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_7410891.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 { 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_7410891.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7410891.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.42, per 1000 atoms: 0.42 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: 0.29 Conformation dependent library (CDL) restraints added in 107.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 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: 410 0.89 - 1.14: 1196 1.14 - 1.40: 576 1.40 - 1.65: 902 1.65 - 1.90: 69 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 165 " pdb=" CA ALA A 165 " ideal model delta sigma weight residual 1.459 1.238 0.221 1.21e-02 6.83e+03 3.35e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.156 0.165 1.00e-02 1.00e+04 2.72e+02 bond pdb=" CA VAL A 33 " pdb=" CB VAL A 33 " ideal model delta sigma weight residual 1.539 1.730 -0.191 1.18e-02 7.18e+03 2.63e+02 bond pdb=" C BLYS A 175 " pdb=" N GLU A 176 " ideal model delta sigma weight residual 1.334 1.540 -0.206 1.27e-02 6.20e+03 2.62e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.428 -0.195 1.21e-02 6.83e+03 2.59e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 3251 4.93 - 9.86: 1858 9.86 - 14.79: 582 14.79 - 19.71: 81 19.71 - 24.64: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALEU A 153 " pdb=" C ALEU A 153 " pdb=" O ALEU A 153 " ideal model delta sigma weight residual 120.30 134.74 -14.44 1.07e+00 8.73e-01 1.82e+02 angle pdb=" O LEU A 92 " pdb=" C LEU A 92 " pdb=" N BLYS A 93 " ideal model delta sigma weight residual 122.07 135.58 -13.51 1.03e+00 9.43e-01 1.72e+02 angle pdb=" O ASP A 60 " pdb=" C ASP A 60 " pdb=" N ALA A 61 " ideal model delta sigma weight residual 122.07 135.53 -13.46 1.03e+00 9.43e-01 1.71e+02 angle pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" O LEU A 82 " ideal model delta sigma weight residual 120.90 134.82 -13.92 1.07e+00 8.73e-01 1.69e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 108.24 10.96 9.00e-01 1.23e+00 1.48e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 1283 16.42 - 32.83: 140 32.83 - 49.24: 41 49.24 - 65.66: 14 65.66 - 82.07: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: 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 122.80 144.29 -21.49 0 2.50e+00 1.60e-01 7.39e+01 dihedral pdb=" N ALA A 104 " pdb=" C ALA A 104 " pdb=" CA ALA A 104 " pdb=" CB ALA A 104 " ideal model delta harmonic sigma weight residual 122.90 142.59 -19.69 0 2.50e+00 1.60e-01 6.20e+01 dihedral pdb=" C BASN A 76 " pdb=" N BASN A 76 " pdb=" CA BASN A 76 " pdb=" CB BASN A 76 " ideal model delta harmonic sigma weight residual -122.60 -104.39 -18.21 0 2.50e+00 1.60e-01 5.30e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 111 0.270 - 0.539: 83 0.539 - 0.809: 39 0.809 - 1.079: 8 1.079 - 1.348: 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 MET A 26 " pdb=" N MET A 26 " pdb=" C MET A 26 " pdb=" CB MET A 26 " both_signs ideal model delta sigma weight residual False 2.51 1.35 1.16 2.00e-01 2.50e+01 3.35e+01 chirality pdb=" CA PRO A 22 " pdb=" N PRO A 22 " pdb=" C PRO A 22 " pdb=" CB PRO A 22 " both_signs ideal model delta sigma weight residual False 2.72 1.70 1.01 2.00e-01 2.50e+01 2.57e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.102 2.00e-02 2.50e+03 7.30e-02 1.60e+02 pdb=" CG PHE A 164 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.128 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.082 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.055 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.065 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG ATYR A 67 " 0.032 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.015 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.098 