Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1446411.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1446411.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1446411.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 =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.79, per 1000 atoms: 0.53 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: 0.52 Conformation dependent library (CDL) restraints added in 105.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.88: 324 0.88 - 1.14: 1275 1.14 - 1.40: 599 1.40 - 1.65: 899 1.65 - 1.91: 56 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.243 1.053 0.190 9.50e-03 1.11e+04 4.02e+02 bond pdb=" C SER A 161 " pdb=" N PHE A 162 " ideal model delta sigma weight residual 1.335 1.079 0.256 1.31e-02 5.83e+03 3.81e+02 bond pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.374 1.564 -0.190 1.10e-02 8.26e+03 2.98e+02 bond pdb=" CA THR A 125 " pdb=" C THR A 125 " ideal model delta sigma weight residual 1.523 1.736 -0.212 1.24e-02 6.50e+03 2.93e+02 bond pdb=" C ALA A 165 " pdb=" O ALA A 165 " ideal model delta sigma weight residual 1.237 1.043 0.193 1.17e-02 7.31e+03 2.73e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 2961 4.31 - 8.63: 1896 8.63 - 12.94: 732 12.94 - 17.26: 168 17.26 - 21.57: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OD1BASN A 76 " pdb=" CG BASN A 76 " pdb=" ND2BASN A 76 " ideal model delta sigma weight residual 122.60 136.71 -14.11 1.00e+00 1.00e+00 1.99e+02 angle pdb=" O SER A 3 " pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 123.03 107.17 15.86 1.13e+00 7.83e-01 1.97e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 106.99 12.21 9.00e-01 1.23e+00 1.84e+02 angle pdb=" C LYS A 89 " pdb=" N BGLU A 90 " pdb=" CA BGLU A 90 " ideal model delta sigma weight residual 120.54 138.79 -18.25 1.35e+00 5.49e-01 1.83e+02 angle pdb=" N LYS A 182 " pdb=" CA LYS A 182 " pdb=" C LYS A 182 " ideal model delta sigma weight residual 111.71 127.15 -15.44 1.15e+00 7.56e-01 1.80e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 17.86: 1310 17.86 - 35.69: 119 35.69 - 53.52: 38 53.52 - 71.35: 11 71.35 - 89.19: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 88 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " pdb=" CB VAL A 88 " ideal model delta harmonic sigma weight residual -122.00 -145.27 23.27 0 2.50e+00 1.60e-01 8.67e+01 dihedral pdb=" N ALA A 39 " pdb=" C ALA A 39 " pdb=" CA ALA A 39 " pdb=" CB ALA A 39 " ideal model delta harmonic sigma weight residual 122.90 103.92 18.98 0 2.50e+00 1.60e-01 5.76e+01 dihedral pdb=" N BGLU A 90 " pdb=" C BGLU A 90 " pdb=" CA BGLU A 90 " pdb=" CB BGLU A 90 " ideal model delta harmonic sigma weight residual 122.80 140.95 -18.15 0 2.50e+00 1.60e-01 5.27e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.248: 110 0.248 - 0.496: 85 0.496 - 0.743: 36 0.743 - 0.991: 10 0.991 - 1.238: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 33 " pdb=" CA VAL A 33 " pdb=" CG1 VAL A 33 " pdb=" CG2 VAL A 33 " both_signs ideal model delta sigma weight residual False -2.63 -1.39 -1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.57 -1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA ASP A 131 " pdb=" N ASP A 131 " pdb=" C ASP A 131 " pdb=" CB ASP A 131 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.170 9.50e-02 1.11e+02 9.09e-02 1.17e+02 pdb=" NE ARG A 145 " -0.068 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " 0.089 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.111 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.021 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.126 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " -0.065 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.008 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.057 2.00e-02 