Starting phenix.refine on Mon May 20 17:15:26 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+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } 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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { 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: 0.00s 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: 1.21, per 1000 atoms: 0.19 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: 1.52 Conformation dependent library (CDL) restraints added in 205.0 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. 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: 0.43 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: 1.39 Time building geometry restraints manager: 1.73 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 { 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 } ramachandran_plot_restraints { 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 ============================ Update phi&psi targets =========================== 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2121 r_free=0.2526 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2121 r_free=0.2526 ========================= Local real-space refinement ========================= Before: r_work=0.2121 r_free=0.2526 106 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 0.408 revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 26 average time/residue: 0.2055 time to fit residues: 7.1107 After: r_work=0.2140 r_free=0.2587 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.218510 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.237935 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 0.2308 0.2516 0.0209 0.002 0.5 2.4 0.0 1.8 0 0.125 0.2277 0.2499 0.0222 0.002 0.5 2.2 0.0 2.1 0 0.250 0.2223 0.2507 0.0283 0.003 0.6 2.2 0.0 2.4 0 0.500 0.2152 0.2525 0.0373 0.004 0.6 2.9 0.0 2.1 0 1.000 0.2076 0.2554 0.0477 0.005 0.7 5.3 0.0 2.1 0 2.000 0.2031 0.2573 0.0542 0.007 0.8 5.7 0.0 3.0 0 3.000 0.1994 0.2574 0.0579 0.009 0.9 6.7 0.0 3.0 0 4.000 0.1969 0.2568 0.0599 0.010 1.0 9.1 0.0 3.6 0 5.000 0.1944 0.2593 0.0650 0.012 1.1 10.0 0.0 3.9 0 6.000 0.1926 0.2594 0.0669 0.013 1.2 10.8 0.0 4.2 0 7.000 0.1908 0.2578 0.0669 0.014 1.3 12.4 0.0 4.5 0 8.000 0.1891 0.2596 0.0705 0.016 1.3 12.6 0.2 5.7 0 9.000 0.1878 0.2606 0.0728 0.017 1.4 14.6 0.2 6.0 0 10.000 0.1930 0.2584 0.0654 0.012 1.2 10.2 0.0 3.6 0 6.609 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2308 0.2516 0.0209 0.002 0.5 2.4 0.0 1.8 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2308 r_free=0.2516 87 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.678 revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.4057 time to fit residues: 3.7638 After: r_work=0.2314 r_free=0.2517 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.14 25.17 2.03 0.478 47.025 0.238 0.064 23.12 25.18 2.06 1.378 47.069 0.007 0.063 22.62 25.12 2.50 1.615 47.076 0.030 0.060 21.82 25.11 3.29 2.804 47.123 0.119 0.056 20.91 25.31 4.40 5.542 47.499 0.238 0.051 20.53 25.32 4.78 6.940 47.874 0.357 0.050 20.36 25.36 5.00 7.751 48.085 0.476 0.049 20.22 25.40 5.18 8.418 48.267 0.595 0.048 20.08 25.45 5.36 9.179 48.486 0.714 0.047 20.01 25.46 5.45 9.615 48.608 0.833 0.047 19.71 25.59 5.89 11.428 49.178 0.952 0.046 19.63 25.68 6.05 12.013 49.356 1.071 0.045 19.59 25.71 6.12 12.384 49.458 1.190 0.045 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: 21.82 25.11 3.29 2.804 47.123 0.119 0.056 Individual atomic B min max mean iso aniso Overall: 18.96 82.36 47.26 2.80 3245 0 Protein: 18.96 82.36 47.26 2.80 3245 0 Chain A: 18.96 82.36 47.26 N/A 3245 0 Histogram: Values Number of atoms 18.96 - 25.30 3 25.30 - 31.64 122 31.64 - 37.98 514 37.98 - 44.32 663 44.32 - 50.66 770 50.66 - 57.00 643 57.00 - 63.34 322 63.34 - 69.68 130 69.68 - 76.02 55 76.02 - 82.36 23 =========================== Idealize ADP of riding H ========================== r_work=0.2182 r_free=0.2511 r_work=0.2163 r_free=0.2504 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2163 r_free= 0.2504 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.055097 | | target function (ls_wunit_k1) not normalized (work): 437.468002 | | target function (ls_wunit_k1) not normalized (free): 30.346278 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2179 0.2163 0.2504 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3483 0.3464 0.3887 n_refl.: 8334 remove outliers: r(all,work,free)=0.3483 0.3464 0.3887 n_refl.: 8334 overall B=-6.05 to atoms: r(all,work,free)=0.3374 0.3355 0.3759 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2175 0.2159 0.2510 n_refl.: 8334 remove outliers: r(all,work,free)=0.2175 0.2159 0.2510 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 0.2150 717.458 691.091 1.118 0.996 0.354 10.272-9.295 91.74 94 6 0.2178 618.392 602.247 1.126 0.989 0.359 9.288-8.400 91.04 120 2 0.1891 636.131 628.418 1.097 0.993 0.364 8.393-7.595 91.58 165 9 0.2025 569.070 556.406 1.138 0.998 0.367 7.592-6.868 92.31 220 8 0.2436 458.229 441.815 1.057 0.992 0.381 6.866-6.210 92.28 299 12 0.2529 390.276 368.171 1.031 0.994 0.383 6.206-5.619 93.06 386 16 0.2419 380.784 366.500 1.016 0.996 0.360 5.613-5.076 93.02 551 22 0.2241 396.573 386.426 0.989 0.995 0.359 5.075-4.591 93.42 709 29 0.1914 438.560 431.141 0.990 0.998 0.320 4.589-4.150 93.88 986 42 0.1849 466.287 457.491 1.017 0.998 0.288 4.148-3.753 94.07 1277 72 0.2003 397.798 389.983 1.037 1.005 0.277 3.750-3.393 94.60 1743 97 0.2216 324.347 311.879 1.069 1.008 0.158 3.392-3.201 94.94 1294 75 0.2684 251.856 237.460 1.029 1.009 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.7559 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2159 r_free=0.2510 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 131 ASN A 223 ASN A 360 GLN Total number of N/Q/H flips: 4 r_work=0.2161 r_free=0.2509 ========================= Local real-space refinement ========================= Before: r_work=0.2161 r_free=0.2509 86 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 1.370 revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.3513 time to fit residues: 2.6306 After: r_work=0.2161 r_free=0.2509 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.706787 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049596 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 0.2523 0.0450 0.003 0.5 3.8 0.0 0.6 0 0.125 0.2013 0.2501 0.0488 0.004 0.6 3.8 0.0 0.3 0 0.250 0.1955 0.2514 0.0559 0.006 0.7 4.9 0.0 1.2 0 0.500 0.1897 0.2531 0.0634 0.010 1.0 7.6 0.2 3.0 0 1.000 0.1823 0.2579 0.0756 0.017 1.4 12.1 0.2 5.4 0 2.000 0.1776 0.2595 0.0818 0.023 1.8 16.6 0.5 6.6 0 3.000 0.1749 0.2611 0.0862 0.028 2.1 20.4 1.0 7.8 0 4.000 0.1723 0.2622 0.0899 0.032 2.3 23.7 1.2 8.7 0 5.000 0.1700 0.2640 0.0940 0.037 2.5 26.1 1.5 9.9 0 6.000 0.1683 0.2643 0.0960 0.041 2.8 28.7 1.5 11.1 0 7.000 0.1672 0.2637 0.0966 0.044 2.9 30.6 1.7 11.7 0 8.000 0.1656 0.2634 0.0978 0.047 3.1 33.3 1.5 12.3 1 9.000 0.1644 0.2639 0.0995 0.050 3.3 37.3 1.7 13.2 1 10.000 0.1867 0.2542 0.0675 0.013 1.2 8.8 0.2 3.6 0 1.353 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2013 0.2501 0.0488 0.004 0.6 3.8 0.0 0.3 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2013 r_free=0.2501 80 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.440 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4521 time