Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2a8z.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2a8z/2a8z.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2a8z/2a8z.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2a8z/2a8z.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2a8z.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2a8z.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 } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6280 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 6280 Classifications: {'peptide': 404} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 388} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N THR A 217 " occ=0.50 ... (12 atoms not shown) pdb="HG23 THR A 217 " occ=0.00 residue: pdb=" N TYR A 381 " occ=0.60 ... (19 atoms not shown) pdb=" HH TYR A 381 " occ=0.00 Time building chain proxies: 2.14, per 1000 atoms: 0.34 Number of scatterers: 6280 At special positions: 0 Unit cell: (77.779, 77.779, 149.634, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 612 8.00 N 555 7.00 C 2066 6.00 H 3035 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 5.05 Conformation dependent library (CDL) restraints added in 754.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 2 sheets defined 48.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 11 through 14 No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 143 through 160 Processing helix chain 'A' and resid 168 through 182 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 219 through 243 removed outlier: 3.558A pdb=" N ASN A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 295 removed outlier: 4.545A pdb=" N ILE A 286 " --> pdb=" O TRP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 318 removed outlier: 3.835A pdb=" N THR A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 removed outlier: 3.532A pdb=" N LEU A 352 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.547A pdb=" N GLU A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 Processing sheet with id= A, first strand: chain 'A' and resid 50 through 55 removed outlier: 5.865A pdb=" N GLU A 55 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N TYR A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 125 through 128 removed outlier: 6.158A pdb=" N LYS A 127 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS A 136 " --> pdb=" O LYS A 127 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3035 1.15 - 1.32: 568 1.32 - 1.49: 1477 1.49 - 1.66: 1273 1.66 - 1.84: 22 Bond restraints: 6375 Sorted by residual: bond pdb=" N THR A 403 " pdb=" H THR A 403 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 228 " pdb=" H VAL A 228 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MET A 89 " pdb=" H MET A 89 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN A 276 " pdb="HE21 GLN A 276 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N SER A 232 " pdb=" H SER A 232 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6370 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.02: 217 106.02 - 113.10: 6605 113.10 - 120.19: 2340 120.19 - 127.27: 2193 127.27 - 134.35: 34 Bond angle restraints: 11389 Sorted by residual: angle pdb=" N ASP A 73 " pdb=" CA ASP A 73 " pdb=" C ASP A 73 " ideal model delta sigma weight residual 110.35 119.54 -9.19 1.40e+00 5.10e-01 4.31e+01 angle pdb=" N LEU A 49 " pdb=" CA LEU A 49 " pdb=" C LEU A 49 " ideal model delta sigma weight residual 114.75 107.29 7.46 1.26e+00 6.30e-01 3.50e+01 angle pdb=" N GLN A 47 " pdb=" CA GLN A 47 " pdb=" C GLN A 47 " ideal model delta sigma weight residual 113.50 107.61 5.89 1.23e+00 6.61e-01 2.30e+01 angle pdb=" N ASN