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_1522381.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_1522381.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1522381.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.29, per 1000 atoms: 0.38 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 107.6 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: 0.63 - 0.89: 391 0.89 - 1.14: 1224 1.14 - 1.40: 582 1.40 - 1.66: 894 1.66 - 1.91: 62 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.237 1.436 -0.199 1.07e-02 8.73e+03 3.47e+02 bond pdb=" C CYS A 106 " pdb=" O CYS A 106 " ideal model delta sigma weight residual 1.235 1.470 -0.234 1.26e-02 6.30e+03 3.46e+02 bond pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 1.459 1.240 0.220 1.19e-02 7.06e+03 3.41e+02 bond pdb=" C ALYS A 99 " pdb=" O ALYS A 99 " ideal model delta sigma weight residual 1.233 1.001 0.232 1.28e-02 6.10e+03 3.28e+02 bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.244 1.064 0.180 1.00e-02 1.00e+04 3.23e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 3295 4.91 - 9.83: 1855 9.83 - 14.74: 547 14.74 - 19.65: 71 19.65 - 24.57: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 25 " pdb=" C VAL A 25 " pdb=" N MET A 26 " ideal model delta sigma weight residual 117.15 134.91 -17.76 1.14e+00 7.69e-01 2.43e+02 angle pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" O THR A 140 " ideal model delta sigma weight residual 120.36 104.85 15.51 1.07e+00 8.73e-01 2.10e+02 angle pdb=" CA ASN A 173 " pdb=" C ASN A 173 " pdb=" O ASN A 173 " ideal model delta sigma weight residual 119.05 133.57 -14.52 1.10e+00 8.26e-01 1.74e+02 angle pdb=" C VAL A 25 " pdb=" N MET A 26 " pdb=" CA MET A 26 " ideal model delta sigma weight residual 120.54 137.66 -17.12 1.35e+00 5.49e-01 1.61e+02 angle pdb=" C ASP A 42 " pdb=" N PRO A 43 " pdb=" CA PRO A 43 " ideal model delta sigma weight residual 120.03 107.87 12.16 9.90e-01 1.02e+00 1.51e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 1310 17.32 - 34.63: 119 34.63 - 51.94: 37 51.94 - 69.26: 12 69.26 - 86.57: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C THR A 124 " pdb=" N THR A 124 " pdb=" CA THR A 124 " pdb=" CB THR A 124 " ideal model delta harmonic sigma weight residual -122.00 -144.62 22.62 0 2.50e+00 1.60e-01 8.18e+01 dihedral pdb=" N MET A 26 " pdb=" C MET A 26 " pdb=" CA MET A 26 " pdb=" CB MET A 26 " ideal model delta harmonic sigma weight residual 122.80 144.61 -21.81 0 2.50e+00 1.60e-01 7.61e+01 dihedral pdb=" N THR A 124 " pdb=" C THR A 124 " pdb=" CA THR A 124 " pdb=" CB THR A 124 " ideal model delta harmonic sigma weight residual 123.40 142.70 -19.30 0 2.50e+00 1.60e-01 5.96e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.008 - 0.276: 120 0.276 - 0.544: 80 0.544 - 0.813: 34 0.813 - 1.081: 7 1.081 - 1.349: 2 Chirality restraints: 243 Sorted by residual: 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 -1.24 -1.35 2.00e-01 2.50e+01 4.55e+01 chirality pdb=" CA THR A 124 " pdb=" N THR A 124 " pdb=" C THR A 124 " pdb=" CB THR A 124 " both_signs ideal model delta sigma weight residual False 2.53 1.39 1.14 2.00e-01 2.50e+01 3.24e+01 chirality pdb=" CA ILE A 152 " pdb=" N ILE A 152 " pdb=" C ILE A 152 " pdb=" CB ILE A 152 " both_signs ideal model delta sigma weight residual False 2.43 3.42 -0.99 2.00e-01 2.50e+01 2.43e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.149 2.00e-02 2.50e+03 7.18e-02 1.55e+02 pdb=" CG TYR A 141 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.117 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.099 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.079 2.00e-02 2.50e+03 6.58e-02 1.30e+02 pdb=" CG PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.099 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.064 