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.080 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.064 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.121 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.066 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.022 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.027 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.070 2.00e-02 2.50e+03 6.39e-02 9.18e+01 pdb=" CG HIS A 138 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.068 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.078 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.084 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.053 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.061 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.34: 1162 2.34 - 2.90: 8204 2.90 - 3.47: 10467 3.47 - 4.03: 15210 4.03 - 4.60: 21605 Nonbonded interactions: 56648 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.771 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.817 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.853 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.873 2.450 x-y,-y,-z-4/3 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.878 2.450 ... (remaining 56643 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_7410891_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= 0.2784 r_free= 0.1802 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.407528 | | target function (ml) not normalized (work): 71591.475545 | | target function (ml) not normalized (free): 3257.093493 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3188 0.2128 7.5696 5.0342| | 2: 3.63 - 2.88 1.00 2711 122 0.2659 0.1675 4.3277 4.3206| | 3: 2.88 - 2.52 1.00 2682 148 0.2520 0.1729 4.1798 4.1771| | 4: 2.52 - 2.29 1.00 2661 139 0.2564 0.1440 3.5014 3.5107| | 5: 2.29 - 2.13 1.00 2678 122 0.2667 0.1581 3.396 3.479| | 6: 2.13 - 2.00 1.00 2692 117 0.2716 0.1796 3.3054 3.4096| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.40 0.77 0.23 1294.73| | 2: 3.63 - 2.88 2711 122 0.83 23.78 1.32 0.23 1294.73| | 3: 2.88 - 2.52 2682 148 0.73 32.70 1.28 0.23 1294.73| | 4: 2.52 - 2.29 2661 139 0.93 11.34 1.30 0.26 130.46| | 5: 2.29 - 2.13 2678 122 0.92 13.30 1.32 0.26 130.46| | 6: 2.13 - 2.00 2692 117 0.90 15.94 1.33 0.26 130.46| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 130.46 max = 1294.73 mean = 719.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.94 mean = 19.08| |phase err.(test): min = 0.00 max = 89.83 mean = 19.41| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.247 1557 Z= 5.376 Angle : 5.408 18.959 2118 Z= 3.798 Chirality : 0.413 1.348 243 Planarity : 0.034 0.086 284 Dihedral : 13.735 82.074 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 1.86 % Favored : 95.65 % Cbeta Deviations : 36.22 % 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: -2.44 (0.44), residues: 224 helix: -2.57 (0.34), residues: 103 sheet: -0.77 (0.90), residues: 28 loop : -0.42 (0.52), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.101 0.024 ARG A 5 TYR 0.069 0.030 TYR A 139 PHE 0.120 0.045 PHE A 164 HIS 0.042 0.017 HIS A 138 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= 0.2784 r_free= 0.1802 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.407528 | | target function (ml) not normalized (work): 71591.475545 | | target function (ml) not normalized (free): 3257.093493 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3569 percent. r_work = 0.2920 r_free = 0.1976 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2867 0.2920 0.1976 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2867 0.2920 0.1976 n_refl.: 17050 remove outliers: r(all,work,free)=0.2158 0.2170 0.1976 n_refl.: 17045 overall B=-0.39 to atoms: r(all,work,free)=0.2132 0.2144 0.1958 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1619 0.1618 0.1635 