Starting phenix.real_space_refine on Sat Sep 12 01:37:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jae_6345/09_2026/3jae_6345.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jae_6345/09_2026/3jae_6345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/3jae_6345/09_2026/3jae_6345.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jae_6345/09_2026/3jae_6345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jae_6345/09_2026/3jae_6345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jae_6345/09_2026/3jae_6345.map" model { file = "/net/cci-nas-00/data/ceres_data/3jae_6345/09_2026/3jae_6345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jae_6345/09_2026/3jae_6345.cif" } resolution = 3.9 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= 1.000 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8360 2.51 5 N 2130 2.21 5 O 2270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12825 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2537 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 9, 'GLN:plan1': 1, 'PHE:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 110 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.14, per 1000 atoms: 0.17 Number of scatterers: 12825 At special positions: 0 Unit cell: (96.0324, 98.4636, 127.638, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2270 8.00 N 2130 7.00 C 8360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 418.7 milliseconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 39.7% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 36 through 40 removed outlier: 4.132A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 235 through 243 removed outlier: 4.666A pdb=" N TYR A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.906A pdb=" N SER A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP A 259 " --> pdb=" O TRP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 288 removed outlier: 4.411A pdb=" N ARG A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 286 " --> pdb=" O GLN A 282 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 removed outlier: 3.847A pdb=" N ILE A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 363 removed outlier: 3.751A pdb=" N THR A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Proline residue: A 347 - end of helix removed outlier: 3.897A pdb=" N ILE A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 361 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 36 through 40 removed outlier: 4.132A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 235 through 243 removed outlier: 4.665A pdb=" N TYR B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 260 removed outlier: 3.907A pdb=" N SER B 247 " --> pdb=" O MET B 243 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP B 259 " --> pdb=" O TRP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 288 removed outlier: 4.411A pdb=" N ARG B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 286 " --> pdb=" O GLN B 282 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 325 removed outlier: 3.847A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 363 removed outlier: 3.751A pdb=" N THR B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) Proline residue: B 347 - end of helix removed outlier: 3.897A pdb=" N ILE B 359 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 Processing helix chain 'C' and resid 36 through 40 removed outlier: 4.133A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 235 through 243 removed outlier: 4.666A pdb=" N TYR C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 260 removed outlier: 3.906A pdb=" N SER C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TRP C 259 " --> pdb=" O TRP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 288 removed outlier: 4.410A pdb=" N ARG C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 286 " --> pdb=" O GLN C 282 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 325 removed outlier: 3.847A pdb=" N ILE C 301 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 363 removed outlier: 3.752A pdb=" N THR C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) Proline residue: C 347 - end of helix removed outlier: 3.897A pdb=" N ILE C 359 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR C 360 " --> pdb=" O PHE C 356 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR C 361 " --> pdb=" O TYR C 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.132A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 235 through 243 removed outlier: 4.665A pdb=" N TYR D 239 " --> pdb=" O GLN D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 260 removed outlier: 3.906A pdb=" N SER D 247 " --> pdb=" O MET D 243 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP D 259 " --> pdb=" O TRP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 288 removed outlier: 4.410A pdb=" N ARG D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D 286 " --> pdb=" O GLN D 282 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 288 " --> pdb=" O SER D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 325 removed outlier: 3.847A pdb=" N ILE D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 363 removed outlier: 3.752A pdb=" N THR D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) Proline residue: D 347 - end of helix removed outlier: 3.897A pdb=" N ILE D 359 " --> pdb=" O ILE D 355 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR D 360 " --> pdb=" O PHE D 356 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR D 361 " --> pdb=" O TYR D 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 36 through 40 removed outlier: 4.132A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 235 through 243 removed outlier: 4.665A pdb=" N TYR E 239 " --> pdb=" O GLN E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 260 removed outlier: 3.907A pdb=" N SER E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL E 256 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP E 259 " --> pdb=" O TRP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 288 removed outlier: 4.411A pdb=" N ARG E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER E 286 " --> pdb=" O GLN E 282 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA E 288 " --> pdb=" O SER