individual atomic B min max mean iso aniso Overall: 5.96 104.14 20.75 4.91 1946 0 Protein: 5.96 104.14 16.68 4.90 1519 0 Water: 8.67 66.37 35.25 N/A 419 0 Other: 27.51 47.83 35.29 N/A 8 0 Chain A: 5.96 104.14 18.31 N/A 1730 0 Chain S: 16.46 66.37 40.30 N/A 216 0 Histogram: Values Number of atoms 5.96 - 15.78 1051 15.78 - 25.60 365 25.60 - 35.41 222 35.41 - 45.23 186 45.23 - 55.05 81 55.05 - 64.87 25 64.87 - 74.68 7 74.68 - 84.50 5 84.50 - 94.32 2 94.32 - 104.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.1120 r_free=0.1542 r_work=0.1120 r_free=0.1542 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1120 r_free = 0.1542 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1113 r_free = 0.1544 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1113 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.938330 | | target function (ml) not normalized (work): 80163.918927 | | target function (ml) not normalized (free): 4174.006035 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1113 0.1544 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1590 0.1578 0.1862 n_refl.: 17040 remove outliers: r(all,work,free)=0.1590 0.1578 0.1862 n_refl.: 17040 overall B=-0.32 to atoms: r(all,work,free)=0.1570 0.1557 0.1849 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1112 0.1540 n_refl.: 17040 remove outliers: r(all,work,free)=0.1133 0.1112 0.1540 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 0.3722 302.488 275.957 0.551 1.002 0.330 11.894-9.307 99.02 97 4 0.1786 486.849 479.562 0.921 1.003 0.320 9.237-7.194 100.00 213 7 0.1775 398.193 398.076 0.983 1.004 0.230 7.162-5.571 100.00 427 22 0.1568 298.844 292.966 0.941 1.003 0.212 5.546-4.326 100.00 867 58 0.0918 410.265 406.694 0.965 1.003 0.197 4.315-3.360 100.00 1859 96 0.0875 390.166 387.908 1.009 1.002 0.191 3.356-2.611 100.00 3867 181 0.1242 256.317 254.283 1.008 1.001 0.131 2.608-2.000 99.99 8818 434 0.1042 167.075 165.904 1.007 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1158 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1112 r_free=0.1540 After: r_work=0.1114 r_free=0.1540 ================================== NQH flips ================================== r_work=0.1114 r_free=0.1540 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1114 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1114 r_free=0.1540 | n_water=419 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1114 r_free=0.1533 | n_water=418 | time (s): 34.180 (total time: 34.800) Filter (q & B) r_work=0.1114 r_free=0.1534 | n_water=417 | time (s): 2.060 (total time: 36.860) Compute maps r_work=0.1114 r_free=0.1534 | n_water=417 | time (s): 0.740 (total time: 37.600) Filter (map) r_work=0.1178 r_free=0.1552 | n_water=330 | time (s): 1.790 (total time: 39.390) Find peaks r_work=0.1178 r_free=0.1552 | n_water=330 | time (s): 0.620 (total time: 40.010) Add new water r_work=0.1288 r_free=0.1641 | n_water=455 | time (s): 2.150 (total time: 42.160) Refine new water occ: r_work=0.1137 r_free=0.1493 adp: r_work=0.1130 r_free=0.1498 occ: r_work=0.1118 r_free=0.1475 adp: r_work=0.1111 r_free=0.1480 occ: r_work=0.1104 r_free=0.1465 adp: r_work=0.1099 r_free=0.1470 ADP+occupancy (water only), MIN, final r_work=0.1099 r_free=0.1470 r_work=0.1099 r_free=0.1470 | n_water=455 | time (s): 30.150 (total time: 72.310) Filter (q & B) r_work=0.1103 r_free=0.1477 | n_water=444 | time (s): 2.040 (total time: 74.350) Filter (dist only) r_work=0.1103 r_free=0.1478 | n_water=443 | time (s): 35.420 (total time: 109.