Starting phenix.real_space_refine on Wed Mar 4 17:42:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2z_15109/03_2026/8a2z_15109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2z_15109/03_2026/8a2z_15109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a2z_15109/03_2026/8a2z_15109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2z_15109/03_2026/8a2z_15109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a2z_15109/03_2026/8a2z_15109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2z_15109/03_2026/8a2z_15109.map" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 10 5.49 5 S 100 5.16 5 C 9145 2.51 5 N 2445 2.21 5 O 3355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15060 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "E" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Restraints were copied for chains: A, B, D, E Time building chain proxies: 2.55, per 1000 atoms: 0.17 Number of scatterers: 15060 At special positions: 0 Unit cell: (95.215, 91.74, 191.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 100 16.00 P 10 15.00 O 3355 8.00 N 2445 7.00 C 9145 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 637.8 milliseconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 30 sheets defined 51.9% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.561A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.958A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.736A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.542A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 351 through 355 removed outlier: 4.038A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.561A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.957A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.736A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.543A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.038A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.560A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.957A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.736A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.543A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.038A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.560A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.957A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.735A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.544A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.038A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.560A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.957A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.736A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.543A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 351 through 355 removed outlier: 4.037A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.537A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.299A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.536A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.300A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.537A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.300A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.537A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.300A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.536A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.300A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 730 hydrogen bonds defined for protein. 1860 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: 3.04 Time building geometry restraints manager: 1.81 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: 4705 1.34 - 1.46: 3130 1.46 - 1.58: 6780 1.58 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14805 Sorted by residual: bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.34e+00 ... (remaining 14800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 19565 1.40 - 2.81: 357 2.81 - 4.21: 122 4.21 - 5.61: 26 5.61 - 7.01: 20 Bond angle restraints: 20090 Sorted by residual: angle pdb=" NE ARG A 39 " pdb=" CZ ARG A 39 " pdb=" NH2 ARG A 39 " ideal model delta sigma weight residual 119.20 121.54 -2.34 9.00e-01 1.23e+00 6.78e+00 angle pdb=" NE ARG D 95 " pdb=" CZ ARG D 95 " pdb=" NH2 ARG D 95 " ideal model delta sigma weight residual 119.20 121.52 -2.32 9.00e-01 1.23e+00 6.66e+00 angle pdb=" NE ARG D 39 " pdb=" CZ ARG D 39 " pdb=" NH2 ARG D 39 " ideal model delta sigma weight residual 119.20 121.52 -2.32 9.00e-01 1.23e+00 6.62e+00 angle pdb=" NE ARG E 256 " pdb=" CZ ARG E 256 " pdb=" NH2 ARG E 256 " ideal model delta sigma weight residual 119.20 121.51 -2.31 9.00e-01 1.23e+00 6.58e+00 angle pdb=" NE ARG A 37 " pdb=" CZ ARG A 37 " pdb=" NH2 ARG A 37 " ideal model delta sigma weight residual 119.20 121.51 -2.31 9.00e-01 1.23e+00 6.58e+00 ... (remaining 20085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 8665 23.67 - 47.34: 195 47.34 - 71.00: 15 71.00 - 94.67: 30 94.67 - 118.34: 5 Dihedral angle restraints: 8910 sinusoidal: 3610 harmonic: 5300 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.34 118.34 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.30 118.29 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 -178.29 118.29 1 2.00e+01 2.50e-03 3.54e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1292 0.031 - 0.063: 625 0.063 - 0.094: 198 0.094 - 0.126: 109 0.126 - 0.157: 6 Chirality restraints: 2230 Sorted by residual: chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.18e-01 chirality pdb=" C3' ADP D 401 " pdb=" C2' ADP D 401 " pdb=" C4' ADP D 401 " pdb=" O3' ADP D 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" C3' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C4' ADP C 401 " pdb=" O3' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 2227 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO C 243 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO D 243 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO A 243 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.014 5.00e-02 4.00e+02 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1058 2.73 - 3.27: 15349 3.27 - 3.82: 27795 3.82 - 4.36: 35515 4.36 - 4.90: 56711 Nonbonded interactions: 136428 Sorted by model distance: nonbonded pdb="CA CA B 402 " pdb=" O HOH B 578 " model vdw 2.190 2.510 nonbonded pdb="CA CA A 402 " pdb=" O HOH A 556 " model vdw 2.206 2.510 nonbonded pdb=" O2B ADP B 401 " pdb="CA CA B 402 " model vdw 2.217 2.510 nonbonded pdb=" O2B ADP E 401 " pdb="CA CA E 402 " model vdw 2.217 2.510 nonbonded pdb=" O2B ADP A 401 " pdb="CA CA A 402 " model vdw 2.217 2.510 ... (remaining 136423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.470 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14805 Z= 0.175 Angle : 0.582 7.015 20090 Z= 0.292 Chirality : 0.043 0.157 2230 Planarity : 0.004 0.033 2565 Dihedral : 11.913 118.341 5510 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.06 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.19), residues: 1795 helix: -1.95 (0.15), residues: 785 sheet: -0.73 (0.27), residues: 320 loop : 1.21 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 210 TYR 0.009 0.001 TYR D 143 PHE 0.008 0.001 PHE E 262 TRP 0.014 0.002 TRP A 340 HIS 0.003 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00389 (14805) covalent geometry : angle 0.58242 (20090) hydrogen bonds : bond 0.21348 ( 720) hydrogen bonds : angle 7.85196 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.621 Fit side-chains REVERT: B 225 ASN cc_start: 0.7901 (m-40) cc_final: 0.7690 (m110) REVERT: B 227 MET cc_start: 0.8770 (mmm) cc_final: 0.8533 (mmm) REVERT: B 286 ASP cc_start: 0.7554 (m-30) cc_final: 0.7347 (m-30) REVERT: D 92 ASN cc_start: 0.8523 (m-40) cc_final: 0.8307 (m110) REVERT: D 128 ASN cc_start: 0.8408 (m-40) cc_final: 0.8200 (m110) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.8121 time to fit residues: 225.6239 Evaluate side-chains 185 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.0870 chunk 149 optimal weight: 4.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN A 59 GLN A 225 ASN A 353 GLN B 59 GLN B 88 HIS B 360 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 353 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098604 restraints weight = 14425.652| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.12 r_work: 0.3003 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14805 Z= 0.179 Angle : 0.639 8.381 20090 Z= 0.317 Chirality : 0.047 0.205 2230 Planarity : 0.004 0.037 2565 Dihedral : 9.747 127.593 2055 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.16 % Allowed : 7.81 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.20), residues: 1795 helix: -0.21 (0.18), residues: 775 sheet: -0.44 (0.26), residues: 320 loop : 1.94 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 183 TYR 0.013 0.001 TYR A 143 PHE 0.011 0.002 PHE B 262 TRP 0.016 0.002 TRP B 340 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00401 (14805) covalent geometry : angle 0.63891 (20090) hydrogen bonds : bond 0.04902 ( 720) hydrogen bonds : angle 5.30043 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.591 Fit side-chains REVERT: B 286 ASP cc_start: 0.7932 (m-30) cc_final: 0.7682 (m-30) REVERT: B 299 MET cc_start: 0.8919 (mtm) cc_final: 0.8703 (mtt) REVERT: B 328 LYS cc_start: 0.8510 (ttmt) cc_final: 0.8303 (mtmm) REVERT: B 355 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8059 (mtm) REVERT: D 41 GLN cc_start: 0.6993 (pm20) cc_final: 0.6533 (mm110) REVERT: D 92 ASN cc_start: 0.8769 (m-40) cc_final: 0.8546 (m110) REVERT: E 95 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7732 (mtp-110) outliers start: 18 outliers final: 7 residues processed: 205 average time/residue: 0.7671 time to fit residues: 169.5034 Evaluate side-chains 186 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 81 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 51 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 HIS A 360 GLN B 161 HIS B 225 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.096693 restraints weight = 14490.760| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.08 r_work: 0.2983 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 14805 Z= 0.295 Angle : 0.724 9.207 20090 Z= 0.365 Chirality : 0.052 0.218 2230 Planarity : 0.005 0.053 2565 Dihedral : 10.160 130.085 2055 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.61 % Allowed : 8.32 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1795 helix: 0.24 (0.19), residues: 790 sheet: -0.25 (0.27), residues: 325 loop : 1.87 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 210 TYR 0.013 0.002 TYR A 143 PHE 0.015 0.002 PHE B 262 TRP 0.021 0.003 TRP D 340 HIS 0.005 0.002 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00677 (14805) covalent geometry : angle 0.72436 (20090) hydrogen bonds : bond 