Starting phenix.refine on Thu Apr 4 08:59:07 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 1OTH_ref.pdb_fitted_modified.pdb Found miller_array, 1fb5.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- main.number_of_mac=5 optimize_xyz=true optimize_adp=true nproc=50 main.max_number_of_iterations=100 ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True overwrite=true Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "1fb5.mtz" } default_miller_array = "1fb5.mtz" model { file = "1OTH_ref.pdb_fitted_modified.pdb" } default_model = "1OTH_ref.pdb_fitted_modified.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 } } main { number_of_macro_cycles = 5 max_number_of_iterations = 100 nproc = 50 } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { enabled = True } } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } output { overwrite = true } Starting job =============================================================================== *** Automatic customization ************************************************** nonbonded_weight=100.000 ******************************************************************************* 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: 2533 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2533 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 307} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 0.58, per 1000 atoms: 0.23 Number of scatterers: 2533 At special positions: 0 Unit cell: (184.7, 184.7, 184.7, 90, 90, 90) Space group: P 43 3 2 (No. 212) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 476 8.00 N 426 7.00 C 1619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 0.23 Conformation dependent library (CDL) restraints added in 116.0 milliseconds 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 602 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 2 sheets defined 43.3% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 50 through 68 Processing helix chain 'A' and resid 92 through 103 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 169 through 183 Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 227 through 240 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 5.012A pdb=" N LYS A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 279 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.985A pdb=" N VAL A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 323 through 342 removed outlier: 4.295A pdb=" N LYS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 107 through 112 removed outlier: 6.646A pdb=" N ALA A 137 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ILE A 85 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 139 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ALA A 140 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 160 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 299 through 302 removed outlier: 6.421A pdb=" N HIS A 214 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TRP A 193 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN A 216 " --> pdb=" O TRP A 193 " (cutoff:3.500A) 96 hydrogen bonds defined for protein. 270 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: 0.40 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 632 1.34 - 1.46: 641 1.46 - 1.58: 1283 1.58 - 1.70: 7 1.70 - 1.82: 22 Bond restraints: 2585 Sorted by residual: bond pdb=" CA VAL A 120 " pdb=" CB VAL A 120 " ideal model delta sigma weight residual 1.540 1.648 -0.108 1.36e-02 5.41e+03 6.34e+01 bond pdb=" CD2 HIS A 214 " pdb=" NE2 HIS A 214 " ideal model delta sigma weight residual 1.374 1.304 0.070 1.10e-02 8.26e+03 4.08e+01 bond pdb=" CD2 HIS A 182 " pdb=" NE2 HIS A 182 " ideal model delta sigma weight residual 1.374 1.306 0.068 1.10e-02 8.26e+03 3.85e+01 bond pdb=" CD2 HIS A 117 " pdb=" NE2 HIS A 117 " ideal model delta sigma weight residual 1.374 1.306 0.068 1.10e-02 8.26e+03 3.77e+01 bond pdb=" CD2 HIS A 107 " pdb=" NE2 HIS A 107 " ideal model delta sigma weight residual 1.374 1.306 0.068 1.10e-02 8.26e+03 3.77e+01 ... (remaining 2580 not shown) Histogram of bond angle deviations from ideal: 98.44 - 106.46: 125 106.46 - 114.47: 1414 114.47 - 122.49: 1584 122.49 - 130.51: 368 130.51 - 138.53: 6 Bond angle restraints: 3497 Sorted by residual: angle pdb=" CA ASP A 312 " pdb=" CB ASP A 312 " pdb=" CG ASP A 312 " ideal model delta sigma weight residual 112.60 121.01 -8.41 1.00e+00 1.00e+00 7.07e+01 angle pdb=" CA ASP A 263 " pdb=" CB ASP A 263 " pdb=" CG ASP A 263 " ideal model delta sigma weight residual 112.60 119.84 -7.24 1.00e+00 1.00e+00 5.24e+01 angle pdb=" N VAL A 323 " pdb=" CA VAL A 323 " pdb=" CB VAL A 323 " ideal model delta sigma weight residual 110.51 103.31 7.20 1.11e+00 8.12e-01 4.21e+01 angle pdb=" CA VAL A 120 " pdb=" C VAL A 120 " pdb=" N ASN A 121 " ideal model delta sigma weight residual 116.60 125.49 -8.89 1.45e+00 4.76e-01 3.76e+01 angle pdb=" CA ASN A 199 " pdb=" CB ASN A 199 " pdb=" CG ASN A 199 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.00e+00 1.00e+00 3.72e+01 ... (remaining 3492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 1448 17.75 - 35.49: 81 35.49 - 53.24: 24 53.24 - 70.98: 8 70.98 - 88.72: 6 Dihedral