2.50e+03 6.23e-02 1.17e+02 pdb=" CG PHE A 164 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.094 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.130 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.024 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.022 2.00e-02 2.50e+03 5.69e-02 9.72e+01 pdb=" CG PHE A 119 " -0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.088 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.061 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1266 2.35 - 2.92: 8275 2.92 - 3.48: 10535 3.48 - 4.04: 15103 4.04 - 4.60: 21473 Nonbonded interactions: 56652 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.792 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.830 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.836 2.100 nonbonded pdb=" HA AASN A 76 " pdb="HD22AASN A 76 " model vdw 1.847 2.270 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.870 2.450 x-y,-y,-z-4/3 ... (remaining 56647 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_1446411_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= 0.2782 r_free= 0.1803 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.415018 | | target function (ml) not normalized (work): 71713.144924 | | target function (ml) not normalized (free): 3262.878550 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3196 0.2061 7.633 5.0286| | 2: 3.63 - 2.88 1.00 2711 122 0.2618 0.1692 4.3173 4.3067| | 3: 2.88 - 2.52 1.00 2682 148 0.2548 0.1758 4.1719 4.181| | 4: 2.52 - 2.29 1.00 2661 139 0.2545 0.1506 3.5121 3.5782| | 5: 2.29 - 2.13 1.00 2678 122 0.2670 0.1567 3.3861 3.4849| | 6: 2.13 - 2.00 1.00 2692 117 0.2740 0.1893 3.3018 3.3897| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.31 0.77 0.23 1265.36| | 2: 3.63 - 2.88 2711 122 0.83 23.44 1.31 0.23 1265.36| | 3: 2.88 - 2.52 2682 148 0.74 32.32 1.28 0.23 1265.36| | 4: 2.52 - 2.29 2661 139 0.93 11.18 1.30 0.26 131.25| | 5: 2.29 - 2.13 2678 122 0.92 13.38 1.32 0.26 131.25| | 6: 2.13 - 2.00 2692 117 0.90 16.03 1.33 0.26 131.25| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 131.25 max = 1265.36 mean = 704.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.96 mean = 18.95| |phase err.(test): min = 0.00 max = 89.21 mean = 19.03| |-----------------------------------------------------------------------------| ----------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 0.261 1557 Z= 5.495 Angle : 5.249 18.248 2118 Z= 3.703 Chirality : 0.391 1.238 243 Planarity : 0.030 0.076 284 Dihedral : 14.342 89.186 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.89 % Cbeta Deviations : 23.24 % 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: -2.68 (0.46), residues: 224 helix: -2.53 (0.35), residues: 109 sheet: -1.11 (0.93), residues: 28 loop : -0.59 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.121 0.035 ARG A 156 TYR 0.032 0.017 TYR A 141 PHE 0.088 0.033 PHE A 119 HIS 0.083 0.030 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2782 r_free= 0.1803 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.415018 | | target function (ml) not normalized (work): 71713.144924 | | target function (ml) not normalized (free): 3262.878550 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2944 percent. r_work = 0.2912 r_free = 0.1930 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2857 0.2912 0.1930 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2857 0.2912 0.1930 n_refl.: 17050 remove outliers: r(all,work,free)=0.2144 0.2157 0.1930 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2118 0.2130 0.1911 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1610 0.1610 0.1610 n_refl.: 17045 remove outliers: r(all,work,free)=0.1609 0.1609 0.1610 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4109 395.134 362.145 0.655 1.018 0.399 11.894-9.307 