0.05555 ( 720) hydrogen bonds : angle 5.28897 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.588 Fit side-chains REVERT: C 125 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: B 241 GLU cc_start: 0.8657 (tt0) cc_final: 0.8445 (tt0) REVERT: D 95 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7562 (mpp-170) REVERT: D 351 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8471 (p) REVERT: E 95 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7697 (mtp-110) REVERT: E 355 MET cc_start: 0.8345 (mtp) cc_final: 0.8025 (mtt) outliers start: 25 outliers final: 10 residues processed: 193 average time/residue: 0.7559 time to fit residues: 157.6770 Evaluate side-chains 189 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 175 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 50 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 88 HIS D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.099877 restraints weight = 14550.406| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.08 r_work: 0.3032 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14805 Z= 0.130 Angle : 0.594 8.184 20090 Z= 0.288 Chirality : 0.045 0.204 2230 Planarity : 0.003 0.032 2565 Dihedral : 9.868 129.460 2055 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.16 % Allowed : 8.97 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.20), residues: 1795 helix: 0.53 (0.19), residues: 790 sheet: -0.25 (0.26), residues: 320 loop : 2.02 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.009 0.001 TYR C 143 PHE 0.008 0.001 PHE D 262 TRP 0.015 0.002 TRP B 340 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00284 (14805) covalent geometry : angle 0.59374 (20090) hydrogen bonds : bond 0.03777 ( 720) hydrogen bonds : angle 4.84776 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.609 Fit side-chains REVERT: B 215 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8474 (mptm) REVERT: D 95 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7558 (mpp-170) REVERT: D 351 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8442 (p) REVERT: E 95 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7720 (mtp-110) REVERT: E 355 MET cc_start: 0.8328 (mtp) cc_final: 0.7964 (mtm) REVERT: E 360 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7641 (mp-120) outliers start: 18 outliers final: 8 residues processed: 191 average time/residue: 0.7767 time to fit residues: 160.5329 Evaluate side-chains 184 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 136 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.098868 restraints weight = 14576.814| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.09 r_work: 0.3021 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14805 Z= 0.157 Angle : 0.611 8.425 20090 Z= 0.298 Chirality : 0.046 0.197 2230 Planarity : 0.004 0.032 2565 Dihedral : 9.850 129.813 2055 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.74 % Allowed : 8.71 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1795 helix: 0.62 (0.19), residues: 790 sheet: -0.23 (0.27), residues: 320 loop : 2.08 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 183 TYR 0.010 0.001 TYR C 143 PHE 0.009 0.001 PHE D 262 TRP 0.016 0.002 TRP B 340 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00349 (14805) covalent geometry : angle 0.61126 (20090) hydrogen bonds : bond 0.04078 ( 720) hydrogen bonds : angle 4.82447 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.659 Fit side-chains REVERT: C 125 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: B 41 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7050 (pm20) REVERT: B 355 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8036 (mtm) REVERT: D 95 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7550 (mpp-170) REVERT: D 351 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8592 (p) REVERT: E 44 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7904 (mmm) REVERT: E 57 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: E 95 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7736 (mtp-110) REVERT: E 314 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8287 (tt0) REVERT: E 355 MET cc_start: 0.8337 (mtp) cc_final: 0.7977 (mtm) REVERT: E 360 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7648 (mp-120) outliers start: 27 outliers final: 10 residues processed: 191 average time/residue: 0.7918 time to fit residues: 163.3816 Evaluate side-chains 191 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 22 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.098344 restraints weight = 14383.363| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.08 r_work: 0.3009 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14805 Z= 0.191 Angle : 0.640 8.595 20090 Z= 0.315 Chirality : 0.047 0.202 2230 Planarity : 0.004 0.032 2565 Dihedral : 9.972 129.937 2055 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.94 % Allowed : 8.65 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1795 helix: 0.63 (0.19), residues: 790 sheet: -0.22 (0.27), residues: 320 loop : 2.09 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 210 TYR 0.009 0.001 TYR C 143 PHE 0.011 0.002 PHE B 262 TRP 0.017 0.003 TRP D 340 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00431 (14805) covalent geometry : angle 0.63993 (20090) hydrogen bonds : bond 0.04436 ( 720) hydrogen bonds : angle 4.89357 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.683 