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.969877 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.168108 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 0.1119 0.1486 0.0367 0.011 1.0 5.4 0.5 0.0 0 0.985 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 14.86 3.67 4.593 20.826 0.168 4.935 11.09 14.72 3.63 4.674 20.852 0.168 4.926 Individual atomic B min max mean iso aniso Overall: 5.39 102.74 20.77 5.04 1970 0 Protein: 5.39 102.74 16.33 5.03 1519 0 Water: 8.42 66.65 35.75 N/A 443 0 Other: 26.99 47.14 34.26 N/A 8 0 Chain A: 5.39 102.74 17.93 N/A 1730 0 Chain S: 15.98 66.65 41.26 N/A 240 0 Histogram: Values Number of atoms 5.39 - 15.13 1030 15.13 - 24.86 376 24.86 - 34.60 215 34.60 - 44.33 199 44.33 - 54.07 103 54.07 - 63.80 29 63.80 - 73.54 9 73.54 - 83.27 4 83.27 - 93.01 1 93.01 - 102.74 4 =========================== Idealize ADP of riding H ========================== r_work=0.1109 r_free=0.1472 r_work=0.1109 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1109 r_free = 0.1471 target_work(ml) = 4.926 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1476 target_work(ml) = 4.922 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1476 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.922306 | | target function (ml) not normalized (work): 79903.793900 | | target function (ml) not normalized (free): 4149.109851 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1115 0.1376 5.4542 5.649| | 2: 3.63 - 2.88 1.00 2711 122 0.1084 0.1428 5.2038 5.3292| | 3: 2.88 - 2.52 1.00 2681 148 0.1343 0.1589 5.1114 5.1611| | 4: 2.52 - 2.29 1.00 2661 139 0.0932 0.1444 4.6124 4.9054| | 5: 2.29 - 2.13 1.00 2678 122 0.0969 0.1483 4.5661 4.8657| | 6: 2.13 - 2.00 1.00 2692 117 0.1119 0.1803 4.5559 4.7986| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.69 1.00 0.96 6028.70| | 2: 3.63 - 2.88 2711 122 0.93 12.48 1.01 0.96 6028.70| | 3: 2.88 - 2.52 2681 148 0.88 18.41 0.99 0.96 6028.70| | 4: 2.52 - 2.29 2661 139 0.93 11.93 1.01 0.97 2029.95| | 5: 2.29 - 2.13 2678 122 0.92 13.89 1.00 0.97 2029.95| | 6: 2.13 - 2.00 2692 117 0.90 16.56 0.99 0.97 2029.95| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2029.95 max = 6028.70 mean = 4050.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.62| |phase err.(test): min = 0.00 max = 88.04 mean = 13.09| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1103 0.1476 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1564 0.1553 0.1799 n_refl.: 17040 remove outliers: r(all,work,free)=0.1564 0.1553 0.1799 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1549 0.1538 0.1791 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1103 0.1477 n_refl.: 17040 remove outliers: r(all,work,free)=0.1122 0.1103 0.1477 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 0.3621 302.488 279.101 0.552 1.005 0.330 11.894-9.307 99.02 97 4 0.1756 486.849 478.553 0.921 1.006 0.330 9.237-7.194 100.00 213 7 0.1723 398.193 400.798 0.984 1.006 0.220 7.162-5.571 100.00 427 22 0.1558 298.844 293.797 0.936 1.005 0.215 5.546-4.326 100.00 867 58 0.0912 410.265 406.759 0.962 1.005 0.198 4.315-3.360 100.00 1859 96 0.0879 390.166 387.861 1.003 1.003 0.187 3.356-2.611 100.00 3867 181 0.1228 256.317 254.173 1.001 1.001 0.151 2.608-2.000 99.99 8818 434 0.1036 167.075 165.763 0.995 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8328 ================= 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 : 0.2787 0.1882 0.082 5.274 8.8 119.3 19.9 258 0.000 1_bss: 0.1611 0.1710 0.082 5.274 8.5 118.9 19.5 258 0.000 1_settarget: 0.1611 