angle restraints: 1567 sinusoidal: 634 harmonic: 933 Sorted by residual: dihedral pdb=" CA PHE A 324 " pdb=" C PHE A 324 " pdb=" N PRO A 325 " pdb=" CA PRO A 325 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CB GLU A 310 " pdb=" CG GLU A 310 " pdb=" CD GLU A 310 " pdb=" OE1 GLU A 310 " ideal model delta sinusoidal sigma weight residual 0.00 -88.72 88.72 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" C VAL A 120 " pdb=" N VAL A 120 " pdb=" CA VAL A 120 " pdb=" CB VAL A 120 " ideal model delta harmonic sigma weight residual -122.00 -129.83 7.83 0 2.50e+00 1.60e-01 9.80e+00 ... (remaining 1564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 209 0.069 - 0.139: 123 0.139 - 0.208: 45 0.208 - 0.277: 17 0.277 - 0.346: 4 Chirality restraints: 398 Sorted by residual: chirality pdb=" CA PRO A 308 " pdb=" N PRO A 308 " pdb=" C PRO A 308 " pdb=" CB PRO A 308 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA PRO A 169 " pdb=" N PRO A 169 " pdb=" C PRO A 169 " pdb=" CB PRO A 169 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ILE A 159 " pdb=" N ILE A 159 " pdb=" C ILE A 159 " pdb=" CB ILE A 159 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 395 not shown) Planarity restraints: 441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 55 " 0.056 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR A 55 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 55 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 55 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 55 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 55 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 55 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 55 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 332 " -0.053 2.00e-02 2.50e+03 2.43e-02 1.47e+01 pdb=" CG TRP A 332 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 332 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 332 " 0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP A 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 332 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 332 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 332 " -0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 332 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 332 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 324 " -0.045 2.00e-02 2.50e+03 2.79e-02 1.36e+01 pdb=" CG PHE A 324 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 324 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 324 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A 324 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 324 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 324 " -0.027 2.00e-02 2.50e+03 ... (remaining 438 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 11 1.87 - 2.62: 44 2.62 - 3.38: 3250 3.38 - 4.14: 7052 4.14 - 4.90: 12042 Nonbonded interactions: 22399 Sorted by model distance: nonbonded pdb=" CD2 TYR A 73 " pdb=" OE1 GLN A 78 " model vdw sym.op. 1.108 3.340 y,z,x nonbonded pdb=" CE2 TYR A 73 " pdb=" CD GLN A 78 " model vdw sym.op. 1.656 3.570 y,z,x nonbonded pdb=" CD2 TYR A 73 " pdb=" CD GLN A 78 " model vdw sym.op. 1.687 3.570 y,z,x nonbonded pdb=" CA GLU A 154 " pdb=" OE2 GLU A 314 " model vdw sym.op. 1.695 3.470 x+1/4,z-1/4,-y-1/4 nonbonded pdb=" O LYS A 153 " pdb=" OE2 GLU A 314 " model vdw sym.op. 1.773 3.040 x+1/4,z-1/4,-y-1/4 ... (remaining 22394 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: 4 Type Number sf(0) Gaussians S 12 15.91 1 O 476 7.97 1 N 426 6.97 1 C 1619 5.97 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 ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 2533 n_use_u_iso = 2533 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 = 2533 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (2533 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 2533 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (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" } } main { number_of_macro_cycles = 5 max_number_of_iterations = 100 nproc = 50 } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 45 through 47 helix_type = alpha pi *3_10 unknown } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 50 through 68 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 92 through 103 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 124 through 134 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 145 through 154 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 169 through 183 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 199 through 205 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 209 through 211 helix_type = alpha pi *3_10 unknown } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 227 through 240 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 250 through 254 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'A' and resid 271 through 280 helix_type = alpha pi *3_10 unknown } helix { serial_number = "12" helix_identifier = "12" selection = chain 'A' and resid 288 through 293 } helix { serial_number = "13" helix_identifier = "13" selection = chain 'A' and resid 313 through 316 } helix { serial_number = "14" helix_identifier = "14" selection = chain 'A' and resid 323 through 342 } sheet { first_strand = chain 'A' and resid 107 through 112 sheet_id = " A" strand { selection = chain 'A' and resid 81 through 86 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 82 and name N bond_start_previous = chain 'A' and resid 107 and name O } strand { selection = chain 'A' and resid 137 through 141 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 137 and name N bond_start_previous = chain 'A' and resid 83 and name O } strand { selection = chain 'A' and resid 158 through 161 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 158 and name N bond_start_previous = chain 'A' and resid 138 and name O } } sheet { first_strand = chain 'A' and resid 299 through 302 sheet_id = " B" strand { selection = chain 'A' and resid 259 through 262 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 260 and name N bond_start_previous = chain 'A' and resid 299 and name O } strand { selection = chain 'A' and resid 190 through 194 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 192 and name N bond_start_previous = chain 'A' and resid 259 and name O } strand { selection = chain 'A' and resid 214 through 218 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 214 and name N bond_start_previous = chain 'A' and resid 191 and name O } strand { selection = chain 'A' and resid 244 through 247 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 245 and name N bond_start_previous = chain 'A' and resid 215 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 = "1OTH_ref.pdb_fitted_modified_refine" serial = 1 target_output_format = None *pdb mmcif overwrite = True } #phil __OFF__ ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 55.69 A, n_refl.=13583 (all), 5.08 % free)------------| | | | r_work= 0.4090 r_free= 0.4042 coordinate error (max.-lik. estimate): 0.54 A | | | | normalized target function (ml) (work): 7.273790 | | target function (ml) not normalized (work): 93780.976437 | | target function (ml) not normalized (free): 4998.164460 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 55.69 - 5.99 0.96 2727 155 0.4821 0.4464 7.8544 7.7052| | 2: 5.98 - 4.75 0.97 2600 136 0.3946 0.3981 7.2962 7.3162| | 3: 4.75 - 4.15 0.98 2607 127 0.3761 0.3873 7.2596 7.2455| | 4: 4.15 - 3.77 0.95 2474 131 0.3604 0.3592 7.0555 7.0458| | 5: 3.77 - 3.50 0.96 2485 141 0.3835 0.3895 6.8453 6.8488| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 55.69 - 5.99 2727 155 0.57 44.56 0.88 0.54 786146.53| | 2: 5.98 - 4.75 2600 136 0.56 46.76 1.13 0.55 558401.74| | 3: 4.75 - 4.15 2607 127 0.66 38.35 1.15 0.55 380794.35| | 4: 4.15 - 3.77 2474 131 0.68 37.45 1.08 0.52 252286.76| | 5: 3.77 - 3.50 2485 141 0.65 39.71 0.97 0.48 173925.52| |alpha: min = 0.48 max = 0.56 mean = 0.53| |beta: min = 173925.52 max = 786146.53 mean = 437815.82| |figures of merit: min = 0.00 max = 1.00 mean = 0.62| |phase err.(work): min = 0.00 max = 90.00 mean = 41.45| |phase err.(test): min = 0.00 max = 89.30 mean = 40.83| |-----------------------------------------------------------------------------| ----------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 : 0.013 0.108 2585 Z= 0.853 Angle : 2.065 12.143 3497 Z= 1.378 Chirality : 0.103 0.346 398 Planarity : 0.009 0.086 441 Dihedral : 14.540 88.723 965 Min Nonbonded Distance : 1.108 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.63 % Allowed : 2.19 % Favored : 97.18 % Rotamer: Outliers : 4.71 % Allowed : 3.62 % Favored : 91.67 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 7.69 % 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: -0.93 (0.46), residues: 319 helix: -0.83 (0.37), residues: 141 sheet: -0.82 (0.60), residues: 55 loop : 0.09 (0.65), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.006 ARG A 330 TYR 0.056 0.011 TYR A 55 PHE 0.045 0.007 PHE A 324 TRP 0.053 0.011 TRP A 332 HIS 0.003 0.001 HIS A 107 Individual atomic B min max mean iso aniso Overall: 7.87 68.00 20.62 2.13 2533 0 Protein: 7.87 68.00 20.62 2.13 2533 0 Chain A: 7.87 68.00 20.62 N/A 2533 0 Histogram: Values Number of atoms 7.87 - 13.88 301 13.88 - 19.90 1238 19.90 - 25.91 581 25.91 - 31.92 196 31.92 - 37.93 103 37.93 - 43.95 37 43.95 - 49.96 28 49.96 - 55.97 28 55.97 - 61.99 13 61.99 - 68.00 8 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13583 (all), 5.08 % free)------------| | | | r_work= 0.4090 r_free= 0.4042 coordinate error (max.