Starting phenix.refine on Sun Dec 29 09:10:03 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=3 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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" } 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: 2.09, per 1000 atoms: 0.62 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 122.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.45 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 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3623 r_free= 0.2082 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.470161 | | target function (ml) not normalized (work): 22037.893042 | | target function (ml) not normalized (free): 1151.691265 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3806 0.2300 4.8557 4.9029| | 2: 3.78 - 3.00 1.00 2430 110 0.3399 0.1712 4.0736 4.1408| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2500 142 0.50 48.91 0.83 0.13 6617.57| | 2: 3.78 - 3.00 2430 110 0.94 11.26 1.48 0.26 448.52| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 378.91 max = 12080.99 mean = 3576.84| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.35| |phase err.(test): min = 0.00 max = 89.98 mean = 33.55| |-----------------------------------------------------------------------------| ----------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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3623 r_free= 0.2082 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.470161 | | target function (ml) not normalized (work): 22037.893042 | | target function (ml) not normalized (free): 1151.691265 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3578 0.3656 0.2156 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3578 0.3656 0.2156 n_refl.: 5182 remove outliers: r(all,work,free)=0.2533 0.2556 0.2156 n_refl.: 5178 overall B=-2.84 to atoms: r(all,work,free)=0.2425 0.2444 0.2115 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1582 0.1579 0.1643 n_refl.: 5178 remove outliers: r(all,work,free)=0.1580 0.1577 0.1643 n_refl.: 5177 ======================== 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 0.4018 444.998 408.992 0.656 1.072 0.394 11.894-9.307 99.02 97 4 0.1861 714.390 693.306 0.935 1.068 0.377 9.237-7.194 100.00 213 7 0.2168 584.229 576.907 0.973 1.060 0.374 7.162-5.571 100.00 427 22 0.2379 438.393 423.030 0.938 1.047 0.304 5.546-4.326 100.00 867 58 0.1422 601.851 594.331 0.979 1.025 0.225 4.315-3.360 100.00 1859 96 0.1322 572.367 565.656 1.055 0.988 0.189 3.356-3.002 100.00 1373 60 0.1592 440.861 433.160 1.072 0.951 0.086 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.6520 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1577 r_free=0.1643 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1577 r_free=0.1643 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.667433 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.772184 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1150 0.1770 0.0620 0.010 1.0 2.2 0.5 0.0 0 9.834 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.50 17.70 6.20 3.013 16.017 1.772 0.018 10.12 17.63 7.51 4.920 16.240 1.772 0.014 Individual atomic B min max mean iso aniso Overall: 2.23 111.46 17.47 5.26 1785 0 Protein: 2.23 110.99 14.77 5.25 1519 0 Water: 4.02 111.46 33.13 N/A 258 0 Other: 17.32 37.83 24.05 N/A 8 0 Chain A: 2.23 111.46 17.47 N/A 1785 0 Histogram: Values Number of atoms 2.23 - 13.15 918 13.15 - 24.08 477 24.08 - 35.00 194 35.00 - 45.92 108 45.92 - 56.84 53 56.84 - 67.77 18 67.77 - 78.69 8 78.69 - 89.61 5 89.61 - 100.53 1 100.53 - 111.