n_refl.: 17045 remove outliers: r(all,work,free)=0.1617 0.1616 0.1635 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 0.4105 391.338 359.280 0.639 1.017 0.380 11.894-9.307 99.02 97 4 0.1863 633.518 616.613 0.922 1.018 0.377 9.237-7.194 100.00 213 7 0.2213 518.154 510.559 0.954 1.018 0.345 7.162-5.571 100.00 427 22 0.2353 388.875 375.982 0.911 1.016 0.289 5.546-4.326 100.00 867 58 0.1396 533.863 528.185 0.959 1.013 0.251 4.315-3.360 100.00 1859 96 0.1295 507.709 503.905 1.013 1.008 0.211 3.356-2.611 100.00 3867 181 0.1662 333.536 328.885 1.013 0.999 0.039 2.608-2.000 99.99 8818 434 0.1645 217.408 213.254 1.034 0.983 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4001 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1616 r_free=0.1635 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1616 r_free=0.1635 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.006372 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.878004 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 0.1640 0.0288 0.009 1.0 1.6 0.5 0.0 0 11.503 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.40 2.88 3.013 18.466 0.878 0.023 12.79 16.60 3.81 3.605 18.683 0.878 0.020 Individual atomic B min max mean iso aniso Overall: 6.02 113.91 19.90 4.08 1785 0 Protein: 6.02 113.08 17.14 4.09 1519 0 Water: 8.55 113.91 36.00 N/A 258 0 Other: 21.78 37.62 26.41 N/A 8 0 Chain A: 6.02 113.91 19.90 N/A 1785 0 Histogram: Values Number of atoms 6.02 - 16.81 1082 16.81 - 27.60 342 27.60 - 38.39 189 38.39 - 49.17 96 49.17 - 59.96 49 59.96 - 70.75 12 70.75 - 81.54 7 81.54 - 92.33 4 92.33 - 103.12 1 103.12 - 113.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1660 r_work=0.1281 r_free=0.1666 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 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 = 0.1276 r_free = 0.1663 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.24 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= 0.1276 r_free= 0.1663 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020083 | | target function (ls_wunit_k1) not normalized (work): 326.066106 | | target function (ls_wunit_k1) not normalized (free): 27.310119 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1276 0.1663 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1900 0.1898 0.2001 n_refl.: 17043 remove outliers: r(all,work,free)=0.1900 0.1898 0.2001 n_refl.: 17043 overall B=-0.51 to atoms: r(all,work,free)=0.1864 0.1861 0.1980 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1656 n_refl.: 17043 remove outliers: r(all,work,free)=0.1292 0.1274 0.1656 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3507 303.635 278.978 0.625 1.002 0.366 11.894-9.307 99.02 97 4 0.1701 488.349 478.589 0.925 1.003 0.364 9.237-7.194 100.00 213 7 0.1815 399.420 396.170 0.965 1.003 0.341 7.162-5.571 100.00 427 22 0.1839 299.765 294.444 0.933 1.003 0.269 5.546-4.326 100.00 867 58 0.1041 411.530 409.403 0.965 1.003 0.221 4.315-3.360 100.00 1859 96 0.0934 391.369 390.346 1.017 1.002 0.202 3.356-2.611 100.00 3867 181 0.1293 257.107 255.678 1.009 1.001 0.102 2.608-2.000 99.99 8818 434 0.1350 167.590 166.330 1.008 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1665 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1656 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1656 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1656 | n_water=258 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1281 r_free=0.1643 | n_water=254 | time (s): 20.870 (total time: 21.570) Filter (q & B) r_work=0.1281 r_free=0.1643 | n_water=252 | time (s): 1.390 (total time: 22.960) Compute maps r_work=0.1281 r_free=0.1643 | n_water=252 | time (s): 0.650 (total time: 23.610) Filter (map) r_work=0.1312 r_free=0.1648 | n_water=216 | time (s): 2.000 (total time: 25.610) Find peaks r_work=0.1312 r_free=0.1648 | n_water=216 | time (s): 0.660 (total time: 26.270) Add new water r_work=0.1529 r_free=0.1873 | n_water=370 | time (s): 1.860 (total time: 28.130) Refine new water occ: r_work=0.1331 r_free=0.1597 adp: r_work=0.1273 r_free=0.1589 occ: r_work=0.1278 r_free=0.1559 adp: r_work=0.1245 r_free=0.1567 occ: r_work=0.1246 r_free=0.1552 adp: r_work=0.1234 r_free=0.1558 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1558 r_work=0.1234 r_free=0.1558 | n_water=370 | time (s): 12.730 (total time: 40.860) Filter (q & B) r_work=0.1236 r_free=0.1560 | n_water=366 | time (s): 2.380 (total time: 43.240) Filter (dist only) r_work=0.1237 r_free=0.1563 | n_water=365 | time (s): 28.580 (total time: 71.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.969421 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.964215 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 0.1209 0.1584 0.0375 0.008 0.9 2.9 0.5 0.0 0 12.485 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 15.84 3.75 4.169 20.905 0.964 0.018 11.96 16.12 4.16 4.229 21.249 0.964 0.018 Individual atomic B min max mean iso aniso Overall: 6.32 107.57 21.38 4.32 1892 0 Protein: 6.32 107.57 17.70 4.30 1519 0 Water: 8.59 68.05 36.39 N/A 365 0 Other: 24.53 48.31 37.04 N/A 8 0 Chain A: 6.32 107.57 19.53 N/A 1743 0 Chain S: 17.06 66.02 43.06 N/A 149 0 Histogram: Values Number of atoms 6.32 - 16.45 1004 16.45 - 26.57 391 26.57 - 36.70 219 36.70 - 46.82 166 46.82 - 56.94 72 56.94 - 67.07 28 67.07 - 77.19 4 77.19 - 87.32 6 87.32 - 97.44 0 97.44 - 107.57 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1612 r_work=0.1198 r_free=0.1615 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1615 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 = 0.1196 r_free = 0.1620 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1196 r_free= 0.1620 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.017071 | | target function (ls_wunit_k1) not normalized (work): 277.149873 | | target function (ls_wunit_k1) not normalized (free): 24.793066 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1196 0.1620 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1748 0.1738 0.1975 n_refl.: 17042 remove outliers: r(all,work,free)=0.1748 0.1738 0.1975 n_refl.: 17042 overall B=-0.46 to atoms: r(all,work,free)=0.1720 0.1709 0.1956 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1192 0.1612 n_refl.: 17042 remove outliers: r(all,work,free)=0.1211 0.1191 0.1612 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 0.3207 300.470 283.609 0.605 1.006 0.350 11.894-9.307 99.02 97 4 0.1518 488.349 486.739 0.918 1.006 0.334 9.237-7.194 100.00 213 7 0.1643 399.420 400.508 0.975 1.006 0.301 7.162-5.571 100.00 427 22 0.1557 299.765 295.988 0.933 1.006 0.261 5.546-4.326 100.00 867 58 0.0881 411.530 409.316 0.964 1.005 0.211 4.315-3.360 100.00 1859 96 0.0823 391.369 390.268 1.014 1.003 0.202 3.356-2.611 100.00 3867 181 0.1203 257.107 256.137 1.009 1.000 0.132 2.608-2.000 99.99 8818 434 0.1335 167.590 166.492 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1555 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1612 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 97 ASN B Total number of N/Q/H flips: 2 r_work=0.1192 r_free=0.1614 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1614 | n_water=365 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1193 r_free=0.1615 | n_water=364 | time (s): 28.740 (total time: 29.420) Filter (q & B) r_work=0.1193 r_free=0.1615 | n_water=364 | time (s): 1.000 (total time: 30.420) Compute maps r_work=0.1193 r_free=0.1615 | n_water=364 | time (s): 0.530 (total time: 30.950) Filter (map) r_work=0.1260 r_free=0.1617 | n_water=265 | time (s): 1.980 (total time: 32.930) Find peaks r_work=0.1260 r_free=0.1617 | n_water=265 | time (s): 0.650 (total time: 33.580) Add new water r_work=0.1441 r_free=0.1781 | n_water=416 | time (s): 1.530 (total time: 35.110) Refine new water occ: r_work=0.1251 r_free=0.1566 adp: r_work=0.1242 r_free=0.1577 occ: r_work=0.1225 r_free=0.1545 adp: r_work=0.1214 r_free=0.1554 occ: r_work=0.1206 r_free=0.1531 adp: r_work=0.1196 r_free=0.1539 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1539 r_work=0.1196 r_free=0.1539 | n_water=416 | time (s): 37.690 (total time: 72.800) Filter (q & B) r_work=0.1198 r_free=0.1557 | n_water=407 | time (s): 1.490 (total time: 74.290) Filter (dist only) r_work=0.1198 r_free=0.1558 | n_water=405 | time (s): 31.670 (total time: 105.