-lik. estimate): 0.54 A | | | | normalized target function (ml) (work): 7.273790 | | target function (ml) not normalized (work): 93780.976437 | | target function (ml) not normalized (free): 4998.164460 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4087 0.4090 0.4042 n_refl.: 13583 re-set all scales: r(all,work,free)=0.4087 0.4090 0.4042 n_refl.: 13583 remove outliers: r(all,work,free)=0.4086 0.4088 0.4042 n_refl.: 13580 overall B=46.49 to atoms: r(all,work,free)=0.4985 0.4996 0.4796 n_refl.: 13580 bulk-solvent and scaling: r(all,work,free)=0.3257 0.3254 0.3304 n_refl.: 13580 remove outliers: r(all,work,free)=0.3257 0.3254 0.3304 n_refl.: 13580 ======================== 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 55.689-19.469 90.27 94 8 0.3192 2358.858 2202.668 1.249 1.069 0.334 19.362-15.234 92.45 91 7 0.3051 2186.374 2101.180 1.117 1.074 0.330 15.182-11.849 95.91 195 16 0.2309 2575.369 2513.588 1.039 1.071 0.334 11.824-9.235 95.44 396 23 0.2197 2842.818 2832.046 1.064 1.065 0.340 9.223-7.200 96.44 830 38 0.2613 2049.759 1985.928 1.026 1.052 0.338 7.195-5.615 96.35 1675 92 0.3330 1362.742 1252.432 0.962 1.030 0.327 5.612-4.379 97.24 3486 178 0.3348 1478.369 1340.665 0.981 0.991 0.291 4.378-3.502 95.73 6123 328 0.3554 1158.408 1021.650 1.075 0.933 0.218 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.2182 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.3254 r_free=0.3304 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 107 HIS A 168 HIS A 171 GLN A 198 ASN A 214 HIS A 216 GLN A 248 ASN A 258 ASN A 348 GLN Total number of N/Q/H flips: 10 r_work=0.3256 r_free=0.3312 ========================= Local real-space refinement ========================= Before: r_work=0.3256 r_free=0.3312 136 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.141 outliers start: 14 outliers final: 6 residues processed: 14 average time/residue: 0.0865 time to fit residues: 2.0354 After: r_work=0.3267 r_free=0.3328 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 20.569130 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.184783 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2624 0.2870 0.0246 0.008 1.0 8.6 0.3 8.0 0 10.285 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2624 r_free=0.2870 131 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.144 outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.0601 time to fit residues: 2.5016 After: r_work=0.2654 r_free=0.2902 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.54 29.02 2.48 2.131 67.112 0.185 0.082 27.24 29.88 2.64 1.022 79.726 0.006 0.087 25.65 28.55 2.90 1.816 69.124 0.023 0.077 24.22 27.57 3.35 3.118 69.781 0.092 0.069 23.53 27.13 3.59 4.762 71.941 0.185 0.066 23.12 26.92 3.80 6.297 73.970 0.277 0.064 22.86 26.78 3.92 7.645 75.173 0.370 0.063 22.66 26.71 4.05 8.850 76.189 0.462 0.062 22.51 26.64 4.13 10.055 76.959 0.554 0.061 22.37 26.60 4.23 11.172 77.598 0.647 0.060 22.27 26.59 4.32 12.255 78.038 0.739 0.060 22.19 26.57 4.38 13.231 78.545 0.832 0.059 22.18 26.60 4.42 13.708 77.954 0.924 0.059 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.832 Accepted refinement result: 22.19 26.57 4.38 13.231 78.545 0.832 0.059 Individual atomic B min max mean iso aniso Overall: 50.40 188.71 78.55 13.23 2533 0 Protein: 50.40 188.71 78.55 13.23 2533 0 Chain A: 50.40 188.71 78.55 N/A 2533 0 Histogram: Values Number of atoms 50.40 - 64.23 965 64.23 - 78.06 699 78.06 - 91.89 347 91.89 - 105.72 162 105.72 - 119.56 126 119.56 - 133.39 78 133.39 - 147.22 57 147.22 - 161.05 54 161.05 - 174.88 25 174.88 - 188.71 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13580 (all), 5.08 % free)------------| | | | r_work= 0.2219 r_free= 0.2657 coordinate error (max.-lik. estimate): 0.36 A | | | | normalized target function (ls_wunit_k1) (work): 0.059481 | | target function (ls_wunit_k1) not normalized (work): 766.716011 | | target function (ls_wunit_k1) not normalized (free): 59.504628 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2241 0.2219 0.2657 n_refl.: 13580 re-set all scales: r(all,work,free)=0.4797 0.4806 0.4649 n_refl.: 13580 remove outliers: r(all,work,free)=0.4797 0.4806 0.4649 n_refl.: 13580 overall B=-11.29 to atoms: r(all,work,free)=0.4354 0.4362 0.4214 n_refl.: 13580 bulk-solvent and scaling: r(all,work,free)=0.2141 0.2122 0.2505 n_refl.: 13580 remove outliers: r(all,work,free)=0.2141 0.2122 0.2505 n_refl.: 13580 ======================== 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 55.689-19.469 90.27 94 8 0.3434 940.412 844.263 1.341 1.128 0.342 19.362-15.234 92.45 91 7 0.2632 871.647 849.154 1.065 1.128 0.318 15.182-11.849 95.91 195 16 0.1830 1026.729 1007.127 1.028 1.122 0.315 11.824-9.235 95.44 396 23 0.1344 1133.353 1133.443 1.028 1.108 0.318 9.223-7.200 96.44 830 38 0.1686 817.182 803.374 1.031 1.084 0.324 7.195-5.615 96.35 1675 92 0.2275 543.288 522.159 0.972 1.043 0.290 5.612-4.379 97.24 3486 178 0.2025 589.385 564.846 0.992 0.975 0.259 4.378-3.502 95.73 6123 328 0.2333 461.826 435.496 1.127 0.871 0.163 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.8731 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2122 r_free=0.2505 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 121 ASN A 168 HIS A 182 HIS A 202 HIS A 350 GLN Total number of N/Q/H flips: 6 r_work=0.2131 r_free=0.2515 ========================= Local real-space refinement ========================= Before: r_work=0.2131 r_free=0.2515 108 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.142 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1924 After: r_work=0.2131 r_free=0.2515 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 33.558066 wxc_scale = 0.046 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.223012 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2358 0.2711 0.0352 0.002 0.5 5.7 0.3 2.5 0 0.125 0.2324 0.2683 0.0358 0.002 0.5 4.5 0.3 2.5 0 0.250 0.2280 0.2647 0.0366 0.002 0.5 4.5 0.3 2.5 0 0.500 0.2200 0.2574 0.0374 0.002 0.5 4.7 0.3 2.9 0 1.000 0.2137 0.2504 0.0366 0.002 0.6 5.9 0.3 4.0 0 2.000 0.2102 0.2475 0.0373 0.003 0.6 6.3 0.3 4.3 0 3.000 0.2078 0.2447 0.0368 0.003 0.7 6.9 0.3 4.3 0 4.000 0.2057 0.2421 0.0363 0.004 0.7 6.9 0.3 5.1 0 5.000 0.2045 0.2415 0.0370 0.004 0.7 7.5 0.3 5.8 0 6.000 0.2031 0.2396 0.0365 0.005 0.8 8.2 0.3 6.2 0 7.000 0.2022 0.2389 0.0368 0.005 0.8 8.2 0.3 6.5 0 8.000 0.2009 0.2373 0.0365 0.006 0.8 7.8 0.3 6.5 0 9.000 0.2002 0.2363 0.0361 0.006 0.9 8.8 0.3 6.9 0 10.000 0.2161 0.2536 0.0375 0.002 0.5 6.1 0.3 4.0 0 1.549 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2137 0.2504 0.0366 0.002 0.6 5.9 0.3 4.0 0 2.