Starting phenix.real_space_refine on Thu Sep 18 01:18:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jae_6345/09_2025/3jae_6345.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jae_6345/09_2025/3jae_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 { model { file = "/net/cci-nas-00/data/ceres_data/3jae_6345/09_2025/3jae_6345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jae_6345/09_2025/3jae_6345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/3jae_6345/09_2025/3jae_6345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jae_6345/09_2025/3jae_6345.map" } 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-2.0-5805/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.54, per 1000 atoms: 0.20 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: 1.19 Conformation dependent library (CDL) restraints added in 634.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.49 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: 2.28 Time building geometry restraints manager: 1.59 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: 7540 16.88 - 33.76: 250 33.76 - 50.63: 20 50.63 - 67.51: 15 67.51 - 84.39: 5 Dihedral angle restraints: 7830 sinusoidal: 2840 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 7827 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: 0.04 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: 0.970 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: 0.040 Process input model: 12.970 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 9.721 84.390 4575 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 aren 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 covalent geometry : bond 0.00635 (13145) covalent geometry : angle 1.25536 (17975) SS BOND : bond 0.00841 ( 5) SS BOND : angle 0.54106 ( 10) hydrogen bonds : bond 0.11711 ( 676) hydrogen bonds : angle 9.03951 ( 2373) link_BETA1-4 : bond 0.00931 ( 5) link_BETA1-4 : angle 0.89503 ( 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: 0.8386 (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: 0.1321 time to fit residues: 61.7806 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 : 0.513 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2968 r_free = 0.2968 target = 0.047036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.034615 restraints weight = 88564.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.035553 restraints weight = 53741.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.036171 restraints weight = 38378.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.036568 restraints weight = 30374.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.036782 restraints weight = 25961.701| |-----------------------------------------------------------------------------| r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13155 Z= 0.240 Angle : 0.884 10.071 18000 Z= 0.443 Chirality : 0.048 0.241 2130 Planarity : 0.005 0.040 2245 Dihedral : 7.989 59.199 2025 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.93 % Allowed : 9.43 % Favored : 87.64 % 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 aren not related in a simple way. whole: -0.38 (0.18), residues: 1670 helix: 0.69 (0.21), residues: 515 sheet: 0.43 (0.26), residues: 355 loop : -1.19 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 43 TYR 0.025 0.002 TYR D 239 PHE 0.028 0.003 PHE B 115 TRP 0.021 0.002 TRP B 255 HIS 0.005 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00512 (13145) covalent geometry : angle 0.88289 (17975) SS BOND : bond 0.01890 ( 5) SS BOND : angle 0.78461 ( 10) hydrogen bonds : bond 0.04733 ( 676) hydrogen bonds : angle 5.87867 ( 2373) link_BETA1-4 : bond 0.00214 ( 5) link_BETA1-4 : angle 1.68925 ( 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 213 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.517 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 100 ASP cc_start: 0.8962 (m-30) cc_final: 0.8699 (m-30) REVERT: A 120 LYS cc_start: 0.9059 (ttpt) cc_final: 0.7858 (ptmm) REVERT: A 132 LYS cc_start: 0.9163 (mttm) cc_final: 0.8883 (mtmt) REVERT: A 146 ILE cc_start: 0.9358 (pt) cc_final: 0.9056 (mm) REVERT: A 156 MET cc_start: 0.8861 (ptp) cc_final: 0.8573 (mmm) REVERT: A 222 LYS cc_start: 0.9347 (pttm) cc_final: 0.8986 (pttp) REVERT: A 353 PHE cc_start: 0.9274 (t80) cc_final: 0.9027 (t80) REVERT: B 73 ASP cc_start: 0.8244 (p0) cc_final: 0.7780 (p0) REVERT: B 105 MET cc_start: 0.8730 (tpp) cc_final: 0.8255 (tpp) REVERT: B 126 GLU cc_start: 0.8648 (mp0) cc_final: 0.8375 (tp30) REVERT: B 132 LYS cc_start: 0.9252 (mttm) cc_final: 0.8805 (mtmt) REVERT: B 156 MET cc_start: 0.8846 (ptp) cc_final: 0.8390 (mmm) REVERT: B 239 TYR cc_start: 0.9345 (m-80) cc_final: 0.8903 (m-80) REVERT: B 303 MET cc_start: 0.9431 (mmm) cc_final: 0.9120 (mmm) REVERT: C 105 MET cc_start: 0.8904 (mmp) cc_final: 0.8701 (mmp) REVERT: C 130 ASP cc_start: 0.8579 (t0) cc_final: 0.8334 (t0) REVERT: C 156 MET cc_start: 0.8723 (ptp) cc_final: 0.8426 (mmm) REVERT: D 100 ASP cc_start: 0.8850 (m-30) cc_final: 0.7910 (t0) REVERT: D 105 MET cc_start: 0.8703 (tpp) cc_final: 0.8398 (tpp) REVERT: D 130 ASP cc_start: 0.8508 (t0) cc_final: 0.8292 (t0) REVERT: D 132 LYS cc_start: 0.9244 (mttm) cc_final: 0.8845 (mtmt) REVERT: D 156 MET cc_start: 0.8731 (ptp) cc_final: 0.8377 (mmm) REVERT: D 292 LYS cc_start: 0.9464 (mtmm) cc_final: 0.9194 (ttmm) REVERT: D 348 LEU cc_start: 0.9311 (mt) cc_final: 0.9101 (pp) REVERT: E 100 ASP cc_start: 0.8783 (m-30) cc_final: 0.7762 (t0) REVERT: E 106 LEU cc_start: 0.9423 (tt) cc_final: 0.9135 (mp) REVERT: E 120 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8909 (ptmt) REVERT: E 279 MET cc_start: 0.9259 (mmm) cc_final: 0.9046 (mmm) REVERT: E 292 LYS cc_start: 0.9475 (mttt) cc_final: 0.9260 (mmtm) outliers start: 36 outliers final: 19 residues processed: 205 average time/residue: 0.1284 time to fit residues: 37.4858 Evaluate side-chains 163 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 256 VAL 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 297 LYS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 168 CYS 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 Chi-restraints excluded: chain E residue 297 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 103 optimal weight: 0.4980 chunk 157 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 217 HIS B 166 GLN ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 HIS C 217 HIS D 166 GLN D 171 GLN D 217 HIS E 171 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.035477 restraints weight = 85565.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.036349 restraints weight = 50295.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.036978 restraints weight = 35437.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.037440 restraints weight = 27454.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.037681 restraints weight = 22898.184| |-----------------------------------------------------------------------------| r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13155 Z= 0.148 Angle : 0.786 10.101 18000 Z= 0.388 Chirality : 0.045 0.262 2130 Planarity : 0.004 0.028 2245 Dihedral : 7.158 59.859 2025 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.28 % Allowed : 10.73 % Favored : 86.99 % 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 aren not related in a simple way. whole: -0.05 (0.19), residues: 1670 helix: 1.60 (0.22), residues: 515 sheet: 0.22 (0.25), residues: 380 loop : -1.32 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 75 TYR 0.023 0.002 TYR D 144 PHE 0.032 0.002 PHE D 353 TRP 0.027 0.002 TRP A 255 HIS 0.003 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00306 (13145) covalent geometry : angle 0.78516 (17975) SS BOND : bond 0.00182 ( 5) SS BOND : angle 1.21198 ( 10) hydrogen bonds : bond 0.04187 ( 676) hydrogen bonds : angle 5.25507 ( 2373) link_BETA1-4 : bond 0.00327 ( 5) link_BETA1-4 : angle 1.30388 ( 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 191 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.540 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 105 MET cc_start: 0.8733 (mmm) cc_final: 0.8402 (mmm) REVERT: A 130 ASP cc_start: 0.8767 (t0) cc_final: 0.8434 (t0) REVERT: A 132 LYS cc_start: 0.9331 (mttm) cc_final: 0.9008 (mtmt) REVERT: A 156 MET cc_start: 0.8896 (ptp) cc_final: 0.8578 (mmm) REVERT: A 179 MET cc_start: 0.9035 (mmm) cc_final: 0.8767 (mmm) REVERT: A 222 LYS cc_start: 0.9223 (pttm) cc_final: 0.9008 (pttm) REVERT: A 279 MET cc_start: 0.9417 (mmm) cc_final: 0.9170 (mmm) REVERT: A 303 MET cc_start: 0.9398 (mmm) cc_final: 0.9063 (mmt) REVERT: B 73 ASP cc_start: 0.8288 (p0) cc_final: 0.7914 (p0) REVERT: B 100 ASP cc_start: 0.8867 (m-30) cc_final: 0.7785 (t0) REVERT: B 105 MET cc_start: 0.8736 (tpp) cc_final: 0.8410 (tpp) REVERT: B 126 GLU cc_start: 0.8825 (mp0) cc_final: 0.8406 (tp30) REVERT: B 132 LYS cc_start: 0.9269 (mttm) cc_final: 0.8895 (mtmt) REVERT: B 156 MET cc_start: 0.8891 (ptp) cc_final: 0.8562 (mtt) REVERT: B 166 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7655 (mm-40) REVERT: B 292 LYS cc_start: 0.9001 (mmtm) cc_final: 0.8746 (ttmm) REVERT: B 303 MET cc_start: 0.9355 (mmm) cc_final: 0.8598 (mmt) REVERT: C 120 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8897 (ptmm) REVERT: C 130 ASP cc_start: 0.8940 (t0) cc_final: 0.8542 (t0) REVERT: C 156 MET cc_start: 0.8699 (ptp) cc_final: 0.8352 (mmm) REVERT: C 179 MET cc_start: 0.9077 (mmm) cc_final: 0.8866 (mmm) REVERT: C 202 GLN cc_start: 0.8520 (mm110) cc_final: 0.8314 (mp10) REVERT: C 287 ARG cc_start: 0.8958 (mmt180) cc_final: 0.8687 (mtt-85) REVERT: D 72 MET cc_start: 0.8907 (tpp) cc_final: 0.8700 (tpp) REVERT: D 73 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7530 (m-30) REVERT: D 100 ASP cc_start: 0.8789 (m-30) cc_final: 0.7781 (t0) REVERT: D 105 MET cc_start: 0.8679 (tpp) cc_final: 0.8361 (tpp) REVERT: D 126 GLU cc_start: 0.8380 (tp30) cc_final: 0.8112 (tp30) REVERT: D 130 ASP cc_start: 0.8820 (t0) cc_final: 0.8269 (t0) REVERT: D 132 LYS cc_start: 0.9303 (mttm) cc_final: 0.8879 (mtmt) REVERT: D 156 MET cc_start: 0.8752 (ptp) cc_final: 0.8295 (mtm) REVERT: D 170 MET cc_start: 0.8287 (pmm) cc_final: 0.7938 (pmm) REVERT: D 179 MET cc_start: 0.8803 (mmm) cc_final: 0.8469 (mmm) REVERT: D 262 MET cc_start: 0.8233 (pmm) cc_final: 0.7983 (mtm) REVERT: D 292 LYS cc_start: 0.9454 (mtmm) cc_final: 0.9167 (mtmm) REVERT: D 314 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8540 (mm) REVERT: E 73 ASP cc_start: 0.8338 (p0) cc_final: 0.7972 (p0) REVERT: E 100 