E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 325 removed outlier: 3.847A pdb=" N ILE E 301 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP E 302 " --> pdb=" O ALA E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 363 removed outlier: 3.751A pdb=" N THR E 340 " --> pdb=" O LYS E 336 " (cutoff:3.500A) Proline residue: E 347 - end of helix removed outlier: 3.897A pdb=" N ILE E 359 " --> pdb=" O ILE E 355 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR E 360 " --> pdb=" O PHE E 356 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR E 361 " --> pdb=" O TYR E 357 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.090A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.931A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET A 170 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET A 170 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.090A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.932A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET B 170 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET B 170 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'C' and resid 98 through 100 removed outlier: 4.090A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.932A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'C' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET C 170 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'C' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET C 170 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing sheet with id=M, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.090A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.932A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET D 170 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing sheet with id=P, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET D 170 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.090A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=R, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.931A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'E' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET E 170 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'E' and resid 115 through 116 removed outlier: 3.848A pdb=" N MET E 170 " --> pdb=" O ALA E 228 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2373 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: 2.49 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3892 1.34 - 1.46: 2535 1.46 - 1.58: 6613 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 13145 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.96e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.86e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.79e+00 ... (remaining 13140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 15290 1.60 - 3.19: 2172 3.19 - 4.79: 368 4.79 - 6.39: 108 6.39 - 7.98: 37 Bond angle restraints: 17975 Sorted by residual: angle pdb=" C THR D 128 " pdb=" CA THR D 128 " pdb=" CB THR D 128 " ideal model delta sigma weight residual 116.63 109.43 7.20 1.16e+00 7.43e-01 3.85e+01 angle pdb=" C THR B 128 " pdb=" CA THR B 128 " pdb=" CB THR B 128 " ideal model delta sigma weight residual 116.63 109.43 7.20 1.16e+00 7.43e-01 3.85e+01 angle pdb=" C THR E 128 " pdb=" CA THR E 128 " pdb=" CB THR E 128 " ideal model delta sigma weight residual 116.63 109.45 7.18 1.16e+00 7.43e-01 3.83e+01 angle pdb=" C THR A 128 " pdb=" CA THR A 128 " pdb=" CB THR A 128 " ideal model delta sigma weight residual 116.63 109.47 7.16 1.16e+00 7.43e-01 3.81e+01 angle pdb=" N GLU E 119 " pdb=" CA GLU E 119 " pdb=" C GLU E 119 " ideal model delta sigma weight residual 111.33 118.79 -7.46 1.21e+00 6.83e-01 3.80e+01 ... (remaining 17970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 7350 16.88 - 33.76: 250 33.76 - 50.63: 10 50.63 - 67.51: 5 67.51 - 84.39: 5 Dihedral angle restraints: 7620 sinusoidal: 2630 harmonic: 4990 Sorted by residual: dihedral pdb=" CB CYS C 214 " pdb=" SG CYS C 214 " pdb=" SG CYS C 225 " pdb=" CB CYS C 225 " ideal model delta sinusoidal sigma weight residual -86.00 -149.65 63.65 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS D 214 " pdb=" SG CYS D 214 " pdb=" SG CYS D 225 " pdb=" CB CYS D 225 " ideal model delta sinusoidal sigma weight residual -86.00 -149.64 63.64 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS E 214 " pdb=" SG CYS E 214 " pdb=" SG CYS E 225 " pdb=" CB CYS E 225 " ideal model delta sinusoidal sigma weight residual -86.00 -149.62 63.62 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 7617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1317 0.037 - 0.074: 602 0.074 - 0.112: 157 0.112 - 0.149: 49 0.149 - 0.186: 5 Chirality restraints: 2130 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.18e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.60e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.45e+00 ... (remaining 2127 not shown) Planarity restraints: 2245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 115 " -0.020 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE C 115 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE C 115 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE C 115 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 115 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 115 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE C 115 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 115 " 0.020 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE E 115 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE E 115 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE E 115 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 115 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 115 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE E 115 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 115 " 0.020 2.00e-02 2.50e+03 2.47e-02 1.07e+01 pdb=" CG PHE A 115 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 115 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE A 115 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 115 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 115 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 115 " -0.003 2.00e-02 2.50e+03 ... (remaining 2242 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1005 2.74 - 3.28: 13587 3.28 - 3.82: 20380 3.82 - 4.36: 23800 4.36 - 4.90: 40392 Nonbonded interactions: 99164 Sorted by model distance: nonbonded pdb=" OG1 THR A 128 " pdb=" O LEU E 114 " model vdw 2.202 3.040 nonbonded pdb=" O VAL B 251 " pdb=" OG SER B 254 " model vdw 2.228 3.040 nonbonded pdb=" O VAL D 251 " pdb=" OG SER D 254 " model vdw 2.229 3.040 nonbonded pdb=" O VAL E 251 " pdb=" OG SER E 254 " model vdw 2.229 3.040 nonbonded pdb=" O VAL A 251 " pdb=" OG SER A 254 " model vdw 2.229 3.040 ... (remaining 99159 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue 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: 0.910 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.750 Find NCS groups from input model: 0.140 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.006 0.049 13155 Z= 0.416 Angle : 1.255 7.985 18000 Z= 0.838 Chirality : 0.046 0.186 2130 Planarity : 0.006 0.059 2245 Dihedral : 9.271 84.390 4365 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: -1.69 (0.17), residues: 1670 helix: -1.72 (0.19), residues: 510 sheet: 0.50 (0.26), residues: 375 loop : -1.46 (0.17), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG C 147 TYR 0.047 0.003 TYR B 74 PHE 0.054 0.004 PHE E 115 TRP 0.047 0.004 TRP A 255 HIS 0.004 0.002 HIS B 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.42 (13145) covalent geometry : angle 1.25536 / 0.84 (17975) SS BOND : bond 0.00841 / 0.47 ( 5) SS BOND : angle 0.54106 / 0.34 ( 10) hydrogen bonds : bond 0.11711 / 7.40 ( 676) hydrogen bonds : angle 9.03951 / 6.27 ( 2373) link_BETA1-4 : bond 0.00931 / 0.51 ( 5) link_BETA1-4 : angle 0.89503 / 0.54 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LYS cc_start: 0.8107 (mttm) cc_final: 0.7869 (mtmt) REVERT: A 204 ILE cc_start: 0.8672 (pt) cc_final: 0.8240 (mm) REVERT: B 73 ASP cc_start: 0.6630 (p0) cc_final: 0.6369 (p0) REVERT: B 132 LYS cc_start: 0.8100 (mttm) cc_final: 0.7832 (mtmt) REVERT: B 303 MET cc_start: 0.8634 (mmm) cc_final: 0.8385 (mmm) REVERT: D 252 ILE cc_start: 0.9528 (mt) cc_final: 0.9296 (mt) REVERT: E 252 ILE cc_start: 0.9487 (mt) cc_final: 0.9245 (mt) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.1094 time to fit residues: 51.8612 Evaluate side-chains 167 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 54 ASN A 83 GLN B 54 ASN B 83 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN D 54 ASN D 83 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 ASN ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.046800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.035478 restraints weight = 89546.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.036418 restraints weight = 51522.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.037077 restraints weight = 35549.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.037514 restraints weight = 27462.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.037853 restraints weight = 23031.832| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13155 Z= 0.240 Angle : 0.877 9.919 18000 Z= 0.440 Chirality : 0.048 0.240 2130 Planarity : 0.005 0.038 2245 Dihedral : 6.405 27.546 1815 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.93 % Allowed : 9.11 % Favored : 87.97 % 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: -0.45 (0.19), residues: 1670 helix: 0.67 (0.21), residues: 515 sheet: 0.38 (0.25), residues: 380 loop : -1.31 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 287 TYR 0.026 0.002 TYR D 239 PHE 0.027 0.003 PHE B 115 TRP 0.020 0.002 TRP B 255 HIS 0.004 0.001 HIS E 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.24 (13145) covalent geometry : angle 0.87601 / 0.44 (17975) SS BOND : bond 0.00760 / 0.41 ( 5) SS BOND : angle 0.95645 / 0.53 ( 10) hydrogen bonds : bond 0.04737 / 3.19 ( 676) hydrogen bonds : angle 5.90408 / 4.08 ( 2373) link_BETA1-4 : bond 0.00463 / 0.22 ( 5) link_BETA1-4 : angle 1.37427 / 0.95 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8947 (m-30) cc_final: 0.8686 (m-30) REVERT: A 105 MET cc_start: 0.8805 (mmp) cc_final: 0.8581 (mmm) REVERT: A 120 LYS cc_start: 0.9083 (ttpt) cc_final: 0.8833 (ptpt) REVERT: A 132 LYS cc_start: 0.9183 (mttm) cc_final: 0.8878 (mtmt) REVERT: A 146 ILE cc_start: 0.9358 (pt) cc_final: 0.9093 (mm) REVERT: A 156 MET cc_start: 0.8852 (ptp) cc_final: 0.8578 (mmm) REVERT: A 353 PHE cc_start: 0.9315 (t80) cc_final: 0.9063 (t80) REVERT: B 73 ASP cc_start: 0.8173 (p0) cc_final: 0.7747 (p0) REVERT: B 105 MET cc_start: 0.8702 (tpp) cc_final: 0.8265 (tpp) REVERT: B 120 LYS cc_start: 0.9054 (ttpt) cc_final: 0.8844 (ttpt) REVERT: B 126 GLU cc_start: 0.8627 (mp0) cc_final: 0.8366 (tp30) REVERT: B 132 LYS cc_start: 0.9249 (mttm) cc_final: 0.8806 (mtmt) REVERT: B 239 TYR cc_start: 0.9336 (m-80) cc_final: 0.8854 (m-80) REVERT: B 303 MET cc_start: 0.9427 (mmm) cc_final: 0.9119 (mmm) REVERT: C 130 ASP cc_start: 0.8547 (t0) cc_final: 0.8340 (t0) REVERT: C 156 MET cc_start: 0.8694 (ptp) cc_final: 0.8376 (mmm) REVERT: D 100 ASP cc_start: 0.8839 (m-30) cc_final: 0.7867 (t0) REVERT: D 105 MET cc_start: 0.8661 (tpp) cc_final: 0.8366 (tpp) REVERT: D 130 ASP cc_start: 0.8483 (t0) cc_final: 0.8248 (t0) REVERT: D 132 LYS cc_start: 0.9239 (mttm) cc_final: 0.8854 (mtmt) REVERT: D 156 MET cc_start: 0.8746 (ptp) cc_final: 0.8311 (mmm) REVERT: D 166 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7463 (mm-40) REVERT: D 292 LYS cc_start: 0.9456 (mtmm) cc_final: 0.9177 (ttmm) REVERT: D 348 LEU cc_start: 0.9311 (mt) cc_final: 0.9104 (pp) REVERT: E 100 ASP cc_start: 0.8797 (m-30) cc_final: 0.7803 (t0) REVERT: E 106 LEU cc_start: 0.9412 (tt) cc_final: 0.9132 (mp) REVERT: E 120 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8895 (ptmt) REVERT: E 279 MET cc_start: 0.9304 (mmm) cc_final: 0.9073 (mmm) outliers start: 36 outliers final: 18 residues processed: 205 average time/residue: 0.1165 time to fit residues: 34.2728 Evaluate side-chains 161 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 136 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 103 optimal weight: 0.0040 chunk 157 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 66 optimal weight: 0.0070 overall best weight: 1.