A 320 " pdb=" CA ASN A 320 " pdb=" C ASN A 320 " ideal model delta sigma weight residual 108.69 116.64 -7.95 1.77e+00 3.19e-01 2.02e+01 angle pdb=" CA PHE A 404 " pdb=" C PHE A 404 " pdb=" O PHE A 404 " ideal model delta sigma weight residual 121.00 134.22 -13.22 3.00e+00 1.11e-01 1.94e+01 ... (remaining 11384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 2647 16.41 - 32.81: 248 32.81 - 49.22: 116 49.22 - 65.63: 50 65.63 - 82.03: 9 Dihedral angle restraints: 3070 sinusoidal: 1572 harmonic: 1498 Sorted by residual: dihedral pdb=" CA PRO A 141 " pdb=" C PRO A 141 " pdb=" N ALA A 142 " pdb=" CA ALA A 142 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ALA A 142 " pdb=" C ALA A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta harmonic sigma weight residual 180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TRP A 277 " pdb=" C TRP A 277 " pdb=" N TYR A 278 " pdb=" CA TYR A 278 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 3067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 273 0.066 - 0.133: 106 0.133 - 0.199: 54 0.199 - 0.265: 12 0.265 - 0.332: 3 Chirality restraints: 448 Sorted by residual: chirality pdb=" CA TRP A 124 " pdb=" N TRP A 124 " pdb=" C TRP A 124 " pdb=" CB TRP A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA TRP A 249 " pdb=" N TRP A 249 " pdb=" C TRP A 249 " pdb=" CB TRP A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA PHE A 364 " pdb=" N PHE A 364 " pdb=" C PHE A 364 " pdb=" CB PHE A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 445 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 37 " -0.002 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" CG PHE A 37 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 37 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 37 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 37 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 37 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 37 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 37 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 37 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 37 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 37 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 37 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 312 " -0.011 2.00e-02 2.50e+03 9.92e-03 2.95e+00 pdb=" CG PHE A 312 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 312 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 312 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 312 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 312 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 312 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 312 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE A 312 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE A 312 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 312 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 124 " 0.013 2.00e-02 2.50e+03 7.84e-03 2.46e+00 pdb=" CG TRP A 124 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 124 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 124 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 124 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 124 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 124 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 124 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 124 " 0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 124 " 0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP A 124 " -0.004 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.69: 49 1.69 - 2.42: 2568 2.42 - 3.14: 20549 3.14 - 3.87: 