ASP cc_start: 0.8770 (m-30) cc_final: 0.7814 (t0) REVERT: E 105 MET cc_start: 0.8649 (mmp) cc_final: 0.8371 (mmp) REVERT: E 120 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8847 (ptmt) REVERT: E 179 MET cc_start: 0.8875 (mmm) cc_final: 0.8545 (mmm) REVERT: E 222 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9036 (pttp) REVERT: E 279 MET cc_start: 0.9283 (mmm) cc_final: 0.9048 (mmm) REVERT: E 292 LYS cc_start: 0.9464 (mttt) cc_final: 0.9237 (mmtm) REVERT: E 303 MET cc_start: 0.9373 (mmm) cc_final: 0.8992 (mmt) outliers start: 28 outliers final: 11 residues processed: 184 average time/residue: 0.1244 time to fit residues: 32.9135 Evaluate side-chains 155 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP 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 130 ASP Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain C residue 120 LYS 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 73 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 Chi-restraints excluded: chain E residue 222 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 24 optimal weight: 0.0470 chunk 13 optimal weight: 0.0060 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 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 = 0.2977 r_free = 0.2977 target = 0.046589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.035208 restraints weight = 87748.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.036100 restraints weight = 51549.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.036675 restraints weight = 35864.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.037116 restraints weight = 28225.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.037422 restraints weight = 23712.191| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4164 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= 0.143 Angle : 0.733 10.081 18000 Z= 0.360 Chirality : 0.044 0.256 2130 Planarity : 0.004 0.028 2245 Dihedral : 6.777 59.944 2025 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.52 % Allowed : 11.63 % 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 aren not related in a simple way. whole: -0.10 (0.19), residues: 1670 helix: 1.58 (0.22), residues: 555 sheet: 0.12 (0.25), residues: 380 loop : -1.49 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 229 TYR 0.022 0.002 TYR C 144 PHE 0.018 0.001 PHE E 353 TRP 0.028 0.001 TRP D 255 HIS 0.003 0.001 HIS E 231 Details of bonding type rmsd covalent geometry : bond 0.00302 (13145) covalent geometry : angle 0.73217 (17975) SS BOND : bond 0.00232 ( 5) SS BOND : angle 0.95685 ( 10) hydrogen bonds : bond 0.03854 ( 676) hydrogen bonds : angle 4.92317 ( 2373) link_BETA1-4 : bond 0.00381 ( 5) link_BETA1-4 : angle 1.25382 ( 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 186 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8674 (mmm) cc_final: 0.8312 (mmm) REVERT: A 130 ASP cc_start: 0.8612 (t0) cc_final: 0.7944 (t0) REVERT: A 132 LYS cc_start: 0.9332 (mttm) cc_final: 0.8970 (mtpt) REVERT: A 156 MET cc_start: 0.8791 (ptp) cc_final: 0.8541 (mmm) REVERT: B 73 ASP cc_start: 0.8355 (p0) cc_final: 0.7968 (p0) REVERT: B 100 ASP cc_start: 0.8844 (m-30) cc_final: 0.7768 (t0) REVERT: B 105 MET cc_start: 0.8812 (tpp) cc_final: 0.8467 (tpp) REVERT: B 126 GLU cc_start: 0.8893 (mp0) cc_final: 0.8359 (tp30) REVERT: B 132 LYS cc_start: 0.9272 (mttm) cc_final: 0.8891 (mtmt) REVERT: B 166 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7283 (mm-40) REVERT: B 179 MET cc_start: 0.8943 (mmm) cc_final: 0.8680 (mmm) REVERT: B 216 LYS cc_start: 0.9496 (mmtp) cc_final: 0.9211 (mmtp) REVERT: C 72 MET cc_start: 0.8806 (tpp) cc_final: 0.8404 (tpp) REVERT: C 109 ILE cc_start: 0.9601 (mp) cc_final: 0.9272 (mm) REVERT: C 132 LYS cc_start: 0.9266 (mttm) cc_final: 0.8887 (mtmt) REVERT: C 156 MET cc_start: 0.8726 (ptp) cc_final: 0.8461 (ptp) REVERT: C 255 TRP cc_start: 0.8275 (m-10) cc_final: 0.7271 (m-90) REVERT: C 287 ARG cc_start: 0.8868 (mmt180) cc_final: 0.8606 (mtt-85) REVERT: C 314 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8765 (mm) REVERT: D 100 ASP cc_start: 0.8753 (m-30) cc_final: 0.7806 (t0) REVERT: D 105 MET cc_start: 0.8793 (tpp) cc_final: 0.8388 (tpp) REVERT: D 126 GLU cc_start: 0.8455 (tp30) cc_final: 0.8116 (tp30) REVERT: D 130 ASP cc_start: 0.8838 (t0) cc_final: 0.7963 (t0) REVERT: D 132 LYS cc_start: 0.9290 (mttm) cc_final: 0.8877 (mtmt) REVERT: D 156 MET cc_start: 0.8598 (ptp) cc_final: 0.8226 (mtm) REVERT: D 169 ILE cc_start: 0.9508 (pt) cc_final: 0.9123 (mp) REVERT: D 279 MET cc_start: 0.9239 (mmm) cc_final: 0.9031 (mmp) REVERT: D 302 TRP cc_start: 0.9232 (t-100) cc_final: 0.8816 (t60) REVERT: D 314 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8606 (mm) REVERT: E 71 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8892 (p) REVERT: E 73 ASP cc_start: 0.8459 (p0) cc_final: 0.8085 (p0) REVERT: E 100 ASP cc_start: 0.8736 (m-30) cc_final: 0.7821 (t0) REVERT: E 106 LEU cc_start: 0.9455 (tt) cc_final: 0.9131 (mp) REVERT: E 120 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8944 (ptmt) REVERT: E 287 ARG cc_start: 0.9094 (mmt180) cc_final: 0.8768 (mtp-110) REVERT: E 292 LYS cc_start: 0.9441 (mttt) cc_final: 0.9098 (mmtm) REVERT: E 302 TRP cc_start: 0.9084 (t-100) cc_final: 0.8521 (t60) outliers start: 31 outliers final: 18 residues processed: 182 average time/residue: 0.1283 time to fit residues: 33.4278 Evaluate side-chains 155 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP 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 C residue 136 ILE 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 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 Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 255 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 70 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 66 optimal weight: 0.4980 chunk 42 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.034922 restraints weight = 86897.