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2137 r_free=0.2504 115 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.145 outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0767 time to fit residues: 1.5263 After: r_work=0.2157 r_free=0.2533 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.57 25.33 3.76 13.231 67.260 0.223 0.056 31.23 33.61 2.38 3.730 102.617 0.007 0.114 26.61 29.15 2.54 3.734 89.054 0.028 0.084 23.34 26.40 3.06 5.627 76.305 0.112 0.065 22.40 25.80 3.40 6.525 73.546 0.223 0.060 21.92 25.54 3.62 7.455 72.321 0.335 0.057 21.64 25.40 3.76 8.102 72.832 0.446 0.056 21.38 25.25 3.87 9.032 71.481 0.558 0.055 21.19 25.20 4.01 9.785 71.527 0.669 0.054 21.05 25.15 4.10 10.542 71.756 0.781 0.053 20.93 25.09 4.16 11.301 70.849 0.892 0.053 20.75 25.05 4.30 11.720 70.604 1.004 0.052 20.65 25.04 4.39 12.307 70.670 1.115 0.051 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 1.115 Accepted refinement result: 20.65 25.04 4.39 12.307 70.670 1.115 0.051 Individual atomic B min max mean iso aniso Overall: 34.11 178.73 70.67 12.31 2533 0 Protein: 34.11 178.73 70.67 12.31 2533 0 Chain A: 34.11 178.73 70.67 N/A 2533 0 Histogram: Values Number of atoms 34.11 - 48.57 503 48.57 - 63.04 764 63.04 - 77.50 562 77.50 - 91.96 261 91.96 - 106.42 143 106.42 - 120.89 105 120.89 - 135.35 70 135.35 - 149.81 71 149.81 - 164.27 33 164.27 - 178.73 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13580 (all), 5.08 % free)------------| | | | r_work= 0.2065 r_free= 0.2504 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ls_wunit_k1) (work): 0.051455 | | target function (ls_wunit_k1) not normalized (work): 663.253279 | | target function (ls_wunit_k1) not normalized (free): 54.280664 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2089 0.2065 0.2504 n_refl.: 13580 re-set all scales: r(all,work,free)=0.4426 0.4433 0.4318 n_refl.: 13580 remove outliers: r(all,work,free)=0.4426 0.4433 0.4318 n_refl.: 13580 overall B=0.00 to atoms: r(all,work,free)=0.4426 0.4433 0.4318 n_refl.: 13580 bulk-solvent and scaling: r(all,work,free)=0.2094 0.2070 0.2515 n_refl.: 13580 remove outliers: r(all,work,free)=0.2094 0.2070 0.2515 n_refl.: 13580 ======================== 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 55.689-19.469 90.27 94 8 0.3274 940.412 852.721 1.357 1.053 0.340 19.362-15.234 92.45 91 7 0.2728 871.647 845.704 1.092 1.055 0.318 15.182-11.849 95.91 195 16 0.1839 1026.729 1012.289 1.054 1.054 0.313 11.824-9.235 95.44 396 23 0.1325 1133.353 1138.559 1.032 1.048 0.310 9.223-7.200 96.44 830 38 0.1661 817.182 810.578 1.034 1.037 0.310 7.195-5.615 96.35 1675 92 0.2187 543.288 524.946 0.978 1.017 0.280 5.612-4.379 97.24 3486 178 0.1966 589.385 565.866 0.955 0.984 0.240 4.378-3.502 95.73 6123 328 0.2281 461.826 437.137 1.059 0.934 0.130 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.5332 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2070 r_free=0.2515 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 114 GLN Total number of N/Q/H flips: 2 r_work=0.2074 r_free=0.2528 ========================= Local real-space refinement ========================= Before: r_work=0.2074 r_free=0.2528 109 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.141 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1926 After: r_work=0.2074 r_free=0.2528 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.949588 wxc_scale = 0.033 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.050704 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2271 0.2707 0.0436 0.002 0.5 5.1 0.3 2.9 0 0.023 0.2185 0.2640 0.0455 0.002 0.5 3.9 0.3 2.9 0 0.069 0.2136 0.2608 0.0472 0.002 0.5 4.7 0.3 2.9 0 0.137 0.2095 0.2588 0.0493 0.002 0.5 5.1 0.3 2.9 0 0.206 0.2068 0.2556 0.0488 0.002 0.5 4.7 0.3 3.3 0 0.274 0.2045 0.2541 0.0496 0.002 0.5 5.3 0.3 2.9 0 0.343 0.2029 0.2523 0.0495 0.002 0.5 5.5 0.3 3.3 0 0.411 0.2014 0.2506 0.0492 0.002 0.6 5.7 0.3 3.3 0 0.480 0.2084 0.2574 0.0490 0.002 0.5 4.7 0.3 3.3 0 0.228 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2185 0.2640 0.0455 0.002 0.5 3.9 0.3 2.9 0 0.069 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2185 r_free=0.2640 128 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.142 outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0628 time to fit residues: 1.0425 After: r_work=0.2191 r_free=0.2658 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.91 26.58 4.66 12.307 70.670 0.051 6.427 28.58 30.94 2.37 3.652 93.472 0.002 6.542 24.87 27.89 3.03 5.449 77.741 0.006 6.496 23.65 27.24 3.60 6.474 