30058 3.87 - 4.60: 45755 Warning: very small nonbonded interaction distances. Nonbonded interactions: 98979 Sorted by model distance: nonbonded pdb=" HG1 THR A 217 " pdb="HD22 ASN A 28 " model vdw sym.op. 0.960 2.100 -x+1,-x+y,-z+1/3 nonbonded pdb="HD22 ASN A 28 " pdb=" HG1 THR A 217 " model vdw sym.op. 0.960 2.100 -x+1,-x+y+1,-z+1/3 nonbonded pdb=" ND2 ASN A 28 " pdb=" HG1 THR A 217 " model vdw sym.op. 1.028 2.600 -x+1,-x+y+1,-z+1/3 nonbonded pdb=" HG1 THR A 217 " pdb=" ND2 ASN A 28 " model vdw sym.op. 1.028 2.600 -x+1,-x+y,-z+1/3 nonbonded pdb=" HB3 PHE A 149 " pdb=" HE3 MET A 175 " model vdw 1.257 2.440 ... (remaining 98974 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: 5 Type Number sf(0) Gaussians S 12 15.96 2 O 612 7.97 1 N 555 6.97 1 C 2066 5.97 2 H 3035 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== Setting occupancies to: 1.000: selected atoms: 3035 of 6280 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6280 n_use_u_iso = 6280 n_use_u_aniso = 0 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 = 6280 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6280 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 6280 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 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 } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 11 through 14 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 20 through 23 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 29 through 41 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 77 through 90 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 93 through 106 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 116 through 118 helix_type = alpha pi *3_10 unknown } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 143 through 160 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 168 through 182 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 201 through 203 helix_type = alpha pi *3_10 unknown } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 206 through 215 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 219 through 243 } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 282 through 295 helix_type = alpha pi *3_10 unknown } helix { serial_number = "13" helix_identifier = "13" selection = chain 'A' and resid 300 through 318 } helix { serial_number = "14" helix_identifier = "14" selection = chain 'A' and resid 342 through 353 } helix { serial_number = "15" helix_identifier = "15" selection = chain 'A' and resid 358 through 369 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'A' and resid 379 through 392 } sheet { first_strand = chain 'A' and resid 50 through 55 sheet_id = " A" strand { selection = chain 'A' and resid 58 through 64 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 63 and name N bond_start_previous = chain 'A' and resid 51 and name O } } sheet { first_strand = chain 'A' and resid 125 through 128 sheet_id = " B" strand { selection = chain 'A' and resid 134 through 138 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 138 and name N bond_start_previous = chain 'A' and resid 125 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "2a8z_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3035 occupancy sum: 3035.00 (% of total atoms 48.91) Rotatable: count: 691 occupancy sum: 691.00 (% of total atoms 11.14) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.20 - 12.00 A, n_refl.