Starting phenix.real_space_refine on Fri Jan 24 10:03:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9in6_60702/01_2025/9in6_60702.cif Found real_map, /net/cci-nas-00/data/ceres_data/9in6_60702/01_2025/9in6_60702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9in6_60702/01_2025/9in6_60702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9in6_60702/01_2025/9in6_60702.map" model { file = "/net/cci-nas-00/data/ceres_data/9in6_60702/01_2025/9in6_60702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9in6_60702/01_2025/9in6_60702.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.814 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 90 5.16 5 C 14131 2.51 5 N 3894 2.21 5 O 4258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 22373 Number of models: 1 Model: "" Number of chains: 8 Chain: "M" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3078 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 16, 'TRANS': 381} Chain: "N" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3078 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 16, 'TRANS': 381} Chain: "O" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3078 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 16, 'TRANS': 381} Chain: "P" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3078 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 16, 'TRANS': 381} Chain: "Q" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3078 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 16, 'TRANS': 381} Chain: "R" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3078 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 16, 'TRANS': 381} Chain: "T" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3078 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 16, 'TRANS': 381} Chain: "c" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 827 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Time building chain proxies: 14.05, per 1000 atoms: 0.63 Number of scatterers: 22373 At special positions: 0 Unit cell: (189.2, 235.4, 81.4, 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 90 16.00 O 4258 8.00 N 3894 7.00 C 14131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.36 Conformation dependent library (CDL) restraints added in 2.8 seconds 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5246 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 39 sheets defined 23.6% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'M' and resid 39 through 43 Processing helix chain 'M' and resid 85 through 89 removed outlier: 3.856A pdb=" N ALA M 88 " --> pdb=" O GLN M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 130 removed outlier: 3.570A pdb=" N GLY M 129 " --> pdb=" O GLY M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 184 Processing helix chain 'M' and resid 191 through 215 removed outlier: 3.527A pdb=" N PHE M 202 " --> pdb=" O LYS M 198 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE M 213 " --> pdb=" O GLU M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 238 removed outlier: 3.582A pdb=" N PHE M 237 " --> pdb=" O GLY M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 264 Processing helix chain 'M' and resid 265 through 267 No H-bonds generated for 'chain 'M' and resid 265 through 267' Processing helix chain 'M' and resid 283 through 296 Processing helix chain 'M' and resid 331 through 336 removed outlier: 3.687A pdb=" N VAL M 336 " --> pdb=" O PRO M 332 " (cutoff:3.500A) Processing helix chain 'M' and resid 339 through 341 No H-bonds generated for 'chain 'M' and resid 339 through 341' Processing helix chain 'M' and resid 348 through 350 No H-bonds generated for 'chain 'M' and resid 348 through 350' Processing helix chain 'M' and resid 388 through 392 Processing helix chain 'N' and resid 9 through 13 removed outlier: 4.272A pdb=" N TRP N 13 " --> pdb=" O THR N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 44 Processing helix chain 'N' and resid 84 through 89 removed outlier: 3.662A pdb=" N TRP N 87 " --> pdb=" O ASP N 84 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA N 88 " --> pdb=" O GLN N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 130 removed outlier: 3.780A pdb=" N GLY N 129 " --> pdb=" O GLY N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 184 Processing helix chain 'N' and resid 191 through 215 Processing helix chain 'N' and resid 233 through 238 removed outlier: 3.571A pdb=" N PHE N 237 " --> pdb=" O GLY N 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 255 through 265 removed outlier: 3.784A pdb=" N ASN N 265 " --> pdb=" O ASP N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 268 No H-bonds generated for 'chain 'N' and resid 266 through 268' Processing helix chain 'N' and resid 283 through 296 Processing helix chain 'N' and resid 331 through 337 removed outlier: 3.642A pdb=" N VAL N 336 " --> pdb=" O PRO N 332 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS N 337 " --> pdb=" O LEU N 333 " (cutoff:3.500A) Processing helix chain 'N' and resid 339 through 342 Processing helix chain 'N' and resid 348 through 350 No H-bonds generated for 'chain 'N' and resid 348 through 350' Processing helix chain 'N' and resid 388 through 392 Processing helix chain 'O' and resid 38 through 43 Processing helix chain 'O' and resid 85 through 89 Processing helix chain 'O' and resid 126 through 130 removed outlier: 3.782A pdb=" N GLY O 129 " --> pdb=" O GLY O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 185 Processing helix chain 'O' and resid 191 through 215 removed outlier: 3.615A pdb=" N ASN O 195 " --> pdb=" O SER O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 238 removed outlier: 3.691A pdb=" N PHE O 237 " --> pdb=" O GLY O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 255 through 265 removed outlier: 3.921A pdb=" N ASN O 265 " --> pdb=" O ASP O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 296 Processing helix chain 'O' and resid 331 through 337 removed outlier: 3.673A pdb=" N VAL O 336 " --> pdb=" O PRO O 332 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS O 337 " --> pdb=" O LEU O 333 " (cutoff:3.500A) Processing helix chain 'O' and resid 339 through 342 Processing helix chain 'O' and resid 348 through 350 No H-bonds generated for 'chain 'O' and resid 348 through 350' Processing helix chain 'O' and resid 388 through 392 removed outlier: 3.540A pdb=" N THR O 391 " --> pdb=" O HIS O 388 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 44 removed outlier: 3.803A pdb=" N LYS P 43 " --> pdb=" O ALA P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 130 removed outlier: 3.835A pdb=" N GLY P 129 " --> pdb=" O GLY P 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 185 Processing helix chain 'P' and resid 191 through 215 removed outlier: 3.513A pdb=" N ASN P 195 " --> pdb=" O SER P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 233 through 238 removed outlier: 3.649A pdb=" N PHE P 237 " --> pdb=" O GLY P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 255 through 263 Processing helix chain 'P' and resid 264 through 268 removed outlier: 3.910A pdb=" N PHE P 267 " --> pdb=" O ALA P 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 283 through 296 Processing helix chain 'P' and resid 331 through 337 removed outlier: 3.528A pdb=" N VAL P 336 " --> pdb=" O PRO P 332 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS P 337 " --> pdb=" O LEU P 333 " (cutoff:3.500A) Processing helix chain 'P' and resid 339 through 342 Processing helix chain 'P' and resid 388 through 392 Processing helix chain 'Q' and resid 38 through 44 removed outlier: 3.639A pdb=" N MET Q 44 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 89 removed outlier: 3.562A pdb=" N ALA Q 88 " --> pdb=" O GLN Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 130 removed outlier: 3.864A pdb=" N GLY Q 129 " --> pdb=" O GLY Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 185 Processing helix chain 'Q' and resid 191 through 215 removed outlier: 3.688A pdb=" N ASN Q 195 " --> pdb=" O SER Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 238 removed outlier: 3.681A pdb=" N PHE Q 237 " --> pdb=" O GLY Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 255 through 265 removed outlier: 3.839A pdb=" N ASN Q 265 " --> pdb=" O ASP Q 261 " (cutoff:3.500A) Processing helix chain 'Q' and resid 283 through 296 Processing helix chain 'Q' and resid 331 through 337 removed outlier: 3.609A pdb=" N VAL Q 336 " --> pdb=" O PRO Q 332 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N HIS Q 337 " --> pdb=" O LEU Q 333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 339 through 341 No H-bonds generated for 'chain 'Q' and resid 339 through 341' Processing helix chain 'Q' and resid 348 through 350 No H-bonds generated for 'chain 'Q' and resid 348 through 350' Processing helix chain 'Q' and resid 388 through 392 removed outlier: 3.525A pdb=" N MET Q 392 " --> pdb=" O GLU Q 389 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 44 removed outlier: 3.592A pdb=" N LYS R 43 " --> pdb=" O ALA R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 89 Processing helix chain 'R' and resid 126 through 130 removed outlier: 3.945A