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.838814 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.192009 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 0.1184 0.1553 0.0368 0.009 0.9 3.5 0.5 0.0 0 0.919 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.84 15.53 3.68 4.365 21.462 0.192 4.997 11.61 15.40 3.79 5.019 21.391 0.192 4.968 Individual atomic B min max mean iso aniso Overall: 6.05 104.39 20.86 4.87 1932 0 Protein: 6.05 104.39 16.84 4.86 1519 0 Water: 8.73 62.94 35.66 N/A 405 0 Other: 27.19 49.25 35.69 N/A 8 0 Chain A: 6.05 104.39 18.65 N/A 1738 0 Chain S: 18.88 62.94 40.66 N/A 194 0 Histogram: Values Number of atoms 6.05 - 15.88 1065 15.88 - 25.71 341 25.71 - 35.55 217 35.55 - 45.38 174 45.38 - 55.22 90 55.22 - 65.05 31 65.05 - 74.88 5 74.88 - 84.72 4 84.72 - 94.55 3 94.55 - 104.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1161 r_free=0.1540 r_work=0.1161 r_free=0.1539 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1161 r_free = 0.1539 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1153 r_free = 0.1529 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1153 r_free= 0.1529 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.960737 | | target function (ml) not normalized (work): 80532.610853 | | target function (ml) not normalized (free): 4175.411652 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1171 0.1153 0.1529 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1653 0.1645 0.1840 n_refl.: 17041 remove outliers: r(all,work,free)=0.1653 0.1645 0.1840 n_refl.: 17041 overall B=-0.34 to atoms: r(all,work,free)=0.1631 0.1622 0.1829 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1170 0.1152 0.1526 n_refl.: 17041 remove outliers: r(all,work,free)=0.1169 0.1151 0.1526 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 0.3350 296.903 280.344 0.577 1.003 0.340 11.894-9.307 99.02 97 4 0.1672 488.349 484.558 0.922 1.004 0.340 9.237-7.194 100.00 213 7 0.1780 399.420 399.654 0.988 1.004 0.290 7.162-5.571 100.00 427 22 0.1614 299.765 293.884 0.939 1.004 0.241 5.546-4.326 100.00 867 58 0.0939 411.530 408.594 0.969 1.004 0.206 4.315-3.360 100.00 1859 96 0.0908 391.369 389.051 1.012 1.003 0.201 3.356-2.611 100.00 3867 181 0.1303 257.107 254.686 1.010 1.001 0.131 2.608-2.000 99.99 8818 434 0.1089 167.590 166.137 1.009 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1691 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1151 r_free=0.1526 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1152 r_free=0.1522 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1152 r_free=0.1522 | n_water=405 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1152 r_free=0.1522 | n_water=405 | time (s): 31.610 (total time: 32.540) Filter (q & B) r_work=0.1152 r_free=0.1522 | n_water=405 | time (s): 0.770 (total time: 33.310) Compute maps r_work=0.1152 r_free=0.1522 | n_water=405 | time (s): 0.590 (total time: 33.900) Filter (map) r_work=0.1205 r_free=0.1527 | n_water=315 | time (s): 1.660 (total time: 35.560) Find peaks r_work=0.1205 r_free=0.1527 | n_water=315 | time (s): 0.510 (total time: 36.070) Add new water r_work=0.1353 r_free=0.1661 | n_water=459 | time (s): 2.090 (total time: 38.160) Refine new water occ: r_work=0.1183 r_free=0.1493 adp: r_work=0.1175 r_free=0.1495 occ: r_work=0.1158 r_free=0.1477 adp: r_work=0.1149 r_free=0.1474 occ: r_work=0.1140 r_free=0.1467 adp: r_work=0.1132 r_free=0.1464 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1464 r_work=0.1132 r_free=0.1464 | n_water=459 | time (s): 28.070 (total time: 66.230) Filter (q & B) r_work=0.1135 r_free=0.1474 | n_water=451 | time (s): 2.010 (total time: 68.240) Filter (dist only) r_work=0.1138 r_free=0.1472 | n_water=449 | time (s): 34.950 (total time: 103.