to fit residues: 2.0507 After: r_work=0.2021 r_free=0.2508 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.21 25.08 4.87 7.001 45.924 0.050 5.961 21.84 25.52 3.67 7.294 47.074 0.001 6.008 20.80 25.11 4.31 7.203 46.044 0.006 5.974 19.64 25.08 5.43 7.442 46.030 0.025 5.942 18.78 25.24 6.45 8.533 46.518 0.050 5.926 18.56 25.33 6.77 9.055 46.593 0.074 5.923 18.46 25.37 6.91 9.351 46.654 0.099 5.923 18.37 25.42 7.05 9.687 46.771 0.124 5.923 18.27 25.49 7.22 10.088 46.923 0.149 5.923 18.24 25.53 7.29 10.273 46.985 0.174 5.923 18.20 25.57 7.38 10.537 47.079 0.198 5.923 18.15 25.64 7.49 10.830 47.184 0.223 5.923 18.11 25.68 7.57 11.079 47.269 0.248 5.923 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.025 Accepted refinement result: 19.64 25.08 5.43 7.442 46.030 0.025 5.942 Individual atomic B min max mean iso aniso Overall: 10.15 82.04 41.41 3.93 3245 0 Protein: 10.15 82.04 41.41 3.93 3245 0 Chain A: 10.15 82.04 41.41 N/A 3245 0 Histogram: Values Number of atoms 10.15 - 17.33 5 17.33 - 24.52 68 24.52 - 31.71 522 31.71 - 38.90 822 38.90 - 46.09 847 46.09 - 53.28 574 53.28 - 60.47 247 60.47 - 67.66 104 67.66 - 74.85 46 74.85 - 82.04 10 =========================== Idealize ADP of riding H ========================== r_work=0.1964 r_free=0.2508 r_work=0.1961 r_free=0.2508 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.1961 r_free= 0.2508 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 5.941442 | | target function (ml) not normalized (work): 47175.048621 | | target function (ml) not normalized (free): 2396.923419 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1986 0.1961 0.2508 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3278 0.3255 0.3767 n_refl.: 8334 remove outliers: r(all,work,free)=0.3278 0.3255 0.3767 n_refl.: 8334 overall B=0.00 to atoms: r(all,work,free)=0.3278 0.3255 0.3767 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.1982 0.1957 0.2493 n_refl.: 8334 remove outliers: r(all,work,free)=0.1982 0.1957 0.2493 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 0.1894 717.458 697.098 1.114 0.995 0.350 10.272-9.295 91.74 94 6 0.1932 618.392 606.954 1.135 0.988 0.367 9.288-8.400 91.04 120 2 0.1756 636.131 632.853 1.105 0.992 0.371 8.393-7.595 91.58 165 9 0.1761 569.070 558.819 1.134 0.996 0.372 7.592-6.868 92.31 220 8 0.2183 458.229 445.643 1.057 0.990 0.377 6.866-6.210 92.28 299 12 0.2285 390.276 371.539 1.038 0.992 0.378 6.206-5.619 93.06 386 16 0.2175 380.784 366.575 1.026 0.993 0.378 5.613-5.076 93.02 551 22 0.2036 396.573 389.039 0.998 0.992 0.358 5.075-4.591 93.42 709 29 0.1759 438.560 432.151 0.999 0.995 0.340 4.589-4.150 93.88 986 42 0.1629 466.287 457.898 1.016 0.993 0.300 4.148-3.753 94.07 1277 72 0.1857 397.798 388.730 1.042 0.999 0.270 3.750-3.393 94.60 1743 97 0.2018 324.347 312.064 1.081 1.001 0.150 3.392-3.201 94.94 1294 75 0.2444 251.856 238.269 1.048 1.002 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=0.1842 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1957 r_free=0.2493 After: r_work=0.1958 r_free=0.2493 ================================== NQH flips ================================== r_work=0.1958 r_free=0.2493 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 109 ASN A 219 GLN A 223 ASN Total number of N/Q/H flips: 4 r_work=0.1960 r_free=0.2492 ========================= Local real-space refinement ========================= Before: r_work=0.1960 r_free=0.2492 78 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.944 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2749 time to fit residues: 1.6035 After: r_work=0.1960 r_free=0.2491 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.955249 