=8335 (all), 4.73 % free)-------------| | | | r_work= 0.3129 r_free= 0.3533 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 5.773695 | | target function (ml) not normalized (work): 45848.910197 | | target function (ml) not normalized (free): 2283.639130 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 12.00 - 4.56 0.92 2698 109 0.3333 0.3782 5.9894 6.0293| | 2: 4.56 - 3.65 0.94 2624 139 0.2857 0.3234 5.8247 5.8395| | 3: 3.65 - 3.20 0.95 2619 146 0.3197 0.3629 5.5004 5.5806| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 12.00 - 4.56 2698 109 0.66 38.31 0.93 0.31 29425.10| | 2: 4.56 - 3.65 2624 139 0.72 33.68 1.09 0.35 19121.17| | 3: 3.65 - 3.20 2619 146 0.70 35.58 1.04 0.38 11437.88| |alpha: min = 0.31 max = 0.38 mean = 0.35| |beta: min = 11437.88 max = 29425.10 mean = 20087.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.69| |phase err.(work): min = 0.00 max = 89.93 mean = 35.88| |phase err.(test): min = 0.00 max = 88.66 mean = 35.84| |-----------------------------------------------------------------------------| ----------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 : 0.008 0.100 3340 Z= 0.544 Angle : 1.367 13.217 4535 Z= 0.896 Chirality : 0.089 0.332 448 Planarity : 0.003 0.010 602 Dihedral : 17.613 81.511 1181 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.71 % Favored : 91.54 % Rotamer: Outliers : 7.81 % Allowed : 9.31 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.33), residues: 402 helix: -2.91 (0.26), residues: 192 sheet: -2.64 (0.92), residues: 22 loop : -2.13 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 337 TYR 0.020 0.003 TYR A 148 PHE 0.022 0.003 PHE A 312 TRP 0.021 0.003 TRP A 124 HIS 0.007 0.001 HIS A 302 Individual atomic B min max mean iso aniso Overall: 3.85 57.10 26.96 0.66 3245 0 Protein: 3.85 57.10 26.96 0.66 3245 0 Chain A: 3.85 57.10 26.96 N/A 3245 0 Histogram: Values Number of atoms 3.85 - 9.18 8 9.18 - 14.50 371 14.50 - 19.83 524 19.83 - 25.15 498 25.15 - 30.48 647 30.48 - 35.80 648 35.80 - 41.12 295 41.12 - 46.45 151 46.45 - 51.78 45 51.78 - 57.10 58 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8335 (all), 4.73 % free)-------------| | | | r_work= 0.3129 r_free= 0.3533 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 5.773695 | | target function (ml) not normalized (work): 45848.910197 | | target function (ml) not normalized (free): 2283.639130 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3148 0.3129 0.3533 n_refl.: 8335 re-set all scales: r(all,work,free)=0.3148 0.3129 0.3533 n_refl.: 8335 remove outliers: r(all,work,free)=0.3147 0.3129 0.3533 n_refl.: 8334 overall B=20.11 to atoms: r(all,work,free)=0.3412 0.3391 0.3856 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2140 0.2121 0.2526 n_refl.: 8334 remove outliers: r(all,work,free)=0.2140 0.2121 0.2526 n_refl.: 8334 ======================== 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 11.998-10.364 91.74 96 4 0.2061 1018.156 981.806 1.016 0.997 0.326 10.272-9.295 90.91 94 6 0.2047 877.570 847.545 1.057 0.990 0.359 9.288-8.400 90.37 120 2 0.1824 902.743 893.544 1.038 0.994 0.356 8.393-7.595 91.10 165 9 0.1960 807.576 781.668 1.078 0.999 0.358 7.592-6.868 91.57 220 8 0.2401 650.279 625.385 1.016 0.993 0.373 6.866-6.210 91.74 299 12 0.2710 553.846 521.628 1.012 0.995 0.366 6.206-5.619 92.63 386 16 0.2364 540.376 514.119 0.988 0.997 0.350 5.613-5.076 92.87 551 22 0.2135 562.783 547.919 0.993 0.996 0.335 5.075-4.591 93.18 709 29 0.1919 622.367 608.134 0.994 0.999 0.298 4.589-4.150 93.71 986 42 0.1839 661.715 646.053 1.033 0.998 0.261 4.148-3.753 93.94 1277 72 0.2027 564.522 549.387 1.068 1.005 0.194 3.750-3.393 94.50 1743 97 0.2146 460.286 441.696 1.126 1.007 0.141 3.392-3.201 94.81 1294 75 0.2541 357.412 335.983 1.120 1.008 0.057 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-5.6730 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.276170 