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.126 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.011 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BASN A 76 " -0.012 2.00e-02 2.50e+03 9.14e-02 1.25e+02 pdb=" CG BASN A 76 " 0.111 2.00e-02 2.50e+03 pdb=" OD1BASN A 76 " -0.086 2.00e-02 2.50e+03 pdb=" ND2BASN A 76 " 0.124 2.00e-02 2.50e+03 pdb="HD21BASN A 76 " -0.013 2.00e-02 2.50e+03 pdb="HD22BASN A 76 " -0.122 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1180 2.33 - 2.90: 8113 2.90 - 3.47: 10476 3.47 - 4.03: 15204 4.03 - 4.60: 21599 Nonbonded interactions: 56572 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.764 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.769 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.795 2.450 nonbonded pdb=" H THR A 124 " pdb=" OG1 THR A 154 " model vdw 1.821 2.450 nonbonded pdb=" H THR A 124 " pdb=" HG1 THR A 154 " model vdw 1.831 2.100 ... (remaining 56567 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_1522381_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2789 r_free= 0.1827 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.410984 | | target function (ml) not normalized (work): 71647.608057 | | target function (ml) not normalized (free): 3268.215212 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3199 0.2168 7.5526 5.0453| | 2: 3.63 - 2.88 1.00 2711 122 0.2642 0.1646 4.3309 4.3112| | 3: 2.88 - 2.52 1.00 2682 148 0.2552 0.1677 4.1812 4.1764| | 4: 2.52 - 2.29 1.00 2661 139 0.2531 0.1439 3.4988 3.5216| | 5: 2.29 - 2.13 1.00 2678 122 0.2684 0.1672 3.425 3.5447| | 6: 2.13 - 2.00 1.00 2692 117 0.2745 0.1982 3.3133 3.4187| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.54 0.77 0.23 1292.41| | 2: 3.63 - 2.88 2711 122 0.83 23.66 1.32 0.23 1292.41| | 3: 2.88 - 2.52 2682 148 0.73 32.78 1.28 0.23 1292.41| | 4: 2.52 - 2.29 2661 139 0.93 11.46 1.29 0.26 136.71| | 5: 2.29 - 2.13 2678 122 0.92 13.61 1.32 0.26 136.71| | 6: 2.13 - 2.00 2692 117 0.90 16.35 1.33 0.26 136.71| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 136.71 max = 1292.41 mean = 721.00| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.95 mean = 19.24| |phase err.(test): min = 0.00 max = 89.48 mean = 19.49| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.253 1557 Z= 5.583 Angle : 5.316 19.200 2118 Z= 3.665 Chirality : 0.401 1.349 243 Planarity : 0.031 0.086 284 Dihedral : 13.837 86.569 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.70 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 5.59 % Favored : 93.17 % Cbeta Deviations : 35.68 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.49), residues: 224 helix: -2.65 (0.39), residues: 103 sheet: -0.39 (0.73), residues: 38 loop : -0.27 (0.63), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.075 0.016 ARG A 156 TYR 0.143 0.050 TYR A 141 PHE 0.116 0.044 PHE A 119 HIS 0.047 0.028 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2789 r_free= 0.1827 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.410984 | | target function (ml) not normalized (work): 71647.608057 | | target function (ml) not normalized (free): 3268.215212 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3036 percent. r_work = 0.2920 r_free = 0.2017 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2920 0.2017 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2920 0.2017 n_refl.: 17050 remove outliers: r(all,work,free)=0.2167 0.2177 0.2017 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2140 0.2150 0.2001 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1622 0.1619 0.1679 n_refl.: 17045 remove outliers: r(all,work,free)=0.1620 0.1617 0.1679 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 0.3873 399.225 362.930 0.658 1.010 0.400 11.894-9.307 99.02 97 4 0.1859 634.064 614.112 0.934 1.011 0.370 9.237-7.194 100.00 213 7 0.2190 518.600 509.738 0.963 