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN A 217 HIS ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS D 166 GLN E 171 GLN E 202 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.047070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.035680 restraints weight = 87866.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.036604 restraints weight = 50715.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.037255 restraints weight = 35029.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.037735 restraints weight = 27000.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.037982 restraints weight = 22369.454| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13155 Z= 0.149 Angle : 0.791 10.397 18000 Z= 0.389 Chirality : 0.045 0.251 2130 Planarity : 0.004 0.031 2245 Dihedral : 5.838 26.326 1815 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.87 % Allowed : 11.30 % Favored : 86.83 % 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: -0.08 (0.19), residues: 1670 helix: 1.55 (0.22), residues: 515 sheet: 0.23 (0.25), residues: 380 loop : -1.34 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 75 TYR 0.027 0.002 TYR A 238 PHE 0.030 0.002 PHE D 353 TRP 0.028 0.002 TRP A 255 HIS 0.003 0.001 HIS B 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (13145) covalent geometry : angle 0.78977 / 0.39 (17975) SS BOND : bond 0.00271 / 0.14 ( 5) SS BOND : angle 1.27451 / 0.73 ( 10) hydrogen bonds : bond 0.04233 / 2.82 ( 676) hydrogen bonds : angle 5.29684 / 3.65 ( 2373) link_BETA1-4 : bond 0.00299 / 0.17 ( 5) link_BETA1-4 : angle 1.19193 / 0.87 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8779 (ptpt) REVERT: A 130 ASP cc_start: 0.8764 (t0) cc_final: 0.8399 (t0) REVERT: A 132 LYS cc_start: 0.9312 (mttm) cc_final: 0.9050 (mtmt) REVERT: A 156 MET cc_start: 0.8930 (ptp) cc_final: 0.8596 (mmm) REVERT: A 179 MET cc_start: 0.9039 (mmm) cc_final: 0.8765 (mmm) REVERT: A 222 LYS cc_start: 0.9247 (pttm) cc_final: 0.9028 (pttm) REVERT: A 279 MET cc_start: 0.9404 (mmm) cc_final: 0.9179 (mmm) REVERT: A 303 MET cc_start: 0.9393 (mmm) cc_final: 0.9053 (mmt) REVERT: B 100 ASP cc_start: 0.8862 (m-30) cc_final: 0.7787 (t0) REVERT: B 105 MET cc_start: 0.8770 (tpp) cc_final: 0.8430 (tpp) REVERT: B 126 GLU cc_start: 0.8782 (mp0) cc_final: 0.8408 (tp30) REVERT: B 130 ASP cc_start: 0.8292 (t0) cc_final: 0.7955 (t0) REVERT: B 132 LYS cc_start: 0.9239 (mttm) cc_final: 0.8888 (mtmt) REVERT: B 279 MET cc_start: 0.9345 (mmm) cc_final: 0.9123 (mmm) REVERT: B 292 LYS cc_start: 0.8913 (mmtm) cc_final: 0.8639 (ttmm) REVERT: B 303 MET cc_start: 0.9364 (mmm) cc_final: 0.8539 (mmt) REVERT: C 72 MET cc_start: 0.8805 (tpp) cc_final: 0.8454 (tpp) REVERT: C 120 LYS cc_start: 0.9208 (ptmm) cc_final: 0.8846 (ptmm) REVERT: C 130 ASP cc_start: 0.8878 (t0) cc_final: 0.8470 (t0) REVERT: C 156 MET cc_start: 0.8778 (ptp) cc_final: 0.8441 (ptp) REVERT: C 179 MET cc_start: 0.9087 (mmm) cc_final: 0.8840 (mmm) REVERT: C 202 GLN cc_start: 0.8516 (mm110) cc_final: 0.8293 (mp10) REVERT: C 287 ARG cc_start: 0.8953 (mmt180) cc_final: 0.8683 (mtt-85) REVERT: D 100 ASP cc_start: 0.8807 (m-30) cc_final: 0.7795 (t0) REVERT: D 105 MET cc_start: 0.8689 (tpp) cc_final: 0.8408 (tpp) REVERT: D 126 GLU cc_start: 0.8267 (tp30) cc_final: 0.7982 (tp30) REVERT: D 130 ASP cc_start: 0.8791 (t0) cc_final: 0.8222 (t0) REVERT: D 132 LYS cc_start: 0.9293 (mttm) cc_final: 0.8811 (mtmt) REVERT: D 156 MET cc_start: 0.8743 (ptp) cc_final: 0.8271 (mtm) REVERT: D 170 MET cc_start: 0.8221 (pmm) cc_final: 0.7951 (pmm) REVERT: D 262 MET cc_start: 0.8146 (pmm) cc_final: 0.7864 (mtm) REVERT: D 292 LYS cc_start: 0.9466 (mtmm) cc_final: 0.9157 (mtmm) REVERT: D 314 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8537 (mm) REVERT: E 73 ASP cc_start: 0.8349 (p0) cc_final: 0.7995 (p0) REVERT: E 100 ASP cc_start: 0.8776 (m-30) cc_final: 0.7816 (t0) REVERT: E 105 MET cc_start: 0.8674 (mmp) cc_final: 0.8388 (mmp) REVERT: E 120 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8810 (ptmt) REVERT: E 179 MET cc_start: 0.8854 (mmm) cc_final: 0.8479 (mmm) REVERT: E 222 LYS cc_start: 0.9318 (pttp) cc_final: 0.9051 (pttp) REVERT: E 279 MET cc_start: 0.9273 (mmm) cc_final: 0.8910 (mmm) REVERT: E 292 LYS cc_start: 0.9223 (mmtm) cc_final: 0.9004 (ttmm) REVERT: E 297 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8786 (mmmm) REVERT: E 303 MET cc_start: 0.9371 (mmm) cc_final: 0.8970 (mmt) outliers start: 23 outliers final: 12 residues processed: 187 average time/residue: 0.1146 time to fit residues: 31.0084 Evaluate side-chains 161 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 297 LYS Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 120 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.034593 restraints weight = 87178.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.035384 restraints weight = 50685.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.035943 restraints weight = 36161.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.036345 restraints weight = 28665.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.036648 restraints weight = 24450.442| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13155 Z= 0.173 Angle : 0.726 9.352 18000 Z= 0.356 Chirality : 0.044 0.241 2130 Planarity : 0.004 0.025 2245 Dihedral : 5.580 25.722 1815 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.44 % Allowed : 11.71 % Favored : 85.85 % 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: 0.22 (0.20), residues: 1670 helix: 1.89 (0.23), residues: 525 sheet: 0.27 (0.26), residues: 360 loop : -1.14 (0.20), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 229 TYR 0.021 0.002 TYR D 144 PHE 0.019 0.002 PHE D 353 TRP 0.022 0.001 TRP D 255 HIS 0.004 0.001 HIS D 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (13145) covalent geometry : angle 0.72481 / 0.36 (17975) SS BOND : bond 0.00178 / 0.10 ( 5) SS BOND : angle 1.05847 / 0.58 ( 10) hydrogen bonds : bond 0.03972 / 2.66 ( 676) hydrogen bonds : angle 5.03264 / 3.45 ( 2373) link_BETA1-4 : bond 0.00353 / 0.20 ( 5) link_BETA1-4 : angle 1.22449 / 0.87 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.9167 (ttpt) cc_final: 0.8903 (ptpt) REVERT: A 132 LYS cc_start: 0.9310 (mttm) cc_final: 0.8994 (mtpt) REVERT: A 156 MET cc_start: 0.8891 (ptp) cc_final: 0.8532 (mmm) REVERT: A 279 MET cc_start: 0.9483 (mmm) cc_final: 0.9184 (mmm) REVERT: A 303 MET cc_start: 0.9475 (mmm) cc_final: 0.8597 (mmt) REVERT: B 105 MET cc_start: 0.8792 (tpp) cc_final: 0.8462 (tpp) REVERT: B 126 GLU cc_start: 0.8866 (mp0) cc_final: 0.8333 (tp30) REVERT: B 130 ASP cc_start: 0.8498 (t0) cc_final: 0.8176 (t0) REVERT: B 132 LYS cc_start: 0.9270 (mttm) cc_final: 0.8945 (mtmt) REVERT: B 303 MET cc_start: 0.9329 (mmm) cc_final: 0.8487 (mmt) REVERT: C 72 MET cc_start: 0.8811 (tpp) cc_final: 0.8477 (tpp) REVERT: C 105 MET cc_start: 0.8691 (tpt) cc_final: 0.8476 (tpt) REVERT: C 156 MET cc_start: 0.8795 (ptp) cc_final: 0.8449 (ptp) REVERT: C 287 ARG cc_start: 0.8904 (mmt180) cc_final: 0.8661 (mtt-85) REVERT: D 105 MET cc_start: 0.8792 (tpp) cc_final: 0.8398 (tpp) REVERT: D 126 GLU cc_start: 0.8434 (tp30) cc_final: 0.8113 (tp30) REVERT: D 130 ASP cc_start: 0.8828 (t0) cc_final: 0.7944 (t0) REVERT: D 132 LYS cc_start: 0.9285 (mttm) cc_final: 0.8896 (mtmt) REVERT: D 156 MET cc_start: 0.8582 (ptp) cc_final: 0.8328 (mtm) REVERT: D 302 TRP cc_start: 0.9250 (t-100) cc_final: 0.8805 (t60) REVERT: D 303 MET cc_start: 0.9387 (mmm) cc_final: 0.9185 (mmp) REVERT: D 314 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8533 (mm) REVERT: E 72 MET cc_start: 0.8667 (tpp) cc_final: 0.7706 (tpp) REVERT: E 73 ASP cc_start: 0.8546 (p0) cc_final: 0.8227 (p0) REVERT: E 100 ASP cc_start: 0.8756 (m-30) cc_final: 0.7910 (t0) REVERT: E 120 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8890 (ptmt) REVERT: E 179 MET cc_start: 0.8846 (mmm) cc_final: 0.8610 (mmm) REVERT: E 222 LYS cc_start: 0.9218 (pttp) cc_final: 0.8974 (pttp) outliers start: 30 outliers final: 20 residues processed: 175 average time/residue: 0.1123 time to fit residues: 28.4622 Evaluate side-chains 152 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 136 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 92 optimal weight: 0.0020 chunk 26 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.034296 restraints weight = 89078.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.035101 restraints weight = 52008.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.035695 restraints weight = 36769.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.036106 restraints weight = 28852.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.036423 restraints weight = 24352.966| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13155 Z= 0.202 Angle : 0.740 9.218 18000 Z= 0.362 Chirality : 0.043 0.234 2130 Planarity : 0.004 0.028 2245 Dihedral : 5.515 27.679 1815 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.76 % Allowed : 12.68 % Favored : 84.55 % 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: 0.38 (0.20), residues: 1670 helix: 2.20 (0.22), residues: 530 sheet: -0.00 (0.26), residues: 365 loop : -1.03 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 287 TYR 0.023 0.002 TYR C 144 PHE 0.019 0.001 PHE D 353 TRP 0.030 0.001 TRP E 255 HIS 0.004 0.001 HIS C 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (13145) covalent geometry : angle 0.73937 / 0.36 (17975) SS BOND : bond 0.00066 / 0.03 ( 5) SS BOND : angle 0.65657 / 0.39 ( 10) hydrogen bonds : bond 0.03882 / 2.59 ( 676) hydrogen bonds : angle 4.82681 / 3.33 ( 2373) link_BETA1-4 : bond 0.00332 / 0.19 ( 5) link_BETA1-4 : angle 1.24652 / 0.87 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8986 (p) REVERT: A 120 LYS cc_start: 0.9262 (ttpt) cc_final: 0.8978 (ptpt) REVERT: A 132 LYS cc_start: 0.9281 (mttm) cc_final: 0.9033 (mtpt) REVERT: A 156 MET cc_start: 0.8950 (ptp) cc_final: 0.8540 (mmm) REVERT: A 279 MET cc_start: 0.9490 (mmm) cc_final: 0.9203 (mmm) REVERT: A 303 MET cc_start: 0.9448 (mmm) cc_final: 0.8727 (mmt) REVERT: B 105 MET cc_start: 0.8822 (tpp) cc_final: 0.8500 (tpp) REVERT: B 126 GLU cc_start: 0.8919 (mp0) cc_final: 0.8293 (tp30) REVERT: B 255 TRP cc_start: 0.8754 (m-10) cc_final: 0.7941 (m-10) REVERT: B 303 MET cc_start: 0.9365 (mmm) cc_final: 0.8589 (mmt) REVERT: C 105 MET cc_start: 0.8902 (tpt) cc_final: 0.8477 (tpt) REVERT: C 169 ILE cc_start: 0.9516 (pt) cc_final: 0.9253 (mp) REVERT: C 255 TRP cc_start: 0.8666 (m-10) cc_final: 0.7640 (m-10) REVERT: C 287 ARG cc_start: 0.8969 (mmt180) cc_final: 0.8715 (mtt-85) REVERT: C 314 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8820 (mm) REVERT: D 105 MET cc_start: 0.8812 (tpp) cc_final: 0.8434 (tpp) REVERT: D 130 ASP cc_start: 0.8858 (t0) cc_final: 0.8281 (t0) REVERT: D 132 LYS cc_start: 0.9293 (mttm) cc_final: 0.8916 (mtmm) REVERT: D 156 MET cc_start: 0.8634 (ptp) cc_final: 0.8388 (mmm) REVERT: D 262 MET cc_start: 0.8477 (pmm) cc_final: 0.8124 (mtp) REVERT: D 302 TRP cc_start: 0.9252 (t-100) cc_final: 0.8817 (t60) REVERT: D 314 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8649 (mm) REVERT: E 71 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8922 (p) REVERT: E 73 ASP cc_start: 0.8564 (p0) cc_final: 0.8140 (p0) REVERT: E 105 MET cc_start: 0.8701 (mmp) cc_final: 0.8484 (mmt) REVERT: E 120 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8925 (ptmt) REVERT: E 156 MET cc_start: 0.7964 (mpp) cc_final: 0.7739 (mpp) REVERT: E 179 MET cc_start: 0.8900 (mmm) cc_final: 0.8641 (mmt) REVERT: E 222 LYS cc_start: 0.9239 (pttp) cc_final: 0.8978 (pttp) REVERT: E 279 MET cc_start: 0.9292 (mmm) cc_final: 0.8935 (mmm) REVERT: E 297 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8773 (mmmm) REVERT: E 302 TRP cc_start: 0.9083 (t-100) cc_final: 0.8380 (t60) REVERT: E 303 MET cc_start: 0.9381 (mmm) cc_final: 0.8841 (mmt) outliers start: 34 outliers final: 22 residues processed: 164 average time/residue: 0.1087 time to fit residues: 26.1009 Evaluate side-chains 153 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS Chi-restraints excluded: chain C residue 181 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 136 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 7 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 0.0270 chunk 105 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 164 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.046476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.035188 restraints weight = 86206.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.036093 restraints weight = 51518.