0.1710 0.082 5.274 8.5 118.9 19.5 258 0.000 1_nqh: 0.1611 0.1710 0.082 5.274 8.5 118.9 19.5 258 0.000 1_weight: 0.1611 0.1710 0.082 5.274 8.5 118.9 19.5 258 0.000 1_xyzrec: 0.1348 0.1641 0.009 0.978 8.5 118.9 19.5 258 0.153 1_adp: 0.1274 0.1661 0.009 0.978 6.3 113.9 20.0 258 0.153 1_regHadp: 0.1277 0.1669 0.009 0.978 6.3 113.9 20.0 258 0.153 1_occ: 0.1272 0.1661 0.009 0.978 6.3 113.9 20.0 258 0.153 2_bss: 0.1272 0.1655 0.009 0.978 5.9 113.5 19.6 258 0.153 2_settarget: 0.1272 0.1655 0.009 0.978 5.9 113.5 19.6 258 0.153 2_updatecdl: 0.1272 0.1655 0.009 0.996 5.9 113.5 19.6 258 0.153 2_nqh: 0.1272 0.1655 0.009 0.996 5.9 113.5 19.6 258 0.153 2_sol: 0.1241 0.1538 0.009 0.996 5.9 112.6 20.9 359 n/a 2_weight: 0.1241 0.1538 0.009 0.996 5.9 112.6 20.9 359 n/a 2_xyzrec: 0.1216 0.1585 0.008 0.932 5.9 112.6 20.9 359 n/a 2_adp: 0.1203 0.1599 0.008 0.932 6.3 107.6 21.4 359 n/a 2_regHadp: 0.1205 0.1598 0.008 0.932 6.3 107.6 21.4 359 n/a 2_occ: 0.1199 0.1608 0.008 0.932 6.3 107.6 21.4 359 n/a 3_bss: 0.1192 0.1597 0.008 0.932 5.9 107.2 21.0 359 n/a 3_settarget: 0.1192 0.1597 0.008 0.932 5.9 107.2 21.0 359 n/a 3_updatecdl: 0.1192 0.1597 0.008 0.932 5.9 107.2 21.0 359 n/a 3_nqh: 0.1193 0.1599 0.008 0.932 5.9 107.2 21.0 359 n/a 3_sol: 0.1198 0.1548 0.008 0.932 5.9 107.2 21.0 396 n/a 3_weight: 0.1198 0.1548 0.008 0.932 5.9 107.2 21.0 396 n/a 3_xyzrec: 0.1173 0.1528 0.009 0.978 5.9 107.2 21.0 396 n/a 3_adp: 0.1155 0.1547 0.009 0.978 6.4 106.5 20.8 396 n/a 3_regHadp: 0.1156 0.1548 0.009 0.978 6.4 106.5 20.8 396 n/a 3_occ: 0.1149 0.1532 0.009 0.978 6.4 106.5 20.8 396 n/a 4_bss: 0.1142 0.1528 0.009 0.978 6.0 106.1 20.4 396 n/a 4_settarget: 0.1142 0.1528 0.009 0.978 6.0 106.1 20.4 396 n/a 4_updatecdl: 0.1142 0.1528 0.009 0.978 6.0 106.1 20.4 396 n/a 4_nqh: 0.1143 0.1525 0.009 0.978 6.0 106.1 20.4 396 n/a 4_sol: 0.1143 0.1493 0.009 0.978 6.0 106.1 20.7 419 n/a 4_weight: 0.1143 0.1493 0.009 0.978 6.0 106.1 20.7 419 n/a 4_xyzrec: 0.1128 0.1540 0.010 1.002 6.0 106.1 20.7 419 n/a 4_adp: 0.1120 0.1542 0.010 1.002 6.0 104.1 20.8 419 n/a 4_regHadp: 0.1120 0.1542 0.010 1.002 6.0 104.1 20.8 419 n/a 4_occ: 0.1113 0.1544 0.010 1.002 6.0 104.1 20.8 419 n/a 5_bss: 0.1112 0.1540 0.010 1.002 5.6 103.8 20.4 419 n/a 5_settarget: 0.1112 0.1540 0.010 1.002 5.6 103.8 20.4 419 n/a 5_updatecdl: 0.1112 0.1540 0.010 1.002 5.6 103.8 20.4 419 n/a 5_setrh: 0.1114 0.1540 0.010 1.002 5.6 103.8 20.4 419 n/a 5_nqh: 0.1114 0.1540 0.010 1.002 5.6 103.8 20.4 419 n/a 5_sol: 0.1103 0.1478 0.010 1.002 5.6 103.8 20.7 443 n/a 5_weight: 0.1103 0.1478 0.010 1.002 5.6 103.8 20.7 443 n/a 5_xyzrec: 0.1119 0.1486 0.011 1.018 5.6 103.8 20.7 443 n/a 5_adp: 0.1109 0.1472 0.011 1.018 5.4 102.7 20.8 443 n/a 5_regHadp: 0.1109 0.1471 0.011 1.018 5.4 102.7 20.8 443 n/a 5_occ: 0.1103 0.1476 0.011 1.018 5.4 102.7 20.8 443 n/a end: 0.1103 0.1477 0.011 1.018 5.2 102.5 20.5 443 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8230669_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8230669_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1900 Refinement macro-cycles (run) : 919.5800 Write final files (write_after_run_outputs) : 19.5400 Total : 942.3100 Total CPU time: 16.10 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:06 PST -0800 (1735494066.92 s) Start R-work = 0.1611, R-free = 0.1710 Final R-work = 0.1103, R-free = 0.1477 =============================================================================== Job complete usr+sys time: 989.76 seconds wall clock time: 16 minutes 52.75 seconds (1012.75 seconds total)