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.237597 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2334 0.2512 0.0178 0.002 0.5 2.1 0.0 3.6 0 0.125 0.2279 0.2490 0.0211 0.002 0.5 2.1 0.0 3.9 0 0.250 0.2218 0.2515 0.0297 0.003 0.5 2.1 0.0 4.2 0 0.500 0.2152 0.2523 0.0371 0.003 0.6 3.5 0.0 4.2 0 1.000 0.2063 0.2520 0.0456 0.005 0.7 5.4 0.0 3.9 0 2.000 0.2019 0.2519 0.0500 0.007 0.8 5.9 0.5 3.9 0 3.000 0.1987 0.2554 0.0567 0.009 0.9 8.3 0.5 3.9 0 4.000 0.1962 0.2562 0.0600 0.010 1.0 9.2 1.0 4.8 0 5.000 0.1939 0.2570 0.0631 0.012 1.1 11.3 1.2 5.4 0 6.000 0.1918 0.2577 0.0659 0.013 1.2 12.6 1.2 6.6 0 7.000 0.1901 0.2572 0.0671 0.014 1.3 13.1 1.2 6.9 0 8.000 0.1887 0.2576 0.0689 0.015 1.3 15.4 1.5 7.8 0 9.000 0.1871 0.2584 0.0712 0.017 1.4 16.2 1.5 8.1 0 10.000 0.1928 0.2564 0.0637 0.012 1.2 12.1 1.2 6.3 0 6.638 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2334 0.2512 0.0178 0.002 0.5 2.1 0.0 3.6 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.34 25.12 1.78 0.478 47.025 0.238 0.065 23.32 25.06 1.75 1.377 47.069 0.007 0.064 22.81 25.01 2.20 1.615 47.077 0.030 0.062 22.03 24.96 2.93 2.818 47.130 0.119 0.057 21.15 25.22 4.07 5.432 47.494 0.238 0.053 20.78 25.30 4.51 6.791 47.858 0.356 0.051 20.60 25.40 4.80 7.588 48.066 0.475 0.050 20.46 25.47 5.01 8.278 48.258 0.594 0.049 20.32 25.53 5.21 8.988 48.467 0.713 0.048 20.24 25.59 5.36 9.416 48.587 0.832 0.048 19.93 25.79 5.86 11.219 49.164 0.950 0.047 19.82 25.84 6.02 11.965 49.406 1.069 0.046 19.74 25.90 6.16 12.598 49.609 1.188 0.046 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.119 Accepted refinement result: 22.03 24.96 2.93 2.818 47.130 0.119 0.057 Individual atomic B min max mean iso aniso Overall: 18.96 82.90 47.27 2.82 3245 0 Protein: 18.96 82.90 47.27 2.82 3245 0 Chain A: 18.96 82.90 47.27 N/A 3245 0 Histogram: Values Number of atoms 18.96 - 25.36 4 25.36 - 31.75 131 31.75 - 38.14 523 38.14 - 44.54 659 44.54 - 50.93 782 50.93 - 57.32 648 57.32 - 63.72 308 63.72 - 70.11 116 70.11 - 76.50 56 76.50 - 82.90 18 =========================== Idealize ADP of riding H ========================== r_work=0.2203 r_free=0.2496 r_work=0.2184 r_free=0.2495 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2184 r_free= 0.2495 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.056129 | | target function (ls_wunit_k1) not normalized (work): 445.661811 | | target function (ls_wunit_k1) not normalized (free): 30.162460 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2198 0.2184 0.2495 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3504 0.3488 0.3855 n_refl.: 8334 remove outliers: r(all,work,free)=0.3504 0.3488 0.3855 n_refl.: 8334 overall B=-6.11 to atoms: r(all,work,free)=0.3394 0.3379 0.3724 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2195 0.2180 0.2495 n_refl.: 8334 remove outliers: r(all,work,free)=0.2195 0.2180 0.2495 n_refl.: 8334 ======================== 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 11.998-10.364 92.59 96 4 0.2156 717.284 690.396 1.111 0.995 0.344 10.272-9.295 91.74 94 6 0.2233 618.242 600.596 1.135 0.988 0.360 9.288-8.400 91.04 120 2 0.1916 635.977 626.945 1.094 0.992 0.364 8.393-7.595 91.58 165 9 0.1984 568.932 557.160 1.138 0.997 0.365 7.592-6.868 92.31 220 8 0.2417 458.117 442.607 1.062 0.992 0.371 6.866-6.210 92.28 299 12 0.2540 390.181 368.526 1.029 0.994 0.373 6.206-5.619 93.06 386 16 0.2380 380.692 367.025 1.019 0.995 0.364 5.613-5.076 93.02 551 22 0.2290 396.477 387.359 0.990 0.995 0.355 5.075-4.591 93.42 709 29 0.1955 438.453 430.107 0.990 0.998 0.320 4.589-4.150 93.88 986 42 0.1841 466.174 458.273 1.019 0.997 0.304 4.148-3.753 94.07 1277 72 0.2037 397.702 389.642 