pdb=" N GLY R 129 " --> pdb=" O GLY R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'R' and resid 191 through 215 removed outlier: 3.540A pdb=" N LYS R 198 " --> pdb=" O ALA R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 238 Processing helix chain 'R' and resid 255 through 265 removed outlier: 4.158A pdb=" N ASN R 265 " --> pdb=" O ASP R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 268 No H-bonds generated for 'chain 'R' and resid 266 through 268' Processing helix chain 'R' and resid 283 through 296 Processing helix chain 'R' and resid 331 through 337 removed outlier: 3.641A pdb=" N VAL R 336 " --> pdb=" O PRO R 332 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS R 337 " --> pdb=" O LEU R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 339 through 341 No H-bonds generated for 'chain 'R' and resid 339 through 341' Processing helix chain 'R' and resid 348 through 350 No H-bonds generated for 'chain 'R' and resid 348 through 350' Processing helix chain 'R' and resid 388 through 392 Processing helix chain 'T' and resid 9 through 13 removed outlier: 4.351A pdb=" N TRP T 13 " --> pdb=" O THR T 10 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 40 Processing helix chain 'T' and resid 84 through 88 removed outlier: 3.752A pdb=" N TRP T 87 " --> pdb=" O ASP T 84 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA T 88 " --> pdb=" O GLN T 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 84 through 88' Processing helix chain 'T' and resid 180 through 185 Processing helix chain 'T' and resid 191 through 215 Processing helix chain 'T' and resid 233 through 238 removed outlier: 3.789A pdb=" N PHE T 237 " --> pdb=" O GLY T 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 255 through 266 removed outlier: 4.192A pdb=" N VAL T 266 " --> pdb=" O PHE T 262 " (cutoff:3.500A) Processing helix chain 'T' and resid 283 through 297 removed outlier: 3.742A pdb=" N ARG T 295 " --> pdb=" O ASN T 291 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN T 296 " --> pdb=" O LYS T 292 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER T 297 " --> pdb=" O LEU T 293 " (cutoff:3.500A) Processing helix chain 'T' and resid 331 through 337 removed outlier: 3.743A pdb=" N VAL T 336 " --> pdb=" O PRO T 332 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS T 337 " --> pdb=" O LEU T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 348 through 350 No H-bonds generated for 'chain 'T' and resid 348 through 350' Processing helix chain 'T' and resid 388 through 392 removed outlier: 3.592A pdb=" N THR T 391 " --> pdb=" O HIS T 388 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 21 through 22 removed outlier: 6.005A pdb=" N LEU M 27 " --> pdb=" O GLU N 59 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.620A pdb=" N SER M 45 " --> pdb=" O GLU M 354 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL M 356 " --> pdb=" O SER M 45 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN M 47 " --> pdb=" O VAL M 356 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ARG M 358 " --> pdb=" O GLN M 47 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU M 381 " --> pdb=" O LEU M 357 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA M 359 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE M 379 " --> pdb=" O ALA M 359 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS M 361 " --> pdb=" O GLN M 377 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN M 377 " --> pdb=" O LYS M 361 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU M 363 " --> pdb=" O LYS M 375 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LYS M 375 " --> pdb=" O GLU M 363 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU M 384 " --> pdb=" O PHE M 168 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N PHE M 168 " --> pdb=" O LEU M 384 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL M 386 " --> pdb=" O ASN M 166 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN M 166 " --> pdb=" O VAL M 386 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLU M 53 " --> pdb=" O ASP R 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.620A pdb=" N SER M 45 " --> pdb=" O GLU M 354 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL M 356 " --> pdb=" O SER M 45 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN M 47 " --> pdb=" O VAL M 356 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ARG M 358 " --> pdb=" O GLN M 47 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU M 381 " --> pdb=" O LEU M 357 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA M 359 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE M 379 " --> pdb=" O ALA M 359 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS M 361 " --> pdb=" O GLN M 377 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN M 377 " --> pdb=" O LYS M 361 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU M 363 " --> pdb=" O LYS M 375 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LYS M 375 " --> pdb=" O GLU M 363 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU M 384 " --> pdb=" O PHE M 168 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N PHE M 168 " --> pdb=" O LEU M 384 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL M 386 " --> pdb=" O ASN M 166 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASN M 166 " --> pdb=" O VAL M 386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 65 through 67 removed outlier: 6.390A pdb=" N ILE M 94 " --> pdb=" O ILE M 144 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP M 93 " --> pdb=" O VAL M 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 218 through 221 Processing sheet with id=AA7, first strand: chain 'M' and resid 242 through 244 removed outlier: 6.863A pdb=" N THR M 243 " --> pdb=" O GLY M 396 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR M 317 " --> pdb=" O PHE M 328 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THR M 330 " --> pdb=" O ASN M 315 " (cutoff:3.500A) removed outlier: 15.866A pdb=" N ASN M 315 " --> pdb=" O THR M 330 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR M 312 " --> pdb=" O VAL N 320 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR N 243 " --> pdb=" O GLY N 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 242 through 244 removed outlier: 6.863A pdb=" N THR M 243 " --> pdb=" O GLY M 396 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR M 317 " --> pdb=" O PHE M 328 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THR M 330 " --> pdb=" O ASN M 315 " (cutoff:3.500A) removed outlier: 15.866A pdb=" N ASN M 315 " --> pdb=" O THR M 330 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN R 310 " --> pdb=" O ASN M 315 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR M 317 " --> pdb=" O GLN R 310 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TYR R 312 " --> pdb=" O THR M 317 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TRP M 319 " --> pdb=" O TYR R 312 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N MET R 314 " --> pdb=" O TRP M 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 300 through 304 removed outlier: 7.814A pdb=" N ARG N 301 " --> pdb=" O THR M 300 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE M 302 " --> pdb=" O ARG N 301 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN N 303 " --> pdb=" O ILE M 302 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE M 304 " --> pdb=" O ASN N 303 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ARG O 301 " --> pdb=" O THR N 300 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE N 302 " --> pdb=" O ARG O 301 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASN O 303 " --> pdb=" O ILE N 302 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE N 304 " --> pdb=" O ASN O 303 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ARG P 301 " --> pdb=" O THR O 300 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE O 302 " --> pdb=" O ARG P 301 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASN P 303 " --> pdb=" O ILE O 302 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE O 304 " --> pdb=" O ASN P 303 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ARG R 301 " --> pdb=" O THR Q 300 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE Q 302 " --> pdb=" O ARG R 301 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN R 303 " --> pdb=" O ILE Q 302 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N PHE Q 304 " --> pdb=" O ASN R 303 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ASP R 305 " --> pdb=" O PHE Q 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 307 through 309 removed outlier: 5.620A pdb=" N VAL M 308 " --> pdb=" O ASN N 315 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR N 312 " --> pdb=" O VAL O 320 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR O 243 " --> pdb=" O GLY O 396 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 163 through 168 removed outlier: 4.866A pdb=" N TRP O 57 " --> pdb=" O ARG N 23 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR N 25 " --> pdb=" O TRP O 57 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N GLU O 59 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU N 27 " --> pdb=" O GLU O 59 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.546A pdb=" N SER N 45 " --> pdb=" O GLU N 354 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL N 356 " --> pdb=" O SER N 45 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN N 47 " --> pdb=" O VAL N 356 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ARG N 358 " --> pdb=" O GLN N 47 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU N 354 " --> pdb=" O GLU N 385 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLU N 385 " --> pdb=" O GLU N 354 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL N 356 " --> pdb=" O GLY N 383 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY N 383 " --> pdb=" O VAL N 356 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR N 360 " --> pdb=" O ILE N 379 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE N 379 " --> pdb=" O THR N 360 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN N 377 " --> pdb=" O PRO N 362 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ASN N 364 " --> pdb=" O LYS N 375 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LYS N 375 " --> pdb=" O ASN N 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 65 through 67 removed outlier: 5.650A pdb=" N ALA N 143 " --> pdb=" O MET N 96 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N MET N 96 " --> pdb=" O ALA N 143 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY N 145 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP N 93 " --> pdb=" O VAL N 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 218 through 221 Processing sheet with id=AB6, first strand: chain 'N' and resid 307 through 308 removed outlier: 6.780A pdb=" N TYR O 312 " --> pdb=" O VAL P 320 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE P 279 " --> pdb=" O LEU P 347 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR P 243 " --> pdb=" O GLY P 396 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 21 through 29 removed outlier: 5.107A pdb=" N TRP P 57 " --> pdb=" O ARG O 23 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR O 25 " --> pdb=" O TRP P 57 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLU P 59 " --> pdb=" O THR O 25 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU O 27 " --> pdb=" O GLU P 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 45 through 48 removed outlier: 3.800A pdb=" N SER O 45 " --> pdb=" O ILE O 352 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU O 381 " --> pdb=" O LEU O 357 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALA O 359 " --> pdb=" O ILE O 379 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE O 379 " --> pdb=" O ALA O 359 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS O 361 " --> pdb=" O GLN O 377 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN O 377 " --> pdb=" O LYS O 361 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLU O 363 " --> pdb=" O LYS O 375 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LYS O 375 " --> pdb=" O GLU O 363 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 65 through 67 removed outlier: 5.597A pdb=" N ALA O 143 " --> pdb=" O MET O 96 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET O 96 " --> pdb=" O ALA O 143 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY O 145 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP O 93 " --> pdb=" O VAL O 111 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 218 through 221 Processing sheet with id=AC2, first strand: chain 'O' and resid 307 through 308 removed outlier: 3.519A pdb=" N VAL O 308 " --> pdb=" O GLY P 313 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N TYR P 312 " --> pdb=" O VAL Q 320 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR Q 243 " --> pdb=" O GLY Q 396 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 21 through 29 removed outlier: 4.875A pdb=" N TRP Q 57 " --> pdb=" O ARG P 23 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR P 25 " --> pdb=" O TRP Q 57 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLU Q 59 " --> pdb=" O THR P 25 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU P 27 " --> pdb=" O GLU Q 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 46 through 48 removed outlier: 6.827A pdb=" N GLU P 381 " --> pdb=" O LEU P 357 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA P 359 " --> pdb=" O ILE P 379 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE P 379 " --> pdb=" O ALA P 359 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS P 361 " --> pdb=" O GLN P 377 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN P 377 " --> pdb=" O LYS P 361 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU P 363 " --> pdb=" O LYS P 375 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS P 375 " --> pdb=" O GLU P 363 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 65 through 67 removed outlier: 6.184A pdb=" N ILE P 94 " --> pdb=" O ILE P 144 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP P 93 " --> pdb=" O VAL P 111 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 218 through 221 Processing sheet with id=AC7, first strand: chain 'Q' and resid 21 through 29 removed outlier: 4.852A pdb=" N TRP R 57 " --> pdb=" O ARG Q 23 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR Q 25 " --> pdb=" O TRP R 57 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLU R 59 " --> pdb=" O THR Q 25 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU Q 27 " --> pdb=" O GLU R 59 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Q' and resid 45 through 48 removed outlier: 6.557A pdb=" N SER Q 45 " --> pdb=" O GLU Q 354 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL Q 356 " --> pdb=" O SER Q 45 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN Q 47 " --> pdb=" O VAL Q 356 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ARG Q 358 " --> pdb=" O GLN Q 47 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU Q 381 " --> pdb=" O LEU Q 357 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA Q 359 " --> pdb=" O ILE Q 379 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE Q 379 " --> pdb=" O ALA Q 359 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS Q 361 " --> pdb=" O GLN Q 377 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLN Q 377 " --> pdb=" O LYS Q 361 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLU Q 363 " --> pdb=" O LYS Q 375 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS Q 375 " --> pdb=" O GLU Q 363 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 65 through 67 removed outlier: 5.479A pdb=" N ALA Q 143 " --> pdb=" O MET Q 96 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET Q 96 " --> pdb=" O ALA Q 143 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY Q 145 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP Q 93 " --> pdb=" O VAL Q 111 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS Q 110 " --> pdb=" O ALA Q 124 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Q' and resid 218 through 221 Processing sheet with id=AD2, first strand: chain 'Q' and resid 311 through 313 removed outlier: 6.502A pdb=" N TYR Q 312 " --> pdb=" O VAL R 320 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR R 243 " --> pdb=" O GLY R 396 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 45 through 48 removed outlier: 6.564A pdb=" N SER R 45 " --> pdb=" O GLU R 354 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N VAL R 356 " --> pdb=" O SER R 45 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN R 47 " --> pdb=" O VAL R 356 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ARG R 358 " --> pdb=" O GLN R 47 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU R 381 " --> pdb=" O LEU R 357 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA R 359 " --> pdb=" O ILE R 379 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE R 379 " --> pdb=" O ALA R 359 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS R 361 " --> pdb=" O GLN R 377 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLN R 377 " --> pdb=" O LYS R 361 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLU R 363 " --> pdb=" O LYS R 375 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS R 375 " --> pdb=" O GLU R 363 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 65 through 67 removed outlier: 5.585A pdb=" N ALA R 143 " --> pdb=" O MET R 96 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N MET R 96 " --> pdb=" O ALA R 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY R 145 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP R 93 " --> pdb=" O VAL R 111 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 218 through 221 Processing sheet with id=AD6, first strand: chain 'T' and resid 46 through 48 removed outlier: 7.238A pdb=" N ARG T 355 " --> pdb=" O GLU T 385 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLU T 385 " --> pdb=" O ARG T 355 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU T 357 " --> pdb=" O GLY T 383 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N GLY T 383 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA T 359 " --> pdb=" O GLU T 381 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLU T 381 " --> pdb=" O ALA