99.02 97 4 0.1890 634.202 615.287 0.927 1.018 0.377 9.237-7.194 100.00 213 7 0.2193 518.713 509.258 0.953 1.017 0.364 7.162-5.571 100.00 427 22 0.2311 389.295 375.621 0.919 1.016 0.289 5.546-4.326 100.00 867 58 0.1380 534.439 528.270 0.956 1.013 0.209 4.315-3.360 100.00 1859 96 0.1290 508.257 504.502 1.014 1.008 0.171 3.356-2.611 100.00 3867 181 0.1644 333.896 329.422 1.011 0.999 0.039 2.608-2.000 99.99 8818 434 0.1649 217.643 213.548 1.034 0.984 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4243 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1609 r_free=0.1610 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=0.1609 r_free=0.1613 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.200086 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.965129 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 0.1352 0.1645 0.0293 0.008 1.0 1.3 0.5 0.0 0 11.100 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.45 2.93 3.013 18.460 0.965 0.023 12.78 16.66 3.87 3.729 18.734 0.965 0.020 Individual atomic B min max mean iso aniso Overall: 6.07 113.90 20.01 4.16 1785 0 Protein: 6.07 112.97 17.23 4.17 1519 0 Water: 9.08 113.90 36.16 N/A 258 0 Other: 21.57 37.11 26.78 N/A 8 0 Chain A: 6.07 113.90 20.01 N/A 1785 0 Histogram: Values Number of atoms 6.07 - 16.85 1080 16.85 - 27.64 339 27.64 - 38.42 189 38.42 - 49.20 98 49.20 - 59.98 50 59.98 - 70.77 14 70.77 - 81.55 7 81.55 - 92.33 4 92.33 - 103.12 1 103.12 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1666 r_work=0.1281 r_free=0.1672 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1672 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 = 0.1276 r_free = 0.1664 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1276 r_free= 0.1664 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020011 | | target function (ls_wunit_k1) not normalized (work): 324.922222 | | target function (ls_wunit_k1) not normalized (free): 27.413714 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1276 0.1664 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1909 0.1908 0.1987 n_refl.: 17044 remove outliers: r(all,work,free)=0.1909 0.1908 0.1987 n_refl.: 17044 overall B=-0.51 to atoms: r(all,work,free)=0.1872 0.1870 0.1967 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1292 0.1274 0.1661 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1274 0.1661 n_refl.: 17044 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 97.92 89 5 0.3716 303.840 281.722 0.644 1.006 0.389 11.894-9.307 99.02 97 4 0.1664 487.672 476.763 0.921 1.007 0.380 9.237-7.194 100.00 213 7 0.1811 398.866 395.225 0.960 1.006 0.351 7.162-5.571 100.00 427 22 0.1809 299.349 294.432 0.933 1.006 0.301 5.546-4.326 100.00 867 58 0.1046 410.959 408.354 0.957 1.005 0.201 4.315-3.360 100.00 1859 96 0.0919 390.826 390.211 1.015 1.004 0.192 3.356-2.611 100.00 3867 181 0.1299 256.750 255.422 1.009 1.001 0.091 2.608-2.000 99.99 8818 434 0.1352 167.357 166.005 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1641 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1661 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1276 r_free=0.1660 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1660 | n_water=258 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1279 r_free=0.1651 | n_water=254 | time (s): 20.370 (total time: 21.070) Filter (q & B) r_work=0.1279 r_free=0.1651 | n_water=252 | time (s): 1.990 (total time: 23.060) Compute maps r_work=0.1279 r_free=0.1651 | n_water=252 | time (s): 0.800 (total time: 23.860) Filter (map) r_work=0.1323 r_free=0.1643 | n_water=208 | time (s): 2.100 (total time: 25.960) Find peaks r_work=0.1323 r_free=0.1643 | n_water=208 | time (s): 0.660 (total time: 26.620) Add new water r_work=0.1553 r_free=0.1867 | n_water=368 | time (s): 2.120 (total time: 28.740) Refine new water occ: r_work=0.1339 r_free=0.1567 adp: r_work=0.1277 r_free=0.1570 occ: r_work=0.1283 r_free=0.1533 adp: r_work=0.1250 r_free=0.1543 occ: r_work=0.1252 r_free=0.1537 adp: r_work=0.1239 r_free=0.1538 ADP+occupancy (water only), MIN, final r_work=0.1239 r_free=0.1538 r_work=0.1239 r_free=0.1538 | n_water=368 | time (s): 18.460 (total time: 47.200) Filter (q & B) r_work=0.1241 r_free=0.1544 | n_water=361 | time (s): 2.080 (total time: 49.280) Filter (dist only) r_work=0.1241 r_free=0.1547 | n_water=360 | time (s): 27.800 (total time: 77.