1.011 0.361 7.162-5.571 100.00 427 22 0.2231 389.210 377.337 0.920 1.010 0.289 5.546-4.326 100.00 867 58 0.1409 534.323 527.735 0.961 1.008 0.220 4.315-3.360 100.00 1859 96 0.1305 508.146 504.253 1.019 1.005 0.191 3.356-2.611 100.00 3867 181 0.1665 333.823 329.400 1.012 1.000 0.091 2.608-2.000 99.99 8818 434 0.1652 217.595 213.634 1.029 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4452 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1617 r_free=0.1679 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1617 r_free=0.1679 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.146007 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.907590 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1350 0.1636 0.0286 0.008 1.0 0.6 0.5 0.0 0 11.073 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.36 2.86 3.013 18.453 0.908 0.023 12.76 16.59 3.83 3.635 18.690 0.908 0.020 Individual atomic B min max mean iso aniso Overall: 5.81 113.89 19.93 4.12 1785 0 Protein: 5.81 113.03 17.15 4.12 1519 0 Water: 8.64 113.89 36.07 N/A 258 0 Other: 21.66 37.66 26.27 N/A 8 0 Chain A: 5.81 113.89 19.93 N/A 1785 0 Histogram: Values Number of atoms 5.81 - 16.62 1064 16.62 - 27.43 356 27.43 - 38.24 188 38.24 - 49.05 98 49.05 - 59.85 52 59.85 - 70.66 11 70.66 - 81.47 8 81.47 - 92.28 4 92.28 - 103.09 1 103.09 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1659 r_work=0.1279 r_free=0.1666 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1666 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 = 0.1273 r_free = 0.1656 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.21 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= 0.1273 r_free= 0.1656 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019899 | | target function (ls_wunit_k1) not normalized (work): 323.077214 | | target function (ls_wunit_k1) not normalized (free): 26.948562 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1273 0.1656 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1897 0.1896 0.1981 n_refl.: 17043 remove outliers: r(all,work,free)=0.1897 0.1896 0.1981 n_refl.: 17043 overall B=-0.47 to atoms: r(all,work,free)=0.1864 0.1862 0.1962 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1289 0.1271 0.1651 n_refl.: 17043 remove outliers: r(all,work,free)=0.1289 0.1271 0.1651 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 0.3567 307.733 286.999 0.654 1.006 0.393 11.894-9.307 99.02 97 4 0.1679 488.753 477.238 0.920 1.006 0.380 9.237-7.194 100.00 213 7 0.1816 399.751 396.406 0.961 1.006 0.351 7.162-5.571 100.00 427 22 0.1833 300.013 294.676 0.932 1.006 0.302 5.546-4.326 100.00 867 58 0.1041 411.870 409.584 0.958 1.005 0.206 4.315-3.360 100.00 1859 96 0.0923 391.693 391.009 1.015 1.003 0.192 3.356-2.611 100.00 3867 181 0.1297 257.320 256.056 1.009 1.001 0.101 2.608-2.000 99.99 8818 434 0.1345 167.728 166.402 1.012 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1734 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1651 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1271 r_free=0.1651 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1271 r_free=0.1651 | n_water=258 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1278 r_free=0.1640 | n_water=253 | time (s): 21.720 (total time: 22.520) Filter (q & B) r_work=0.1277 r_free=0.1638 | n_water=251 | time (s): 1.580 (total time: 24.100) Compute maps r_work=0.1277 r_free=0.1638 | n_water=251 | time (s): 0.660 (total time: 24.760) Filter (map) r_work=0.1316 r_free=0.1636 | n_water=208 | time (s): 1.780 (total time: 26.540) Find peaks r_work=0.1316 r_free=0.1636 | n_water=208 | time (s): 0.600 (total time: 27.140) Add new water r_work=0.1545 r_free=0.1871 | n_water=363 | time (s): 1.500 (total time: 28.640) Refine new water occ: r_work=0.1335 r_free=0.1591 adp: r_work=0.1277 r_free=0.1578 occ: r_work=0.1279 r_free=0.1554 adp: r_work=0.1250 r_free=0.1558 occ: r_work=0.1250 r_free=0.1548 adp: r_work=0.1239 r_free=0.1553 ADP+occupancy (water only), MIN, final r_work=0.1239 r_free=0.1553 r_work=0.1239 r_free=0.1553 | n_water=363 | time (s): 13.440 (total time: 42.080) Filter (q & B) r_work=0.1240 r_free=0.1554 | n_water=355 | time (s): 1.590 (total time: 43.670) Filter (dist only) r_work=0.1240 r_free=0.1554 | n_water=355 | time (s): 26.990 (total time: 70.