73.771 0.025 6.466 22.72 26.74 4.02 8.097 70.999 0.051 6.440 22.45 26.54 4.09 8.888 70.760 0.076 6.429 22.19 26.36 4.17 9.869 70.374 0.101 6.421 22.00 26.23 4.23 10.766 70.318 0.127 6.414 21.84 26.12 4.28 11.620 70.335 0.152 6.409 21.71 26.05 4.34 12.416 70.454 0.177 6.404 21.60 25.99 4.39 13.138 70.572 0.203 6.401 21.51 25.93 4.42 13.711 70.623 0.228 6.398 21.44 25.90 4.46 14.306 70.805 0.254 6.395 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.254 Accepted refinement result: 21.44 25.90 4.46 14.306 70.805 0.254 6.395 Individual atomic B min max mean iso aniso Overall: 29.11 179.64 70.81 14.31 2533 0 Protein: 29.11 179.64 70.81 14.31 2533 0 Chain A: 29.11 179.64 70.81 N/A 2533 0 Histogram: Values Number of atoms 29.11 - 44.17 362 44.17 - 59.22 766 59.22 - 74.27 585 74.27 - 89.32 285 89.32 - 104.38 174 104.38 - 119.43 125 119.43 - 134.48 85 134.48 - 149.53 75 149.53 - 164.59 52 164.59 - 179.64 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13580 (all), 5.08 % free)------------| | | | r_work= 0.2144 r_free= 0.2590 coordinate error (max.-lik. estimate): 0.46 A | | | | normalized target function (ml) (work): 6.395420 | | target function (ml) not normalized (work): 82436.961124 | | target function (ml) not normalized (free): 4490.793631 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2167 0.2144 0.2590 n_refl.: 13580 re-set all scales: r(all,work,free)=0.4392 0.4398 0.4297 n_refl.: 13580 remove outliers: r(all,work,free)=0.4392 0.4398 0.4297 n_refl.: 13580 overall B=0.00 to atoms: r(all,work,free)=0.4392 0.4398 0.4297 n_refl.: 13580 bulk-solvent and scaling: r(all,work,free)=0.2164 0.2141 0.2582 n_refl.: 13580 remove outliers: r(all,work,free)=0.2164 0.2141 0.2582 n_refl.: 13580 ======================== 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 55.689-19.469 90.27 94 8 0.3349 940.412 848.049 1.449 1.053 0.340 19.362-15.234 92.45 91 7 0.3090 871.647 827.076 1.115 1.056 0.318 15.182-11.849 95.91 195 16 0.1923 1026.729 1011.566 1.082 1.055 0.312 11.824-9.235 95.44 396 23 0.1441 1133.353 1136.906 1.051 1.049 0.310 9.223-7.200 96.44 830 38 0.1838 817.182 806.658 1.052 1.038 0.310 7.195-5.615 96.35 1675 92 0.2386 543.288 517.677 1.009 1.019 0.280 5.612-4.379 97.24 3486 178 0.2088 589.385 561.989 0.973 0.986 0.230 4.378-3.502 95.73 6123 328 0.2233 461.826 435.460 1.070 0.936 0.130 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=1.6041 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2141 r_free=0.2582 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS A 348 GLN Total number of N/Q/H flips: 2 r_work=0.2141 r_free=0.2582 ========================= Local real-space refinement ========================= Before: r_work=0.2141 r_free=0.2582 121 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.141 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1922 After: r_work=0.2141 r_free=0.2582 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.093393 wxc_scale = 0.023 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.052308 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2281 0.2665 0.0384 0.001 0.5 5.5 0.3 2.5 0 0.016 0.2182 0.2600 0.0417 0.001 0.5 4.1 0.3 1.8 0 0.049 0.2141 0.2573 0.0432 0.001 0.5 4.3 0.3 2.5 0 0.099 0.2103 0.2543 0.0440 0.001 0.5 4.1 0.3 2.5 0 0.148 0.2073 0.2516 0.0443 0.002 0.5 4.5 0.3 2.5 0 0.197 0.2054 0.2489 0.0435 0.002 0.5 4.3 0.3 2.5 0 0.247 0.2043 0.2480 0.0438 0.002 0.5 4.3 0.3 2.5 0 0.296 0.2030 0.2468 0.0438 0.002 0.5 5.1 0.3 2.5 0 0.345 0.2090 0.2532 0.0441 0.002 0.5 4.5 0.3 2.5 0 0.164 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2182 0.2600 0.0417 0.001 0.5 4.1 0.3 1.8 0 0.049 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2182 r_free=0.2600 120 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.158 outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0505 time to fit residues: 0.6686 After: r_work=0.2190 r_free=0.2612 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.90 26.12 4.22 14.306 70.805 0.052 6.410 29.74 31.69 1.95 3.857 96.421 0.002 6.556 25.54 28.10 2.56 5.690 80.194 0.007 6.506 23.85 26.98 3.13 7.331 74.026 0.026 6.466 22.91 26.47 3.57 9.263 71.054 0.052 6.438 22.66 26.38 3.72 9.980 70.318 0.078 6.430 22.45 26.22 3.77 10.736 69.821 0.105 6.422 22.28 26.11 3.83 11.510 69.532 0.131 6.416 22.13 26.04 3.91 12.373 69.369 0.157 6.411 21.99 25.98 4.00 13.203 69.326 0.183 6.406 21.85 25.96 4.11 14.046 69.368 0.209 6.402 21.76 25.93 4.17 14.705 69.427 0.235 6.399 21.68 25.91 4.23 15.271 69.498 0.262 6.397 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.262 Accepted refinement result: 21.68 25.91 4.23 15.271 69.498 0.262 6.397 Individual atomic B min max mean iso aniso Overall: 25.21 181.87 69.50 15.27 2533 0 Protein: 25.21 181.87 69.50 15.27 2533 0 Chain A: 25.21 181.87 69.50 N/A 2533 0 Histogram: Values Number of atoms 25.21 - 40.88 326 40.88 - 56.54 772 56.54 - 72.21 603 72.21 - 87.87 285 87.87 - 103.54 175 103.54 - 119.20 123 119.20 - 134.87 96 134.87 - 150.54 71 150.54 - 166.20 56 166.20 - 181.87 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13580 (all), 5.08 % free)------------| | | | r_work= 0.2168 r_free= 0.2591 coordinate error (max.