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.745553 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.992884 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 0.1214 0.1607 0.0393 0.008 0.9 2.2 0.5 0.0 0 12.373 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.14 16.07 3.93 4.222 21.003 0.993 0.018 12.01 16.27 4.25 4.258 21.277 0.993 0.018 Individual atomic B min max mean iso aniso Overall: 6.94 107.46 21.32 4.29 1887 0 Protein: 6.94 107.46 17.65 4.27 1519 0 Water: 8.56 68.05 36.47 N/A 360 0 Other: 24.55 46.70 35.73 N/A 8 0 Chain A: 6.94 107.46 19.32 N/A 1735 0 Chain S: 17.46 66.42 44.04 N/A 152 0 Histogram: Values Number of atoms 6.94 - 17.00 1059 17.00 - 27.05 346 27.05 - 37.10 213 37.10 - 47.15 155 47.15 - 57.20 79 57.20 - 67.25 23 67.25 - 77.30 5 77.30 - 87.35 4 87.35 - 97.40 1 97.40 - 107.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1627 r_work=0.1203 r_free=0.1628 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1628 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1622 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1201 r_free= 0.1622 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017309 | | target function (ls_wunit_k1) not normalized (work): 281.052871 | | target function (ls_wunit_k1) not normalized (free): 25.503214 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1201 0.1622 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1812 0.1808 0.1963 n_refl.: 17044 remove outliers: r(all,work,free)=0.1812 0.1808 0.1963 n_refl.: 17044 overall B=-0.46 to atoms: r(all,work,free)=0.1780 0.1775 0.1943 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1217 0.1197 0.1617 n_refl.: 17044 remove outliers: r(all,work,free)=0.1214 0.1194 0.1617 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 0.3282 300.054 276.165 0.597 1.008 0.350 11.894-9.307 99.02 97 4 0.1541 487.672 484.354 0.918 1.008 0.340 9.237-7.194 100.00 213 7 0.1682 398.866 401.160 0.970 1.008 0.311 7.162-5.571 100.00 427 22 0.1569 299.349 296.119 0.939 1.007 0.251 5.546-4.326 100.00 867 58 0.0879 410.959 408.530 0.959 1.006 0.211 4.315-3.360 100.00 1859 96 0.0834 390.826 390.369 1.014 1.004 0.202 3.356-2.611 100.00 3867 181 0.1215 256.750 255.818 1.009 1.001 0.063 2.608-2.000 99.99 8818 434 0.1324 167.357 166.254 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9585 b_overall=-1.1428 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1617 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1617 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1617 | n_water=360 | time (s): 0.800 (total time: 0.800) Filter (dist) r_work=0.1195 r_free=0.1620 | n_water=357 | time (s): 28.880 (total time: 29.680) Filter (q & B) r_work=0.1195 r_free=0.1620 | n_water=357 | time (s): 1.220 (total time: 30.900) Compute maps r_work=0.1195 r_free=0.1620 | n_water=357 | time (s): 0.610 (total time: 31.510) Filter (map) r_work=0.1260 r_free=0.1634 | n_water=258 | time (s): 1.860 (total time: 33.370) Find peaks r_work=0.1260 r_free=0.1634 | n_water=258 | time (s): 0.440 (total time: 33.810) Add new water r_work=0.1438 r_free=0.1809 | n_water=398 | time (s): 1.500 (total time: 35.310) Refine new water occ: r_work=0.1247 r_free=0.1574 adp: r_work=0.1238 r_free=0.1586 occ: r_work=0.1223 r_free=0.1545 adp: r_work=0.1212 r_free=0.1553 occ: r_work=0.1205 r_free=0.1531 adp: r_work=0.1196 r_free=0.1536 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1536 r_work=0.1196 r_free=0.1536 | n_water=398 | time (s): 52.210 (total time: 87.520) Filter (q & B) r_work=0.1198 r_free=0.1536 | n_water=390 | time (s): 1.780 (total time: 89.300) Filter (dist only) r_work=0.1198 r_free=0.1537 | n_water=389 | time (s): 32.630 (total time: 121.