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.1012 r_free=0.1763 r_work=0.1006 r_free=0.1770 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1006 r_free = 0.1770 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1010 r_free = 0.1781 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1010 r_free= 0.1781 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014017 | | target function (ls_wunit_k1) not normalized (work): 69.031968 | | target function (ls_wunit_k1) not normalized (free): 10.324554 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1049 0.1010 0.1781 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2105 0.2105 0.2224 n_refl.: 5177 remove outliers: r(all,work,free)=0.2105 0.2105 0.2224 n_refl.: 5177 overall B=-1.02 to atoms: r(all,work,free)=0.2062 0.2059 0.2212 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1054 0.1015 0.1790 n_refl.: 5177 remove outliers: r(all,work,free)=0.1052 0.1013 0.1790 n_refl.: 5176 ======================== 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 0.3382 323.635 309.865 0.660 1.012 0.370 11.894-9.307 99.02 97 4 0.1526 524.028 517.085 0.985 1.013 0.351 9.237-7.194 100.00 213 7 0.1660 428.551 428.825 1.024 1.012 0.323 7.162-5.571 100.00 427 22 0.1625 321.575 318.510 0.987 1.010 0.302 5.546-4.326 100.00 867 58 0.0906 441.477 438.626 0.997 1.005 0.198 4.315-3.360 100.00 1859 96 0.0769 419.850 419.653 1.047 0.998 0.196 3.356-3.002 100.00 1373 60 0.1000 323.386 321.701 1.023 0.990 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.6257 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1013 r_free=0.1790 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1013 r_free=0.1790 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1013 r_free=0.1790 | n_water=258 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1040 r_free=0.1784 | n_water=248 | time (s): 21.940 (total time: 22.550) Filter (q & B) r_work=0.1041 r_free=0.1786 | n_water=245 | time (s): 1.890 (total time: 24.440) Compute maps r_work=0.1041 r_free=0.1786 | n_water=245 | time (s): 0.600 (total time: 25.040) Filter (map) r_work=0.1328 r_free=0.1909 | n_water=149 | time (s): 1.510 (total time: 26.550) Find peaks r_work=0.1328 r_free=0.1909 | n_water=149 | time (s): 0.590 (total time: 27.140) Add new water r_work=0.1677 r_free=0.2172 | n_water=237 | time (s): 1.770 (total time: 28.910) Refine new water occ: r_work=0.1155 r_free=0.1715 adp: r_work=0.1136 r_free=0.1728 occ: r_work=0.1129 r_free=0.1702 adp: r_work=0.1121 r_free=0.1714 occ: r_work=0.1119 r_free=0.1694 adp: r_work=0.1116 r_free=0.1699 ADP+occupancy (water only), MIN, final r_work=0.1116 r_free=0.1699 r_work=0.1116 r_free=0.1699 | n_water=237 | time (s): 3.390 (total time: 32.300) Filter (q & B) r_work=0.1116 r_free=0.1699 | n_water=237 | time (s): 0.770 (total time: 33.070) Filter (dist only) r_work=0.1124 r_free=0.1679 | n_water=234 | time (s): 20.090 (total time: 53.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.755930 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.728244 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1019 0.1803 0.0784 0.009 1.0 3.8 0.5 0.6 0 10.878 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.19 18.03 7.84 4.648 16.806 2.728 0.014 9.47 18.19 8.73 5.411 17.096 2.728 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.33 16.48 6.36 1761 0 Protein: 0.00 108.33 14.79 6.36 1519 0 Water: 0.00 62.72 27.29 N/A 234 0 Other: 11.66 31.81 20.00 N/A 8 0 