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.960679 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.166708 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1128 0.1554 0.0426 0.010 1.0 4.8 0.5 0.0 0 0.980 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.28 15.54 4.26 4.585 21.080 0.167 4.958 11.18 15.65 4.47 4.695 21.113 0.167 4.954 Individual atomic B min max mean iso aniso Overall: 5.63 102.14 21.08 4.84 1976 0 Protein: 5.63 102.14 16.47 4.83 1519 0 Water: 8.31 66.07 36.45 N/A 449 0 Other: 26.76 46.79 34.49 N/A 8 0 Chain A: 5.63 102.14 18.23 N/A 1737 0 Chain S: 13.59 66.07 41.80 N/A 239 0 Histogram: Values Number of atoms 5.63 - 15.28 1030 15.28 - 24.93 379 24.93 - 34.59 201 34.59 - 44.24 200 44.24 - 53.89 113 53.89 - 63.54 35 63.54 - 73.19 9 73.19 - 82.84 2 82.84 - 92.49 4 92.49 - 102.14 3 =========================== Idealize ADP of riding H ========================== r_work=0.1118 r_free=0.1565 r_work=0.1118 r_free=0.1567 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1118 r_free = 0.1567 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1107 r_free = 0.1572 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.18 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= 0.1107 r_free= 0.1572 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.952273 | | target function (ml) not normalized (work): 80390.255455 | | target function (ml) not normalized (free): 4194.602163 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1107 0.1572 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1588 0.1575 0.1872 n_refl.: 17040 remove outliers: r(all,work,free)=0.1588 0.1575 0.1872 n_refl.: 17040 overall B=-0.27 to atoms: r(all,work,free)=0.1571 0.1558 0.1864 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1126 0.1103 0.1563 n_refl.: 17040 remove outliers: r(all,work,free)=0.1126 0.1103 0.1563 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 0.3530 296.903 278.761 0.553 1.002 0.314 11.894-9.307 99.02 97 4 0.1752 488.349 481.590 0.925 1.003 0.304 9.237-7.194 100.00 213 7 0.1666 399.420 401.361 0.997 1.003 0.240 7.162-5.571 100.00 427 22 0.1551 299.765 294.225 0.938 1.003 0.224 5.546-4.326 100.00 867 58 0.0905 411.530 407.581 0.966 1.003 0.195 4.315-3.360 100.00 1859 96 0.0855 391.369 389.065 1.006 1.002 0.165 3.356-2.611 100.00 3867 181 0.1254 257.107 254.769 1.002 1.001 0.141 2.608-2.000 99.99 8818 434 0.1038 167.590 166.471 0.998 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9402 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1103 r_free=0.1563 After: r_work=0.1106 r_free=0.1562 ================================== NQH flips ================================== r_work=0.1106 r_free=0.1562 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1107 r_free=0.1564 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1107 r_free=0.1564 | n_water=449 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1107 r_free=0.1564 | n_water=449 | time (s): 36.050 (total time: 36.710) Filter (q & B) r_work=0.1107 r_free=0.1561 | n_water=448 | time (s): 1.680 (total time: 38.390) Compute maps r_work=0.1107 r_free=0.1561 | n_water=448 | time (s): 0.550 (total time: 38.940) Filter (map) r_work=0.1186 r_free=0.1554 | n_water=326 | time (s): 1.570 (total time: 40.510) Find peaks r_work=0.1186 r_free=0.1554 | n_water=326 | time (s): 0.550 (total time: 41.060) Add new water r_work=0.1303 