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.850843 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.161940 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 0.1176 0.1545 0.0368 0.009 1.0 4.5 0.5 0.0 0 0.925 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 15.45 3.68 4.348 21.269 0.162 4.992 11.55 15.48 3.93 4.939 21.169 0.162 4.970 Individual atomic B min max mean iso aniso Overall: 6.16 104.82 20.52 4.72 1916 0 Protein: 6.16 104.82 16.79 4.71 1519 0 Water: 7.95 60.89 34.78 N/A 389 0 Other: 27.29 47.20 35.33 N/A 8 0 Chain A: 6.16 104.82 18.50 N/A 1732 0 Chain S: 12.49 60.89 39.53 N/A 184 0 Histogram: Values Number of atoms 6.16 - 16.03 1067 16.03 - 25.89 352 25.89 - 35.76 218 35.76 - 45.62 166 45.62 - 55.49 74 55.49 - 65.35 26 65.35 - 75.22 4 75.22 - 85.08 5 85.08 - 94.95 2 94.95 - 104.82 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1548 r_work=0.1156 r_free=0.1549 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1549 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1536 target_work(ml) = 4.967 | | 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= 0.1150 r_free= 0.1536 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.966757 | | target function (ml) not normalized (work): 80630.332463 | | target function (ml) not normalized (free): 4183.894819 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1169 0.1150 0.1536 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1669 0.1660 0.1884 n_refl.: 17041 remove outliers: r(all,work,free)=0.1669 0.1660 0.1884 n_refl.: 17041 overall B=-0.32 to atoms: r(all,work,free)=0.1648 0.1638 0.1873 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1169 0.1150 0.1541 n_refl.: 17041 remove outliers: r(all,work,free)=0.1168 0.1150 0.1541 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3517 296.491 279.241 0.571 1.006 0.340 11.894-9.307 99.02 97 4 0.1796 487.672 482.904 0.918 1.007 0.327 9.237-7.194 100.00 213 7 0.1757 398.866 401.140 0.984 1.007 0.270 7.162-5.571 100.00 427 22 0.1636 299.349 294.395 0.943 1.007 0.251 5.546-4.326 100.00 867 58 0.0940 410.959 407.158 0.963 1.006 0.216 4.315-3.360 100.00 1859 96 0.0880 390.826 388.951 1.011 1.004 0.211 3.356-2.611 100.00 3867 181 0.1291 256.750 254.640 1.009 1.000 0.141 2.608-2.000 99.99 8818 434 0.1100 167.357 165.947 1.011 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1207 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1150 r_free=0.1541 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1150 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1150 r_free=0.1541 | n_water=389 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1150 r_free=0.1541 | n_water=389 | time (s): 29.150 (total time: 29.800) Filter (q & B) r_work=0.1150 r_free=0.1538 | n_water=388 | time (s): 1.900 (total time: 31.700) Compute maps r_work=0.1150 r_free=0.1538 | n_water=388 | time (s): 0.860 (total time: 32.560) Filter (map) r_work=0.1202 r_free=0.1559 | n_water=307 | time (s): 2.040 (total time: 34.600) Find peaks r_work=0.1202 r_free=0.1559 | n_water=307 | time (s): 0.560 (total time: 35.160) Add new water r_work=0.1336 r_free=0.1657 | n_water=432 | time (s): 2.200 (total time: 37.360) Refine new water occ: r_work=0.1188 r_free=0.1511 adp: r_work=0.1180 r_free=0.1507 occ: r_work=0.1166 r_free=0.1501 adp: r_work=0.1158 r_free=0.1495 occ: r_work=0.1151 r_free=0.1498 adp: r_work=0.1144 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1144 r_free=0.1491 r_work=0.1144 r_free=0.1491 | n_water=432 | time (s): 36.150 (total time: 73.510) Filter (q & B) r_work=0.1147 r_free=0.1498 | n_water=420 | time (s): 2.000 (total time: 75.510) Filter (dist only) r_work=0.1147 r_free=0.1498 | n_water=420 | time (s): 32.700 (total time: 108.