-lik. estimate): 0.46 A | | | | normalized target function (ml) (work): 6.396662 | | target function (ml) not normalized (work): 82452.969677 | | target function (ml) not normalized (free): 4489.551119 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2190 0.2168 0.2591 n_refl.: 13580 re-set all scales: r(all,work,free)=0.4310 0.4314 0.4241 n_refl.: 13580 remove outliers: r(all,work,free)=0.4310 0.4314 0.4241 n_refl.: 13580 overall B=0.00 to atoms: r(all,work,free)=0.4310 0.4314 0.4241 n_refl.: 13580 bulk-solvent and scaling: r(all,work,free)=0.2175 0.2153 0.2567 n_refl.: 13580 remove outliers: r(all,work,free)=0.2175 0.2153 0.2567 n_refl.: 13580 ======================== 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 55.689-19.469 90.27 94 8 0.3419 1073.723 967.398 1.420 1.113 0.340 19.362-15.234 92.45 91 7 0.3147 995.211 944.206 1.044 1.113 0.310 15.182-11.849 95.91 195 16 0.2081 1172.276 1149.565 1.045 1.108 0.310 11.824-9.235 95.44 396 23 0.1470 1294.016 1293.306 1.026 1.096 0.310 9.223-7.200 96.44 830 38 0.1891 933.025 917.828 1.031 1.075 0.310 7.195-5.615 96.35 1675 92 0.2427 620.303 588.709 1.012 1.039 0.290 5.612-4.379 97.24 3486 178 0.2102 672.935 642.008 0.994 0.979 0.230 4.378-3.502 95.73 6123 328 0.2208 527.293 497.957 1.128 0.888 0.140 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.8896 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2153 r_free=0.2567 After: r_work=0.2153 r_free=0.2567 ================================== NQH flips ================================== r_work=0.2153 r_free=0.2567 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2153 r_free=0.2567 ========================= Local real-space refinement ========================= Before: r_work=0.2153 r_free=0.2567 118 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.141 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1923 After: r_work=0.2153 r_free=0.2567 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.009696 wxc_scale = 0.023 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.054659 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2275 0.2665 0.0390 0.001 0.4 5.9 0.3 2.2 0 0.016 0.2217 0.2624 0.0407 0.001 0.4 6.3 0.3 2.2 0 0.048 0.2138 0.2560 0.0421 0.001 0.4 4.5 0.3 1.4 0 0.096 0.2102 0.2528 0.0426 0.001 0.4 4.5 0.3 1.4 0 0.144 0.2072 0.2499 0.0428 0.002 0.5 4.7 0.3 1.4 0 0.192 0.2048 0.2466 0.0419 0.002 0.5 4.7 0.3 1.4 0 0.240 0.2034 0.2453 0.0419 0.002 0.5 4.7 0.3 1.4 0 0.288 0.2020 0.2437 0.0416 0.002 0.5 4.9 0.3 1.4 0 0.336 0.2096 0.2524 0.0428 0.001 0.4 4.5 0.3 1.4 0 0.160 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2096 0.2524 0.0428 0.001 0.4 4.5 0.3 1.4 0 0.160 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2096 r_free=0.2524 120 residues out of total 277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 0.143 outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0731 time to fit residues: 0.6525 After: r_work=0.2101 r_free=0.2529 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.01 25.29 4.28 15.271 69.498 0.055 6.502 29.32 31.45 2.13 4.112 95.657 0.002 6.667 24.77 27.60 2.82 6.162 79.085 0.007 6.610 22.92 26.21 3.29 8.084 72.544 0.027 6.564 22.14 25.69 3.55 9.595 70.134 0.055 6.539 21.81 25.54 3.73 10.608 69.122 0.082 6.527 21.58 25.43 3.85 11.504 68.536 0.109 6.519 21.43 25.37 3.94 12.129 68.191 0.137 6.514 21.28 25.32 4.04 12.924 68.011 0.164 6.509 21.15 25.29 4.13 13.719 67.943 0.191 6.505 21.03 25.26 4.23 14.520 67.961 0.219 6.501 20.93 25.25 4.31 15.260 68.009 0.246 6.497 20.84 25.23 4.39 15.958 68.078 0.273 6.495 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.273 Accepted refinement result: 20.84 25.23 4.39 15.958 68.078 0.273 6.495 Individual atomic B min max mean iso aniso Overall: 20.21 184.36 68.08 15.96 2533 0 Protein: 20.21 184.36 68.08 15.96 2533 0 Chain A: 20.21 184.36 68.08 N/A 2533 0 Histogram: Values Number of atoms 20.21 - 36.63 242 36.63 - 53.04 807 53.04 - 69.46 627 69.46 - 85.87 299 85.87 - 102.29 177 102.29 - 118.70 121 118.70 - 135.12 101 135.12 - 151.53 72 151.53 - 167.95 60 167.95 - 184.36 27 ----------X-ray data---------- |--(resolution: 3.50 - 55.69 A, n_refl.=13580 (all), 5.08 % free)------------| | | | r_work= 0.2084 r_free= 0.2523 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 6.494710 | | target function (ml) not normalized (work): 83716.807225 | | target function (ml) not normalized (free): 4562.934702 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 55.69 - 5.99 0.96 2724 155 0.2090 0.2431 6.839 6.956| | 2: 5.98 - 4.75 0.97 2600 136 0.2217 0.2806 6.58 6.7191| | 3: 4.75 - 4.15 0.98 2607 127 0.1877 0.2495 6.4823 6.642| | 4: 4.15 - 3.77 0.95 2474 131 0.2006 0.2208 6.3487 6.4181| | 5: 3.77 - 3.50 0.96 2485 141 0.2300 0.2732 6.1864 6.2884| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 55.69 - 5.99 2724 155 0.83 22.10 1.00 0.92 137210.59| | 2: 5.98 - 4.75 2600 136 0.81 25.31 1.02 0.93 106210.37| | 3: 4.75 - 4.15 2607 127 0.86 20.41 1.00 0.91 80224.18| | 4: 4.15 - 3.77 2474 131 0.85 21.47 1.00 0.89 59093.82| | 5: 3.77 - 3.50 2485 141 0.84 23.15 0.96 0.85 43074.76| |alpha: min = 0.85 max = 0.93 mean = 0.90| |beta: min = 43074.76 max = 137210.59 mean = 86291.