Fit side-chains REVERT: C 125 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: B 41 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7076 (pm20) REVERT: B 215 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8528 (mptm) REVERT: B 241 GLU cc_start: 0.8633 (tt0) cc_final: 0.8416 (tt0) REVERT: B 286 ASP cc_start: 0.7963 (m-30) cc_final: 0.7708 (m-30) REVERT: D 28 ARG cc_start: 0.8448 (tpp-160) cc_final: 0.8226 (mtt-85) REVERT: D 95 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7570 (mpp-170) REVERT: D 354 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7750 (pp30) REVERT: E 44 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7833 (mmm) REVERT: E 57 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: E 95 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7728 (mtp-110) REVERT: E 314 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: E 355 MET cc_start: 0.8347 (mtp) cc_final: 0.7971 (mtm) REVERT: E 360 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7667 (mp-120) outliers start: 30 outliers final: 11 residues processed: 192 average time/residue: 0.7904 time to fit residues: 164.0115 Evaluate side-chains 191 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 354 GLN Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 170 optimal weight: 0.0770 chunk 14 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN D 246 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.098894 restraints weight = 14488.459| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.13 r_work: 0.3021 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14805 Z= 0.169 Angle : 0.623 8.407 20090 Z= 0.305 Chirality : 0.047 0.202 2230 Planarity : 0.004 0.031 2565 Dihedral : 9.932 129.802 2055 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.61 % Allowed : 8.97 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.20), residues: 1795 helix: 0.69 (0.19), residues: 790 sheet: -0.22 (0.27), residues: 320 loop : 2.10 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 28 TYR 0.009 0.001 TYR C 143 PHE 0.010 0.001 PHE B 262 TRP 0.016 0.002 TRP D 340 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00379 (14805) covalent geometry : angle 0.62270 (20090) hydrogen bonds : bond 0.04160 ( 720) hydrogen bonds : angle 4.81686 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.550 Fit side-chains REVERT: C 125 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: B 41 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7335 (pm20) REVERT: B 215 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8505 (mptm) REVERT: B 241 GLU cc_start: 0.8651 (tt0) cc_final: 0.8426 (tt0) REVERT: B 286 ASP cc_start: 0.7958 (m-30) cc_final: 0.7708 (m-30) REVERT: D 28 ARG cc_start: 0.8489 (tpp-160) cc_final: 0.8260 (mtt-85) REVERT: D 41 GLN cc_start: 0.7121 (pt0) cc_final: 0.6887 (pm20) REVERT: D 95 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7559 (mpp-170) REVERT: E 57 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7887 (pt0) REVERT: E 95 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7738 (mtp-110) REVERT: E 314 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: E 355 MET cc_start: 0.8372 (mtp) cc_final: 0.7981 (mtm) REVERT: E 360 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7688 (mp-120) outliers start: 25 outliers final: 12 residues processed: 189 average time/residue: 0.7419 time to fit residues: 151.8490 Evaluate side-chains 191 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 158 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100082 restraints weight = 14701.053| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.14 r_work: 0.3039 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14805 Z= 0.132 Angle : 0.592 8.114 20090 Z= 0.287 Chirality : 0.045 0.194 2230 Planarity : 0.003 0.032 2565 Dihedral : 9.791 129.034 2055 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.23 % Allowed : 9.48 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.20), residues: 1795 helix: 0.79 (0.19), residues: 790 sheet: -0.22 (0.27), residues: 320 loop : 2.14 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 95 TYR 0.008 0.001 TYR C 143 PHE 0.008 0.001 PHE D 262 TRP 0.015 0.002 TRP D 340 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00289 (14805) covalent geometry : angle 0.59160 (20090) hydrogen bonds : bond 0.03692 ( 720) hydrogen bonds : angle 4.68385 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.466 Fit side-chains REVERT: C 125 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: A 57 GLU cc_start: 0.8279 (tt0) cc_final: 0.8033 (pt0) REVERT: B 41 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: B 215 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8472 (mptm) REVERT: B 241 GLU cc_start: 0.8621 (tt0) cc_final: 0.8401 (tt0) REVERT: D 28 ARG cc_start: 0.8489 (tpp-160) cc_final: 0.8256 (mtt-85) REVERT: D 41 GLN cc_start: 0.7129 (pt0) cc_final: 0.6912 (pm20) REVERT: D 95 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7545 (mpp-170) REVERT: E 57 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7834 (pt0) REVERT: E 95 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7718 (mtp-110) REVERT: E 355 MET cc_start: 0.8379 (mtp) cc_final: 0.7988 (mtm) REVERT: E 360 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7657 (mp-120) outliers start: 19 outliers final: 8 residues processed: 185 average time/residue: 