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.048689 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 0.1968 0.2493 0.0525 0.003 0.6 4.6 0.0 0.0 0 0.125 0.1961 0.2490 0.0529 0.004 0.6 4.5 0.0 0.0 0 0.250 0.1948 0.2492 0.0544 0.005 0.6 4.6 0.0 0.0 0 0.500 0.1870 0.2476 0.0606 0.013 1.0 5.7 0.0 0.3 0 1.000 0.1780 0.2515 0.0736 0.019 1.8 14.6 0.5 3.0 0 2.000 0.1778 0.2533 0.0755 0.020 1.8 15.4 0.5 4.2 0 3.000 0.1736 0.2553 0.0817 0.026 2.2 21.2 1.5 5.7 0 4.000 0.1705 0.2562 0.0857 0.031 2.8 23.9 1.5 5.4 0 5.000 0.1691 0.2563 0.0872 0.035 3.0 24.7 1.5 5.7 0 6.000 0.1673 0.2564 0.0891 0.038 3.2 28.2 1.5 6.3 0 7.000 0.1656 0.2571 0.0916 0.041 3.4 30.9 1.5 6.6 1 8.000 0.1641 0.2579 0.0939 0.045 3.6 33.8 1.5 7.5 1 9.000 0.1628 0.2589 0.0961 0.047 3.8 35.4 1.7 7.8 1 10.000 0.1817 0.2490 0.0673 0.017 1.5 9.6 0.0 1.2 0 1.478 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1961 0.2490 0.0529 0.004 0.6 4.5 0.0 0.0 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1961 r_free=0.2490 77 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.246 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8154 After: r_work=0.1961 r_free=0.2490 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.61 24.90 5.29 6.552 45.463 0.049 5.943 21.76 25.17 3.40 5.754 48.052 0.001 6.002 20.73 24.85 4.12 6.504 45.530 0.006 5.973 19.61 24.90 5.29 6.552 45.463 0.024 5.943 19.22 24.94 5.72 6.914 45.449 0.049 5.934 18.60 25.08 6.49 7.926 45.568 0.073 5.922 18.27 25.32 7.05 8.805 45.798 0.097 5.920 18.15 25.40 7.25 9.261 45.961 0.122 5.920 18.07 25.47 7.40 9.653 46.101 0.146 5.920 18.01 25.53 7.52 9.959 46.211 0.170 5.920 17.97 25.59 7.62 10.250 46.315 0.195 5.920 17.94 25.65 7.71 10.499 46.402 0.219 5.920 17.91 25.70 7.79 10.721 46.480 0.243 5.921 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: 20.73 24.85 4.12 6.504 45.530 0.006 5.973 Individual atomic B min max mean iso aniso Overall: 22.99 77.04 41.54 1.67 3245 0 Protein: 22.99 77.04 41.54 1.67 3245 0 Chain A: 22.99 77.04 41.54 N/A 3245 0 Histogram: Values Number of atoms 22.99 - 28.40 161 28.40 - 33.80 544 33.80 - 39.21 690 39.21 - 44.61 774 44.61 - 50.02 552 50.02 - 55.42 269 55.42 - 60.83 129 60.83 - 66.23 75 66.23 - 71.64 40 71.64 - 77.04 11 =========================== Idealize ADP of riding H ========================== r_work=0.2073 r_free=0.2485 r_work=0.2084 r_free=0.2486 ----------X-ray data---------- |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2084 r_free= 0.2486 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.976348 | | target function (ml) not normalized (work): 47452.206402 | | target function (ml) not normalized (free): 2396.351166 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2022 0.2410 6.1259 6.2769| | 2: 4.56 - 3.65 0.94 2624 139 0.1919 0.2172 5.9924 6.0706| | 3: 3.65 - 3.20 0.95 2619 146 0.2430 0.3006 5.8063 5.9477| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 22.24 1.00 0.91 34420.59| | 2: 4.56 - 3.65 2624 139 0.85 21.56 1.00 0.91 27984.61| | 3: 3.65 - 3.20 2619 146 0.78 28.47 0.99 0.90 22833.41| |alpha: min = 0.90 max = 0.91 mean = 0.91| |beta: min = 22833.41 max = 34420.59 mean = 28471.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.82| |phase err.(work): min = 0.00 max = 89.83 mean = 24.07| |phase err.