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.035827 restraints weight = 51072.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.036439 restraints weight = 35753.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.036896 restraints weight = 27707.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.037221 restraints weight = 23014.123| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13155 Z= 0.153 Angle : 0.734 11.068 18000 Z= 0.355 Chirality : 0.043 0.248 2130 Planarity : 0.003 0.029 2245 Dihedral : 6.629 59.952 2025 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.44 % Allowed : 12.93 % Favored : 84.63 % 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 aren not related in a simple way. whole: 0.03 (0.20), residues: 1670 helix: 1.75 (0.22), residues: 565 sheet: -0.05 (0.25), residues: 385 loop : -1.37 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 75 TYR 0.021 0.002 TYR C 144 PHE 0.018 0.001 PHE D 353 TRP 0.027 0.001 TRP D 255 HIS 0.004 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00327 (13145) covalent geometry : angle 0.73307 (17975) SS BOND : bond 0.00080 ( 5) SS BOND : angle 0.62734 ( 10) hydrogen bonds : bond 0.03752 ( 676) hydrogen bonds : angle 4.64941 ( 2373) link_BETA1-4 : bond 0.00462 ( 5) link_BETA1-4 : angle 1.27518 ( 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 173 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8786 (mmm) cc_final: 0.8484 (mmm) REVERT: A 130 ASP cc_start: 0.8591 (t0) cc_final: 0.7598 (t0) REVERT: A 132 LYS cc_start: 0.9303 (mttm) cc_final: 0.9093 (mttp) REVERT: A 156 MET cc_start: 0.8893 (ptp) cc_final: 0.8521 (mmm) REVERT: A 216 LYS cc_start: 0.9549 (mmtp) cc_final: 0.9195 (mmmt) REVERT: A 279 MET cc_start: 0.9407 (mmm) cc_final: 0.9130 (mmp) REVERT: A 303 MET cc_start: 0.9453 (mmm) cc_final: 0.8717 (mmt) REVERT: B 73 ASP cc_start: 0.8362 (p0) cc_final: 0.8079 (p0) REVERT: B 105 MET cc_start: 0.8791 (tpp) cc_final: 0.8457 (tpp) REVERT: B 126 GLU cc_start: 0.8911 (mp0) cc_final: 0.8417 (tp30) REVERT: B 216 LYS cc_start: 0.9479 (mmtp) cc_final: 0.9219 (mmtp) REVERT: B 255 TRP cc_start: 0.8679 (m-10) cc_final: 0.7473 (m-10) REVERT: C 132 LYS cc_start: 0.9202 (mttm) cc_final: 0.8979 (mtmt) REVERT: C 156 MET cc_start: 0.8888 (ptp) cc_final: 0.8546 (mmm) REVERT: C 169 ILE cc_start: 0.9494 (pt) cc_final: 0.9220 (mp) REVERT: C 255 TRP cc_start: 0.8323 (m-10) cc_final: 0.6800 (m-10) REVERT: C 287 ARG cc_start: 0.8857 (mmt180) cc_final: 0.8601 (mtt-85) REVERT: C 314 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8809 (mm) REVERT: D 105 MET cc_start: 0.8784 (tpp) cc_final: 0.8383 (tpp) REVERT: D 130 ASP cc_start: 0.8838 (t0) cc_final: 0.8525 (t0) REVERT: D 132 LYS cc_start: 0.9308 (mttm) cc_final: 0.8851 (mtmt) REVERT: D 156 MET cc_start: 0.8564 (ptp) cc_final: 0.8316 (mtm) REVERT: D 169 ILE cc_start: 0.9493 (pt) cc_final: 0.9153 (mp) REVERT: D 262 MET cc_start: 0.8600 (pmm) cc_final: 0.8198 (mtp) REVERT: D 292 LYS cc_start: 0.9467 (mtmm) cc_final: 0.9158 (mttm) REVERT: D 302 TRP cc_start: 0.9215 (t-100) cc_final: 0.8873 (t60) REVERT: D 314 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8659 (mm) REVERT: E 73 ASP cc_start: 0.8539 (p0) cc_final: 0.8232 (p0) REVERT: E 100 ASP cc_start: 0.8737 (m-30) cc_final: 0.7899 (t0) REVERT: E 105 MET cc_start: 0.8657 (mmp) cc_final: 0.8442 (mmt) REVERT: E 179 MET cc_start: 0.8881 (mmm) cc_final: 0.8255 (mmm) REVERT: E 222 LYS cc_start: 0.9245 (pttp) cc_final: 0.9044 (pttp) REVERT: E 279 MET cc_start: 0.9320 (mmm) cc_final: 0.8973 (mmm) REVERT: E 287 ARG cc_start: 0.9079 (mmt180) cc_final: 0.8788 (mtp-110) REVERT: E 292 LYS cc_start: 0.9468 (mttt) cc_final: 0.9166 (mmtm) REVERT: E 302 TRP cc_start: 0.9087 (t-100) cc_final: 0.8336 (t60) REVERT: E 303 MET cc_start: 0.9441 (mmm) cc_final: 0.8877 (mmt) outliers start: 30 outliers final: 19 residues processed: 171 average time/residue: 0.1210 time to fit residues: 29.9394 Evaluate side-chains 152 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 255 TRP 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 314 LEU Chi-restraints excluded: chain C residue 136 ILE 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 D residue 113 ASP Chi-restraints excluded: chain D residue 136 ILE 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 136 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 255 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 7 optimal weight: 0.0770 chunk 154 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 0.0170 chunk 164 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.2998 r_free = 0.2998 target = 0.047201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.035656 restraints weight = 86524.