0.7536 time to fit residues: 150.5620 Evaluate side-chains 187 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 149 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN D 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.098452 restraints weight = 14652.034| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.14 r_work: 0.3011 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14805 Z= 0.194 Angle : 0.643 8.617 20090 Z= 0.316 Chirality : 0.047 0.199 2230 Planarity : 0.004 0.031 2565 Dihedral : 9.961 129.937 2055 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.61 % Allowed : 9.16 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1795 helix: 0.73 (0.19), residues: 790 sheet: -0.23 (0.27), residues: 320 loop : 2.10 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 28 TYR 0.009 0.001 TYR C 143 PHE 0.011 0.002 PHE B 262 TRP 0.017 0.002 TRP D 340 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00437 (14805) covalent geometry : angle 0.64298 (20090) hydrogen bonds : bond 0.04418 ( 720) hydrogen bonds : angle 4.84346 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.493 Fit side-chains REVERT: C 125 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: A 57 GLU cc_start: 0.8306 (tt0) cc_final: 0.8045 (pt0) REVERT: B 41 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: B 241 GLU cc_start: 0.8664 (tt0) cc_final: 0.8438 (tt0) REVERT: D 28 ARG cc_start: 0.8493 (tpp-160) cc_final: 0.8249 (mtt-85) REVERT: D 41 GLN cc_start: 0.7144 (pt0) cc_final: 0.6899 (pm20) REVERT: D 95 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7567 (mpp-170) REVERT: E 44 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.8019 (mtp) REVERT: E 57 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7896 (pt0) REVERT: E 95 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7733 (mtp-110) REVERT: E 314 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: E 355 MET cc_start: 0.8392 (mtp) cc_final: 0.8000 (mtm) REVERT: E 360 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7688 (mp-120) outliers start: 25 outliers final: 10 residues processed: 188 average time/residue: 0.7469 time to fit residues: 151.9430 Evaluate side-chains 189 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN D 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.118930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097993 restraints weight = 14690.514| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.14 r_work: 0.3004 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14805 Z= 0.220 Angle : 0.666 8.811 20090 Z= 0.330 Chirality : 0.049 0.204 2230 Planarity : 0.004 0.036 2565 Dihedral : 10.075 130.335 2055 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.29 % Allowed : 9.55 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1795 helix: 0.70 (0.19), residues: 790 sheet: -0.26 (0.27), residues: 320 loop : 2.07 (0.26), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 210 TYR 0.009 0.001 TYR C 143 PHE 0.012 0.002 PHE B 262 TRP 0.018 0.003 TRP B 340 HIS 0.005 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00500 (14805) covalent geometry : angle 0.66649 (20090) hydrogen bonds : bond 0.04662 ( 720) hydrogen bonds : angle 4.92227 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.582 Fit side-chains REVERT: C 125 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: B 41 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: B 241 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: D 28 ARG cc_start: 0.8491 (tpp-160) cc_final: 0.8241 (mtt-85) REVERT: D 41 GLN cc_start: 0.7183 (pt0) cc_final: 0.6944 (pm20) REVERT: D 95 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7540 (mpp-170) REVERT: E 57 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: E 95 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7721 (mtp-110) REVERT: E 314 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: E 355 MET cc_start: 0.8391 (mtp) cc_final: 0.8012 (mtm) REVERT: E 360 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7668 (mp-120) outliers start: 20 outliers final: 10 residues processed: 179 average time/residue: 0.7651 time to fit residues: 147.8756 Evaluate side-chains 187 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 368 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 0.0970 chunk 56 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.122528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.102048 restraints weight = 14645.107| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.13 r_work: 0.3073 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14805 Z= 0.102 Angle : 0.567 7.471 20090 Z= 0.272 Chirality : 0.044 0.186 2230 Planarity : 0.003 0.034 2565 Dihedral : 9.668 129.670 2055 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.90 % Allowed : 9.87 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.21), residues: 1795 helix: 0.96 (0.19), residues: 780 sheet: -0.09 (0.25), residues: 340 loop : 2.36 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 28 TYR 0.009 0.001 TYR C 143 PHE 0.007 0.001 PHE D 31 TRP 0.012 0.002 TRP D 340 HIS 0.005 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00214 (14805) covalent geometry : angle 0.56656 (20090) hydrogen bonds : bond 0.03149 ( 720) hydrogen bonds : angle 4.53293 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6748.99 seconds wall clock time: 115 minutes 30.31 seconds (6930.31 seconds total)