Chain A: 0.00 108.33 15.57 N/A 1674 0 Chain S: 1.21 60.22 34.03 N/A 87 0 Histogram: Values Number of atoms 0.00 - 10.83 679 10.83 - 21.67 675 21.67 - 32.50 217 32.50 - 43.33 111 43.33 - 54.17 38 54.17 - 65.00 30 65.00 - 75.83 4 75.83 - 86.67 2 86.67 - 97.50 3 97.50 - 108.33 2 =========================== Idealize ADP of riding H ========================== r_work=0.0947 r_free=0.1819 r_work=0.0943 r_free=0.1817 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0943 r_free = 0.1817 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0941 r_free = 0.1814 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0941 r_free= 0.1814 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012028 | | target function (ls_wunit_k1) not normalized (work): 59.226930 | | target function (ls_wunit_k1) not normalized (free): 9.710166 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0984 0.0941 0.1814 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2126 0.2128 0.2231 n_refl.: 5176 remove outliers: r(all,work,free)=0.2126 0.2128 0.2231 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2126 0.2128 0.2231 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0982 0.0938 0.1824 n_refl.: 5176 remove outliers: r(all,work,free)=0.0980 0.0936 0.1824 n_refl.: 5175 ======================== 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 0.3142 325.749 307.843 0.659 1.006 0.360 11.894-9.307 99.02 97 4 0.1398 524.028 519.176 0.984 1.008 0.340 9.237-7.194 100.00 213 7 0.1466 428.551 429.537 1.025 1.008 0.304 7.162-5.571 100.00 427 22 0.1439 321.575 319.469 0.999 1.006 0.290 5.546-4.326 100.00 867 58 0.0796 441.477 438.886 1.008 1.004 0.230 4.315-3.360 100.00 1859 96 0.0724 419.850 419.720 1.055 1.000 0.210 3.356-3.002 100.00 1373 60 0.0969 323.386 322.038 1.032 0.995 0.100 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9553 b_overall=-4.1872 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0936 r_free=0.1824 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0937 r_free=0.1828 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0937 r_free=0.1828 | n_water=234 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.0966 r_free=0.1816 | n_water=228 | time (s): 17.520 (total time: 18.240) Filter (q & B) r_work=0.0994 r_free=0.1836 | n_water=227 | time (s): 1.330 (total time: 19.570) Compute maps r_work=0.0994 r_free=0.1836 | n_water=227 | time (s): 0.510 (total time: 20.080) Filter (map) r_work=0.1264 r_free=0.1880 | n_water=150 | time (s): 1.520 (total time: 21.600) Find peaks r_work=0.1264 r_free=0.1880 | n_water=150 | time (s): 0.400 (total time: 22.000) Add new water r_work=0.1652 r_free=0.2244 | n_water=235 | time (s): 1.490 (total time: 23.490) Refine new water occ: r_work=0.1073 r_free=0.1784 adp: r_work=0.1070 r_free=0.1788 occ: r_work=0.1057 r_free=0.1768 adp: r_work=0.1057 r_free=0.1774 occ: r_work=0.1046 r_free=0.1757 adp: r_work=0.1046 r_free=0.1762 ADP+occupancy (water only), MIN, final r_work=0.1046 r_free=0.1762 r_work=0.1046 r_free=0.1762 | n_water=235 | time (s): 11.820 (total time: 35.310) Filter (q & B) r_work=0.1047 r_free=0.1774 | n_water=233 | time (s): 1.830 (total time: 37.140) Filter (dist only) r_work=0.1056 r_free=0.1780 | n_water=231 | time (s): 18.310 (total time: 55.