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.036560 restraints weight = 51994.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.037179 restraints weight = 36480.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.037645 restraints weight = 28521.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.037984 restraints weight = 23759.193| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13155 Z= 0.123 Angle : 0.729 12.703 18000 Z= 0.347 Chirality : 0.043 0.254 2130 Planarity : 0.003 0.032 2245 Dihedral : 6.407 59.890 2025 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.54 % Allowed : 14.31 % Favored : 84.15 % 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 aren not related in a simple way. whole: 0.07 (0.20), residues: 1670 helix: 1.78 (0.21), residues: 565 sheet: 0.07 (0.25), residues: 380 loop : -1.40 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 75 TYR 0.021 0.001 TYR C 144 PHE 0.015 0.001 PHE E 353 TRP 0.026 0.001 TRP D 255 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00255 (13145) covalent geometry : angle 0.72812 (17975) SS BOND : bond 0.00086 ( 5) SS BOND : angle 0.48250 ( 10) hydrogen bonds : bond 0.03588 ( 676) hydrogen bonds : angle 4.48992 ( 2373) link_BETA1-4 : bond 0.00401 ( 5) link_BETA1-4 : angle 1.20671 ( 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 170 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8654 (mmm) cc_final: 0.8354 (mmm) REVERT: A 130 ASP cc_start: 0.8604 (t0) cc_final: 0.8375 (t0) REVERT: A 132 LYS cc_start: 0.9331 (mttm) cc_final: 0.8987 (mtmt) REVERT: A 156 MET cc_start: 0.8881 (ptp) cc_final: 0.8576 (mmm) REVERT: A 216 LYS cc_start: 0.9544 (mmtp) cc_final: 0.9184 (mmmt) REVERT: B 105 MET cc_start: 0.8774 (tpp) cc_final: 0.8454 (tpp) REVERT: B 120 LYS cc_start: 0.8529 (pttt) cc_final: 0.8298 (pttm) REVERT: B 126 GLU cc_start: 0.8924 (mp0) cc_final: 0.8423 (tp30) REVERT: B 132 LYS cc_start: 0.9282 (mttm) cc_final: 0.8891 (mtmt) REVERT: B 216 LYS cc_start: 0.9458 (mmtp) cc_final: 0.9250 (mmtp) REVERT: B 255 TRP cc_start: 0.8563 (m-10) cc_final: 0.7687 (m-10) REVERT: B 303 MET cc_start: 0.9120 (mmm) cc_final: 0.8747 (tpt) REVERT: C 132 LYS cc_start: 0.9166 (mttm) cc_final: 0.8951 (mtmt) REVERT: C 156 MET cc_start: 0.8789 (ptp) cc_final: 0.8399 (ptp) REVERT: C 169 ILE cc_start: 0.9515 (pt) cc_final: 0.9248 (mp) REVERT: C 255 TRP cc_start: 0.8300 (m-10) cc_final: 0.6694 (m-10) REVERT: C 287 ARG cc_start: 0.8844 (mmt180) cc_final: 0.8593 (mtt-85) REVERT: D 100 ASP cc_start: 0.8642 (m-30) cc_final: 0.7811 (t0) REVERT: D 105 MET cc_start: 0.8728 (tpp) cc_final: 0.8368 (tpp) REVERT: D 126 GLU cc_start: 0.8335 (tp30) cc_final: 0.7852 (tp30) REVERT: D 130 ASP cc_start: 0.8887 (t0) cc_final: 0.7957 (t0) REVERT: D 132 LYS cc_start: 0.9296 (mttm) cc_final: 0.8903 (mtmt) REVERT: D 169 ILE cc_start: 0.9463 (pt) cc_final: 0.9066 (mp) REVERT: D 262 MET cc_start: 0.8531 (pmm) cc_final: 0.8167 (mtp) REVERT: D 292 LYS cc_start: 0.9464 (mtmm) cc_final: 0.9231 (mmmm) REVERT: D 302 TRP cc_start: 0.9131 (t-100) cc_final: 0.8723 (t60) REVERT: D 303 MET cc_start: 0.9244 (mmp) cc_final: 0.8776 (mmm) REVERT: E 71 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8884 (p) REVERT: E 73 ASP cc_start: 0.8430 (p0) cc_final: 0.7963 (p0) REVERT: E 100 ASP cc_start: 0.8687 (m-30) cc_final: 0.7903 (t0) REVERT: E 106 LEU cc_start: 0.9451 (tt) cc_final: 0.9101 (mp) REVERT: E 126 GLU cc_start: 0.8977 (mp0) cc_final: 0.8522 (tp30) REVERT: E 179 MET cc_start: 0.8945 (mmm) cc_final: 0.8416 (mmm) REVERT: E 287 ARG cc_start: 0.9066 (mmt180) cc_final: 0.8695 (mtp-110) REVERT: E 292 LYS cc_start: 0.9427 (mttt) cc_final: 0.9174 (mmtm) REVERT: E 303 MET cc_start: 0.9478 (mmm) cc_final: 0.9087 (mmt) outliers start: 19 outliers final: 14 residues processed: 169 average time/residue: 0.1235 time to fit residues: 30.0427 Evaluate side-chains 149 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 181 ASP 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 181 ASP Chi-restraints excluded: chain B residue 314 LEU 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 D residue 315 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 255 TRP 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: 0.0170 chunk 103 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 96 optimal weight: 40.0000 chunk 77 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 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** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 166 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 = 0.2975 r_free = 0.2975 target = 0.046226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.034961 restraints weight = 88199.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.035813 restraints weight = 53537.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.036405 restraints weight = 37817.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.036848 restraints weight = 29686.