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.719323 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.967027 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 0.1588 0.0372 0.008 0.9 2.2 0.5 0.0 0 12.360 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.16 15.88 3.72 4.189 20.916 0.967 0.018 12.04 16.05 4.02 4.274 21.243 0.967 0.018 Individual atomic B min max mean iso aniso Overall: 6.51 107.56 21.31 4.38 1882 0 Protein: 6.51 107.56 17.74 4.36 1519 0 Water: 8.61 65.71 36.29 N/A 355 0 Other: 24.57 47.08 35.56 N/A 8 0 Chain A: 6.51 107.56 19.39 N/A 1735 0 Chain S: 16.70 60.61 43.99 N/A 147 0 Histogram: Values Number of atoms 6.51 - 16.61 1017 16.61 - 26.72 375 26.72 - 36.82 225 36.82 - 46.93 156 46.93 - 57.03 75 57.03 - 67.14 23 67.14 - 77.25 3 77.25 - 87.35 5 87.35 - 97.46 1 97.46 - 107.56 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1605 r_work=0.1206 r_free=0.1607 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1607 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1615 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.28 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= 0.1206 r_free= 0.1615 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017318 | | target function (ls_wunit_k1) not normalized (work): 281.171105 | | target function (ls_wunit_k1) not normalized (free): 25.715554 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1226 0.1206 0.1615 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1812 0.1807 0.1964 n_refl.: 17043 remove outliers: r(all,work,free)=0.1812 0.1807 0.1964 n_refl.: 17043 overall B=-0.46 to atoms: r(all,work,free)=0.1781 0.1774 0.1943 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1221 0.1201 0.1605 n_refl.: 17043 remove outliers: r(all,work,free)=0.1219 0.1200 0.1605 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3351 307.170 280.101 0.610 1.008 0.360 11.894-9.307 99.02 97 4 0.1541 488.753 485.758 0.924 1.008 0.360 9.237-7.194 100.00 213 7 0.1627 399.751 400.888 0.973 1.007 0.311 7.162-5.571 100.00 427 22 0.1574 300.013 296.232 0.934 1.007 0.240 5.546-4.326 100.00 867 58 0.0878 411.870 409.307 0.959 1.006 0.211 4.315-3.360 100.00 1859 96 0.0847 391.693 391.030 1.015 1.004 0.202 3.356-2.611 100.00 3867 181 0.1215 257.320 256.326 1.009 1.001 0.101 2.608-2.000 99.99 8818 434 0.1333 167.728 166.623 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1548 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1605 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1605 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1605 | n_water=355 | time (s): 0.750 (total time: 0.750) Filter (dist) r_work=0.1200 r_free=0.1608 | n_water=353 | time (s): 27.330 (total time: 28.080) Filter (q & B) r_work=0.1200 r_free=0.1608 | n_water=353 | time (s): 0.900 (total time: 28.980) Compute maps r_work=0.1200 r_free=0.1608 | n_water=353 | time (s): 0.810 (total time: 29.790) Filter (map) r_work=0.1261 r_free=0.1625 | n_water=260 | time (s): 2.120 (total time: 31.910) Find peaks r_work=0.1261 r_free=0.1625 | n_water=260 | time (s): 0.590 (total time: 32.500) Add new water r_work=0.1448 r_free=0.1839 | n_water=409 | time (s): 1.610 (total time: 34.110) Refine new water occ: r_work=0.1248 r_free=0.1595 adp: r_work=0.1239 r_free=0.1600 occ: r_work=0.1224 r_free=0.1566 adp: r_work=0.1212 r_free=0.1570 occ: r_work=0.1206 r_free=0.1553 adp: r_work=0.1195 r_free=0.1554 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1554 r_work=0.1195 r_free=0.1554 | n_water=409 | time (s): 43.040 (total time: 77.150) Filter (q & B) r_work=0.1198 r_free=0.1561 | n_water=399 | time (s): 1.590 (total time: 78.740) Filter (dist only) r_work=0.1198 r_free=0.1561 | n_water=399 | time (s): 30.870 (total time: 109.