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.114767 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.225762 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0951 0.1838 0.0887 0.011 1.1 3.8 0.5 0.0 0 0.557 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.51 18.38 8.87 5.319 17.503 0.226 5.165 9.06 18.20 9.14 7.055 17.512 0.226 5.073 Individual atomic B min max mean iso aniso Overall: 0.00 107.63 16.18 8.71 1758 0 Protein: 0.00 107.63 14.95 8.71 1519 0 Water: 0.00 60.93 24.05 N/A 231 0 Other: 8.98 36.71 21.61 N/A 8 0 Chain A: 0.00 107.63 15.60 N/A 1659 0 Chain S: 0.00 60.93 25.78 N/A 99 0 Histogram: Values Number of atoms 0.00 - 10.76 684 10.76 - 21.53 658 21.53 - 32.29 239 32.29 - 43.05 111 43.05 - 53.82 30 53.82 - 64.58 16 64.58 - 75.34 13 75.34 - 86.11 2 86.11 - 96.87 4 96.87 - 107.63 1 =========================== Idealize ADP of riding H ========================== r_work=0.0906 r_free=0.1820 r_work=0.0910 r_free=0.1828 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0910 r_free = 0.1828 target_work(ml) = 5.076 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0899 r_free = 0.1815 target_work(ml) = 5.069 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0899 r_free= 0.1815 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.069114 | | target function (ml) not normalized (work): 24955.249888 | | target function (ml) not normalized (free): 1826.448261 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0946 0.0899 0.1815 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2060 0.2059 0.2193 n_refl.: 5175 remove outliers: r(all,work,free)=0.2060 0.2059 0.2193 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2060 0.2059 0.2193 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0935 0.0890 0.1801 n_refl.: 5175 remove outliers: r(all,work,free)=0.0935 0.0890 0.1801 n_refl.: 5175 ======================== 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 0.3723 325.749 298.798 0.589 0.991 0.324 11.894-9.307 99.02 97 4 0.1832 524.028 506.029 0.950 0.995 0.320 9.237-7.194 100.00 213 7 0.1861 428.551 422.584 1.008 0.997 0.310 7.162-5.571 100.00 427 22 0.1817 321.575 312.133 0.980 0.998 0.280 5.546-4.326 100.00 867 58 0.0909 441.477 436.134 1.004 1.000 0.230 4.315-3.360 100.00 1859 96 0.0597 419.850 419.422 1.056 1.002 0.220 3.356-3.002 100.00 1373 60 0.0613 323.386 323.134 1.034 1.004 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.4469 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0890 r_free=0.1801 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0890 r_free=0.1801 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0890 r_free=0.1801 | n_water=231 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.0908 r_free=0.1796 | n_water=226 | time (s): 17.900 (total time: 18.610) Filter (q & B) r_work=0.0949 r_free=0.1821 | n_water=224 | time (s): 1.570 (total time: 20.180) Compute maps r_work=0.0949 r_free=0.1821 | n_water=224 | time (s): 0.460 (total time: 20.640) Filter (map) r_work=0.1241 r_free=0.1875 | n_water=158 | time (s): 1.250 (total time: 21.890) Find peaks r_work=0.1241 r_free=0.1875 | n_water=158 | time (s): 0.570 (total time: 22.460) Add new water r_work=0.1572 r_free=0.2114 | n_water=232 | time (s): 1.630 (total time: 24.090) Refine new water occ: r_work=0.1006 r_free=0.1793 adp: r_work=0.1003 r_free=0.1800 occ: r_work=0.0993 r_free=0.1782 adp: r_work=0.0993 r_free=0.1787 occ: r_work=0.0982 r_free=0.1770 adp: r_work=0.0983 r_free=0.1774 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1774 r_work=0.0983 r_free=0.1774 | n_water=232 | time (s): 11.060 (total time: 35.150) Filter (q & B) r_work=0.0983 r_free=0.1774 | n_water=232 | time (s): 0.990 (total time: 36.140) Filter (dist only) r_work=0.0984 r_free=0.1771 | n_water=230 | time (s): 18.200 (total time: 54.