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.037187 restraints weight = 24890.379| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13155 Z= 0.160 Angle : 0.740 15.456 18000 Z= 0.350 Chirality : 0.043 0.243 2130 Planarity : 0.003 0.035 2245 Dihedral : 6.446 59.893 2025 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.28 % Allowed : 14.55 % Favored : 83.17 % 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 aren not related in a simple way. whole: 0.20 (0.20), residues: 1670 helix: 2.03 (0.22), residues: 565 sheet: -0.05 (0.26), residues: 390 loop : -1.34 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 75 TYR 0.023 0.002 TYR C 144 PHE 0.019 0.001 PHE D 353 TRP 0.026 0.001 TRP D 255 HIS 0.004 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00341 (13145) covalent geometry : angle 0.73962 (17975) SS BOND : bond 0.00042 ( 5) SS BOND : angle 0.35080 ( 10) hydrogen bonds : bond 0.03627 ( 676) hydrogen bonds : angle 4.46460 ( 2373) link_BETA1-4 : bond 0.00407 ( 5) link_BETA1-4 : angle 1.19999 ( 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 164 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8686 (mmm) cc_final: 0.8413 (mmm) REVERT: A 132 LYS cc_start: 0.9300 (mttm) cc_final: 0.8975 (mtpt) REVERT: A 156 MET cc_start: 0.8876 (ptp) cc_final: 0.8527 (mmm) REVERT: A 216 LYS cc_start: 0.9542 (mmtp) cc_final: 0.9211 (mmmt) REVERT: B 105 MET cc_start: 0.8743 (tpp) cc_final: 0.8440 (tpp) REVERT: B 120 LYS cc_start: 0.8724 (pttt) cc_final: 0.8465 (pttm) REVERT: B 169 ILE cc_start: 0.9525 (pt) cc_final: 0.9268 (mp) REVERT: B 216 LYS cc_start: 0.9481 (mmtp) cc_final: 0.9276 (mmtp) REVERT: B 255 TRP cc_start: 0.8600 (m-10) cc_final: 0.7735 (m-10) REVERT: B 303 MET cc_start: 0.9239 (mmm) cc_final: 0.8928 (tpt) REVERT: B 350 PHE cc_start: 0.9607 (t80) cc_final: 0.9386 (t80) REVERT: C 169 ILE cc_start: 0.9526 (pt) cc_final: 0.9266 (mp) REVERT: C 255 TRP cc_start: 0.8326 (m-10) cc_final: 0.6677 (m-10) REVERT: C 287 ARG cc_start: 0.8895 (mmt180) cc_final: 0.8619 (mtt-85) REVERT: C 314 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8827 (mm) REVERT: D 105 MET cc_start: 0.8679 (tpp) cc_final: 0.8297 (tpp) REVERT: D 130 ASP cc_start: 0.8861 (t0) cc_final: 0.8325 (t0) REVERT: D 132 LYS cc_start: 0.9282 (mttm) cc_final: 0.8898 (mtmm) REVERT: D 262 MET cc_start: 0.8114 (pmm) cc_final: 0.7864 (mtp) REVERT: D 292 LYS cc_start: 0.9452 (mtmm) cc_final: 0.8987 (mmmm) REVERT: E 100 ASP cc_start: 0.8673 (m-30) cc_final: 0.7884 (t0) REVERT: E 279 MET cc_start: 0.9255 (mmm) cc_final: 0.9018 (mmm) REVERT: E 287 ARG cc_start: 0.9076 (mmt180) cc_final: 0.8837 (mtt-85) REVERT: E 292 LYS cc_start: 0.9433 (mttt) cc_final: 0.9193 (mmtm) REVERT: E 303 MET cc_start: 0.9451 (mmm) cc_final: 0.8833 (mmt) outliers start: 28 outliers final: 18 residues processed: 161 average time/residue: 0.1243 time to fit residues: 29.2007 Evaluate side-chains 144 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 181 ASP 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 181 ASP 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 136 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 255 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 164 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 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 83 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.035543 restraints weight = 87210.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.036458 restraints weight = 51309.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.037123 restraints weight = 35573.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.037587 restraints weight = 27420.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.037900 restraints weight = 22684.714| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13155 Z= 0.124 Angle : 0.760 13.904 18000 Z= 0.357 Chirality : 0.044 0.247 2130 Planarity : 0.003 0.036 2245 Dihedral : 6.286 59.915 2025 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.54 % Allowed : 15.28 % Favored : 83.17 % 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 aren not related in a simple way. whole: 0.23 (0.20), residues: 1670 helix: 1.94 (0.22), residues: 565 sheet: 0.08 (0.26), residues: 395 loop : -1.31 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 75 TYR 0.023 0.001 TYR C 144 PHE 0.017 0.001 PHE D 353 TRP 0.027 0.001 TRP D 255 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00263 (13145) covalent geometry : angle 0.75974 (17975) SS BOND : bond 0.00089 ( 5) SS BOND : angle 0.33672 ( 10) hydrogen bonds : bond 0.03504 ( 676) hydrogen bonds : angle 4.38140 ( 2373) link_BETA1-4 : bond 0.00363 ( 5) link_BETA1-4 : angle 1.21190 ( 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 159 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 0.501 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 105 MET cc_start: 0.8773 (mmm) cc_final: 0.8482 (mmm) REVERT: A 132 LYS cc_start: 0.9289 (mttm) cc_final: 0.8987 (mtpt) REVERT: A 156 MET cc_start: 0.8846 (ptp) cc_final: 0.8502 (mmm) REVERT: A 216 LYS cc_start: 0.9530 (mmtp) cc_final: 0.9181 (mmmt) REVERT: A 303 MET cc_start: 0.9412 (mmm) cc_final: 0.8752 (mmt) REVERT: B 105 MET cc_start: 0.8753 (tpp) cc_final: 0.8434 (tpp) REVERT: B 169 ILE cc_start: 0.9521 (pt) cc_final: 0.9172 (mp) REVERT: B 216 LYS cc_start: 0.9449 (mmtp) cc_final: 0.9248 (mmtp) REVERT: B 255 TRP cc_start: 0.8579 (m-10) cc_final: 0.7662 (m-10) REVERT: B 303 MET cc_start: 0.9275 (mmm) cc_final: 