T 359 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 53 through 58 Processing sheet with id=AD8, first strand: chain 'T' and resid 65 through 67 removed outlier: 5.623A pdb=" N ALA T 143 " --> pdb=" O MET T 96 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET T 96 " --> pdb=" O ALA T 143 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY T 145 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP T 93 " --> pdb=" O VAL T 111 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE T 108 " --> pdb=" O GLY T 126 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY T 126 " --> pdb=" O ILE T 108 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 218 through 221 Processing sheet with id=AE1, first strand: chain 'T' and resid 242 through 244 removed outlier: 6.351A pdb=" N THR T 243 " --> pdb=" O GLY T 396 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'c' and resid 2 through 6 removed outlier: 7.520A pdb=" N VAL c 105 " --> pdb=" O VAL c 3 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR c 5 " --> pdb=" O VAL c 103 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL c 103 " --> pdb=" O TYR c 5 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'c' and resid 14 through 16 removed outlier: 3.775A pdb=" N GLY c 66 " --> pdb=" O PHE c 53 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLY c 55 " --> pdb=" O LEU c 64 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU c 64 " --> pdb=" O GLY c 55 " (cutoff:3.500A) 773 hydrogen bonds defined for protein. 2094 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: 8.30 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3839 1.32 - 1.44: 5961 1.44 - 1.56: 12869 1.56 - 1.68: 0 1.68 - 1.81: 164 Bond restraints: 22833 Sorted by residual: bond pdb=" CA ASN T 32 " pdb=" C ASN T 32 " ideal model delta sigma weight residual 1.525 1.473 0.052 1.27e-02 6.20e+03 1.67e+01 bond pdb=" C VAL O 320 " pdb=" O VAL O 320 " ideal model delta sigma weight residual 1.237 1.197 0.039 1.13e-02 7.83e+03 1.22e+01 bond pdb=" C LEU O 321 " pdb=" O LEU O 321 " ideal model delta sigma weight residual 1.235 1.207 0.028 8.20e-03 1.49e+04 1.17e+01 bond pdb=" CA ALA T 35 " pdb=" CB ALA T 35 " ideal model delta sigma weight residual 1.528 1.480 0.048 1.57e-02 4.06e+03 9.40e+00 bond pdb=" N ALA T 35 " pdb=" CA ALA T 35 " ideal model delta sigma weight residual 1.455 1.416 0.040 1.39e-02 5.18e+03 8.11e+00 ... (remaining 22828 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 30604 2.27 - 4.54: 291 4.54 - 6.80: 16 6.80 - 9.07: 5 9.07 - 11.34: 1 Bond angle restraints: 30917 Sorted by residual: angle pdb=" N ASN T 32 " pdb=" CA ASN T 32 " pdb=" C ASN T 32 " ideal model delta sigma weight residual 111.87 100.53 11.34 1.41e+00 5.03e-01 6.47e+01 angle pdb=" N GLN O 323 " pdb=" CA GLN O 323 " pdb=" C GLN O 323 " ideal model delta sigma weight residual 111.36 119.93 -8.57 1.09e+00 8.42e-01 6.18e+01 angle pdb=" N GLN T 34 " pdb=" CA GLN T 34 " pdb=" C GLN T 34 " ideal model delta sigma weight residual 110.53 102.67 7.86 1.32e+00 5.74e-01 3.55e+01 angle pdb=" N GLU O 325 " pdb=" CA GLU O 325 " pdb=" C GLU O 325 " ideal model delta sigma weight residual 109.85 118.59 -8.74 1.58e+00 4.01e-01 3.06e+01 angle pdb=" N GLY T 33 " pdb=" CA GLY T 33 " pdb=" C GLY T 33 " ideal model delta sigma weight residual 113.18 104.35 8.83 2.37e+00 1.78e-01 1.39e+01 ... (remaining 30912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 12572 17.89 - 35.79: 864 35.79 - 53.68: 98 53.68 - 71.58: 16 71.58 - 89.47: 10 Dihedral angle restraints: 13560 sinusoidal: 5377 harmonic: 8183 Sorted by residual: dihedral pdb=" CA VAL O 308 " pdb=" C VAL O 308 " pdb=" N THR O 309 " pdb=" CA THR O 309 " ideal model delta harmonic sigma weight residual -180.00 -157.06 -22.94 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA VAL N 308 " pdb=" C VAL N 308 " pdb=" N THR N 309 " pdb=" CA THR N 309 " ideal model delta harmonic sigma weight residual -180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA THR M 309 " pdb=" C THR M 309 " pdb=" N GLN M 310 " pdb=" CA GLN M 310 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 13557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2999 0.066 - 0.132: 407 0.132 - 0.198: 17 0.198 - 0.265: 0 0.265 - 0.331: 1 Chirality restraints: 3424 Sorted by residual: chirality pdb=" CA GLN O 323 " pdb=" N GLN O 323 " pdb=" C GLN O 323 " pdb=" CB GLN O 323 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA LEU O 321 " pdb=" N LEU O 321 " pdb=" C LEU O 321 " pdb=" CB LEU O 321 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CA GLU O 325 " pdb=" N GLU O 325 " pdb=" C GLU O 325 " pdb=" CB GLU O 325 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.86e-01 ... (remaining 3421 not shown) Planarity restraints: 4038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP M 51 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO M 52 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO M 52 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO M 52 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 13 " 0.017 2.00e-02 2.50e+03 1.24e-02 3.87e+00 pdb=" CG TRP M 13 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP M 13 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP M 13 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP M 13 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP M 13 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP M 13 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 13 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 13 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP M 13 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR c 43 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO c 44 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO c 44 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO c 44 " -0.025 5.00e-02 4.00e+02 ... (remaining 4035 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 5433 2.79 - 3.32: 18848 3.32 - 3.85: 34965 3.85 - 4.37: 41598 4.37 - 4.90: 74550 Nonbonded interactions: 175394 Sorted by model distance: nonbonded pdb=" OG1 THR P 10 " pdb=" OE2 GLU R 150 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR c 37 " pdb=" OD2 ASP c 104 " model vdw 2.267 3.040 nonbonded pdb=" OE1 GLN O 47 " pdb=" NZ LYS O 353 " model vdw 2.269 3.120 nonbonded pdb=" OE1 GLU T 256 " pdb=" OG SER T 297 " model vdw 2.278 3.040 nonbonded pdb=" O GLY c 99 " pdb=" OG1 THR c 100 " model vdw 2.285 3.040 ... (remaining 175389 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: 0.00 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.050 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: 0.040 Extract box with map and model: 0.920 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 51.560 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 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:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22833 Z= 0.294 Angle : 0.576 11.338 30917 Z= 0.325 Chirality : 0.044 0.331 3424 Planarity : 0.004 0.053 4038 Dihedral : 12.032 89.470 8314 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.13 % Allowed : 0.09 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 2881 helix: 1.32 (0.26), residues: 485 sheet: 0.35 (0.16), residues: 930 loop : -1.07 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M 13 HIS 0.005 0.001 HIS N 331 PHE 0.028 0.001 PHE O 212 TYR 0.015 0.002 TYR R 214 ARG 0.005 0.000 ARG T 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 347 time to evaluate : 2.677 Fit side-chains REVERT: N 180 LYS cc_start: 0.9107 (mttt) cc_final: 0.8568 (pptt) REVERT: N 257 ASP cc_start: 0.8347 (m-30) cc_final: 0.8062 (m-30) REVERT: O 8 ARG cc_start: 0.8170 (ttt90) cc_final: 0.7097 (pmt-80) REVERT: P 93 ASP cc_start: 0.8235 (m-30) cc_final: 0.7914 (m-30) REVERT: P 205 TYR cc_start: 0.9192 (m-10) cc_final: 0.8947 (m-10) REVERT: Q 64 ASN cc_start: 0.9019 (t0) cc_final: 0.8706 (t0) REVERT: Q 122 LYS cc_start: 0.8817 (tptm) cc_final: 0.8539 (tppt) REVERT: Q 177 GLU cc_start: 0.5180 (pp20) cc_final: 0.4574 (tm-30) REVERT: Q 186 LYS cc_start: 0.8536 (ttpp) cc_final: 0.8199 (mptt) REVERT: R 180 LYS cc_start: 0.9138 (mttp) cc_final: 0.8181 (pptt) REVERT: T 29 MET cc_start: 0.7621 (mmt) cc_final: 0.5645 (ptt) REVERT: T 41 MET cc_start: 0.7640 (mtp) cc_final: 0.5896 (mtp) REVERT: T 186 LYS cc_start: 0.9037 (ttmt) cc_final: 0.8705 (pmtt) REVERT: T 210 MET cc_start: 0.9011 (mmm) cc_final: 0.7988 (ptt) REVERT: T 295 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8591 (tpt170) REVERT: T 317 THR cc_start: 0.9223 (m) cc_final: 0.8677 (t) REVERT: T 323 GLN cc_start: 0.8746 (mp10) cc_final: 0.8475 (mp10) REVERT: T 331 HIS cc_start: 0.8977 (t-90) cc_final: 0.8596 (t-90) REVERT: T 337 HIS cc_start: 0.8633 (t-90) cc_final: 0.8288 (t-90) REVERT: T 342 LYS cc_start: 0.9195 (mttt) cc_final: 0.8107 (pptt) outliers start: 3 outliers final: 0 residues processed: 350 average time/residue: 1.4371 time to fit residues: 569.6383 Evaluate side-chains 238 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN N 310 GLN O 244 GLN P 291 ASN Q 388 HIS T 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.057277 restraints weight = 