1.037 1.005 0.277 3.750-3.393 94.60 1743 97 0.2275 324.269 310.895 1.068 1.008 0.169 3.392-3.201 94.94 1294 75 0.2679 251.794 237.885 1.031 1.010 0.058 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.7635 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.719841 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.050498 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2073 0.2502 0.0429 0.002 0.5 2.7 0.0 1.8 0 0.125 0.2012 0.2513 0.0501 0.004 0.6 4.1 0.5 2.4 0 0.250 0.1959 0.2524 0.0565 0.006 0.7 5.4 0.5 3.0 0 0.500 0.1894 0.2528 0.0634 0.010 1.0 7.3 1.2 4.5 0 1.000 0.1823 0.2580 0.0758 0.017 1.4 12.7 2.0 6.6 0 2.000 0.1786 0.2610 0.0824 0.022 1.7 17.2 2.0 7.8 0 3.000 0.1751 0.2622 0.0871 0.027 2.1 21.0 2.5 9.6 0 4.000 0.1727 0.2621 0.0894 0.032 2.3 24.4 2.2 11.1 0 5.000 0.1708 0.2626 0.0918 0.036 2.5 25.2 2.7 11.1 0 6.000 0.1689 0.2644 0.0955 0.039 2.7 28.8 3.7 12.9 0 7.000 0.1674 0.2633 0.0959 0.042 2.9 28.7 3.5 11.7 0 8.000 0.1658 0.2653 0.0995 0.046 3.1 34.1 3.7 13.2 1 9.000 0.1647 0.2672 0.1024 0.049 3.3 39.3 4.7 14.7 1 10.000 0.1868 0.2551 0.0684 0.013 1.1 9.2 1.5 5.4 0 1.360 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2073 0.2502 0.0429 0.002 0.5 2.7 0.0 1.8 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.73 25.02 4.29 7.003 45.865 0.050 5.980 22.38 25.54 3.16 7.300 46.992 0.002 6.028 21.34 25.03 3.69 7.178 45.928 0.006 5.993 20.26 25.07 4.81 7.393 45.888 0.025 5.964 19.33 25.35 6.02 8.643 46.364 0.050 5.944 19.16 25.41 6.25 9.011 46.363 0.076 5.942 19.02 25.51 6.49 9.402 46.509 0.101 5.941 18.88 25.63 6.76 9.907 46.716 0.126 5.940 18.81 25.70 6.89 10.216 46.833 0.151 5.939 18.75 25.77 7.02 10.488 46.935 0.177 5.940 18.70 25.82 7.12 10.739 47.028 0.202 5.939 18.66 25.88 7.22 11.007 47.126 0.227 5.940 18.63 25.92 7.29 11.186 47.190 0.252 5.940 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 21.34 25.03 3.69 7.178 45.928 0.006 5.993 Individual atomic B min max mean iso aniso Overall: 21.27 74.37 41.28 1.62 3245 0 Protein: 21.27 74.37 41.28 1.62 3245 0 Chain A: 21.27 74.37 41.28 N/A 3245 0 Histogram: Values Number of atoms 21.27 - 26.58 75 26.58 - 31.89 450 31.89 - 37.20 666 37.20 - 42.51 666 42.51 - 47.82 682 47.82 - 53.13 370 53.13 - 58.44 185 58.44 - 63.75 79 63.75 - 69.06 54 69.06 - 74.37 18 =========================== Idealize ADP of riding H ========================== r_work=0.2134 r_free=0.2503 r_work=0.2141 r_free=0.2505 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2141 r_free= 0.2505 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.995049 | | target function (ml) not normalized (work): 47600.688210 | | target function (ml) not normalized (free): 2394.775082 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2158 0.2141 0.2505 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3377 0.3360 0.3751 n_refl.: 8334 remove outliers: r(all,work,free)=0.3377 0.3360 0.3751 n_refl.: 8334 overall B=0.00 to atoms: r(all,work,free)=0.3377 0.3360 0.3751 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2155 0.2138 0.2498 n_refl.: 8334 remove outliers: r(all,work,free)=0.2155 0.2138 0.2498 n_refl.: 8334 ======================== 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 11.998-10.364 92.59 96 4 0.2041 717.284 693.924 1.108 0.996 0.350 10.272-9.295 91.74 94 6 0.2072 618.242 604.858 1.138 0.989 0.370 9.288-8.400 91.04 120 2 0.1804 635.977 631.058 1.100 0.993 0.372 8.393-7.595 91.58 165 9 0.1828 568.932 557.521 1.129 0.998 0.373 7.592-6.868 92.31 220 8 0.2297 458.117 444.521 1.063 0.992 0.380 6.866-6.210 92.28 299 12 0.2450 390.181 368.636 1.033 0.994 0.380 6.206-5.619 93.06 386 16 0.2287 380.692 366.350 1.022 0.995 0.379 