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.016113 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.169179 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 0.1138 0.1574 0.0436 0.010 1.0 4.8 0.5 0.0 0 1.008 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.38 15.74 4.36 4.498 20.798 0.169 4.970 11.27 15.75 4.48 4.635 20.820 0.169 4.962 Individual atomic B min max mean iso aniso Overall: 5.59 103.29 20.61 4.81 1947 0 Protein: 5.59 103.29 16.40 4.80 1519 0 Water: 7.75 64.07 35.58 N/A 420 0 Other: 25.69 44.20 32.92 N/A 8 0 Chain A: 5.59 103.29 18.06 N/A 1732 0 Chain S: 14.21 64.07 41.16 N/A 215 0 Histogram: Values Number of atoms 5.59 - 15.36 1043 15.36 - 25.13 363 25.13 - 34.90 227 34.90 - 44.67 171 44.67 - 54.44 100 54.44 - 64.21 29 64.21 - 73.98 6 73.98 - 83.75 3 83.75 - 93.52 3 93.52 - 103.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1127 r_free=0.1575 r_work=0.1127 r_free=0.1576 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1127 r_free = 0.1576 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1119 r_free = 0.1587 target_work(ml) = 4.960 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1119 r_free= 0.1587 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.960291 | | target function (ml) not normalized (work): 80520.397560 | | target function (ml) not normalized (free): 4196.582523 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1142 0.1119 0.1587 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1615 0.1601 0.1929 n_refl.: 17040 remove outliers: r(all,work,free)=0.1615 0.1601 0.1929 n_refl.: 17040 overall B=-0.26 to atoms: r(all,work,free)=0.1599 0.1584 0.1920 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1139 0.1117 0.1586 n_refl.: 17040 remove outliers: r(all,work,free)=0.1139 0.1117 0.1586 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3665 296.491 273.415 0.549 1.003 0.330 11.894-9.307 99.02 97 4 0.1817 487.672 481.024 0.919 1.004 0.330 9.237-7.194 100.00 213 7 0.1755 398.866 400.446 0.990 1.004 0.240 7.162-5.571 100.00 427 22 0.1587 299.349 293.537 0.939 1.004 0.230 5.546-4.326 100.00 867 58 0.0901 410.959 407.245 0.963 1.004 0.201 4.315-3.360 100.00 1859 96 0.0863 390.826 388.729 1.006 1.003 0.201 3.356-2.611 100.00 3867 181 0.1262 256.750 254.509 1.001 1.001 0.121 2.608-2.000 99.99 8818 434 0.1052 167.357 166.047 0.997 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8895 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1117 r_free=0.1586 After: r_work=0.1119 r_free=0.1585 ================================== NQH flips ================================== r_work=0.1119 r_free=0.1585 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1119 r_free=0.1585 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1119 r_free=0.1585 | n_water=420 | time (s): 0.690 (total time: 0.690) Filter (dist) r_work=0.1119 r_free=0.1585 | n_water=420 | time (s): 34.560 (total time: 35.250) Filter (q & B) r_work=0.1119 r_free=0.1584 | n_water=418 | time (s): 2.340 (total time: 37.590) Compute maps r_work=0.1119 r_free=0.1584 | n_water=418 | time (s): 0.650 (total time: 38.240) Filter (map) r_work=0.1176 r_free=0.1573 | n_water=328 | time (s): 2.200 (total time: 40.440) Find peaks r_work=0.1176 r_free=0.1573 | n_water=328 | time (s): 0.670 (total time: 41.110) Add new water r_work=0.1302 r_free=0.1677 | n_water=461 | time (s): 1.910 (total time: 43.020) Refine new water occ: r_work=0.1148 r_free=0.1536 adp: r_work=0.1141 r_free=0.1539 occ: r_work=0.1126 r_free=0.1528 adp: r_work=0.1119 r_free=0.1528 occ: r_work=0.1112 r_free=0.1522 adp: r_work=0.1107 r_free=0.1520 ADP+occupancy (water only), MIN, final r_work=0.1107 r_free=0.1520 r_work=0.1107 r_free=0.1520 | n_water=461 | time (s): 46.500 (total time: 89.520) Filter (q & B) r_work=0.1110 r_free=0.1533 | n_water=451 | time (s): 1.760 (total time: 91.280) Filter (dist only) r_work=0.1110 r_free=0.1536 | n_water=450 | time (s): 37.560 (total time: 128.