r_free=0.1650 | n_water=472 | time (s): 2.100 (total time: 43.160) Refine new water occ: r_work=0.1144 r_free=0.1508 adp: r_work=0.1137 r_free=0.1512 occ: r_work=0.1124 r_free=0.1494 adp: r_work=0.1116 r_free=0.1498 occ: r_work=0.1109 r_free=0.1489 adp: r_work=0.1103 r_free=0.1490 ADP+occupancy (water only), MIN, final r_work=0.1103 r_free=0.1490 r_work=0.1103 r_free=0.1490 | n_water=472 | time (s): 28.830 (total time: 71.990) Filter (q & B) r_work=0.1108 r_free=0.1505 | n_water=458 | time (s): 2.360 (total time: 74.350) Filter (dist only) r_work=0.1108 r_free=0.1507 | n_water=457 | time (s): 39.430 (total time: 113.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.994833 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.192013 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 0.1130 0.1536 0.0405 0.011 1.1 6.4 0.5 0.0 0 0.997 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.36 4.05 4.535 20.794 0.192 4.954 11.17 15.25 4.08 4.676 20.859 0.192 4.943 Individual atomic B min max mean iso aniso Overall: 5.55 101.85 20.95 5.08 1984 0 Protein: 5.55 101.85 16.20 5.07 1519 0 Water: 8.18 65.06 36.50 N/A 457 0 Other: 26.53 46.96 34.45 N/A 8 0 Chain A: 5.55 101.85 17.95 N/A 1737 0 Chain S: 17.05 65.06 42.00 N/A 247 0 Histogram: Values Number of atoms 5.55 - 15.18 1052 15.18 - 24.81 363 24.81 - 34.44 193 34.44 - 44.07 197 44.07 - 53.70 122 53.70 - 63.33 39 63.33 - 72.96 9 72.96 - 82.59 2 82.59 - 92.22 3 92.22 - 101.85 4 =========================== Idealize ADP of riding H ========================== r_work=0.1117 r_free=0.1525 r_work=0.1117 r_free=0.1525 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1117 r_free = 0.1525 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1110 r_free = 0.1536 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1110 r_free= 0.1536 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.941005 | | target function (ml) not normalized (work): 80207.334976 | | target function (ml) not normalized (free): 4175.692396 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1136 0.1508 5.468 5.7218| | 2: 3.63 - 2.88 1.00 2711 122 0.1100 0.1479 5.2361 5.3478| | 3: 2.88 - 2.52 1.00 2681 148 0.1349 0.1624 5.1463 5.2035| | 4: 2.52 - 2.29 1.00 2661 139 0.0933 0.1532 4.6249 4.97| | 5: 2.29 - 2.13 1.00 2678 122 0.0950 0.1455 4.5738 4.873| | 6: 2.13 - 2.00 1.00 2692 117 0.1111 0.1724 4.5671 4.7696| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 9.28 1.00 0.96 6740.99| | 2: 3.63 - 2.88 2711 122 0.92 13.27 1.01 0.96 6740.99| | 3: 2.88 - 2.52 2681 148 0.87 19.53 0.99 0.96 6740.99| | 4: 2.52 - 2.29 2661 139 0.93 12.01 1.01 0.97 2100.22| | 5: 2.29 - 2.13 2678 122 0.92 14.04 1.00 0.97 2100.22| | 6: 2.13 - 2.00 2692 117 0.89 16.73 0.99 0.97 2100.22| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2100.22 max = 6740.99 mean = 4445.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.98 mean = 14.11| |phase err.(test): min = 0.00 max = 85.24 mean = 13.75| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1131 0.1110 0.1536 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1570 0.1558 0.1835 n_refl.: 17040 remove outliers: r(all,work,free)=0.1570 0.1558 0.1835 n_refl.: 17040 overall B=-0.22 to atoms: r(all,work,free)=0.1557 0.1545 0.1828 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1131 0.1110 0.1540 n_refl.: 17040 remove outliers: r(all,work,free)=0.1131 0.1110 0.1540 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3629 296.903 276.396 0.544 1.004 0.329 11.894-9.307 99.02 97 4 0.1833 488.349 481.580 0.921 1.005 0.329 9.237-7.194 100.00 213 7 0.1780 399.420 402.518 0.988 1.005 0.220 7.162-5.571 100.00 427 22 0.1632 299.765 293.582 0.930 1.005 0.211 5.546-4.326 100.00 867 58 0.0943 411.530 407.920 0.964 1.004 0.200 4.315-3.360 100.00 1859 96 0.0867 391.369 389.073 1.003 1.003 0.181 3.356-2.611 100.00 3867 181 0.1245 257.107 254.890 