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.924649 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.179959 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 0.1174 0.1558 0.0384 0.009 1.0 2.9 0.5 0.0 0 0.962 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.74 15.58 3.84 4.398 21.447 0.180 5.004 11.54 15.61 4.08 5.011 21.304 0.180 4.981 Individual atomic B min max mean iso aniso Overall: 6.09 105.24 20.66 4.73 1926 0 Protein: 6.09 105.24 16.79 4.72 1519 0 Water: 8.62 60.57 35.09 N/A 399 0 Other: 26.33 47.83 35.36 N/A 8 0 Chain A: 6.09 105.24 18.52 N/A 1733 0 Chain S: 18.39 60.57 39.82 N/A 193 0 Histogram: Values Number of atoms 6.09 - 16.00 1068 16.00 - 25.92 336 25.92 - 35.83 227 35.83 - 45.75 184 45.75 - 55.66 72 55.66 - 65.58 27 65.58 - 75.49 4 75.49 - 85.41 4 85.41 - 95.32 2 95.32 - 105.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1154 r_free=0.1561 r_work=0.1154 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1154 r_free = 0.1563 target_work(ml) = 4.981 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1554 target_work(ml) = 4.974 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1145 r_free= 0.1554 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.973575 | | target function (ml) not normalized (work): 80741.014246 | | target function (ml) not normalized (free): 4198.069737 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1165 0.1145 0.1554 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1644 0.1634 0.1867 n_refl.: 17041 remove outliers: r(all,work,free)=0.1644 0.1634 0.1867 n_refl.: 17041 overall B=-0.33 to atoms: r(all,work,free)=0.1623 0.1613 0.1855 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1164 0.1144 0.1550 n_refl.: 17041 remove outliers: r(all,work,free)=0.1162 0.1142 0.1550 n_refl.: 17039 ======================== 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 92.71 84 5 0.3377 300.431 284.503 0.584 1.007 0.344 11.894-9.307 99.02 97 4 0.1778 488.753 482.745 0.914 1.008 0.340 9.237-7.194 100.00 213 7 0.1740 399.751 400.330 0.985 1.008 0.290 7.162-5.571 100.00 427 22 0.1608 300.013 295.717 0.943 1.007 0.230 5.546-4.326 100.00 867 58 0.0933 411.870 408.039 0.961 1.006 0.206 4.315-3.360 100.00 1859 96 0.0890 391.693 389.621 1.012 1.004 0.201 3.356-2.611 100.00 3867 181 0.1284 257.320 254.921 1.009 1.000 0.121 2.608-2.000 99.99 8818 434 0.1088 167.728 166.165 1.012 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9584 b_overall=-1.1381 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1142 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1142 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1142 r_free=0.1550 | n_water=399 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1142 r_free=0.1553 | n_water=397 | time (s): 32.370 (total time: 33.010) Filter (q & B) r_work=0.1142 r_free=0.1553 | n_water=397 | time (s): 0.780 (total time: 33.790) Compute maps r_work=0.1142 r_free=0.1553 | n_water=397 | time (s): 0.790 (total time: 34.580) Filter (map) r_work=0.1193 r_free=0.1577 | n_water=314 | time (s): 1.780 (total time: 36.360) Find peaks r_work=0.1193 r_free=0.1577 | n_water=314 | time (s): 0.440 (total time: 36.800) Add new water r_work=0.1340 r_free=0.1720 | n_water=458 | time (s): 1.560 (total time: 38.360) Refine new water occ: r_work=0.1175 r_free=0.1547 adp: r_work=0.1167 r_free=0.1551 occ: r_work=0.1153 r_free=0.1528 adp: r_work=0.1144 r_free=0.1529 occ: r_work=0.1139 r_free=0.1518 adp: r_work=0.1132 r_free=0.1519 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1519 r_work=0.1132 r_free=0.1519 | n_water=458 | time (s): 24.880 (total time: 63.240) Filter (q & B) r_work=0.1135 r_free=0.1522 | n_water=447 | time (s): 1.600 (total time: 64.840) Filter (dist only) r_work=0.1135 r_free=0.1522 | n_water=446 | time (s): 37.290 (total time: 102.