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.036703 restraints weight = 36179.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.037161 restraints weight = 28180.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.037474 restraints weight = 23512.332| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13155 Z= 0.126 Angle : 0.705 9.527 18000 Z= 0.341 Chirality : 0.044 0.248 2130 Planarity : 0.003 0.030 2245 Dihedral : 5.176 26.128 1815 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.71 % Allowed : 13.90 % Favored : 84.39 % 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: 0.42 (0.20), residues: 1670 helix: 2.19 (0.22), residues: 535 sheet: 0.12 (0.25), residues: 395 loop : -1.08 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 75 TYR 0.020 0.001 TYR C 144 PHE 0.015 0.001 PHE D 353 TRP 0.039 0.001 TRP E 255 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (13145) covalent geometry : angle 0.70438 / 0.34 (17975) SS BOND : bond 0.00109 / 0.05 ( 5) SS BOND : angle 0.55785 / 0.32 ( 10) hydrogen bonds : bond 0.03566 / 2.38 ( 676) hydrogen bonds : angle 4.50442 / 3.10 ( 2373) link_BETA1-4 : bond 0.00407 / 0.24 ( 5) link_BETA1-4 : angle 1.17482 / 0.89 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LYS cc_start: 0.9306 (mttm) cc_final: 0.9000 (mtmt) REVERT: A 156 MET cc_start: 0.8950 (ptp) cc_final: 0.8730 (mmm) REVERT: A 216 LYS cc_start: 0.9517 (mmtp) cc_final: 0.9225 (mmmt) REVERT: A 279 MET cc_start: 0.9545 (mmm) cc_final: 0.9276 (mmm) REVERT: A 303 MET cc_start: 0.9422 (mmm) cc_final: 0.8728 (mmt) REVERT: B 105 MET cc_start: 0.8790 (tpp) cc_final: 0.8475 (tpp) REVERT: B 120 LYS cc_start: 0.8968 (pttt) cc_final: 0.8752 (pttm) REVERT: B 126 GLU cc_start: 0.8959 (mp0) cc_final: 0.8451 (tp30) REVERT: B 179 MET cc_start: 0.8937 (mmm) cc_final: 0.8616 (mmm) REVERT: B 255 TRP cc_start: 0.8687 (m-10) cc_final: 0.7854 (m-10) REVERT: B 279 MET cc_start: 0.9459 (mmm) cc_final: 0.9253 (mmm) REVERT: B 282 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8840 (mm-40) REVERT: C 105 MET cc_start: 0.8898 (tpt) cc_final: 0.8419 (tpt) REVERT: C 169 ILE cc_start: 0.9510 (pt) cc_final: 0.9278 (mp) REVERT: C 255 TRP cc_start: 0.8606 (m-10) cc_final: 0.7750 (m-10) REVERT: C 287 ARG cc_start: 0.8841 (mmt180) cc_final: 0.8590 (mtt-85) REVERT: C 314 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8808 (mm) REVERT: D 100 ASP cc_start: 0.8683 (m-30) cc_final: 0.7877 (t0) REVERT: D 105 MET cc_start: 0.8766 (tpp) cc_final: 0.8406 (tpp) REVERT: D 130 ASP cc_start: 0.8945 (t0) cc_final: 0.8644 (t0) REVERT: D 132 LYS cc_start: 0.9312 (mttm) cc_final: 0.8887 (mtmt) REVERT: D 262 MET cc_start: 0.8257 (pmm) cc_final: 0.7775 (mtp) REVERT: D 279 MET cc_start: 0.9225 (mmm) cc_final: 0.8984 (mmt) REVERT: D 292 LYS cc_start: 0.9357 (mtmm) cc_final: 0.9048 (mttm) REVERT: D 302 TRP cc_start: 0.9234 (t-100) cc_final: 0.8664 (t60) REVERT: E 71 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8940 (p) REVERT: E 73 ASP cc_start: 0.8432 (p0) cc_final: 0.7907 (p0) REVERT: E 100 ASP cc_start: 0.8793 (m-30) cc_final: 0.7806 (t0) REVERT: E 120 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8940 (ptmt) REVERT: E 179 MET cc_start: 0.9001 (mmm) cc_final: 0.8795 (mmm) REVERT: E 279 MET cc_start: 0.9329 (mmm) cc_final: 0.8910 (mmm) REVERT: E 292 LYS cc_start: 0.9239 (mmtm) cc_final: 0.8968 (mmtm) REVERT: E 297 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8671 (mmmm) REVERT: E 303 MET cc_start: 0.9407 (mmm) cc_final: 0.8809 (mmt) outliers start: 21 outliers final: 9 residues processed: 174 average time/residue: 0.1139 time to fit residues: 28.6214 Evaluate side-chains 147 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 120 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 9.9990 chunk 140 optimal weight: 0.3980 chunk 103 optimal weight: 0.0770 chunk 128 optimal weight: 7.9990 chunk 96 optimal weight: 40.0000 chunk 77 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.046456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.035483 restraints weight = 89330.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.036362 restraints weight = 52379.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.036989 restraints weight = 36509.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.037436 restraints weight = 28262.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.037688 restraints weight = 23474.668| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13155 Z= 0.135 Angle : 0.722 12.411 18000 Z= 0.347 Chirality : 0.043 0.248 2130 Planarity : 0.003 0.031 2245 Dihedral : 5.120 25.150 1815 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.63 % Allowed : 15.04 % Favored : 83.33 % 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: 0.44 (0.20), residues: 1670 helix: 2.30 (0.22), residues: 535 sheet: 0.11 (0.26), residues: 395 loop : -1.13 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 75 TYR 0.023 0.001 TYR C 144 PHE 0.014 0.001 PHE D 353 TRP 0.037 0.001 TRP E 255 HIS 0.002 0.001 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (13145) covalent geometry : angle 0.72198 / 0.35 (17975) SS BOND : bond 0.00152 / 0.07 ( 5) SS BOND : angle 0.46893 / 0.29 ( 10) hydrogen bonds : bond 0.03557 / 2.38 ( 676) hydrogen bonds : angle 4.43301 / 3.05 ( 2373) link_BETA1-4 : bond 0.00492 / 0.26 ( 5) link_BETA1-4 : angle 1.20817 / 0.87 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8256 (m-30) REVERT: A 179 MET cc_start: 0.8821 (mmm) cc_final: 0.8598 (mmm) REVERT: A 216 LYS cc_start: 0.9525 (mmtp) cc_final: 0.9210 (mmmt) REVERT: A 279 MET cc_start: 0.9548 (mmm) cc_final: 0.9340 (mmm) REVERT: B 100 ASP cc_start: 0.8640 (m-30) cc_final: 0.7690 (t0) REVERT: B 105 MET cc_start: 0.8763 (tpp) cc_final: 0.8456 (tpp) REVERT: B 169 ILE cc_start: 0.9489 (pt) cc_final: 0.9151 (mp) REVERT: B 216 LYS cc_start: 0.9501 (mmmt) cc_final: 0.9221 (mmtt) REVERT: B 255 TRP cc_start: 0.8760 (m-10) cc_final: 0.7854 (m-10) REVERT: B 282 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8823 (mm-40) REVERT: C 105 MET cc_start: 0.8756 (tpt) cc_final: 0.8391 (tpt) REVERT: C 169 ILE cc_start: 0.9512 (pt) cc_final: 0.9280 (mp) REVERT: C 255 TRP cc_start: 0.8584 (m-10) cc_final: 0.7743 (m-10) REVERT: C 287 ARG cc_start: 0.8873 (mmt180) cc_final: 0.8622 (mtt-85) REVERT: C 314 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8816 (mm) REVERT: D 105 MET cc_start: 0.8743 (tpp) cc_final: 0.8377 (tpp) REVERT: D 130 ASP cc_start: 0.8883 (t0) cc_final: 0.8345 (t0) REVERT: D 132 LYS cc_start: 0.9297 (mttm) cc_final: 0.8901 (mtmm) REVERT: D 262 MET cc_start: 0.8098 (pmm) cc_final: 0.7750 (mtp) REVERT: D 292 LYS cc_start: 0.9363 (mtmm) cc_final: 0.9045 (mttm) REVERT: D 303 MET cc_start: 0.9366 (mmm) cc_final: 0.8651 (mmt) REVERT: E 71 THR cc_start: 0.9186 (OUTLIER) cc_final: 0.8928 (p) REVERT: E 73 ASP cc_start: 0.8475 (p0) cc_final: 0.7919 (p0) REVERT: E 100 ASP cc_start: 0.8782 (m-30) cc_final: 0.7832 (t0) REVERT: E 120 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8948 (ptmt) REVERT: E 279 MET cc_start: 0.9394 (mmm) cc_final: 0.9045 (mmm) REVERT: E 303 MET cc_start: 0.9405 (mmm) cc_final: 0.8587 (mmt) outliers start: 20 outliers final: 12 residues processed: 163 average time/residue: 0.1163 time to fit residues: 27.5988 Evaluate side-chains 145 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 136 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 164 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 4 optimal weight: 0.0570 overall best weight: 2.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.035327 restraints weight = 89429.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.036192 restraints weight = 51809.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.036832 restraints weight = 35952.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.037275 restraints weight = 27856.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.037563 restraints weight = 23121.608| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13155 Z= 0.152 Angle : 0.756 15.304 18000 Z= 0.360 Chirality : 0.043 0.243 2130 Planarity : 0.004 0.034 2245 Dihedral : 5.138 26.476 1815 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.71 % Allowed : 16.02 % Favored : 82.28 % 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: 0.44 (0.20), residues: 1670 helix: 2.38 (0.22), residues: 535 sheet: 0.03 (0.26), residues: 395 loop : -1.16 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 75 TYR 0.040 0.002 TYR A 238 PHE 0.018 0.001 PHE D 353 TRP 0.038 0.001 TRP E 255 HIS 0.006 0.001 HIS E 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (13145) covalent geometry : angle 0.75598 / 0.36 (17975) SS BOND : bond 0.00084 / 0.04 ( 5) SS BOND : angle 0.46039 / 0.29 ( 10) hydrogen bonds : bond 0.03566 / 2.38 ( 676) hydrogen bonds : angle 4.41854 / 3.04 ( 2373) link_BETA1-4 : bond 0.00353 / 0.19 ( 5) link_BETA1-4 : angle 1.13821 / 0.81 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 GLU cc_start: 0.8638 (mp0) cc_final: 0.8270 (mp0) REVERT: A 179 MET cc_start: 0.8790 (mmm) cc_final: 0.8585 (mmm) REVERT: A 216 LYS cc_start: 0.9514 (mmtp) cc_final: 0.9245 (mmmt) REVERT: A 279 MET cc_start: 0.9544 (mmm) cc_final: 0.9159 (mmm) REVERT: A 303 MET cc_start: 0.9424 (mmm) cc_final: 0.8676 (mmt) REVERT: B 105 MET cc_start: 0.8707 (tpp) cc_final: 0.8418 (tpp) REVERT: B 169 ILE cc_start: 0.9482 (pt) cc_final: 0.9132 (mp) REVERT: B 216 LYS cc_start: 0.9484 (mmmt) cc_final: 0.9213 (mmtm) REVERT: B 255 TRP cc_start: 0.8653 (m-10) cc_final: 0.7782 (m-10) REVERT: B 282 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8850 (mm-40) REVERT: C 105 MET cc_start: 0.8711 (tpt) cc_final: 0.8352 (tpt) REVERT: C 169 ILE cc_start: 0.9510 (pt) cc_final: 0.9288 (mp) REVERT: C 255 TRP cc_start: 0.8491 (m-10) cc_final: 0.7568 (m-10) REVERT: C 287 ARG cc_start: 0.8869 (mmt180) cc_final: 0.8625 (mtt-85) REVERT: C 314 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8831 (mm) REVERT: D 105 MET cc_start: 0.8707 (tpp) cc_final: 0.8345 (tpp) REVERT: D 130 ASP cc_start: 0.8857 (t0) cc_final: 0.8310 (t0) REVERT: D 132 LYS cc_start: 0.9270 (mttm) cc_final: 0.8911 (mtmm) REVERT: D 179 MET cc_start: 0.8775 (mmm) cc_final: 0.8555 (mmm) REVERT: D 262 MET cc_start: 0.8083 (pmm) cc_final: 0.7738 (mtp) REVERT: D 292 LYS cc_start: 0.9367 (mtmm) cc_final: 0.9140 (mmmm) REVERT: E 71 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8938 (p) REVERT: E 73 ASP cc_start: 0.8482 (p0) cc_final: 0.7941 (p0) REVERT: E 100 ASP cc_start: 0.8769 (m-30) cc_final: 0.7855 (t0) REVERT: E 120 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8914 (ptmt) REVERT: E 279 MET cc_start: 0.9410 (mmm) cc_final: 0.9058 (mmm) REVERT: E 297 LYS cc_start: 0.9142 (mtpp) cc_final: 0.8823 (mmmm) REVERT: E 303 MET cc_start: 0.9407 (mmm) cc_final: 0.8689 (mmt) outliers start: 21 outliers final: 15 residues processed: 156 average time/residue: 0.1108 time to fit residues: 24.9860 Evaluate side-chains 149 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 255 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.034252 restraints weight = 92833.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.035116 restraints weight = 54117.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.035707 restraints weight = 37712.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.036167 restraints weight = 29379.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.036474 restraints weight = 24487.670| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13155 Z= 0.220 Angle : 0.807 13.513 18000 Z= 0.384 Chirality : 0.044 0.227 2130 Planarity : 0.004 0.048 2245 Dihedral : 5.324 27.288 1815 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.95 % Allowed : 16.02 % Favored : 82.03 % 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: 0.33 (0.21), residues: 1670 helix: 2.38 (0.22), residues: 565 sheet: -0.20 (0.26), residues: 395 loop : -1.37 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 75 TYR 0.027 0.002 TYR A 238 PHE 0.019 0.002 PHE E 115 TRP 0.037 0.001 TRP E 255 HIS 0.004 0.002 HIS C 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (13145) covalent geometry : angle 0.80629 / 0.38 (17975) SS BOND : bond 0.00088 / 0.05 ( 5) SS BOND : angle 0.45966 / 0.30 ( 10) hydrogen bonds : bond 0.03813 / 2.55 ( 676) hydrogen bonds : angle 4.51124 / 3.11 ( 2373) link_BETA1-4 : bond 0.00228 / 0.13 ( 5) link_BETA1-4 : angle 1.19518 / 0.81 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 LYS cc_start: 0.9001 (mtmm) cc_final: 0.8332 (mmtm) REVERT: A 279 MET cc_start: 0.9569 (mmm) cc_final: 0.9199 (mmm) REVERT: A 303 MET cc_start: 0.9423 (mmm) cc_final: 0.8651 (mmt) REVERT: B 105 MET cc_start: 0.8713 (tpp) cc_final: 0.8440 (tpp) REVERT: B 126 GLU cc_start: 0.8200 (tp30) cc_final: 0.7888 (tp30) REVERT: B 130 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8335 (t0) REVERT: B 132 LYS cc_start: 0.9329 (mttm) cc_final: 0.9072 (mtpt) REVERT: B 169 ILE cc_start: 0.9479 (pt) cc_final: 0.9131 (mp) REVERT: B 303 MET cc_start: 0.9365 (mmm) cc_final: 0.8433 (mmt) REVERT: C 105 MET cc_start: 0.8653 (tpt) cc_final: 0.8282 (tpt) REVERT: C 169 ILE cc_start: 0.9482 (pt) cc_final: 0.9267 (mp) REVERT: C 287 ARG cc_start: 0.8975 (mmt180) cc_final: 0.8711 (mtp-110) REVERT: D 105 MET cc_start: 0.8760 (tpp) cc_final: 0.8347 (tpp) REVERT: D 132 LYS cc_start: 0.9239 (mttm) cc_final: 0.9030 (mtpt) REVERT: D 292 LYS cc_start: 0.9375 (mtmm) cc_final: 0.9146 (mmmm) REVERT: E 100 ASP cc_start: 0.8731 (m-30) cc_final: 0.8053 (t0) REVERT: E 120 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8864 (ptmt) REVERT: E 172 LEU cc_start: 0.9515 (mp) cc_final: 0.9250 (mp) REVERT: E 297 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8815 (mmmm) outliers start: 24 outliers final: 15 residues processed: 149 average time/residue: 0.0997 time to fit residues: 21.9112 Evaluate side-chains 139 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 255 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 28 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 92 optimal weight: 0.2980 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.034000 restraints weight = 92684.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.034846 restraints weight = 54191.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.035428 restraints weight = 37972.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.035866 restraints weight = 29629.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.036112 restraints weight = 24800.516| |-----------------------------------------------------------------------------| r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13155 Z= 0.235 Angle : 0.849 18.171 18000 Z= 0.400 Chirality : 0.044 0.239 2130 Planarity : 0.004 0.058 2245 Dihedral : 5.415 27.881 1815 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.71 % Allowed : 16.50 % Favored : 81.79 % 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: 0.26 (0.21), residues: 1670 helix: 2.33 (0.23), residues: 565 sheet: -0.29 (0.26), residues: 395 loop : -1.38 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 75 TYR 0.029 0.002 TYR A 238 PHE 0.019 0.002 PHE D 353 TRP 0.036 0.002 TRP E 255 HIS 0.005 0.001 HIS E 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (13145) covalent geometry : angle 0.84834 / 0.40 (17975) SS BOND : bond 0.00100 / 0.06 ( 5) SS BOND : angle 0.53805 / 0.36 ( 10) hydrogen bonds : bond 0.03877 / 2.60 ( 676) hydrogen bonds : angle 4.59556 / 3.18 ( 2373) link_BETA1-4 : bond 0.00244 / 0.15 ( 5) link_BETA1-4 : angle 1.15508 / 0.82 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.9246 (ptmm) cc_final: 0.8924 (ptmm) REVERT: A 132 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8296 (mmtm) REVERT: A 279 MET cc_start: 0.9569 (mmm) cc_final: 0.9191 (mmm) REVERT: A 303 MET cc_start: 0.9422 (mmm) cc_final: 0.8653 (mmt) REVERT: B 105 MET cc_start: 0.8744 (tpp) cc_final: 0.8464 (tpp) REVERT: B 126 GLU cc_start: 0.8150 (tp30) cc_final: 0.7930 (tp30) REVERT: B 202 GLN cc_start: 0.8669 (pm20) cc_final: 0.8454 (pm20) REVERT: B 303 MET cc_start: 0.9371 (mmm) cc_final: 0.8443 (mmt) REVERT: C 105 MET cc_start: 0.8588 (tpt) cc_final: 0.8206 (tpt) REVERT: C 169 ILE cc_start: 0.9467 (pt) cc_final: 0.9202 (mp) REVERT: D 105 MET cc_start: 0.8807 (tpp) cc_final: 0.8435 (tpp) REVERT: D 179 MET cc_start: 0.8707 (mmm) cc_final: 0.8491 (mmm) REVERT: D 292 LYS cc_start: 0.9368 (mtmm) cc_final: 0.9137 (mmmm) REVERT: D 303 MET cc_start: 0.9258 (mmm) cc_final: 0.8991 (tpt) REVERT: E 172 LEU cc_start: 0.9525 (mp) cc_final: 0.9266 (mp) REVERT: E 292 LYS cc_start: 0.8687 (tppt) cc_final: 0.8310 (mmmm) REVERT: E 297 LYS cc_start: 0.9234 (mtpp) cc_final: 0.8866 (mmmm) outliers start: 21 outliers final: 16 residues processed: 145 average time/residue: 0.1164 time to fit residues: 24.8465 Evaluate side-chains 135 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 113 ASP Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 255 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 0.7980 chunk 40 optimal weight: 0.0070 chunk 124 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 149 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 83 GLN ** 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 = 0.2990 r_free = 0.2990 target = 0.046254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.035275 restraints weight = 90816.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.036215 restraints weight = 52394.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.036844 restraints weight = 36187.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.037298 restraints weight = 28016.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.037599 restraints weight = 23225.948| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13155 Z= 0.138 Angle : 0.861 16.965 18000 Z= 0.395 Chirality : 0.045 0.257 2130 Planarity : 0.004 0.060 2245 Dihedral : 5.139 30.015 1815 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.30 % Allowed : 17.15 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.22 (0.21), residues: 1670 helix: 2.12 (0.22), residues: 565 sheet: -0.16 (0.26), residues: 395 loop : -1.34 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 75 TYR 0.023 0.002 TYR B 238 PHE 0.017 0.001 PHE D 353 TRP 0.037 0.001 TRP E 255 HIS 0.002 0.001 HIS E 231 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (13145) covalent geometry : angle 0.86058 / 0.39 (17975) SS BOND : bond 0.00164 / 0.08 ( 5) SS BOND : angle 0.46516 / 0.29 ( 10) hydrogen bonds : bond 0.03587 / 2.38 ( 676) hydrogen bonds : angle 4.40664 / 3.05 ( 2373) link_BETA1-4 : bond 0.00486 / 0.25 ( 5) link_BETA1-4 : angle 1.26746 / 0.94 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.83 seconds wall clock time: 30 minutes 46.62 seconds (1846.62 seconds total)