5.613-5.076 93.02 551 22 0.2211 396.477 387.726 0.991 0.994 0.360 5.075-4.591 93.42 709 29 0.1933 438.453 430.770 0.995 0.996 0.330 4.589-4.150 93.88 986 42 0.1794 466.174 457.385 1.016 0.994 0.310 4.148-3.753 94.07 1277 72 0.2038 397.702 387.652 1.037 1.000 0.290 3.750-3.393 94.60 1743 97 0.2258 324.269 309.597 1.069 1.002 0.170 3.392-3.201 94.94 1294 75 0.2688 251.794 236.088 1.036 1.002 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.8200 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2138 r_free=0.2498 After: r_work=0.2139 r_free=0.2497 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.643270 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049183 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2139 0.2489 0.0350 0.002 0.5 3.0 0.0 1.8 0 0.125 0.2131 0.2491 0.0360 0.003 0.5 3.0 0.0 1.8 0 0.250 0.2072 0.2487 0.0415 0.008 0.7 4.1 0.0 2.1 0 0.500 0.1952 0.2506 0.0553 0.013 1.4 9.6 1.0 2.7 0 1.000 0.1900 0.2543 0.0643 0.017 1.8 16.1 1.5 3.6 0 2.000 0.1844 0.2551 0.0707 0.024 2.3 21.2 1.5 5.7 0 3.000 0.1812 0.2586 0.0774 0.029 2.5 24.2 2.0 7.8 0 4.000 0.1796 0.2600 0.0804 0.032 2.7 28.2 2.5 9.3 0 5.000 0.1760 0.2624 0.0864 0.037 3.1 34.1 3.0 11.1 0 6.000 0.1741 0.2625 0.0885 0.040 3.4 36.8 3.2 11.1 1 7.000 0.1717 0.2627 0.0909 0.045 3.8 39.8 3.2 12.3 2 8.000 0.1701 0.2637 0.0936 0.049 4.1 42.2 3.5 12.6 2 9.000 0.1694 0.2612 0.0918 0.052 4.2 40.0 3.0 11.1 4 10.000 0.1936 0.2518 0.0583 0.015 1.5 13.1 1.2 3.3 0 1.322 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2139 0.2489 0.0350 0.002 0.5 3.0 0.0 1.8 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.39 24.89 3.50 5.951 45.268 0.049 5.995 22.07 25.00 2.93 6.162 45.391 0.001 6.018 21.37 24.93 3.56 5.982 45.360 0.006 5.995 20.50 24.99 4.49 6.376 45.313 0.025 5.969 19.60 25.20 5.60 7.610 45.682 0.049 5.949 19.33 25.35 6.01 8.303 45.947 0.074 5.945 19.18 25.47 6.29 8.870 46.154 0.098 5.943 19.06 25.55 6.49 9.367 46.330 0.123 5.943 18.95 25.66 6.71 9.920 46.523 0.148 5.942 18.90 25.72 6.82 10.252 46.632 0.172 5.942 18.84 25.79 6.95 10.617 46.751 0.197 5.942 18.79 25.85 7.06 10.948 46.857 0.221 5.942 18.76 25.90 7.14 11.201 46.935 0.246 5.943 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 21.37 24.93 3.56 5.982 45.360 0.006 5.995 Individual atomic B min max mean iso aniso Overall: 21.75 73.58 41.46 1.67 3245 0 Protein: 21.75 73.58 41.46 1.67 3245 0 Chain A: 21.75 73.58 41.46 N/A 3245 0 Histogram: Values Number of atoms 21.75 - 26.93 50 26.93 - 32.11 394 32.11 - 37.30 694 37.30 - 42.48 770 42.48 - 47.66 653 47.66 - 52.85 364 52.85 - 58.03 161 58.03 - 63.21 85 63.21 - 68.40 55 68.40 - 73.58 19 =========================== Idealize ADP of riding H ========================== r_work=0.2137 r_free=0.2493 r_work=0.2137 r_free=0.2494 ----------X-ray data---------- |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2137 r_free= 0.2494 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.994736 | | target function (ml) not normalized (work): 47598.200206 | | target function (ml) not normalized (free): 2394.897465 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 12.00 - 4.56 0.92 2697 109 0.2094 0.2465 6.1528 6.2862| | 2: 4.56 - 3.65 0.94 2624 139 0.1958 0.2158 6.0093 6.0558| | 3: 3.65 - 3.20 0.95 2619 146 0.2473 0.2984 5.8174 5.9448| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 12.00 - 4.56 2697 109 0.83 22.23 1.00 0.92 34677.89| | 2: 4.56 - 3.65 2624 139 0.85 21.59 1.00 0.91 28125.70| | 3: 3.65 - 3.20 2619 146 0.78 28.92 1.00 0.90 23270.67| |alpha: min = 0.90 max = 0.92 mean = 0.91| |beta: min = 23270.67 max = 34677.89 mean = 28749.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.82| |phase err.