0.8941 (tpt) REVERT: B 350 PHE cc_start: 0.9608 (t80) cc_final: 0.9400 (t80) REVERT: C 169 ILE cc_start: 0.9520 (pt) cc_final: 0.9251 (mp) REVERT: C 255 TRP cc_start: 0.8304 (m-10) cc_final: 0.6716 (m-10) REVERT: C 287 ARG cc_start: 0.8845 (mmt180) cc_final: 0.8588 (mtt-85) REVERT: C 314 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8735 (mm) REVERT: D 105 MET cc_start: 0.8716 (tpp) cc_final: 0.8342 (tpp) REVERT: D 130 ASP cc_start: 0.8893 (t0) cc_final: 0.8608 (t0) REVERT: D 132 LYS cc_start: 0.9234 (mttm) cc_final: 0.8792 (mtmm) REVERT: D 169 ILE cc_start: 0.9487 (pt) cc_final: 0.9135 (mp) REVERT: D 262 MET cc_start: 0.8087 (pmm) cc_final: 0.7808 (mtp) REVERT: D 292 LYS cc_start: 0.9383 (mtmm) cc_final: 0.9050 (mttm) REVERT: D 308 LEU cc_start: 0.9637 (tt) cc_final: 0.9372 (mm) REVERT: E 100 ASP cc_start: 0.8634 (m-30) cc_final: 0.7883 (t0) REVERT: E 126 GLU cc_start: 0.8580 (mp0) cc_final: 0.8362 (tp30) REVERT: E 169 ILE cc_start: 0.9527 (pt) cc_final: 0.9182 (mp) REVERT: E 287 ARG cc_start: 0.9012 (mmt180) cc_final: 0.8639 (mtp-110) REVERT: E 292 LYS cc_start: 0.9468 (mttt) cc_final: 0.8986 (mmtm) outliers start: 19 outliers final: 13 residues processed: 157 average time/residue: 0.1284 time to fit residues: 29.0660 Evaluate side-chains 144 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 181 ASP 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 181 ASP 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 156 MET 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: 9.9990 chunk 134 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 149 optimal weight: 0.0870 chunk 10 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 110 optimal weight: 9.9990 overall best weight: 2.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.046336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.035244 restraints weight = 89784.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.036148 restraints weight = 52507.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.036791 restraints weight = 36549.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.037253 restraints weight = 28245.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.037541 restraints weight = 23432.630| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13155 Z= 0.155 Angle : 0.772 16.107 18000 Z= 0.360 Chirality : 0.043 0.239 2130 Planarity : 0.003 0.039 2245 Dihedral : 6.340 59.792 2025 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.71 % Allowed : 15.45 % Favored : 82.85 % 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 aren not related in a simple way. whole: 0.29 (0.20), residues: 1670 helix: 2.11 (0.22), residues: 565 sheet: -0.03 (0.26), residues: 395 loop : -1.29 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 75 TYR 0.022 0.002 TYR C 144 PHE 0.017 0.001 PHE D 353 TRP 0.027 0.001 TRP D 255 HIS 0.004 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00334 (13145) covalent geometry : angle 0.77215 (17975) SS BOND : bond 0.00063 ( 5) SS BOND : angle 0.28511 ( 10) hydrogen bonds : bond 0.03541 ( 676) hydrogen bonds : angle 4.39395 ( 2373) link_BETA1-4 : bond 0.00429 ( 5) link_BETA1-4 : angle 1.22866 ( 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 154 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.509 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 105 MET cc_start: 0.8862 (mmm) cc_final: 0.8543 (mmm) REVERT: A 132 LYS cc_start: 0.9283 (mttm) cc_final: 0.9008 (mtpt) REVERT: A 156 MET cc_start: 0.8860 (ptp) cc_final: 0.8488 (mmm) REVERT: A 279 MET cc_start: 0.9413 (mmp) cc_final: 0.9206 (mmp) REVERT: A 303 MET cc_start: 0.9493 (mmm) cc_final: 0.8714 (mmt) REVERT: B 105 MET cc_start: 0.8725 (tpp) cc_final: 0.8427 (tpp) REVERT: B 120 LYS cc_start: 0.8544 (pttt) cc_final: 0.8282 (pttm) REVERT: B 126 GLU cc_start: 0.8042 (tp30) cc_final: 0.7718 (tp30) REVERT: B 169 ILE cc_start: 0.9519 (pt) cc_final: 0.9182 (mp) REVERT: B 255 TRP cc_start: 0.8615 (m-10) cc_final: 0.7662 (m-10) REVERT: B 303 MET cc_start: 0.9299 (mmm) cc_final: 0.8809 (mmt) REVERT: B 350 PHE cc_start: 0.9611 (t80) cc_final: 0.9376 (t80) REVERT: C 169 ILE cc_start: 0.9485 (pt) cc_final: 0.9235 (mp) REVERT: C 255 TRP cc_start: 0.8290 (m-10) cc_final: 0.6747 (m-10) REVERT: C 287 ARG cc_start: 0.8899 (mmt180) cc_final: 0.8635 (mtt-85) REVERT: D 105 MET cc_start: 0.8746 (tpp) cc_final: 0.8368 (tpp) REVERT: D 130 ASP cc_start: 0.8821 (t0) cc_final: 0.8238 (t0) REVERT: D 132 LYS cc_start: 0.9198 (mttm) cc_final: 0.8859 (mtmm) REVERT: D 166 GLN cc_start: 0.7436 (tm-30) cc_final: 0.7219 (tm-30) REVERT: D 169 ILE cc_start: 0.9516 (pt) cc_final: 0.9154 (mp) REVERT: D 262 MET cc_start: 0.8111 (pmm) cc_final: 0.7718 (mtp) REVERT: D 292 LYS cc_start: 0.9391 (mtmm) cc_final: 0.9160 (mmmm) REVERT: D 308 LEU cc_start: 0.9640 (tt) cc_final: 0.9378 (mm) REVERT: E 126 GLU cc_start: 0.8480 (mp0) cc_final: 0.8115 (tp30) REVERT: E 287 ARG cc_start: 0.9033 (mmt180) cc_final: 0.8790 (mtt-85) REVERT: E 292 LYS cc_start: 0.9347 (mttt) cc_final: 0.9133 (mmtm) REVERT: E 303 MET cc_start: 0.9431 (mmm) cc_final: 0.9157 (mmt) outliers start: 21 outliers final: 16 residues processed: 152 average time/residue: 0.1257 time to fit residues: 27.5749 Evaluate side-chains 143 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP 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 136 ILE 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 D residue 255 TRP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 181 ASP 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: 0.9990 chunk 121 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 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 = 0.2977 r_free = 0.2977 target = 0.045941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.034799 restraints weight = 90436.