45587.099| |-----------------------------------------------------------------------------| r_work (start): 0.2588 rms_B_bonded: 2.18 r_work: 0.2484 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2381 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.055 22833 Z= 0.620 Angle : 0.717 13.827 30917 Z= 0.386 Chirality : 0.049 0.185 3424 Planarity : 0.005 0.053 4038 Dihedral : 5.158 25.053 3072 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.05 % Allowed : 8.63 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 2881 helix: 1.00 (0.24), residues: 538 sheet: 0.31 (0.17), residues: 920 loop : -1.19 (0.15), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 13 HIS 0.006 0.002 HIS Q 337 PHE 0.024 0.002 PHE R 212 TYR 0.024 0.002 TYR T 204 ARG 0.006 0.001 ARG R 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 2.842 Fit side-chains REVERT: N 180 LYS cc_start: 0.9314 (mttt) cc_final: 0.8484 (pptt) REVERT: N 186 LYS cc_start: 0.5786 (OUTLIER) cc_final: 0.4500 (ptpt) REVERT: N 363 GLU cc_start: 0.8633 (tt0) cc_final: 0.8419 (tt0) REVERT: N 398 ILE cc_start: 0.8572 (mt) cc_final: 0.8265 (tt) REVERT: O 8 ARG cc_start: 0.8281 (ttt90) cc_final: 0.6786 (pmt-80) REVERT: O 13 TRP cc_start: 0.9316 (OUTLIER) cc_final: 0.8126 (m-10) REVERT: P 93 ASP cc_start: 0.9005 (m-30) cc_final: 0.8420 (m-30) REVERT: P 186 LYS cc_start: 0.5809 (OUTLIER) cc_final: 0.4996 (pmtt) REVERT: P 205 TYR cc_start: 0.9445 (m-10) cc_final: 0.9234 (m-10) REVERT: Q 64 ASN cc_start: 0.9408 (t0) cc_final: 0.9131 (t0) REVERT: Q 122 LYS cc_start: 0.9055 (tptm) cc_final: 0.8583 (tmtm) REVERT: Q 177 GLU cc_start: 0.5473 (pp20) cc_final: 0.4336 (pp20) REVERT: Q 186 LYS cc_start: 0.9088 (ttpp) cc_final: 0.8297 (mptt) REVERT: Q 270 ASP cc_start: 0.8882 (p0) cc_final: 0.8452 (t70) REVERT: Q 314 MET cc_start: 0.9323 (ptp) cc_final: 0.9021 (ptt) REVERT: R 270 ASP cc_start: 0.8886 (t0) cc_final: 0.8533 (t0) REVERT: T 29 MET cc_start: 0.7460 (mmt) cc_final: 0.5183 (ptt) REVERT: T 186 LYS cc_start: 0.9462 (ttmt) cc_final: 0.8589 (pmtt) REVERT: T 210 MET cc_start: 0.9006 (mmm) cc_final: 0.7756 (ptt) REVERT: T 295 ARG cc_start: 0.8994 (ttp80) cc_final: 0.8413 (mpt180) REVERT: T 318 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7199 (ttp-170) REVERT: T 323 GLN cc_start: 0.8609 (mp10) cc_final: 0.8256 (mp10) REVERT: T 331 HIS cc_start: 0.8567 (t-90) cc_final: 0.8049 (t-90) REVERT: c 11 MET cc_start: 0.8677 (mmm) cc_final: 0.8341 (mmp) outliers start: 48 outliers final: 17 residues processed: 259 average time/residue: 1.5074 time to fit residues: 440.6633 Evaluate side-chains 240 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 2.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 346 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 186 LYS Chi-restraints excluded: chain N residue 356 VAL Chi-restraints excluded: chain O residue 13 TRP Chi-restraints excluded: chain O residue 15 ASN Chi-restraints excluded: chain O residue 247 THR Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 186 LYS Chi-restraints excluded: chain P residue 346 VAL Chi-restraints excluded: chain P residue 369 VAL Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 247 THR Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 96 MET Chi-restraints excluded: chain T residue 259 LEU Chi-restraints excluded: chain T residue 318 ARG Chi-restraints excluded: chain c residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 129 optimal weight: 0.4980 chunk 252 optimal weight: 20.0000 chunk 234 optimal weight: 30.0000 chunk 73 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 310 GLN O 244 GLN P 377 GLN R 244 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.061299 restraints weight = 44855.048| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.20 r_work: 0.2569 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22833 Z= 0.166 Angle : 0.509 9.547 30917 Z= 0.273 Chirality : 0.042 0.171 3424 Planarity : 0.004 0.048 4038 Dihedral : 4.556 23.544 3072 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.24 % Allowed : 10.97 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 2881 helix: 1.50 (0.24), residues: 537 sheet: 0.45 (0.17), residues: 898 loop : -1.08 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 13 HIS 0.003 0.000 HIS N 388 PHE 0.012 0.001 PHE R 212 TYR 0.019 0.001 TYR T 204 ARG 0.002 0.000 ARG R 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 2.624 Fit side-chains REVERT: M 24 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8891 (mt-10) REVERT: M 277 GLN cc_start: 0.9416 (mt0) cc_final: 0.9195 (mt0) REVERT: N 180 LYS cc_start: 0.9221 (mttt) cc_final: 0.8499 (pptt) REVERT: N 186 LYS cc_start: 0.5883 (mptt) cc_final: 0.4656 (ptpt) REVERT: N 363 GLU cc_start: 0.8621 (tt0) cc_final: 0.8335 (tt0) REVERT: O 7 LEU cc_start: 0.8874 (mm) cc_final: 0.8329 (tm) REVERT: O 8 ARG cc_start: 0.8044 (ttt90) cc_final: 0.6393 (pmt-80) REVERT: O 13 TRP cc_start: 0.9313 (OUTLIER) cc_final: 0.8244 (m-10) REVERT: O 325 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8864 (mt-10) REVERT: P 25 THR cc_start: 0.9171 (m) cc_final: 0.8834 (p) REVERT: P 93 ASP cc_start: 0.8968 (m-30) cc_final: 0.8440 (m-30) REVERT: P 186 LYS cc_start: 0.5735 (OUTLIER) cc_final: 0.4835 (pttm) REVERT: P 219 GLU cc_start: 0.9181 (tt0) cc_final: 0.8676 (tp30) REVERT: Q 64 ASN cc_start: 0.9447 (t0) cc_final: 0.9229 (t0) REVERT: Q 93 ASP cc_start: 0.9036 (m-30) cc_final: 0.8713 (m-30) REVERT: Q 122 LYS cc_start: 0.8885 (tptm) cc_final: 0.8516 (tppp) REVERT: Q 177 GLU cc_start: 0.4873 (pp20) cc_final: 0.3851 (tm-30) REVERT: Q 186 LYS cc_start: 0.9089 (ttpp) cc_final: 0.8363 (mptt) REVERT: Q 201 MET cc_start: 0.9422 (tpp) cc_final: 0.8979 (tpp) REVERT: R 270 ASP cc_start: 0.8713 (t0) cc_final: 0.8289 (t0) REVERT: T 24 GLU cc_start: 0.8710 (mp0) cc_final: 0.8144 (tm-30) REVERT: T 29 MET cc_start: 0.7414 (mmt) cc_final: 0.5135 (ptt) REVERT: T 122 LYS cc_start: 0.9402 (tttp) cc_final: 0.9061 (mmmm) REVERT: T 177 GLU cc_start: 0.4954 (OUTLIER) cc_final: 0.3639 (tm-30) REVERT: T 186 LYS cc_start: 0.9431 (ttmt) cc_final: 0.8462 (pmtt) REVERT: T 210 MET cc_start: 0.8976 (mmm) cc_final: 0.7737 (ttp) REVERT: T 295 ARG cc_start: 0.9075 (ttp80) cc_final: 0.8488 (mpt180) REVERT: T 323 GLN cc_start: 0.8592 (mp10) cc_final: 0.7912 (mp10) REVERT: T 331 HIS cc_start: 0.8583 (t-90) cc_final: 0.8152 (t-90) REVERT: T 342 LYS cc_start: 0.9062 (mttt) cc_final: 0.7898 (pptt) REVERT: T 378 TRP cc_start: 0.9315 (m100) cc_final: 0.8876 (m100) REVERT: T 392 MET cc_start: 0.8829 (mtt) cc_final: 0.8236 (mmt) outliers start: 29 outliers final: 9 residues processed: 269 average time/residue: 1.4993 time to fit residues: 456.2390 Evaluate side-chains 250 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 237 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 24 GLU Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 13 TRP Chi-restraints excluded: chain O residue 15 ASN Chi-restraints excluded: chain P residue 186 LYS Chi-restraints excluded: chain P residue 369 VAL Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 177 GLU Chi-restraints excluded: chain T residue 314 MET Chi-restraints excluded: chain c residue 34 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 104 optimal weight: 6.9990 chunk 226 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 281 optimal weight: 50.0000 chunk 201 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 92 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 244 GLN P 16 GLN P 310 GLN T 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.058309 restraints weight = 45869.821| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 2.23 r_work: 0.2512 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2411 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 22833 Z= 0.369 Angle : 0.570 11.355 30917 Z= 0.306 Chirality : 0.044 0.162 3424 Planarity : 0.004 0.047 4038 Dihedral : 4.695 21.759 3072 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.49 % Allowed : 12.98 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 2881 helix: 1.42 (0.24), residues: 542 sheet: 0.41 (0.17), residues: 919 loop : -1.09 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 378 HIS 0.003 0.001 HIS M 63 PHE 0.016 0.001 PHE N 316 TYR 0.024 0.002 TYR T 204 ARG 0.004 0.000 ARG R 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 2.739 Fit side-chains REVERT: M 24 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8945 (mt-10) REVERT: M 277 GLN cc_start: 0.9435 (mt0) cc_final: 0.9230 (mt0) REVERT: N 180 LYS cc_start: 0.9305 (mttt) cc_final: 0.8501 (pptt) REVERT: N 186 LYS cc_start: 0.5809 (mptt) cc_final: 0.4623 (ptpt) REVERT: N 363 GLU cc_start: 0.8702 (tt0) cc_final: 0.8442 (tt0) REVERT: O 7 LEU cc_start: 0.8952 (mm) cc_final: 0.8609 (tt) REVERT: O 8 ARG cc_start: 0.8072 (ttt90) cc_final: 0.6498 (pmt-80) REVERT: O 13 TRP cc_start: 0.9279 (OUTLIER) cc_final: 0.8048 (m-10) REVERT: O 325 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8949 (mt-10) REVERT: P 25 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8834 (p) REVERT: P 93 ASP cc_start: 0.8972 (m-30) cc_final: 0.8368 (m-30) REVERT: Q 64 ASN cc_start: 0.9462 (t0) cc_final: 0.9187 (t0) REVERT: Q 96 MET cc_start: 0.9442 (ttt) cc_final: 