(work): min = 0.00 max = 89.98 mean = 24.23| |phase err.(test): min = 0.00 max = 86.61 mean = 24.17| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2153 0.2137 0.2494 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3387 0.3369 0.3763 n_refl.: 8334 remove outliers: r(all,work,free)=0.3387 0.3369 0.3763 n_refl.: 8334 overall B=0.00 to atoms: r(all,work,free)=0.3387 0.3369 0.3763 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2152 0.2136 0.2491 n_refl.: 8334 remove outliers: r(all,work,free)=0.2152 0.2136 0.2491 n_refl.: 8334 ======================== 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 11.998-10.364 92.59 96 4 0.2049 717.284 693.713 1.107 0.997 0.350 10.272-9.295 91.74 94 6 0.2079 618.242 604.587 1.135 0.989 0.367 9.288-8.400 91.04 120 2 0.1803 635.977 630.842 1.103 0.994 0.372 8.393-7.595 91.58 165 9 0.1830 568.932 557.388 1.130 0.998 0.373 7.592-6.868 92.31 220 8 0.2303 458.117 444.137 1.065 0.992 0.380 6.866-6.210 92.28 299 12 0.2446 390.181 368.413 1.036 0.994 0.383 6.206-5.619 93.06 386 16 0.2299 380.692 366.028 1.024 0.995 0.379 5.613-5.076 93.02 551 22 0.2211 396.477 387.634 0.998 0.994 0.370 5.075-4.591 93.42 709 29 0.1933 438.453 430.907 0.998 0.996 0.330 4.589-4.150 93.88 986 42 0.1792 466.174 457.321 1.021 0.995 0.310 4.148-3.753 94.07 1277 72 0.2039 397.702 387.844 1.044 1.001 0.280 3.750-3.393 94.60 1743 97 0.2249 324.269 309.773 1.078 1.002 0.170 3.392-3.201 94.94 1294 75 0.2678 251.794 236.355 1.046 1.002 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.3731 ================= 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) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3129 0.3533 0.008 1.367 3.9 57.1 27.0 0 0.000 1_bss: 0.2121 0.2526 0.008 1.367 24.0 77.2 47.1 0 0.000 1_settarget: 0.2121 0.2526 0.008 1.367 24.0 77.2 47.1 0 0.000 1_weight: 0.2121 0.2526 0.008 1.367 24.0 77.2 47.1 0 0.000 1_xyzrec: 0.2334 0.2512 0.002 0.486 24.0 77.2 47.1 0 0.193 1_adp: 0.2203 0.2496 0.002 0.486 19.0 82.9 47.3 0 0.193 1_regHadp: 0.2184 0.2495 0.002 0.486 19.0 82.9 47.3 0 0.193 2_bss: 0.2180 0.2495 0.002 0.486 12.9 76.8 41.2 0 0.193 2_settarget: 0.2180 0.2495 0.002 0.486 12.9 76.8 41.2 0 0.193 2_updatecdl: 0.2180 0.2495 0.002 0.544 12.9 76.8 41.2 0 0.193 2_weight: 0.2180 0.2495 0.002 0.544 12.9 76.8 41.2 0 0.193 2_xyzrec: 0.2073 0.2502 0.002 0.502 12.9 76.8 41.2 0 0.217 2_adp: 0.2134 0.2503 0.002 0.502 21.3 74.4 41.3 0 0.217 2_regHadp: 0.2141 0.2505 0.002 0.502 21.3 74.4 41.3 0 0.217 3_bss: 0.2138 0.2498 0.002 0.502 21.3 74.4 41.3 0 0.217 3_settarget: 0.2138 0.2498 0.002 0.502 21.3 74.4 41.3 0 0.217 3_updatecdl: 0.2138 0.2498 0.003 0.524 21.3 74.4 41.3 0 0.217 3_setrh: 0.2139 0.2497 0.003 0.524 21.3 74.4 41.3 0 0.217 3_weight: 0.2139 0.2497 0.003 0.524 21.3 74.4 41.3 0 0.217 3_xyzrec: 0.2139 0.2489 0.002 0.503 21.3 74.4 41.3 0 0.218 3_adp: 0.2137 0.2493 0.002 0.503 21.7 73.6 41.5 0 0.218 3_regHadp: 0.2137 0.2494 0.002 0.503 21.7 73.6 41.5 0 0.218 end: 0.2136 0.2491 0.002 0.503 21.7 73.6 41.5 0 0.218 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2a8z_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/2a8z_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 9.6600 Refinement macro-cycles (run) : 226.0500 Write final files (write_after_run_outputs) : 23.2200 Total : 258.9300 Total CPU time: 5.00 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:10 PDT -0700 (1716251650.23 s) Start R-work = 0.2121, R-free = 0.2526 Final R-work = 0.2136, R-free = 0.2491 =============================================================================== Job complete usr+sys time: 322.44 seconds wall clock time: 17 minutes 3.21 seconds (1023.21 seconds total)