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.035708 restraints weight = 53117.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.036333 restraints weight = 37066.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.036790 restraints weight = 28773.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.037026 restraints weight = 23914.313| |-----------------------------------------------------------------------------| r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13155 Z= 0.173 Angle : 0.806 13.605 18000 Z= 0.377 Chirality : 0.044 0.233 2130 Planarity : 0.004 0.042 2245 Dihedral : 6.360 59.294 2025 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.38 % Allowed : 15.77 % Favored : 82.85 % 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 aren not related in a simple way. whole: 0.26 (0.20), residues: 1670 helix: 2.12 (0.22), residues: 565 sheet: -0.16 (0.25), residues: 400 loop : -1.27 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 75 TYR 0.021 0.002 TYR C 144 PHE 0.017 0.001 PHE D 353 TRP 0.025 0.001 TRP D 255 HIS 0.004 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00374 (13145) covalent geometry : angle 0.80609 (17975) SS BOND : bond 0.00051 ( 5) SS BOND : angle 0.34593 ( 10) hydrogen bonds : bond 0.03659 ( 676) hydrogen bonds : angle 4.41929 ( 2373) link_BETA1-4 : bond 0.00340 ( 5) link_BETA1-4 : angle 1.23652 ( 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 144 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.8844 (mmm) cc_final: 0.8523 (mmm) REVERT: A 132 LYS cc_start: 0.9279 (mttm) cc_final: 0.9023 (mtpt) REVERT: A 156 MET cc_start: 0.8860 (ptp) cc_final: 0.8387 (mtm) REVERT: A 303 MET cc_start: 0.9478 (mmm) cc_final: 0.9184 (mmt) REVERT: B 105 MET cc_start: 0.8696 (tpp) cc_final: 0.8401 (tpp) REVERT: B 120 LYS cc_start: 0.8671 (pttt) cc_final: 0.8441 (pttt) REVERT: B 126 GLU cc_start: 0.8070 (tp30) cc_final: 0.7785 (tp30) REVERT: B 169 ILE cc_start: 0.9507 (pt) cc_final: 0.9192 (mp) REVERT: B 255 TRP cc_start: 0.8548 (m-10) cc_final: 0.7636 (m-10) REVERT: B 350 PHE cc_start: 0.9617 (t80) cc_final: 0.9378 (t80) REVERT: C 169 ILE cc_start: 0.9472 (pt) cc_final: 0.9203 (mp) REVERT: C 255 TRP cc_start: 0.8311 (m-10) cc_final: 0.6806 (m-10) REVERT: D 105 MET cc_start: 0.8776 (tpp) cc_final: 0.8397 (tpp) REVERT: D 130 ASP cc_start: 0.8834 (t0) cc_final: 0.8485 (t0) REVERT: D 132 LYS cc_start: 0.9269 (mttm) cc_final: 0.8871 (mtmt) REVERT: D 292 LYS cc_start: 0.9402 (mtmm) cc_final: 0.9164 (mmmm) REVERT: E 100 ASP cc_start: 0.8746 (m-30) cc_final: 0.8011 (t0) REVERT: E 303 MET cc_start: 0.9422 (mmm) cc_final: 0.9168 (mmt) outliers start: 17 outliers final: 14 residues processed: 143 average time/residue: 0.1245 time to fit residues: 25.6286 Evaluate side-chains 134 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 315 LEU 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 142 VAL Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 255 TRP Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 181 ASP 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: 1.9990 chunk 40 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 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 = 0.2995 r_free = 0.2995 target = 0.046552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.035522 restraints weight = 90542.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.036431 restraints weight = 52637.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.037113 restraints weight = 36482.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.037563 restraints weight = 27962.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.037874 restraints weight = 23174.007| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13155 Z= 0.138 Angle : 0.834 18.068 18000 Z= 0.388 Chirality : 0.045 0.244 2130 Planarity : 0.003 0.041 2245 Dihedral : 6.282 59.532 2025 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.06 % Allowed : 16.91 % 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 aren not related in a simple way. whole: 0.15 (0.20), residues: 1670 helix: 1.91 (0.22), residues: 565 sheet: -0.09 (0.25), residues: 395 loop : -1.30 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 75 TYR 0.042 0.002 TYR D 238 PHE 0.015 0.001 PHE D 353 TRP 0.026 0.001 TRP D 255 HIS 0.003 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00303 (13145) covalent geometry : angle 0.83421 (17975) SS BOND : bond 0.00065 ( 5) SS BOND : angle 0.34820 ( 10) hydrogen bonds : bond 0.03558 ( 676) hydrogen bonds : angle 4.36964 ( 2373) link_BETA1-4 : bond 0.00359 ( 5) link_BETA1-4 : angle 1.22723 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1843.17 seconds wall clock time: 32 minutes 56.16 seconds (1976.16 seconds total)