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.950680 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.176903 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1123 0.1570 0.0447 0.009 1.0 3.5 0.5 0.0 0 0.975 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 15.70 4.47 4.508 20.954 0.177 4.961 11.10 15.60 4.50 4.669 20.959 0.177 4.953 Individual atomic B min max mean iso aniso Overall: 5.54 103.08 20.86 4.85 1973 0 Protein: 5.54 103.08 16.36 4.84 1519 0 Water: 8.49 66.99 35.95 N/A 446 0 Other: 25.94 45.13 33.73 N/A 8 0 Chain A: 5.54 103.08 18.05 N/A 1733 0 Chain S: 16.76 66.99 41.17 N/A 240 0 Histogram: Values Number of atoms 5.54 - 15.29 1040 15.29 - 25.04 363 25.04 - 34.80 220 34.80 - 44.55 196 44.55 - 54.31 107 54.31 - 64.06 32 64.06 - 73.81 6 73.81 - 83.57 4 83.57 - 93.32 3 93.32 - 103.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1110 r_free=0.1560 r_work=0.1110 r_free=0.1561 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1110 r_free = 0.1561 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1569 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1101 r_free= 0.1569 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.949498 | | target function (ml) not normalized (work): 80340.249405 | | target function (ml) not normalized (free): 4187.422765 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1124 0.1101 0.1569 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1565 0.1549 0.1892 n_refl.: 17039 remove outliers: r(all,work,free)=0.1565 0.1549 0.1892 n_refl.: 17039 overall B=-0.24 to atoms: r(all,work,free)=0.1551 0.1534 0.1884 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1122 0.1099 0.1567 n_refl.: 17039 remove outliers: r(all,work,free)=0.1122 0.1099 0.1567 n_refl.: 17039 ======================== 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 92.71 84 5 0.3486 300.431 275.870 0.564 1.004 0.340 11.894-9.307 99.02 97 4 0.1741 488.753 483.535 0.911 1.005 0.330 9.237-7.194 100.00 213 7 0.1750 399.751 400.994 0.984 1.005 0.260 7.162-5.571 100.00 427 22 0.1488 300.013 294.588 0.941 1.004 0.205 5.546-4.326 100.00 867 58 0.0888 411.870 408.895 0.963 1.004 0.195 4.315-3.360 100.00 1859 96 0.0857 391.693 389.365 1.005 1.003 0.191 3.356-2.611 100.00 3867 181 0.1239 257.320 254.989 1.000 1.001 0.121 2.608-2.000 99.99 8818 434 0.1041 167.728 166.422 0.996 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8483 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1099 r_free=0.1567 After: r_work=0.1101 r_free=0.1564 ================================== NQH flips ================================== r_work=0.1101 r_free=0.1564 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1101 r_free=0.1564 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1101 r_free=0.1564 | n_water=446 | time (s): 0.950 (total time: 0.950) Filter (dist) r_work=0.1101 r_free=0.1559 | n_water=445 | time (s): 37.720 (total time: 38.670) Filter (q & B) r_work=0.1101 r_free=0.1559 | n_water=445 | time (s): 1.060 (total time: 39.730) Compute maps r_work=0.1101 r_free=0.1559 | n_water=445 | time (s): 0.610 (total time: 40.340) Filter (map) r_work=0.1178 r_free=0.1582 | n_water=342 | time (s): 1.790 (total time: 42.130) Find peaks r_work=0.1178 r_free=0.1582 | n_water=342 | time (s): 0.610 (total time: 42.740) Add new water r_work=0.1304 r_free=0.1661 | n_water=483 | time (s): 2.120 (total time: 44.860) Refine new water occ: r_work=0.1137 r_free=0.1537 adp: r_work=0.1129 r_free=0.1538 occ: r_work=0.1115 r_free=0.1525 adp: r_work=0.1105 r_free=0.1526 occ: r_work=0.1100 r_free=0.1516 adp: r_work=0.1093 r_free=0.1517 ADP+occupancy (water only), MIN, final r_work=0.1093 r_free=0.1517 r_work=0.1093 r_free=0.1517 | n_water=483 | time (s): 29.400 (total time: 74.260) Filter (q & B) r_work=0.1096 r_free=0.1527 | n_water=473 | time (s): 2.080 (total time: 76.340) Filter (dist only) r_work=0.1096 r_free=0.1526 | n_water=472 | time (s): 37.700 (total time: 114.