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.980851 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.216182 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0897 0.1776 0.0879 0.011 1.1 4.5 0.5 0.0 0 0.490 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.97 17.76 8.79 6.806 17.702 0.216 5.029 8.73 17.94 9.22 8.184 17.863 0.216 4.962 Individual atomic B min max mean iso aniso Overall: 0.00 111.03 16.55 10.74 1757 0 Protein: 0.00 111.03 15.45 10.73 1519 0 Water: 0.00 59.86 23.59 N/A 230 0 Other: 11.07 36.01 22.27 N/A 8 0 Chain A: 0.00 111.03 15.97 N/A 1648 0 Chain S: 0.38 59.86 25.26 N/A 109 0 Histogram: Values Number of atoms 0.00 - 11.10 713 11.10 - 22.21 635 22.21 - 33.31 235 33.31 - 44.41 106 44.41 - 55.51 34 55.51 - 66.62 14 66.62 - 77.72 13 77.72 - 88.82 3 88.82 - 99.92 3 99.92 - 111.03 1 =========================== Idealize ADP of riding H ========================== r_work=0.0873 r_free=0.1794 r_work=0.0877 r_free=0.1801 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0877 r_free = 0.1801 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0869 r_free = 0.1784 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0869 r_free= 0.1784 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.960956 | | target function (ml) not normalized (work): 24422.785247 | | target function (ml) not normalized (free): 2074.868136 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0915 0.0869 0.1784 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2107 0.2112 0.2142 n_refl.: 5175 remove outliers: r(all,work,free)=0.2107 0.2112 0.2142 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2107 0.2112 0.2142 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0914 0.0869 0.1783 n_refl.: 5175 remove outliers: r(all,work,free)=0.0914 0.0869 0.1783 n_refl.: 5175 ======================== 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 0.3746 325.749 300.220 0.582 0.987 0.318 11.894-9.307 99.02 97 4 0.1970 524.028 502.910 0.942 0.992 0.308 9.237-7.194 100.00 213 7 0.2058 428.551 422.155 1.011 0.995 0.290 7.162-5.571 100.00 427 22 0.1972 321.575 311.593 0.991 0.997 0.280 5.546-4.326 100.00 867 58 0.0961 441.477 436.508 1.014 0.999 0.234 4.315-3.360 100.00 1859 96 0.0555 419.850 419.819 1.075 1.002 0.220 3.356-3.002 100.00 1373 60 0.0448 323.386 323.343 1.053 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.2781 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0869 r_free=0.1783 After: r_work=0.0872 r_free=0.1782 ================================== NQH flips ================================== r_work=0.0872 r_free=0.1782 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0872 r_free=0.1782 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0872 r_free=0.1782 | n_water=230 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.0884 r_free=0.1792 | n_water=227 | time (s): 18.500 (total time: 19.200) Filter (q & B) r_work=0.0985 r_free=0.1847 | n_water=224 | time (s): 1.350 (total time: 20.550) Compute maps r_work=0.0985 r_free=0.1847 | n_water=224 | time (s): 0.510 (total time: 21.060) Filter (map) r_work=0.1234 r_free=0.1957 | n_water=165 | time (s): 1.490 (total time: 22.550) Find peaks r_work=0.1234 r_free=0.1957 | n_water=165 | time (s): 0.580 (total time: 23.130) Add new water r_work=0.1517 r_free=0.2216 | n_water=232 | time (s): 1.770 (total time: 24.900) Refine new water occ: r_work=0.0976 r_free=0.1788 adp: r_work=0.0967 r_free=0.1791 occ: r_work=0.0961 r_free=0.1774 adp: r_work=0.0960 r_free=0.1782 occ: r_work=0.0954 r_free=0.1766 adp: r_work=0.0953 r_free=0.1774 ADP+occupancy (water only), MIN, final r_work=0.0953 r_free=0.1774 r_work=0.0953 r_free=0.1774 | n_water=232 | time (s): 9.650 (total time: 34.550) Filter (q & B) r_work=0.0954 r_free=0.1774 | n_water=231 | time (s): 1.300 (total time: 35.850) Filter (dist only) r_work=0.0952 r_free=0.1780 | n_water=230 | time (s): 18.450 (total time: 54.