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.025526 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.165667 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 0.1133 0.1551 0.0418 0.010 1.1 5.1 0.5 0.0 0 1.013 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 15.51 4.18 4.516 20.644 0.166 4.954 11.22 15.43 4.20 4.626 20.734 0.166 4.944 Individual atomic B min max mean iso aniso Overall: 5.43 102.55 20.78 4.95 1977 0 Protein: 5.43 102.55 16.12 4.94 1519 0 Water: 7.70 68.29 36.28 N/A 450 0 Other: 26.53 43.14 33.46 N/A 8 0 Chain A: 5.43 102.55 17.77 N/A 1732 0 Chain S: 13.95 68.29 42.05 N/A 245 0 Histogram: Values Number of atoms 5.43 - 15.14 1051 15.14 - 24.85 361 24.85 - 34.56 225 34.56 - 44.28 174 44.28 - 53.99 114 53.99 - 63.70 32 63.70 - 73.41 11 73.41 - 83.12 4 83.12 - 92.83 2 92.83 - 102.55 3 =========================== Idealize ADP of riding H ========================== r_work=0.1122 r_free=0.1543 r_work=0.1123 r_free=0.1543 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1123 r_free = 0.1543 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1116 r_free = 0.1540 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1116 r_free= 0.1540 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.939970 | | target function (ml) not normalized (work): 80190.530920 | | target function (ml) not normalized (free): 4167.762785 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1130 0.1462 5.4701 5.6801| | 2: 3.63 - 2.88 1.00 2711 122 0.1116 0.1519 5.2492 5.3816| | 3: 2.88 - 2.52 1.00 2681 148 0.1380 0.1783 5.1548 5.2417| | 4: 2.52 - 2.29 1.00 2661 139 0.0927 0.1459 4.6136 4.9217| | 5: 2.29 - 2.13 1.00 2678 122 0.0954 0.1429 4.5631 4.8408| | 6: 2.13 - 2.00 1.00 2692 117 0.1110 0.1713 4.5587 4.7658| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.94 9.54 1.00 0.95 6797.08| | 2: 3.63 - 2.88 2711 122 0.92 13.31 1.01 0.95 6797.08| | 3: 2.88 - 2.52 2681 148 0.87 19.67 0.99 0.95 6797.08| | 4: 2.52 - 2.29 2661 139 0.93 11.80 1.01 0.98 2035.73| | 5: 2.29 - 2.13 2678 122 0.92 13.91 1.00 0.98 2035.73| | 6: 2.13 - 2.00 2692 117 0.90 16.46 0.99 0.98 2035.73| |alpha: min = 0.95 max = 0.98 mean = 0.96| |beta: min = 2035.73 max = 6797.08 mean = 4441.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.98 mean = 14.08| |phase err.(test): min = 0.00 max = 89.43 mean = 13.72| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1116 0.1540 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1581 0.1568 0.1871 n_refl.: 17040 remove outliers: r(all,work,free)=0.1581 0.1568 0.1871 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1568 0.1554 0.1863 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1137 0.1117 0.1542 n_refl.: 17040 remove outliers: r(all,work,free)=0.1137 0.1117 0.1542 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3631 296.491 278.509 0.536 1.002 0.308 11.894-9.307 99.02 97 4 0.1806 487.672 480.181 0.918 1.004 0.300 9.237-7.194 100.00 213 7 0.1761 398.866 401.273 0.991 1.004 0.240 7.162-5.571 100.00 427 22 0.1580 299.349 293.527 0.935 1.004 0.213 5.546-4.326 100.00 867 58 0.0933 410.959 407.241 0.963 1.004 0.195 4.315-3.360 100.00 1859 96 0.0895 390.826 388.847 1.005 1.003 0.191 3.356-2.611 100.00 3867 181 0.1256 256.750 254.555 0.999 1.001 0.063 2.608-2.000 99.99 8818 434 0.1033 167.357 166.016 