0.9122 (tpp) REVERT: Q 122 LYS cc_start: 0.8920 (tptm) cc_final: 0.8620 (tppt) REVERT: Q 177 GLU cc_start: 0.5298 (pp20) cc_final: 0.4300 (pp20) REVERT: Q 186 LYS cc_start: 0.9132 (ttpp) cc_final: 0.8338 (mptt) REVERT: Q 270 ASP cc_start: 0.8689 (p0) cc_final: 0.8374 (t70) REVERT: R 270 ASP cc_start: 0.8822 (t0) cc_final: 0.8350 (t0) REVERT: R 347 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9001 (pp) REVERT: T 24 GLU cc_start: 0.8728 (mp0) cc_final: 0.8159 (tm-30) REVERT: T 29 MET cc_start: 0.7384 (mmt) cc_final: 0.5155 (ptt) REVERT: T 96 MET cc_start: 0.8451 (ttt) cc_final: 0.7599 (tpp) REVERT: T 122 LYS cc_start: 0.9409 (tttp) cc_final: 0.9063 (mmmm) REVERT: T 186 LYS cc_start: 0.9380 (ttmt) cc_final: 0.8505 (pmtt) REVERT: T 210 MET cc_start: 0.8906 (mmm) cc_final: 0.7750 (ttp) REVERT: T 295 ARG cc_start: 0.9088 (ttp80) cc_final: 0.8489 (mpt180) REVERT: T 318 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7102 (ttp-170) REVERT: T 323 GLN cc_start: 0.8552 (mp10) cc_final: 0.8215 (mp10) REVERT: T 331 HIS cc_start: 0.8623 (t-90) cc_final: 0.8164 (t-90) REVERT: T 342 LYS cc_start: 0.9061 (mttt) cc_final: 0.7968 (pptt) REVERT: c 11 MET cc_start: 0.8817 (mmm) cc_final: 0.8576 (mmm) outliers start: 35 outliers final: 15 residues processed: 249 average time/residue: 1.5172 time to fit residues: 427.2918 Evaluate side-chains 240 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 24 GLU Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 363 GLU Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 13 TRP Chi-restraints excluded: chain O residue 15 ASN Chi-restraints excluded: chain O residue 247 THR Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 369 VAL Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 314 MET Chi-restraints excluded: chain T residue 318 ARG Chi-restraints excluded: chain c residue 34 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 59 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 269 optimal weight: 20.0000 chunk 179 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 310 GLN Q 291 ASN Q 388 HIS T 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.058782 restraints weight = 45359.378| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 2.18 r_work: 0.2522 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 22833 Z= 0.324 Angle : 0.553 11.305 30917 Z= 0.296 Chirality : 0.043 0.164 3424 Planarity : 0.004 0.047 4038 Dihedral : 4.638 22.538 3072 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.09 % Allowed : 13.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 2881 helix: 1.49 (0.24), residues: 540 sheet: 0.33 (0.17), residues: 907 loop : -1.08 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 378 HIS 0.003 0.001 HIS M 63 PHE 0.014 0.001 PHE R 212 TYR 0.025 0.001 TYR T 204 ARG 0.004 0.000 ARG N 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 2.668 Fit side-chains REVERT: M 24 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8916 (mt-10) REVERT: M 277 GLN cc_start: 0.9417 (mt0) cc_final: 0.9216 (mt0) REVERT: N 180 LYS cc_start: 0.9282 (mttt) cc_final: 0.8472 (pptt) REVERT: N 186 LYS cc_start: 0.5839 (OUTLIER) cc_final: 0.4624 (ptpt) REVERT: N 363 GLU cc_start: 0.8674 (tt0) cc_final: 0.8401 (tt0) REVERT: O 7 LEU cc_start: 0.8979 (mm) cc_final: 0.8392 (tm) REVERT: O 8 ARG cc_start: 0.8031 (ttt90) cc_final: 0.6494 (pmt-80) REVERT: O 13 TRP cc_start: 0.9251 (OUTLIER) cc_final: 0.7975 (m-10) REVERT: O 325 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8928 (mt-10) REVERT: P 25 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8862 (p) REVERT: P 30 GLU cc_start: 0.9223 (mt-10) cc_final: 0.9010 (mp0) REVERT: P 93 ASP cc_start: 0.8974 (m-30) cc_final: 0.8364 (m-30) REVERT: P 186 LYS cc_start: 0.6020 (OUTLIER) cc_final: 0.5500 (pmtt) REVERT: P 219 GLU cc_start: 0.9187 (tt0) cc_final: 0.8692 (tp30) REVERT: P 270 ASP cc_start: 0.8744 (t0) cc_final: 0.8413 (t70) REVERT: Q 93 ASP cc_start: 0.9022 (m-30) cc_final: 0.8718 (m-30) REVERT: Q 122 LYS cc_start: 0.8919 (tptm) cc_final: 0.8628 (tppt) REVERT: Q 177 GLU cc_start: 0.5180 (pp20) cc_final: 0.4225 (pp20) REVERT: Q 186 LYS cc_start: 0.9107 (ttpp) cc_final: 0.8372 (mptt) REVERT: Q 270 ASP cc_start: 0.8652 (p0) cc_final: 0.8435 (t70) REVERT: R 270 ASP cc_start: 0.8789 (t0) cc_final: 0.8323 (t0) REVERT: T 24 GLU cc_start: 0.8781 (mp0) cc_final: 0.8211 (tm-30) REVERT: T 29 MET cc_start: 0.7291 (mmt) cc_final: 0.5091 (ptt) REVERT: T 93 ASP cc_start: 0.9036 (m-30) cc_final: 0.8710 (m-30) REVERT: T 96 MET cc_start: 0.8647 (ttt) cc_final: 0.7876 (tpp) REVERT: T 122 LYS cc_start: 0.9424 (tttp) cc_final: 0.9067 (mmmm) REVERT: T 186 LYS cc_start: 0.9374 (ttmt) cc_final: 0.8520 (pmtt) REVERT: T 210 MET cc_start: 0.8926 (mmm) cc_final: 0.7768 (ttp) REVERT: T 295 ARG cc_start: 0.9108 (ttp80) cc_final: 0.8496 (mpt180) REVERT: T 323 GLN cc_start: 0.8584 (mp10) cc_final: 0.8142 (mp10) REVERT: T 331 HIS cc_start: 0.8645 (t-90) cc_final: 0.8209 (t-90) REVERT: T 342 LYS cc_start: 0.9066 (mttt) cc_final: 0.7972 (pptt) REVERT: T 378 TRP cc_start: 0.9327 (m100) cc_final: 0.8976 (m100) REVERT: c 11 MET cc_start: 0.8732 (mmm) cc_final: 0.8455 (mmm) outliers start: 49 outliers final: 16 residues processed: 262 average time/residue: 1.4956 time to fit residues: 442.8899 Evaluate side-chains 240 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 24 GLU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 346 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 186 LYS Chi-restraints excluded: chain O residue 13 TRP Chi-restraints excluded: chain O residue 15 ASN Chi-restraints excluded: chain O residue 160 ARG Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 186 LYS Chi-restraints excluded: chain P residue 346 VAL Chi-restraints excluded: chain P residue 369 VAL Chi-restraints excluded: chain Q residue 84 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 247 THR Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain c residue 34 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 13 optimal weight: 4.9990 chunk 268 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 222 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 277 optimal weight: 40.0000 chunk 152 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 231 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 303 ASN P 310 GLN Q 291 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.093380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.061020 restraints weight = 45207.498| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.20 r_work: 0.2572 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22833 Z= 0.161 Angle : 0.493 12.113 30917 Z= 0.261 Chirality : 0.041 0.154 3424 Planarity : 0.004 0.047 4038 Dihedral : 4.334 23.125 3072 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.88 % Allowed : 13.83 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2881 helix: 1.82 (0.25), residues: 530 sheet: 0.41 (0.17), residues: 915 loop : -0.97 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP T 378 HIS 0.005 0.000 HIS N 388 PHE 0.009 0.001 PHE P 394 TYR 0.023 0.001 TYR T 204 ARG 0.002 0.000 ARG N 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 2.556 Fit side-chains REVERT: M 24 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8877 (mt-10) REVERT: M 277 GLN cc_start: 0.9426 (mt0) cc_final: 0.9200 (mt0) REVERT: N 180 LYS cc_start: 0.9234 (mttt) cc_final: 0.8485 (pptt) REVERT: N 186 LYS cc_start: 0.5821 (OUTLIER) cc_final: 0.4610 (ptpt) REVERT: N 363 GLU cc_start: 0.8655 (tt0) cc_final: 0.8365 (tt0) REVERT: O 7 LEU cc_start: 0.8893 (mm) cc_final: 0.8339 (tm) REVERT: O 8 ARG cc_start: 0.8055 (ttt90) cc_final: 0.6390 (pmt-80) REVERT: O 13 TRP cc_start: 0.9197 (OUTLIER) cc_final: 0.7971 (m-10) REVERT: P 13 TRP cc_start: 0.9404 (OUTLIER) cc_final: 0.8800 (m-90) REVERT: P 25 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8853 (p) REVERT: P 41 MET cc_start: 0.9168 (mmm) cc_final: 0.8965 (mmm) REVERT: P 82 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8854 (m-30) REVERT: P 93 ASP cc_start: 0.8971 (m-30) cc_final: 0.8403 (m-30) REVERT: P 186 LYS cc_start: 0.6158 (OUTLIER) cc_final: 0.5603 (pmtt) REVERT: P 219 GLU cc_start: 0.9201 (tt0) cc_final: 0.8735 (tp30) REVERT: P 270 ASP cc_start: 0.8726 (t0) cc_final: 0.8483 (t70) REVERT: Q 64 ASN cc_start: 0.9495 (t0) cc_final: 0.9204 (t0) REVERT: Q 93 ASP cc_start: 0.8994 (m-30) cc_final: 0.8729 (m-30) REVERT: Q 122 LYS cc_start: 0.8881 (tptm) cc_final: 0.8517 (tppp) REVERT: Q 177 GLU cc_start: 0.5175 (pp20) cc_final: 0.4484 (pp20) REVERT: Q 186 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8369 (mptt) REVERT: Q 270 ASP cc_start: 0.8603 (p0) cc_final: 0.8329 (t70) REVERT: R 270 ASP cc_start: 0.8666 (t0) cc_final: 0.8263 (t0) REVERT: R 347 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8955 (pp) REVERT: T 24 GLU cc_start: 0.8791 (mp0) cc_final: 0.8235 (tm-30) REVERT: T 29 MET cc_start: 0.7223 (mmt) cc_final: 0.5093 (ptt) REVERT: T 93 ASP cc_start: 0.9044 (m-30) cc_final: 0.8710 (m-30) REVERT: T 96 MET cc_start: 0.8689 (ttt) cc_final: 0.7947 (tpp) REVERT: T 122 LYS cc_start: 0.9416 (tttp) cc_final: 0.9075 (mmmm) REVERT: T 186 LYS cc_start: 0.9348 (ttmt) cc_final: 0.8517 (pmtt) REVERT: T 210 MET cc_start: 0.8887 (mmm) cc_final: 0.7652 (ttp) REVERT: T 295 ARG cc_start: 0.9104 (ttp80) cc_final: 0.8488 (mpt180) REVERT: T 318 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7390 (ttp-170) REVERT: T 323 GLN cc_start: 0.8526 (mp10) cc_final: 0.8235 (mp10) REVERT: T 331 HIS cc_start: 0.8542 (t-90) cc_final: 0.8116 (t-90) REVERT: T 342 LYS cc_start: 0.9042 (mttt) cc_final: 0.7907 (pptt) outliers start: 44 outliers final: 17 residues processed: 274 average time/residue: 1.4569 time to fit residues: 452.3861 Evaluate side-chains 261 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 24 GLU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 346 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 186 LYS Chi-restraints excluded: chain O residue 13 TRP Chi-restraints excluded: chain O residue 15 ASN Chi-restraints excluded: chain O residue 160 ARG Chi-restraints excluded: chain O residue 221 VAL Chi-restraints excluded: chain P residue 13 TRP Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 29 MET Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 186 LYS Chi-restraints excluded: chain P residue 346 VAL Chi-restraints excluded: chain P residue 369 VAL Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 317 THR Chi-restraints excluded: chain T residue 318 ARG Chi-restraints excluded: chain c residue 34 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 151 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 277 optimal weight: 30.0000 chunk 232 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 234 optimal weight: 30.0000 chunk 168 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 310 GLN Q 291 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.057960 restraints weight = 45912.969| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 2.19 r_work: 0.2501 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 22833 Z= 0.458 Angle : 0.608 11.810 30917 Z= 0.324 Chirality : 0.045 0.180 3424 Planarity : 0.005 0.047 4038 Dihedral : 4.689 21.805 3072 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.05 % Allowed : 14.18 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 2881 helix: 1.50 (0.24), residues: 540 sheet: 0.29 (0.17), residues: 910 loop : -1.06 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 378 HIS 0.004 0.001 HIS Q 337 PHE 0.017 0.001 PHE N 316 TYR 0.027 0.002 TYR T 204 ARG 0.006 0.001 ARG N 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 2.439 Fit side-chains REVERT: N 180 LYS cc_start: 0.9313 (mttt) cc_final: 0.8466 (pptt) REVERT: N 186 LYS cc_start: 0.5839 (OUTLIER) cc_final: 0.4661 (ptpt) REVERT: N 363 GLU cc_start: 0.8700 (tt0) cc_final: 0.8425 (tt0) REVERT: O 8 ARG cc_start: 0.8119 (ttt90) cc_final: 0.6590 (pmt-80) REVERT: O 13 TRP cc_start: 0.9238 (OUTLIER) cc_final: 0.7994 (m-10) REVERT: P 13 TRP cc_start: 0.9449 (OUTLIER) cc_final: 0.8772 (m-90) REVERT: P 25 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8893 (p) REVERT: P 93 ASP cc_start: 0.8976 (m-30) cc_final: 0.8355 (m-30) REVERT: P 186 LYS cc_start: 0.6142 (OUTLIER) cc_final: 0.5701 (pmtt) REVERT: P 219 GLU cc_start: 0.9163 (tt0) cc_final: 0.8677 (tp30) REVERT: P 270 ASP cc_start: 0.8798 (t0) cc_final: 0.8470 (t70) REVERT: Q 93 ASP cc_start: 0.9014 (m-30) cc_final: 0.8727 (m-30) REVERT: Q 122 LYS cc_start: 0.8902 (tptm) cc_final: 0.8512 (tppp) REVERT: Q 177 GLU cc_start: 0.5384 (pp20) cc_final: 0.4431 (pp20) REVERT: Q 186 LYS cc_start: 0.9134 (ttpp) cc_final: 0.8402 (mptt) REVERT: R 270 ASP cc_start: 0.8771 (t0) cc_final: 0.8286 (t0) REVERT: R 347 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8498 (pp) REVERT: R 392 MET cc_start: 0.9581 (OUTLIER) cc_final: 0.7598 (mmt) REVERT: T 24 GLU cc_start: 0.8835 (mp0) cc_final: 0.8232 (tm-30) REVERT: T 93 ASP cc_start: 0.9005 (m-30) cc_final: 0.8652 (m-30) REVERT: T 96 MET cc_start: 0.8747 (ttt) cc_final: 0.8039 (tpp) REVERT: T 122 LYS cc_start: 0.9386 (tttp) cc_final: 0.9020 (mmmm) REVERT: T 186 LYS cc_start: 0.9370 (ttmt) cc_final: 0.8484 (pmtt) REVERT: T 210 MET cc_start: 0.8893 (mmm) cc_final: 0.7762 (ttp) REVERT: T 295 ARG cc_start: 0.9092 (ttp80) cc_final: 0.8495 (mpt180) REVERT: T 317 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7528 (t) REVERT: T 318 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7392 (ttp-170) REVERT: T 323 GLN cc_start: 0.8648 (mp10) cc_final: 0.8264 (mp10) REVERT: T 331 HIS cc_start: 0.8657 (t-90) cc_final: 0.8214 (t-90) REVERT: T 342 LYS cc_start: 0.8969 (mttt) cc_final: 0.7836 (pptt) REVERT: c 11 MET cc_start: 0.8764 (mmm) cc_final: 0.8497 (mmm) outliers start: 48 outliers final: 26 residues processed: 253 average time/residue: 1.4988 time to fit residues: 430.2244 Evaluate side-chains 248 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 234 LEU Chi-restraints excluded: chain M residue 346 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 186 LYS Chi-restraints excluded: chain N residue 356 VAL Chi-restraints excluded: chain O residue 13 TRP Chi-restraints excluded: chain O residue 15 ASN Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 160 ARG Chi-restraints excluded: chain O residue 221 VAL Chi-restraints excluded: chain O residue 259 LEU Chi-restraints excluded: chain P residue 13 TRP Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 186 LYS Chi-restraints excluded: chain P residue 346 VAL Chi-restraints excluded: chain P residue 369 VAL Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 247 THR Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 347 LEU Chi-restraints excluded: chain R residue 392 MET Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 317 THR Chi-restraints excluded: chain T residue 318 ARG Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 40 optimal weight: 0.0980 chunk 64 optimal weight: 0.0270 chunk 144 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 310 GLN Q 291 ASN T 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.093974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.061769 restraints weight = 45084.668| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.20 r_work: 0.2587 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22833 Z= 0.141 Angle : 0.497 9.865 30917 Z= 0.261 Chirality : 0.041 0.155 3424 Planarity : 0.004 0.047 4038 Dihedral : 4.269 22.974 3072 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.54 % Allowed : 15.20 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2881 helix: 1.85 (0.25), residues: 530 sheet: 0.36 (0.17), residues: 902 loop : -0.92 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP T 378 HIS 0.002 0.000 HIS M 63 PHE 0.010 0.001 PHE N 22 TYR 0.023 0.001 TYR T 204 ARG 0.002 0.000 ARG N 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 249 time to evaluate : 2.601 Fit side-chains REVERT: M 24 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8845 (mt-10) REVERT: M 277 GLN cc_start: 0.9411 (mt0) cc_final: 0.9207 (mt0) REVERT: N 180 LYS cc_start: 0.9218 (mttt) cc_final: 0.8487 (pptt) REVERT: N 186 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.4615 (ptpt) REVERT: N 363 GLU cc_start: 0.8649 (tt0) cc_final: 0.8358 (tt0) REVERT: O 7 LEU cc_start: 0.8984 (mm) cc_final: 0.8439 (tm) REVERT: O 8 ARG cc_start: 0.8017 (ttt90) cc_final: 0.6358 (pmt-80) REVERT: O 13 TRP cc_start: 0.9177 (OUTLIER) cc_final: 0.7997 (m-10) REVERT: P 13 TRP cc_start: 0.9394 (OUTLIER) cc_final: 0.8929 (m-90) REVERT: P 25 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8869 (p) REVERT: P 29 MET cc_start: 0.8479 (ttp) cc_final: 0.8269 (mtm) REVERT: P 41 MET cc_start: 0.9269 (tpp) cc_final: 0.9039 (mmm) REVERT: P 82 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8868 (m-30) REVERT: P 93 ASP cc_start: 0.8975 (m-30) cc_final: 0.8410 (m-30) REVERT: P 113 GLU cc_start: 0.8936 (tp30) cc_final: 0.8708 (tp30) REVERT: P 186 LYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5596 (pmtt) REVERT: P 219 GLU cc_start: 0.9176 (tt0) cc_final: 0.8725 (tp30) REVERT: Q 93 ASP cc_start: 0.8987 (m-30) cc_final: 0.8707 (m-30) REVERT: Q 122 LYS cc_start: 0.8837 (tptm) cc_final: 0.8470 (tppp) REVERT: Q 177 GLU cc_start: 0.5122 (pp20) cc_final: 0.4523 (pp20) REVERT: Q 186 LYS cc_start: 0.9081 (ttpp) cc_final: 0.8365 (mptt) REVERT: R 270 ASP cc_start: 0.8620 (t0) cc_final: 0.8271 (t0) REVERT: T 24 GLU cc_start: 0.8807 (mp0) cc_final: 0.8246 (tm-30) REVERT: T 93 ASP cc_start: 0.9041 (m-30) cc_final: 0.8689 (m-30) REVERT: T 96 MET cc_start: 0.8736 (ttt) cc_final: 0.7989 (tpp) REVERT: T 122 LYS cc_start: 0.9394 (tttp) cc_final: 0.9137 (tptm) REVERT: T 186 LYS cc_start: 0.9365 (ttmt) cc_final: 0.8498 (pmtt) REVERT: T 210 MET cc_start: 0.8764 (mmm) cc_final: 0.7510 (tmt) REVERT: T 295 ARG cc_start: 0.9106 (ttp80) cc_final: 0.8493 (mpt180) REVERT: T 303 ASN cc_start: 0.8805 (m-40) cc_final: 0.8551 (m-40) REVERT: T 323 GLN cc_start: 0.8493 (mp10) cc_final: 0.8215 (mp10) REVERT: T 331 HIS cc_start: 0.8555 (t-90) cc_final: 0.8196 (t-90) REVERT: T 342 LYS cc_start: 0.9012 (mttt) cc_final: 0.7832 (pptt) REVERT: c 11 MET cc_start: 0.8764 (mmm) cc_final: 0.8534 (mmm) outliers start: 36 outliers final: 15 residues processed: 272 average time/residue: 1.4487 time to fit residues: 447.0918 Evaluate