1.000 1.001 0.063 2.608-2.000 99.99 8818 434 0.1029 167.590 166.356 0.991 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7595 ================= 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 : 0.2784 0.1802 0.080 5.408 8.8 119.3 19.9 258 0.000 1_bss: 0.1616 0.1635 0.080 5.408 8.5 118.9 19.5 258 0.000 1_settarget: 0.1616 0.1635 0.080 5.408 8.5 118.9 19.5 258 0.000 1_nqh: 0.1616 0.1635 0.080 5.408 8.5 118.9 19.5 258 0.000 1_weight: 0.1616 0.1635 0.080 5.408 8.5 118.9 19.5 258 0.000 1_xyzrec: 0.1352 0.1640 0.009 0.981 8.5 118.9 19.5 258 0.145 1_adp: 0.1279 0.1660 0.009 0.981 6.0 113.9 19.9 258 0.145 1_regHadp: 0.1281 0.1666 0.009 0.981 6.0 113.9 19.9 258 0.145 1_occ: 0.1276 0.1663 0.009 0.981 6.0 113.9 19.9 258 0.145 2_bss: 0.1274 0.1656 0.009 0.981 5.5 113.4 19.4 258 0.145 2_settarget: 0.1274 0.1656 0.009 0.981 5.5 113.4 19.4 258 0.145 2_updatecdl: 0.1274 0.1656 0.009 0.996 5.5 113.4 19.4 258 0.145 2_nqh: 0.1274 0.1656 0.009 0.996 5.5 113.4 19.4 258 0.145 2_sol: 0.1237 0.1563 0.009 0.996 5.5 112.6 20.7 365 n/a 2_weight: 0.1237 0.1563 0.009 0.996 5.5 112.6 20.7 365 n/a 2_xyzrec: 0.1209 0.1584 0.008 0.937 5.5 112.6 20.7 365 n/a 2_adp: 0.1196 0.1612 0.008 0.937 6.3 107.6 21.4 365 n/a 2_regHadp: 0.1198 0.1615 0.008 0.937 6.3 107.6 21.4 365 n/a 2_occ: 0.1196 0.1620 0.008 0.937 6.3 107.6 21.4 365 n/a 3_bss: 0.1191 0.1612 0.008 0.937 5.9 107.1 20.9 365 n/a 3_settarget: 0.1191 0.1612 0.008 0.937 5.9 107.1 20.9 365 n/a 3_updatecdl: 0.1191 0.1612 0.008 0.937 5.9 107.1 20.9 365 n/a 3_nqh: 0.1192 0.1614 0.008 0.937 5.9 107.1 20.9 365 n/a 3_sol: 0.1198 0.1558 0.008 0.937 5.9 107.1 21.0 405 n/a 3_weight: 0.1198 0.1558 0.008 0.937 5.9 107.1 21.0 405 n/a 3_xyzrec: 0.1184 0.1553 0.009 0.948 5.9 107.1 21.0 405 n/a 3_adp: 0.1161 0.1540 0.009 0.948 6.0 104.4 20.9 405 n/a 3_regHadp: 0.1161 0.1539 0.009 0.948 6.0 104.4 20.9 405 n/a 3_occ: 0.1153 0.1529 0.009 0.948 6.0 104.4 20.9 405 n/a 4_bss: 0.1151 0.1526 0.009 0.948 5.7 104.0 20.5 405 n/a 4_settarget: 0.1151 0.1526 0.009 0.948 5.7 104.0 20.5 405 n/a 4_updatecdl: 0.1151 0.1526 0.009 0.950 5.7 104.0 20.5 405 n/a 4_nqh: 0.1152 0.1522 0.009 0.950 5.7 104.0 20.5 405 n/a 4_sol: 0.1138 0.1472 0.009 0.950 5.7 104.0 21.0 449 n/a 4_weight: 0.1138 0.1472 0.009 0.950 5.7 104.0 21.0 449 n/a 4_xyzrec: 0.1128 0.1554 0.010 0.988 5.7 104.0 21.0 449 n/a 4_adp: 0.1118 0.1565 0.010 0.988 5.6 102.1 21.1 449 n/a 4_regHadp: 0.1118 0.1567 0.010 0.988 5.6 102.1 21.1 449 n/a 4_occ: 0.1107 0.1572 0.010 0.988 5.6 102.1 21.1 449 n/a 5_bss: 0.1103 0.1563 0.010 0.988 5.4 101.9 20.8 449 n/a 5_settarget: 0.1103 0.1563 0.010 0.988 5.4 101.9 20.8 449 n/a 5_updatecdl: 0.1103 0.1563 0.010 0.990 5.4 101.9 20.8 449 n/a 5_setrh: 0.1106 0.1562 0.010 0.990 5.4 101.9 20.8 449 n/a 5_nqh: 0.1107 0.1564 0.010 0.990 5.4 101.9 20.8 449 n/a 5_sol: 0.1108 0.1507 0.010 0.990 5.4 101.9 20.8 457 n/a 5_weight: 0.1108 0.1507 0.010 0.990 5.4 101.9 20.8 457 n/a 5_xyzrec: 0.1130 0.1536 0.011 1.061 5.4 101.9 20.8 457 n/a 5_adp: 0.1117 0.1525 0.011 1.061 5.5 101.9 20.9 457 n/a 5_regHadp: 0.1117 0.1525 0.011 1.061 5.5 101.9 20.9 457 n/a 5_occ: 0.1110 0.1536 0.011 1.061 5.5 101.9 20.9 457 n/a end: 0.1110 0.1540 0.011 1.061 5.3 101.6 20.7 457 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7410891_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7410891_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.8600 Refinement macro-cycles (run) : 923.9200 Write final files (write_after_run_outputs) : 19.9600 Total : 946.7400 Total CPU time: 16.11 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:08 PST -0800 (1735494068.35 s) Start R-work = 0.1616, R-free = 0.1635 Final R-work = 0.1110, R-free = 0.1540 =============================================================================== Job complete usr+sys time: 990.49 seconds wall clock time: 16 minutes 54.12 seconds (1014.12 seconds total)