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.968081 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.234127 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0893 0.1772 0.0878 0.011 1.2 6.4 0.5 0.6 0 0.484 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.93 17.72 8.78 8.161 18.205 0.234 4.981 8.78 17.90 9.12 9.164 18.319 0.234 4.937 Individual atomic B min max mean iso aniso Overall: 0.00 115.97 16.84 12.18 1757 0 Protein: 0.00 115.97 15.85 12.17 1519 0 Water: 0.00 56.40 23.18 N/A 230 0 Other: 9.37 35.16 21.41 N/A 8 0 Chain A: 0.00 115.97 16.31 N/A 1641 0 Chain S: 0.00 53.21 24.38 N/A 116 0 Histogram: Values Number of atoms 0.00 - 11.60 718 11.60 - 23.19 633 23.19 - 34.79 241 34.79 - 46.39 103 46.39 - 57.99 31 57.99 - 69.58 12 69.58 - 81.18 13 81.18 - 92.78 3 92.78 - 104.38 2 104.38 - 115.97 1 =========================== Idealize ADP of riding H ========================== r_work=0.0878 r_free=0.1790 r_work=0.0881 r_free=0.1795 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0881 r_free = 0.1795 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0875 r_free = 0.1781 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0875 r_free= 0.1781 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 4.937326 | | target function (ml) not normalized (work): 24306.454356 | | target function (ml) not normalized (free): 2129.030723 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1246 0.1744 5.5153 6.2121| | 2: 3.78 - 3.00 1.00 2430 110 0.0422 0.1846 4.3444 11.336| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2493 142 0.92 12.01 1.00 0.98 12943.09| | 2: 3.78 - 3.00 2430 110 0.99 1.80 1.00 1.00 883.14| |alpha: min = 0.96 max = 1.00 mean = 0.99| |beta: min = 569.40 max = 21855.98 mean = 6990.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.82 mean = 6.97| |phase err.(test): min = 0.00 max = 82.66 mean = 7.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0920 0.0875 0.1781 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2142 0.2149 0.2160 n_refl.: 5175 remove outliers: r(all,work,free)=0.2142 0.2149 0.2160 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2142 0.2149 0.2160 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0920 0.0875 0.1782 n_refl.: 5175 remove outliers: r(all,work,free)=0.0920 0.0875 0.1782 n_refl.: 5175 ======================== 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 0.3790 325.749 299.220 0.580 0.989 0.320 11.894-9.307 99.02 97 4 0.1889 524.028 505.720 0.948 0.995 0.315 9.237-7.194 100.00 213 7 0.2132 428.551 420.825 1.008 0.998 0.294 7.162-5.571 100.00 427 22 0.2066 321.575 310.994 0.990 1.000 0.280 5.546-4.326 100.00 867 58 0.1011 441.477 436.108 1.021 1.001 0.233 4.315-3.360 100.00 1859 96 0.0549 419.850 419.789 1.094 1.002 0.227 3.356-3.002 100.00 1373 60 0.0402 323.386 323.007 1.073 1.003 0.054 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.0849 ================= 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 : 0.3623 0.2082 0.082 5.274 8.8 119.3 19.9 258 0.000 1_bss: 0.1577 0.1643 0.082 5.274 6.0 116.5 17.0 258 0.000 1_settarget: 0.1577 