(test): min = 0.00 max = 86.76 mean = 23.92| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2102 0.2084 0.2486 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3344 0.3323 0.3777 n_refl.: 8334 remove outliers: r(all,work,free)=0.3344 0.3323 0.3777 n_refl.: 8334 overall B=0.00 to atoms: r(all,work,free)=0.3344 0.3323 0.3777 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2102 0.2084 0.2492 n_refl.: 8334 remove outliers: r(all,work,free)=0.2102 0.2084 0.2492 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 0.1916 717.458 696.921 1.113 0.997 0.350 10.272-9.295 91.74 94 6 0.1960 618.392 607.074 1.135 0.989 0.370 9.288-8.400 91.04 120 2 0.1775 636.131 632.638 1.103 0.993 0.371 8.393-7.595 91.58 165 9 0.1799 569.070 558.396 1.132 0.998 0.372 7.592-6.868 92.31 220 8 0.2244 458.229 444.637 1.053 0.992 0.377 6.866-6.210 92.28 299 12 0.2362 390.276 369.349 1.036 0.994 0.378 6.206-5.619 93.06 386 16 0.2254 380.784 366.281 1.023 0.995 0.378 5.613-5.076 93.02 551 22 0.2121 396.573 388.085 0.991 0.993 0.350 5.075-4.591 93.42 709 29 0.1861 438.560 432.110 0.998 0.996 0.330 4.589-4.150 93.88 986 42 0.1752 466.287 457.366 1.018 0.994 0.290 4.148-3.753 94.07 1277 72 0.1993 397.798 387.826 1.043 1.000 0.270 3.750-3.393 94.60 1743 97 0.2194 324.347 310.656 1.079 1.002 0.160 3.392-3.201 94.94 1294 75 0.2671 251.856 236.180 1.046 1.002 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=0.2487 ================= 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_updatephipsi: 0.2121 0.2526 0.008 1.367 24.0 77.2 47.1 0 0.000 1_nqh: 0.2121 0.2526 0.008 1.367 24.0 77.2 47.1 0 0.000 1_realsrl: 0.2140 0.2587 0.008 1.367 24.0 77.2 47.1 0 0.020 1_weight: 0.2140 0.2587 0.008 1.367 24.0 77.2 47.1 0 0.020 1_xyzrec: 0.2308 0.2516 0.002 0.528 24.0 77.2 47.1 0 0.198 1_realsrl2: 0.2314 0.2517 0.002 0.528 24.0 77.2 47.1 0 0.201 1_adp: 0.2182 0.2511 0.002 0.528 19.0 82.4 47.3 0 0.201 1_regHadp: 0.2163 0.2504 0.002 0.528 19.0 82.4 47.3 0 0.201 2_bss: 0.2159 0.2510 0.002 0.528 12.9 76.3 41.2 0 0.201 2_settarget: 0.2159 0.2510 0.002 0.528 12.9 76.3 41.2 0 0.201 2_updatephipsi: 0.2159 0.2510 0.002 0.528 12.9 76.3 41.2 0 0.201 2_updatecdl: 0.2159 0.2510 0.002 0.551 12.9 76.3 41.2 0 0.201 2_nqh: 0.2161 0.2509 0.002 0.551 12.9 76.3 41.2 0 0.207 2_realsrl: 0.2161 0.2509 0.002 0.551 12.9 76.3 41.2 0 0.206 2_weight: 0.2161 0.2509 0.002 0.551 12.9 76.3 41.2 0 0.206 2_xyzrec: 0.2013 0.2501 0.004 0.593 12.9 76.3 41.2 0 0.228 2_realsrl2: 0.2021 0.2508 0.004 0.593 12.9 76.3 41.2 0 0.228 2_adp: 0.1964 0.2508 0.004 0.593 10.1 82.0 41.4 0 0.228 2_regHadp: 0.1961 0.2508 0.004 0.593 10.1 82.0 41.4 0 0.228 3_bss: 0.1957 0.2493 0.004 0.593 10.1 82.0 41.4 0 0.228 3_settarget: 0.1957 0.2493 0.004 0.593 10.1 82.0 41.4 0 0.228 3_updatephipsi: 0.1957 0.2493 0.004 0.593 10.1 82.0 41.4 0 0.228 3_updatecdl: 0.1957 0.2493 0.004 0.605 10.1 82.0 41.4 0 0.228 3_setrh: 0.1958 0.2493 0.004 0.605 10.1 82.0 41.4 0 0.228 3_nqh: 0.1960 0.2492 0.004 0.605 10.1 82.0 41.4 0 0.231 3_realsrl: 0.1960 0.2491 0.004 0.605 10.1 82.0 41.4 0 0.230 3_weight: 0.1960 0.2491 0.004 0.605 10.1 82.0 41.4 0 0.230 3_xyzrec: 0.1961 0.2490 0.004 0.601 10.1 82.0 41.4 0 0.230 3_realsrl2: 0.1961 0.2490 0.004 0.601 10.1 82.0 41.4 0 0.230 3_adp: 0.2073 0.2485 0.004 0.601 23.0 77.0 41.5 0 0.230 3_regHadp: 0.2084 0.2486 0.004 0.601 23.0 77.0 41.5 0 0.230 end: 0.2084 0.2492 0.004 0.601 23.0 77.0 41.5 0 0.230 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2a8z_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/2a8z_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.9200 Refinement macro-cycles (run) : 293.4100 Write final files (write_after_run_outputs) : 24.1000 Total : 322.4300 Total CPU time: 5.76 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:32:10 PDT -0700 (1716251530.50 s) Start R-work = 0.2121, R-free = 0.2526 Final R-work = 0.2084, R-free = 0.2492 =============================================================================== Job complete usr+sys time: 367.54 seconds wall clock time: 17 minutes 13.47 seconds (1033.47 seconds total)