0.991 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7747 ================= 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 : 0.2782 0.1803 0.082 5.249 8.8 119.3 19.9 258 0.000 1_bss: 0.1609 0.1610 0.082 5.249 8.4 118.9 19.5 258 0.000 1_settarget: 0.1609 0.1610 0.082 5.249 8.4 118.9 19.5 258 0.000 1_nqh: 0.1609 0.1613 0.082 5.249 8.4 118.9 19.5 258 0.003 1_weight: 0.1609 0.1613 0.082 5.249 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1352 0.1645 0.008 0.951 8.4 118.9 19.5 258 0.154 1_adp: 0.1278 0.1666 0.008 0.951 6.1 113.9 20.0 258 0.154 1_regHadp: 0.1281 0.1672 0.008 0.951 6.1 113.9 20.0 258 0.154 1_occ: 0.1276 0.1664 0.008 0.951 6.1 113.9 20.0 258 0.154 2_bss: 0.1274 0.1661 0.008 0.951 5.6 113.4 19.5 258 0.154 2_settarget: 0.1274 0.1661 0.008 0.951 5.6 113.4 19.5 258 0.154 2_updatecdl: 0.1274 0.1661 0.008 0.978 5.6 113.4 19.5 258 0.154 2_nqh: 0.1276 0.1660 0.008 0.978 5.6 113.4 19.5 258 0.151 2_sol: 0.1241 0.1547 0.008 0.978 5.6 112.5 20.8 360 n/a 2_weight: 0.1241 0.1547 0.008 0.978 5.6 112.5 20.8 360 n/a 2_xyzrec: 0.1214 0.1607 0.008 0.921 5.6 112.5 20.8 360 n/a 2_adp: 0.1201 0.1627 0.008 0.921 6.9 107.5 21.3 360 n/a 2_regHadp: 0.1203 0.1628 0.008 0.921 6.9 107.5 21.3 360 n/a 2_occ: 0.1201 0.1622 0.008 0.921 6.9 107.5 21.3 360 n/a 3_bss: 0.1194 0.1617 0.008 0.921 6.5 107.0 20.9 360 n/a 3_settarget: 0.1194 0.1617 0.008 0.921 6.5 107.0 20.9 360 n/a 3_updatecdl: 0.1194 0.1617 0.008 0.920 6.5 107.0 20.9 360 n/a 3_nqh: 0.1194 0.1617 0.008 0.920 6.5 107.0 20.9 360 n/a 3_sol: 0.1198 0.1537 0.008 0.920 6.5 107.0 20.7 389 n/a 3_weight: 0.1198 0.1537 0.008 0.920 6.5 107.0 20.7 389 n/a 3_xyzrec: 0.1176 0.1545 0.009 0.956 6.5 107.0 20.7 389 n/a 3_adp: 0.1155 0.1548 0.009 0.956 6.2 104.8 20.5 389 n/a 3_regHadp: 0.1156 0.1549 0.009 0.956 6.2 104.8 20.5 389 n/a 3_occ: 0.1150 0.1536 0.009 0.956 6.2 104.8 20.5 389 n/a 4_bss: 0.1150 0.1541 0.009 0.956 5.8 104.5 20.2 389 n/a 4_settarget: 0.1150 0.1541 0.009 0.956 5.8 104.5 20.2 389 n/a 4_updatecdl: 0.1150 0.1541 0.009 0.956 5.8 104.5 20.2 389 n/a 4_nqh: 0.1150 0.1541 0.009 0.956 5.8 104.5 20.2 389 n/a 4_sol: 0.1147 0.1498 0.009 0.956 5.8 104.5 20.6 420 n/a 4_weight: 0.1147 0.1498 0.009 0.956 5.8 104.5 20.6 420 n/a 4_xyzrec: 0.1138 0.1574 0.010 0.997 5.8 104.5 20.6 420 n/a 4_adp: 0.1127 0.1575 0.010 0.997 5.6 103.3 20.6 420 n/a 4_regHadp: 0.1127 0.1576 0.010 0.997 5.6 103.3 20.6 420 n/a 4_occ: 0.1119 0.1587 0.010 0.997 5.6 103.3 20.6 420 n/a 5_bss: 0.1117 0.1586 0.010 0.997 5.3 103.0 20.3 420 n/a 5_settarget: 0.1117 0.1586 0.010 0.997 5.3 103.0 20.3 420 n/a 5_updatecdl: 0.1117 0.1586 0.010 0.998 5.3 103.0 20.3 420 n/a 5_setrh: 0.1119 0.1585 0.010 0.998 5.3 103.0 20.3 420 n/a 5_nqh: 0.1119 0.1585 0.010 0.998 5.3 103.0 20.3 420 n/a 5_sol: 0.1110 0.1536 0.010 0.998 5.3 103.0 20.6 450 n/a 5_weight: 0.1110 0.1536 0.010 0.998 5.3 103.0 20.6 450 n/a 5_xyzrec: 0.1133 0.1551 0.010 1.068 5.3 103.0 20.6 450 n/a 5_adp: 0.1122 0.1543 0.010 1.068 5.4 102.5 20.8 450 n/a 5_regHadp: 0.1123 0.1543 0.010 1.068 5.4 102.5 20.8 450 n/a 5_occ: 0.1116 0.1540 0.010 1.068 5.4 102.5 20.8 450 n/a end: 0.1117 0.1542 0.010 1.068 5.2 102.3 20.6 450 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1446411_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_1446411_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8900 Refinement macro-cycles (run) : 960.5800 Write final files (write_after_run_outputs) : 17.1000 Total : 980.5700 Total CPU time: 16.73 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:45 PST -0800 (1735494105.39 s) Start R-work = 0.1609, R-free = 0.1610 Final R-work = 0.1117, R-free = 0.1542 =============================================================================== Job complete usr+sys time: 1022.28 seconds wall clock time: 17 minutes 25.26 seconds (1045.26 seconds total)