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.922806 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.183048 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 0.1111 0.1534 0.0422 0.011 1.0 4.8 0.5 0.0 0 0.961 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.11 15.34 4.22 4.543 20.770 0.183 4.945 10.98 15.26 4.28 4.694 20.822 0.183 4.935 Individual atomic B min max mean iso aniso Overall: 5.27 102.65 20.96 5.09 1999 0 Protein: 5.27 102.65 16.06 5.07 1519 0 Water: 8.16 65.47 36.49 N/A 472 0 Other: 25.48 42.73 33.19 N/A 8 0 Chain A: 5.27 102.65 17.73 N/A 1733 0 Chain S: 16.30 65.47 42.00 N/A 266 0 Histogram: Values Number of atoms 5.27 - 15.01 1042 15.01 - 24.75 360 24.75 - 34.48 233 34.48 - 44.22 189 44.22 - 53.96 118 53.96 - 63.70 36 63.70 - 73.44 12 73.44 - 83.18 3 83.18 - 92.91 2 92.91 - 102.65 4 =========================== Idealize ADP of riding H ========================== r_work=0.1098 r_free=0.1526 r_work=0.1098 r_free=0.1525 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1098 r_free = 0.1525 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1090 r_free = 0.1526 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1090 r_free= 0.1526 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.931739 | | target function (ml) not normalized (work): 80051.989217 | | target function (ml) not normalized (free): 4161.490334 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2809 159 0.1088 0.1369 5.4359 5.6069| | 2: 3.63 - 2.88 1.00 2711 122 0.1066 0.1495 5.209 5.3579| | 3: 2.88 - 2.52 1.00 2681 148 0.1336 0.1812 5.1243 5.2167| | 4: 2.52 - 2.29 1.00 2661 139 0.0940 0.1507 4.632 4.9423| | 5: 2.29 - 2.13 1.00 2678 122 0.0972 0.1504 4.586 4.9004| | 6: 2.13 - 2.00 1.00 2692 117 0.1109 0.1736 4.5749 4.7815| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2809 159 0.95 9.05 1.00 0.96 6294.56| | 2: 3.63 - 2.88 2711 122 0.92 12.75 1.01 0.96 6294.56| | 3: 2.88 - 2.52 2681 148 0.88 18.82 0.99 0.96 6294.56| | 4: 2.52 - 2.29 2661 139 0.93 12.24 1.01 0.97 2145.41| | 5: 2.29 - 2.13 2678 122 0.91 14.24 1.00 0.97 2145.41| | 6: 2.13 - 2.00 2692 117 0.89 16.91 0.99 0.97 2145.41| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2145.41 max = 6294.56 mean = 4241.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.89 mean = 13.96| |phase err.(test): min = 0.00 max = 88.41 mean = 13.78| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1112 0.1090 0.1526 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1527 0.1511 0.1851 n_refl.: 17039 remove outliers: r(all,work,free)=0.1527 0.1511 0.1851 n_refl.: 17039 overall B=-0.19 to atoms: r(all,work,free)=0.1517 0.1501 0.1845 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1113 0.1091 0.1526 n_refl.: 17039 remove outliers: r(all,work,free)=0.1113 0.1091 0.1526 n_refl.: 17039 ======================== 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 92.71 84 5 0.3432 300.431 278.743 0.565 1.005 0.334 11.894-9.307 99.02 97 4 0.1695 488.753 482.366 0.921 1.006 0.330 9.237-7.194 100.00 213 7 0.1676 399.751 402.454 0.990 1.006 0.230 7.162-5.571 100.00 427 22 0.1560 300.013 294.550 0.942 1.005 0.202 5.546-4.326 100.00 867 58 0.0884 411.870 408.773 0.968 1.004 0.194 4.315-3.360 100.00 1859 96 0.0867 391.693 389.645 1.007 1.003 0.161 3.356-2.611 100.00 3867 181 0.1206 257.320 254.961 1.003 1.000 0.111 