side-chains 258 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 24 GLU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 186 LYS Chi-restraints excluded: chain O residue 13 TRP Chi-restraints excluded: chain O residue 15 ASN Chi-restraints excluded: chain O residue 221 VAL Chi-restraints excluded: chain P residue 13 TRP Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 186 LYS Chi-restraints excluded: chain P residue 346 VAL Chi-restraints excluded: chain P residue 369 VAL Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 317 THR Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 138 optimal weight: 6.9990 chunk 243 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 291 ASN P 310 GLN Q 291 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.089839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.057139 restraints weight = 46004.653| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 2.19 r_work: 0.2488 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2388 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 22833 Z= 0.556 Angle : 0.663 13.077 30917 Z= 0.353 Chirality : 0.047 0.179 3424 Planarity : 0.005 0.049 4038 Dihedral : 4.790 21.424 3072 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.41 % Allowed : 15.80 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 2881 helix: 1.37 (0.24), residues: 544 sheet: 0.22 (0.17), residues: 887 loop : -1.06 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 378 HIS 0.006 0.001 HIS N 388 PHE 0.019 0.002 PHE N 316 TYR 0.027 0.002 TYR T 204 ARG 0.006 0.001 ARG N 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 2.702 Fit side-chains REVERT: N 180 LYS cc_start: 0.9326 (mttt) cc_final: 0.8454 (pptt) REVERT: N 186 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.4632 (ptpt) REVERT: N 363 GLU cc_start: 0.8718 (tt0) cc_final: 0.8486 (tt0) REVERT: N 398 ILE cc_start: 0.8596 (mt) cc_final: 0.8355 (tt) REVERT: O 8 ARG cc_start: 0.8169 (ttt90) cc_final: 0.6621 (pmt-80) REVERT: O 13 TRP cc_start: 0.9219 (OUTLIER) cc_final: 0.7893 (m-10) REVERT: P 13 TRP cc_start: 0.9450 (OUTLIER) cc_final: 0.8858 (m-90) REVERT: P 25 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8916 (p) REVERT: P 29 MET cc_start: 0.8733 (ttp) cc_final: 0.8440 (mtm) REVERT: P 93 ASP cc_start: 0.8969 (m-30) cc_final: 0.8337 (m-30) REVERT: P 219 GLU cc_start: 0.9154 (tt0) cc_final: 0.8690 (tp30) REVERT: Q 93 ASP cc_start: 0.9013 (m-30) cc_final: 0.8745 (m-30) REVERT: Q 122 LYS cc_start: 0.8888 (tptm) cc_final: 0.8494 (tppp) REVERT: Q 177 GLU cc_start: 0.5529 (pp20) cc_final: 0.4552 (pp20) REVERT: Q 186 LYS cc_start: 0.9136 (ttpp) cc_final: 0.8388 (mptt) REVERT: R 270 ASP cc_start: 0.8794 (t0) cc_final: 0.8296 (t0) REVERT: T 24 GLU cc_start: 0.8818 (mp0) cc_final: 0.8228 (tm-30) REVERT: T 93 ASP cc_start: 0.9013 (m-30) cc_final: 0.8643 (m-30) REVERT: T 96 MET cc_start: 0.8770 (ttt) cc_final: 0.8075 (tpp) REVERT: T 122 LYS cc_start: 0.9385 (tttp) cc_final: 0.9046 (mmmm) REVERT: T 186 LYS cc_start: 0.9406 (ttmt) cc_final: 0.8510 (pmtt) REVERT: T 210 MET cc_start: 0.8900 (mmm) cc_final: 0.7764 (ttp) REVERT: T 295 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8498 (mpt180) REVERT: T 317 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7702 (t) REVERT: T 323 GLN cc_start: 0.8813 (mp10) cc_final: 0.8421 (mp10) REVERT: T 331 HIS cc_start: 0.8706 (t-90) cc_final: 0.8309 (t-90) REVERT: T 342 LYS cc_start: 0.8922 (mttt) cc_final: 0.7732 (pptt) REVERT: c 11 MET cc_start: 0.8741 (mmm) cc_final: 0.8507 (mmm) outliers start: 33 outliers final: 20 residues processed: 244 average time/residue: 1.5214 time to fit residues: 422.2332 Evaluate side-chains 243 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 346 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 186 LYS Chi-restraints excluded: chain O residue 13 TRP Chi-restraints excluded: chain O residue 15 ASN Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 221 VAL Chi-restraints excluded: chain P residue 13 TRP Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 270 ASP Chi-restraints excluded: chain P residue 346 VAL Chi-restraints excluded: chain P residue 369 VAL Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 208 VAL Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 317 THR Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 48 optimal weight: 1.9990 chunk 279 optimal weight: 30.0000 chunk 67 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.057555 restraints weight = 45853.895| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 2.19 r_work: 0.2497 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 22833 Z= 0.382 Angle : 0.796 61.598 30917 Z= 0.401 Chirality : 0.045 0.592 3424 Planarity : 0.005 0.050 4038 Dihedral : 4.795 21.576 3072 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.15 % Allowed : 16.18 % Favored : 82.66 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2881 helix: 1.37 (0.24), residues: 544 sheet: 0.20 (0.17), residues: 888 loop : -1.06 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP M 378 HIS 0.005 0.001 HIS N 388 PHE 0.017 0.001 PHE N 316 TYR 0.027 0.002 TYR T 204 ARG 0.003 0.000 ARG N 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 2.709 Fit side-chains REVERT: N 180 LYS cc_start: 0.9323 (mttt) cc_final: 0.8461 (pptt) REVERT: N 186 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.4695 (ptpt) REVERT: N 363 GLU cc_start: 0.8710 (tt0) cc_final: 0.8477 (tt0) REVERT: N 398 ILE cc_start: 0.8577 (mt) cc_final: 0.8341 (tt) REVERT: O 8 ARG cc_start: 0.8155 (ttt90) cc_final: 0.6617 (pmt-80) REVERT: O 13 TRP cc_start: 0.9222 (OUTLIER) cc_final: 0.7916 (m-10) REVERT: P 13 TRP cc_start: 0.9445 (OUTLIER) cc_final: 0.8853 (m-90) REVERT: P 25 THR cc_start: 0.9206 (OUTLIER) cc_final: 0.8913 (p) REVERT: P 29 MET cc_start: 0.8728 (ttp) cc_final: 0.8429 (mtm) REVERT: P 93 ASP cc_start: 0.8959 (m-30) cc_final: 0.8328 (m-30) REVERT: P 186 LYS cc_start: 0.5208 (pmtt) cc_final: 0.4891 (pmtt) REVERT: Q 93 ASP cc_start: 0.9013 (m-30) cc_final: 0.8740 (m-30) REVERT: Q 122 LYS cc_start: 0.8887 (tptm) cc_final: 0.8493 (tppp) REVERT: Q 177 GLU cc_start: 0.5621 (pp20) cc_final: 0.4635 (pp20) REVERT: Q 186 LYS cc_start: 0.9144 (ttpp) cc_final: 0.8388 (mptt) REVERT: R 270 ASP cc_start: 0.8788 (t0) cc_final: 0.8319 (t0) REVERT: T 24 GLU cc_start: 0.8814 (mp0) cc_final: 0.8231 (tm-30) REVERT: T 29 MET cc_start: 0.5171 (OUTLIER) cc_final: 0.4665 (tpt) REVERT: T 93 ASP cc_start: 0.9018 (m-30) cc_final: 0.8645 (m-30) REVERT: T 96 MET cc_start: 0.8786 (ttt) cc_final: 0.8084 (tpp) REVERT: T 122 LYS cc_start: 0.9390 (tttp) cc_final: 0.9050 (mmmm) REVERT: T 186 LYS cc_start: 0.9402 (ttmt) cc_final: 0.8506 (pmtt) REVERT: T 210 MET cc_start: 0.8898 (mmm) cc_final: 0.7760 (ttp) REVERT: T 295 ARG cc_start: 0.9116 (ttp80) cc_final: 0.8499 (mpt180) REVERT: T 317 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7732 (t) REVERT: T 323 GLN cc_start: 0.8775 (mp10) cc_final: 0.8439 (mp10) REVERT: T 331 HIS cc_start: 0.8726 (t-90) cc_final: 0.8265 (t-90) REVERT: T 342 LYS cc_start: 0.8925 (mttt) cc_final: 0.7731 (pptt) REVERT: c 11 MET cc_start: 0.8718 (mmm) cc_final: 0.8488 (mmm) outliers start: 27 outliers final: 19 residues processed: 241 average time/residue: 1.5044 time to fit residues: 409.9122 Evaluate side-chains 244 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 346 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 186 LYS Chi-restraints excluded: chain N residue 356 VAL Chi-restraints excluded: chain O residue 13 TRP Chi-restraints excluded: chain O residue 15 ASN Chi-restraints excluded: chain O residue 37 LEU Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 221 VAL Chi-restraints excluded: chain P residue 13 TRP Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 346 VAL Chi-restraints excluded: chain P residue 369 VAL Chi-restraints excluded: chain Q residue 139 THR Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 29 MET Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 254 LEU Chi-restraints excluded: chain T residue 317 THR Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 222 optimal weight: 0.9980 chunk 219 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 193 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 310 GLN Q 291 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.062093 restraints weight = 45063.624| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 2.18 r_work: 0.2596 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22833 Z= 0.158 Angle : 0.558 23.972 30917 Z= 0.287 Chirality : 0.042 0.274 3424 Planarity : 0.004 0.121 4038 Dihedral : 4.292 23.536 3072 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.90 % Allowed : 16.52 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2881 helix: 1.67 (0.25), residues: 541 sheet: 0.32 (0.17), residues: 900 loop : -0.92 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 378 HIS 0.002 0.000 HIS O 331 PHE 0.011 0.001 PHE N 22 TYR 0.022 0.001 TYR T 204 ARG 0.003 0.000 ARG R 23 =============================================================================== Job complete usr+sys time: 18832.12 seconds wall clock time: 341 minutes 51.64 seconds (20511.64 seconds total)