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.95 mean = 22.49| |phase err.(test): min = 0.00 max = 87.95 mean = 22.81| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2105 0.2082 0.2522 n_refl.: 13580 re-set all scales: r(all,work,free)=0.4207 0.4211 0.4157 n_refl.: 13580 remove outliers: r(all,work,free)=0.4207 0.4211 0.4157 n_refl.: 13580 overall B=0.00 to atoms: r(all,work,free)=0.4207 0.4211 0.4157 n_refl.: 13580 bulk-solvent and scaling: r(all,work,free)=0.2094 0.2071 0.2512 n_refl.: 13580 remove outliers: r(all,work,free)=0.2094 0.2071 0.2512 n_refl.: 13580 ======================== 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 55.689-19.469 90.27 94 8 0.3576 1073.723 958.566 1.356 1.165 0.340 19.362-15.234 92.45 91 7 0.3108 995.211 935.744 1.030 1.162 0.314 15.182-11.849 95.91 195 16 0.2111 1172.276 1145.617 1.031 1.154 0.311 11.824-9.235 95.44 396 23 0.1455 1294.016 1290.435 1.006 1.137 0.310 9.223-7.200 96.44 830 38 0.1872 933.025 917.118 1.015 1.107 0.310 7.195-5.615 96.35 1675 92 0.2414 620.303 587.299 1.008 1.057 0.290 5.612-4.379 97.24 3486 178 0.1997 672.935 643.978 1.016 0.973 0.240 4.378-3.502 95.73 6123 328 0.2079 527.293 500.209 1.178 0.847 0.150 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.3863 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.4090 0.4042 0.013 2.065 7.9 68.0 20.6 0 0.000 1_bss: 0.3254 0.3304 0.013 2.065 54.4 114.5 67.1 0 0.000 1_settarget: 0.3254 0.3304 0.013 2.065 54.4 114.5 67.1 0 0.000 1_updatephipsi: 0.3254 0.3304 0.013 2.065 54.4 114.5 67.1 0 0.000 1_nqh: 0.3256 0.3312 0.013 2.065 54.4 114.5 67.1 0 0.021 1_realsrl: 0.3267 0.3328 0.013 2.065 54.4 114.5 67.1 0 0.034 1_weight: 0.3267 0.3328 0.013 2.065 54.4 114.5 67.1 0 0.034 1_xyzrec: 0.2624 0.2870 0.008 0.964 54.4 114.5 67.1 0 0.406 1_realsrl2: 0.2654 0.2902 0.008 0.964 54.4 114.5 67.1 0 0.409 1_adp: 0.2219 0.2657 0.008 0.964 50.4 188.7 78.5 0 0.409 2_bss: 0.2122 0.2505 0.008 0.964 39.1 177.4 67.3 0 0.409 2_settarget: 0.2122 0.2505 0.008 0.964 39.1 177.4 67.3 0 0.409 2_updatephipsi: 0.2122 0.2505 0.008 0.964 39.1 177.4 67.3 0 0.409 2_updatecdl: 0.2122 0.2505 0.008 0.985 39.1 177.4 67.3 0 0.409 2_nqh: 0.2131 0.2515 0.008 0.985 39.1 177.4 67.3 0 0.415 2_realsrl: 0.2131 0.2515 0.008 0.985 39.1 177.4 67.3 0 0.415 2_weight: 0.2131 0.2515 0.008 0.985 39.1 177.4 67.3 0 0.415 2_xyzrec: 0.2137 0.2504 0.002 0.573 39.1 177.4 67.3 0 0.452 2_realsrl2: 0.2157 0.2533 0.002 0.573 39.1 177.4 67.3 0 0.453 2_adp: 0.2065 0.2504 0.002 0.573 34.1 178.7 70.7 0 0.453 3_bss: 0.2070 0.2515 0.002 0.573 34.1 178.7 70.7 0 0.453 3_settarget: 0.2070 0.2515 0.002 0.573 34.1 178.7 70.7 0 0.453 3_updatephipsi: 0.2070 0.2515 0.002 0.573 34.1 178.7 70.7 0 0.453 3_updatecdl: 0.2070 0.2515 0.002 0.586 34.1 178.7 70.7 0 0.453 3_nqh: 0.2074 0.2528 0.002 0.586 34.1 178.7 70.7 0 0.450 3_realsrl: 0.2074 0.2528 0.002 0.586 34.1 178.7 70.7 0 0.450 3_weight: 0.2074 0.2528 0.002 0.586 34.1 178.7 70.7 0 0.450 3_xyzrec: 0.2185 0.2640 0.002 0.469 34.1 178.7 70.7 0 0.461 3_realsrl2: 0.2191 0.2658 0.002 0.469 34.1 178.7 70.7 0 0.461 3_adp: 0.2144 0.2590 0.002 0.469 29.1 179.6 70.8 0 0.461 4_bss: 0.2141 0.2582 0.002 0.469 29.1 179.6 70.8 0 0.461 4_settarget: 0.2141 0.2582 0.002 0.469 29.1 179.6 70.8 0 0.461 4_updatephipsi: 0.2141 0.2582 0.002 0.469 29.1 179.6 70.8 0 0.461 4_updatecdl: 0.2141 0.2582 0.002 0.486 29.1 179.6 70.8 0 0.461 4_nqh: 0.2141 0.2582 0.002 0.486 29.1 179.6 70.8 0 0.461 4_realsrl: 0.2141 0.2582 0.002 0.486 29.1 179.6 70.8 0 0.461 4_weight: 0.2141 0.2582 0.002 0.486 29.1 179.6 70.8 0 0.461 4_xyzrec: 0.2182 0.2600 0.001 0.455 29.1 179.6 70.8 0 0.471 4_realsrl2: 0.2190 0.2612 0.001 0.455 29.1 179.6 70.8 0 0.472 4_adp: 0.2168 0.2591 0.001 0.455 25.2 181.9 69.5 0 0.472 5_bss: 0.2153 0.2567 0.001 0.455 25.2 181.9 69.5 0 0.472 5_settarget: 0.2153 0.2567 0.001 0.455 25.2 181.9 69.5 0 0.472 5_updatephipsi: 0.2153 0.2567 0.001 0.455 25.2 181.9 69.5 0 0.472 5_updatecdl: 0.2153 0.2567 0.001 0.465 25.2 181.9 69.5 0 0.472 5_setrh: 0.2153 0.2567 0.001 0.465 25.2 181.9 69.5 0 0.472 5_nqh: 0.2153 0.2567 0.001 0.465 25.2 181.9 69.5 0 0.472 5_realsrl: 0.2153 0.2567 0.001 0.465 25.2 181.9 69.5 0 0.472 5_weight: 0.2153 0.2567 0.001 0.465 25.2 181.9 69.5 0 0.472 5_xyzrec: 0.2096 0.2524 0.001 0.449 25.2 181.9 69.5 0 0.484 5_realsrl2: 0.2101 0.2529 0.001 0.449 25.2 181.9 69.5 0 0.484 5_adp: 0.2084 0.2523 0.001 0.449 20.2 184.4 68.1 0 0.484 end: 0.2071 0.2512 0.001 0.449 20.2 184.4 68.1 0 0.484 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1OTH_ref.pdb_fitted_modified_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1OTH_ref.pdb_fitted_modified_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 1.4700 Refinement macro-cycles (run) : 261.6700 Write final files (write_after_run_outputs) : 14.9800 Total : 278.1200 Total CPU time: 4.89 minutes =========================== phenix.refine: finished =========================== # Date 2024-04-04 Time 09:07:13 PDT -0700 (1712246833.78 s) Start R-work = 0.3254, R-free = 0.3304 Final R-work = 0.2071, R-free = 0.2512 =============================================================================== Job complete usr+sys time: 312.21 seconds wall clock time: 8 minutes 26.50 seconds (506.50 seconds total)