2.608-2.000 99.99 8818 434 0.1041 167.728 166.296 0.994 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.6562 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2789 0.1827 0.084 5.316 8.8 119.3 19.9 258 0.000 1_bss: 0.1617 0.1679 0.084 5.316 8.4 118.9 19.5 258 0.000 1_settarget: 0.1617 0.1679 0.084 5.316 8.4 118.9 19.5 258 0.000 1_nqh: 0.1617 0.1679 0.084 5.316 8.4 118.9 19.5 258 0.000 1_weight: 0.1617 0.1679 0.084 5.316 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1350 0.1636 0.008 0.971 8.4 118.9 19.5 258 0.152 1_adp: 0.1276 0.1659 0.008 0.971 5.8 113.9 19.9 258 0.152 1_regHadp: 0.1279 0.1666 0.008 0.971 5.8 113.9 19.9 258 0.152 1_occ: 0.1273 0.1656 0.008 0.971 5.8 113.9 19.9 258 0.152 2_bss: 0.1271 0.1651 0.008 0.971 5.3 113.4 19.5 258 0.152 2_settarget: 0.1271 0.1651 0.008 0.971 5.3 113.4 19.5 258 0.152 2_updatecdl: 0.1271 0.1651 0.008 0.982 5.3 113.4 19.5 258 0.152 2_nqh: 0.1271 0.1651 0.008 0.982 5.3 113.4 19.5 258 0.152 2_sol: 0.1240 0.1554 0.008 0.982 5.3 112.6 20.7 355 n/a 2_weight: 0.1240 0.1554 0.008 0.982 5.3 112.6 20.7 355 n/a 2_xyzrec: 0.1216 0.1588 0.008 0.928 5.3 112.6 20.7 355 n/a 2_adp: 0.1204 0.1605 0.008 0.928 6.5 107.6 21.3 355 n/a 2_regHadp: 0.1206 0.1607 0.008 0.928 6.5 107.6 21.3 355 n/a 2_occ: 0.1206 0.1615 0.008 0.928 6.5 107.6 21.3 355 n/a 3_bss: 0.1200 0.1605 0.008 0.928 6.0 107.1 20.8 355 n/a 3_settarget: 0.1200 0.1605 0.008 0.928 6.0 107.1 20.8 355 n/a 3_updatecdl: 0.1200 0.1605 0.008 0.927 6.0 107.1 20.8 355 n/a 3_nqh: 0.1200 0.1605 0.008 0.927 6.0 107.1 20.8 355 n/a 3_sol: 0.1198 0.1561 0.008 0.927 6.0 107.1 20.9 399 n/a 3_weight: 0.1198 0.1561 0.008 0.927 6.0 107.1 20.9 399 n/a 3_xyzrec: 0.1174 0.1558 0.009 0.953 6.0 107.1 20.9 399 n/a 3_adp: 0.1154 0.1561 0.009 0.953 6.1 105.2 20.7 399 n/a 3_regHadp: 0.1154 0.1563 0.009 0.953 6.1 105.2 20.7 399 n/a 3_occ: 0.1145 0.1554 0.009 0.953 6.1 105.2 20.7 399 n/a 4_bss: 0.1142 0.1550 0.009 0.953 5.8 104.9 20.3 399 n/a 4_settarget: 0.1142 0.1550 0.009 0.953 5.8 104.9 20.3 399 n/a 4_updatecdl: 0.1142 0.1550 0.009 0.953 5.8 104.9 20.3 399 n/a 4_nqh: 0.1142 0.1550 0.009 0.953 5.8 104.9 20.3 399 n/a 4_sol: 0.1135 0.1522 0.009 0.953 5.8 104.9 20.9 446 n/a 4_weight: 0.1135 0.1522 0.009 0.953 5.8 104.9 20.9 446 n/a 4_xyzrec: 0.1123 0.1570 0.009 0.972 5.8 104.9 20.9 446 n/a 4_adp: 0.1110 0.1560 0.009 0.972 5.5 103.1 20.9 446 n/a 4_regHadp: 0.1110 0.1561 0.009 0.972 5.5 103.1 20.9 446 n/a 4_occ: 0.1101 0.1569 0.009 0.972 5.5 103.1 20.9 446 n/a 5_bss: 0.1099 0.1567 0.009 0.972 5.3 102.8 20.6 446 n/a 5_settarget: 0.1099 0.1567 0.009 0.972 5.3 102.8 20.6 446 n/a 5_updatecdl: 0.1099 0.1567 0.009 0.973 5.3 102.8 20.6 446 n/a 5_setrh: 0.1101 0.1564 0.009 0.973 5.3 102.8 20.6 446 n/a 5_nqh: 0.1101 0.1564 0.009 0.973 5.3 102.8 20.6 446 n/a 5_sol: 0.1096 0.1526 0.009 0.973 5.3 102.8 20.9 472 n/a 5_weight: 0.1096 0.1526 0.009 0.973 5.3 102.8 20.9 472 n/a 5_xyzrec: 0.1111 0.1534 0.011 1.031 5.3 102.8 20.9 472 n/a 5_adp: 0.1098 0.1526 0.011 1.031 5.3 102.7 21.0 472 n/a 5_regHadp: 0.1098 0.1525 0.011 1.031 5.3 102.7 21.0 472 n/a 5_occ: 0.1090 0.1526 0.011 1.031 5.3 102.7 21.0 472 n/a end: 0.1091 0.1526 0.011 1.031 5.1 102.5 20.8 472 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1522381_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1522381_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0300 Refinement macro-cycles (run) : 933.4700 Write final files (write_after_run_outputs) : 20.2700 Total : 956.7700 Total CPU time: 16.27 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:18 PST -0800 (1735494078.13 s) Start R-work = 0.1617, R-free = 0.1679 Final R-work = 0.1091, R-free = 0.1526 =============================================================================== Job complete usr+sys time: 996.99 seconds wall clock time: 17 minutes 0.70 seconds (1020.70 seconds total)