0.1643 0.082 5.274 6.0 116.5 17.0 258 0.000 1_nqh: 0.1577 0.1643 0.082 5.274 6.0 116.5 17.0 258 0.000 1_weight: 0.1577 0.1643 0.082 5.274 6.0 116.5 17.0 258 0.000 1_xyzrec: 0.1150 0.1770 0.010 0.973 6.0 116.5 17.0 258 0.210 1_adp: 0.1012 0.1763 0.010 0.973 2.2 111.5 17.5 258 0.210 1_regHadp: 0.1006 0.1770 0.010 0.973 2.2 111.5 17.5 258 0.210 1_occ: 0.1010 0.1781 0.010 0.973 2.2 111.5 17.5 258 0.210 2_bss: 0.1013 0.1790 0.010 0.973 1.2 110.4 16.4 258 0.210 2_settarget: 0.1013 0.1790 0.010 0.973 1.2 110.4 16.4 258 0.210 2_updatecdl: 0.1013 0.1790 0.010 0.994 1.2 110.4 16.4 258 0.210 2_nqh: 0.1013 0.1790 0.010 0.994 1.2 110.4 16.4 258 0.210 2_sol: 0.1124 0.1679 0.010 0.994 1.0 110.0 15.9 234 n/a 2_weight: 0.1124 0.1679 0.010 0.994 1.0 110.0 15.9 234 n/a 2_xyzrec: 0.1019 0.1803 0.009 0.962 1.0 110.0 15.9 234 n/a 2_adp: 0.0947 0.1819 0.009 0.962 0.0 108.3 16.5 234 n/a 2_regHadp: 0.0943 0.1817 0.009 0.962 0.0 108.3 16.5 234 n/a 2_occ: 0.0941 0.1814 0.009 0.962 0.0 108.3 16.5 234 n/a 3_bss: 0.0936 0.1824 0.009 0.962 0.0 108.3 16.5 234 n/a 3_settarget: 0.0936 0.1824 0.009 0.962 0.0 108.3 16.5 234 n/a 3_updatecdl: 0.0936 0.1824 0.009 0.968 0.0 108.3 16.5 234 n/a 3_nqh: 0.0937 0.1828 0.009 0.968 0.0 108.3 16.5 234 n/a 3_sol: 0.1056 0.1780 0.009 0.968 0.0 108.3 16.2 231 n/a 3_weight: 0.1056 0.1780 0.009 0.968 0.0 108.3 16.2 231 n/a 3_xyzrec: 0.0951 0.1838 0.011 1.074 0.0 108.3 16.2 231 n/a 3_adp: 0.0906 0.1820 0.011 1.074 0.0 107.6 16.2 231 n/a 3_regHadp: 0.0910 0.1828 0.011 1.074 0.0 107.6 16.2 231 n/a 3_occ: 0.0899 0.1815 0.011 1.074 0.0 107.6 16.2 231 n/a 4_bss: 0.0890 0.1801 0.011 1.074 0.0 107.6 16.2 231 n/a 4_settarget: 0.0890 0.1801 0.011 1.074 0.0 107.6 16.2 231 n/a 4_updatecdl: 0.0890 0.1801 0.011 1.086 0.0 107.6 16.2 231 n/a 4_nqh: 0.0890 0.1801 0.011 1.086 0.0 107.6 16.2 231 n/a 4_sol: 0.0984 0.1771 0.011 1.086 0.0 107.6 16.2 230 n/a 4_weight: 0.0984 0.1771 0.011 1.086 0.0 107.6 16.2 230 n/a 4_xyzrec: 0.0897 0.1776 0.011 1.057 0.0 107.6 16.2 230 n/a 4_adp: 0.0873 0.1794 0.011 1.057 0.0 111.0 16.5 230 n/a 4_regHadp: 0.0877 0.1801 0.011 1.057 0.0 111.0 16.5 230 n/a 4_occ: 0.0869 0.1784 0.011 1.057 0.0 111.0 16.5 230 n/a 5_bss: 0.0869 0.1783 0.011 1.057 0.0 111.0 16.5 230 n/a 5_settarget: 0.0869 0.1783 0.011 1.057 0.0 111.0 16.5 230 n/a 5_updatecdl: 0.0869 0.1783 0.011 1.072 0.0 111.0 16.5 230 n/a 5_setrh: 0.0872 0.1782 0.011 1.072 0.0 111.0 16.5 230 n/a 5_nqh: 0.0872 0.1782 0.011 1.072 0.0 111.0 16.5 230 n/a 5_sol: 0.0952 0.1780 0.011 1.072 0.0 111.0 16.6 230 n/a 5_weight: 0.0952 0.1780 0.011 1.072 0.0 111.0 16.6 230 n/a 5_xyzrec: 0.0893 0.1772 0.011 1.151 0.0 111.0 16.6 230 n/a 5_adp: 0.0878 0.1790 0.011 1.151 0.0 116.0 16.8 230 n/a 5_regHadp: 0.0881 0.1795 0.011 1.151 0.0 116.0 16.8 230 n/a 5_occ: 0.0875 0.1781 0.011 1.151 0.0 116.0 16.8 230 n/a end: 0.0875 0.1782 0.011 1.151 0.0 116.0 16.8 230 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8230669_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8230669_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9800 Refinement macro-cycles (run) : 480.4800 Write final files (write_after_run_outputs) : 11.4200 Total : 494.8800 Total CPU time: 8.63 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:59 PST -0800 (1735492739.70 s) Start R-work = 0.1577, R-free = 0.1643 Final R-work = 0.0875, R-free = 0.1782 =============================================================================== Job complete usr+sys time: 525.17 seconds wall clock time: 9 minutes 8.21 seconds (548.21 seconds total)