Starting phenix.real_space_refine on Fri Sep 19 00:48:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9in6_60702/09_2025/9in6_60702.cif Found real_map, /net/cci-nas-00/data/ceres_data/9in6_60702/09_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_60702/09_2025/9in6_60702.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9in6_60702/09_2025/9in6_60702.map" model { file = "/net/cci-nas-00/data/ceres_data/9in6_60702/09_2025/9in6_60702.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9in6_60702/09_2025/9in6_60702.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.57, per 1000 atoms: 0.25 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: 1.80 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.9 microseconds 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: 1.17 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: 4.85 Time building geometry restraints manager: 2.40 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.260 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.910 ------------------------------------------------------------------------------- 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= 0.206 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 : 4.09 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (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 ARG 0.005 0.000 ARG T 200 TYR 0.015 0.002 TYR R 214 PHE 0.028 0.001 PHE O 212 TRP 0.034 0.001 TRP M 13 HIS 0.005 0.001 HIS N 331 Details of bonding type rmsd covalent geometry : bond 0.00449 (22833) covalent geometry : angle 0.57578 (30917) hydrogen bonds : bond 0.22764 ( 734) hydrogen bonds : angle 7.11443 ( 2094) *********************** 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 : 0.958 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: 0.6843 time to fit residues: 270.2368 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 : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.4980 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 310 GLN P 291 ASN P 377 GLN Q 388 HIS T 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.091245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.058503 restraints weight = 45361.562| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 2.19 r_work: 0.2518 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 22833 Z= 0.276 Angle : 0.637 14.287 30917 Z= 0.342 Chirality : 0.046 0.191 3424 Planarity : 0.005 0.051 4038 Dihedral : 4.903 21.777 3072 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.58 % Allowed : 8.54 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.15), residues: 2881 helix: 1.07 (0.24), residues: 553 sheet: 0.38 (0.17), residues: 898 loop : -1.12 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 301 TYR 0.022 0.002 TYR T 204 PHE 0.018 0.002 PHE T 202 TRP 0.028 0.002 TRP M 13 HIS 0.004 0.001 HIS M 388 Details of bonding type rmsd covalent geometry : bond 0.00660 (22833) covalent geometry : angle 0.63688 (30917) hydrogen bonds : bond 0.05483 ( 734) hydrogen bonds : angle 5.33311 ( 2094) *********************** 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 275 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 0.860 Fit side-chains REVERT: M 24 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8933 (mt-10) REVERT: N 180 LYS cc_start: 0.9265 (mttt) cc_final: 0.8507 (pptt) REVERT: N 186 LYS cc_start: 0.5754 (mptt) cc_final: 0.4541 (mptt) REVERT: N 363 GLU cc_start: 0.8597 (tt0) cc_final: 0.8305 (tt0) REVERT: O 8 ARG cc_start: 0.8071 (ttt90) cc_final: 0.6574 (pmt-80) REVERT: P 24 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8970 (mt-10) REVERT: P 25 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8860 (p) REVERT: P 93 ASP cc_start: 0.9006 (m-30) cc_final: 0.8408 (m-30) REVERT: P 186 LYS cc_start: 0.5667 (OUTLIER) cc_final: 0.5034 (pmtt) REVERT: P 205 TYR cc_start: 0.9418 (m-10) cc_final: 0.9167 (m-10) REVERT: Q 64 ASN cc_start: 0.9403 (t0) cc_final: 0.9117 (t0) REVERT: Q 122 LYS cc_start: 0.9032 (tptm) cc_final: 0.8611 (tppp) REVERT: Q 177 GLU cc_start: 0.5226 (pp20) cc_final: 0.4100 (tm-30) REVERT: Q 186 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8244 (mptt) REVERT: Q 314 MET cc_start: 0.9289 (ptp) cc_final: 0.9026 (ptt) REVERT: R 270 ASP cc_start: 0.8860 (t0) cc_final: 0.8524 (t0) REVERT: T 29 MET cc_start: 0.7413 (mmt) cc_final: 0.5108 (ptt) REVERT: T 122 LYS cc_start: 0.9362 (tttp) cc_final: 0.9003 (mmmm) REVERT: T 177 GLU cc_start: 0.5220 (OUTLIER) cc_final: 0.3896 (tm-30) REVERT: T 186 LYS cc_start: 0.9418 (ttmt) cc_final: 0.8561 (pmtt) REVERT: T 210 MET cc_start: 0.9024 (mmm) cc_final: 0.7753 (ptt) REVERT: T 295 ARG cc_start: 0.8986 (ttp80) cc_final: 0.8437 (mpt180) REVERT: T 318 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7154 (ttp-170) REVERT: T 323 GLN cc_start: 0.8636 (mp10) cc_final: 0.8221 (mp10) REVERT: T 331 HIS cc_start: 0.8491 (t-90) cc_final: 0.8037 (t-90) REVERT: T 342 LYS cc_start: 0.9043 (mttt) cc_final: 0.7892 (pptt) outliers start: 37 outliers final: 12 residues processed: 255 average time/residue: 0.6912 time to fit residues: 199.6609 Evaluate side-chains 243 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 226 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 24 GLU Chi-restraints excluded: chain M residue 346 VAL Chi-restraints excluded: chain N residue 40 LEU 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 O residue 369 VAL Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 186 LYS 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 177 GLU 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 200 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 228 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 234 optimal weight: 30.0000 chunk 88 optimal weight: 4.9990 chunk 260 optimal weight: 20.0000 chunk 252 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN O 244 GLN R 244 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 = 0.3287 r_free = 0.3287 target = 0.092398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.059767 restraints weight = 45336.502| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 2.21 r_work: 0.2542 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22833 Z= 0.162 Angle : 0.532 10.456 30917 Z= 0.286 Chirality : 0.043 0.164 3424 Planarity : 0.004 0.049 4038 Dihedral : 4.600 22.717 3072 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.45 % Allowed : 10.72 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.15), residues: 2881 helix: 1.45 (0.24), residues: 543 sheet: 0.45 (0.17), residues: 896 loop : -1.07 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 229 TYR 0.015 0.001 TYR T 204 PHE 0.014 0.001 PHE R 212 TRP 0.013 0.001 TRP M 13 HIS 0.003 0.001 HIS M 63 Details of bonding type rmsd covalent geometry : bond 0.00383 (22833) covalent geometry : angle 0.53234 (30917) hydrogen bonds : bond 0.04527 ( 734) hydrogen bonds : angle 4.98563 ( 2094) *********************** 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 282 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.870 Fit side-chains REVERT: M 24 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8901 (mt-10) REVERT: M 277 GLN cc_start: 0.9443 (mt0) cc_final: 0.9231 (mt0) REVERT: N 180 LYS cc_start: 0.9265 (mttt) cc_final: 0.8514 (pptt) REVERT: N 186 LYS cc_start: 0.5805 (OUTLIER) cc_final: 0.4677 (pttm) REVERT: N 363 GLU cc_start: 0.8657 (tt0) cc_final: 0.8404 (tt0) REVERT: O 7 LEU cc_start: 0.8901 (mm) cc_final: 0.8355 (tm) REVERT: O 8 ARG cc_start: 0.7972 (ttt90) cc_final: 0.6388 (pmt-80) REVERT: O 13 TRP cc_start: 0.9282 (OUTLIER) cc_final: 0.8082 (m-10) REVERT: O 325 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8894 (mt-10) REVERT: P 25 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8837 (p) REVERT: P 41 MET cc_start: 0.9169 (tpp) cc_final: 0.8910 (mmm) REVERT: P 93 ASP cc_start: 0.9022 (m-30) cc_final: 0.8400 (m-30) REVERT: P 205 TYR cc_start: 0.9430 (m-10) cc_final: 0.9203 (m-10) REVERT: P 219 GLU cc_start: 0.9173 (tt0) cc_final: 0.8684 (tp30) REVERT: Q 64 ASN cc_start: 0.9445 (t0) cc_final: 0.9218 (t0) REVERT: Q 93 ASP cc_start: 0.9058 (m-30) cc_final: 0.8763 (m-30) REVERT: Q 122 LYS cc_start: 0.9040 (tptm) cc_final: 0.8601 (tppp) REVERT: Q 177 GLU cc_start: 0.4988 (pp20) cc_final: 0.3893 (tm-30) REVERT: Q 186 LYS cc_start: 0.9083 (ttpp) cc_final: 0.8299 (mptt) REVERT: R 270 ASP cc_start: 0.8743 (t0) cc_final: 0.8320 (t0) REVERT: T 24 GLU cc_start: 0.8730 (mp0) cc_final: 0.8133 (tm-30) REVERT: T 29 MET cc_start: 0.7375 (mmt) cc_final: 0.5082 (ptt) REVERT: T 93 ASP cc_start: 0.9004 (m-30) cc_final: 0.8740 (m-30) REVERT: T 96 MET cc_start: 0.8449 (ttt) cc_final: 0.7620 (tpp) REVERT: T 122 LYS cc_start: 0.9398 (tttp) cc_final: 0.9053 (mmmm) REVERT: T 177 GLU cc_start: 0.5513 (OUTLIER) cc_final: 0.4266 (tm-30) REVERT: T 186 LYS cc_start: 0.9429 (ttmt) cc_final: 0.8486 (pmtt) REVERT: T 210 MET cc_start: 0.8913 (mmm) cc_final: 0.7680 (ttp) REVERT: T 295 ARG cc_start: 0.9066 (ttp80) cc_final: 0.8489 (mpt180) REVERT: T 323 GLN cc_start: 0.8582 (mp10) cc_final: 0.7961 (mp10) REVERT: T 331 HIS cc_start: 0.8592 (t-90) cc_final: 0.8129 (t-90) REVERT: T 342 LYS cc_start: 0.9068 (mttt) cc_final: 0.7910 (pptt) REVERT: T 392 MET cc_start: 0.8789 (mtt) cc_final: 0.8214 (mmt) outliers start: 34 outliers final: 12 residues processed: 265 average time/residue: 0.6726 time to fit residues: 201.8079 Evaluate side-chains 246 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 229 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 24 GLU 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 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 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 T residue 7 LEU Chi-restraints excluded: chain T residue 177 GLU Chi-restraints excluded: chain T residue 259 LEU 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 15 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 222 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 GLN T 303 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.060735 restraints weight = 45252.197| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 2.21 r_work: 0.2563 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2462 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.1994 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= 0.122 Angle : 0.498 9.631 30917 Z= 0.266 Chirality : 0.042 0.157 3424 Planarity : 0.004 0.045 4038 Dihedral : 4.398 22.351 3072 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.49 % Allowed : 12.47 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.16), residues: 2881 helix: 1.70 (0.25), residues: 537 sheet: 0.47 (0.17), residues: 910 loop : -0.98 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 229 TYR 0.016 0.001 TYR T 214 PHE 0.011 0.001 PHE R 212 TRP 0.014 0.001 TRP P 378 HIS 0.002 0.000 HIS M 63 Details of bonding type rmsd covalent geometry : bond 0.00286 (22833) covalent geometry : angle 0.49773 (30917) hydrogen bonds : bond 0.03948 ( 734) hydrogen bonds : angle 4.75597 ( 2094) *********************** 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 283 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.989 Fit side-chains REVERT: M 24 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8872 (mt-10) REVERT: M 277 GLN cc_start: 0.9430 (mt0) cc_final: 0.9224 (mt0) REVERT: N 180 LYS cc_start: 0.9255 (mttt) cc_final: 0.8525 (pptt) REVERT: N 186 LYS cc_start: 0.5638 (OUTLIER) cc_final: 0.4458 (pttm) REVERT: N 363 GLU cc_start: 0.8660 (tt0) cc_final: 0.8394 (tt0) REVERT: O 7 LEU cc_start: 0.8879 (mm) cc_final: 0.8313 (tm) REVERT: O 8 ARG cc_start: 0.8006 (ttt90) cc_final: 0.6420 (pmt-80) REVERT: O 13 TRP cc_start: 0.9240 (OUTLIER) cc_final: 0.7977 (m-10) REVERT: O 325 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8905 (mt-10) REVERT: P 25 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8824 (p) REVERT: P 30 GLU cc_start: 0.9219 (mt-10) cc_final: 0.9019 (mt-10) REVERT: P 41 MET cc_start: 0.9183 (tpp) cc_final: 0.8931 (mmm) REVERT: P 93 ASP cc_start: 0.9016 (m-30) cc_final: 0.8370 (m-30) REVERT: P 186 LYS cc_start: 0.5905 (OUTLIER) cc_final: 0.5316 (pmtt) REVERT: Q 64 ASN cc_start: 0.9477 (t0) cc_final: 0.9181 (t0) REVERT: Q 96 MET cc_start: 0.9391 (ttt) cc_final: 0.9172 (tpp) REVERT: Q 122 LYS cc_start: 0.9049 (tptm) cc_final: 0.8495 (tppp) REVERT: Q 177 GLU cc_start: 0.4839 (pp20) cc_final: 0.4112 (pp20) REVERT: Q 186 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8331 (mptt) REVERT: R 270 ASP cc_start: 0.8720 (t0) cc_final: 0.8300 (t0) REVERT: T 24 GLU cc_start: 0.8737 (mp0) cc_final: 0.8154 (tm-30) REVERT: T 29 MET cc_start: 0.7245 (mmt) cc_final: 0.4900 (ptt) REVERT: T 93 ASP cc_start: 0.9008 (m-30) cc_final: 0.8695 (m-30) REVERT: T 96 MET cc_start: 0.8600 (ttt) cc_final: 0.7810 (tpp) REVERT: T 122 LYS cc_start: 0.9405 (tttp) cc_final: 0.9064 (mmmm) REVERT: T 186 LYS cc_start: 0.9331 (ttmt) cc_final: 0.8475 (pmtt) REVERT: T 210 MET cc_start: 0.8926 (mmm) cc_final: 0.7675 (ttp) REVERT: T 295 ARG cc_start: 0.9084 (ttp80) cc_final: 0.8490 (mpt180) REVERT: T 318 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7163 (ttp-170) REVERT: T 323 GLN cc_start: 0.8581 (mp10) cc_final: 0.8175 (mp10) REVERT: T 331 HIS cc_start: 0.8510 (t-90) cc_final: 0.8072 (t-90) REVERT: T 342 LYS cc_start: 0.9052 (mttt) cc_final: 0.7907 (pptt) outliers start: 35 outliers final: 13 residues processed: 268 average time/residue: 0.6773 time to fit residues: 205.3359 Evaluate side-chains 255 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 24 GLU Chi-restraints excluded: chain M residue 234 LEU 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 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 152 SER Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 201 MET Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain T residue 7 LEU 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 265 optimal weight: 8.9990 chunk 209 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 243 optimal weight: 30.0000 chunk 114 optimal weight: 8.9990 chunk 270 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 310 GLN Q 388 HIS T 303 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.091289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.058538 restraints weight = 45165.734| |-----------------------------------------------------------------------------| r_work (start): 0.2623 rms_B_bonded: 2.20 r_work: 0.2519 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2419 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.2071 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= 0.234 Angle : 0.565 11.354 30917 Z= 0.301 Chirality : 0.044 0.169 3424 Planarity : 0.004 0.046 4038 Dihedral : 4.591 21.496 3072 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.92 % Allowed : 12.77 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.16), residues: 2881 helix: 1.55 (0.24), residues: 541 sheet: 0.41 (0.17), residues: 922 loop : -1.02 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 125 TYR 0.025 0.001 TYR T 204 PHE 0.017 0.001 PHE N 316 TRP 0.017 0.001 TRP P 378 HIS 0.003 0.001 HIS N 388 Details of bonding type rmsd covalent geometry : bond 0.00558 (22833) covalent geometry : angle 0.56463 (30917) hydrogen bonds : bond 0.04829 ( 734) hydrogen bonds : angle 4.88486 ( 2094) *********************** 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 280 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 235 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: M 277 GLN cc_start: 0.9428 (mt0) cc_final: 0.9214 (mt0) REVERT: N 180 LYS cc_start: 0.9320 (mttt) cc_final: 0.8501 (pptt) REVERT: N 186 LYS cc_start: 0.5736 (OUTLIER) cc_final: 0.4545 (ptpt) REVERT: N 363 GLU cc_start: 0.8693 (tt0) cc_final: 0.8409 (tt0) REVERT: O 8 ARG cc_start: 0.8122 (ttt90) cc_final: 0.6527 (pmt-80) REVERT: O 13 TRP cc_start: 0.9263 (OUTLIER) cc_final: 0.7948 (m-10) REVERT: O 24 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8216 (mm-30) REVERT: O 325 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8962 (mt-10) REVERT: P 13 TRP cc_start: 0.9431 (OUTLIER) cc_final: 0.8694 (m-90) REVERT: P 25 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8821 (p) REVERT: P 41 MET cc_start: 0.9203 (tpp) cc_final: 0.8872 (mmm) REVERT: P 93 ASP cc_start: 0.9014 (m-30) cc_final: 0.8362 (m-30) REVERT: P 219 GLU cc_start: 0.9171 (tt0) cc_final: 0.8680 (tp30) REVERT: P 270 ASP cc_start: 0.8751 (t0) cc_final: 0.8428 (t70) REVERT: P 344 MET cc_start: 0.9449 (ttp) cc_final: 0.8976 (ttp) REVERT: Q 64 ASN cc_start: 0.9460 (t0) cc_final: 0.9184 (t0) REVERT: Q 93 ASP cc_start: 0.9045 (m-30) cc_final: 0.8766 (m-30) REVERT: Q 122 LYS cc_start: 0.9072 (tptm) cc_final: 0.8491 (tppp) REVERT: Q 177 GLU cc_start: 0.5221 (pp20) cc_final: 0.4338 (pp20) REVERT: Q 186 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8357 (mptt) REVERT: Q 270 ASP cc_start: 0.8726 (p0) cc_final: 0.8341 (t70) REVERT: R 270 ASP cc_start: 0.8787 (t0) cc_final: 0.8309 (t0) REVERT: T 24 GLU cc_start: 0.8758 (mp0) cc_final: 0.8186 (tm-30) REVERT: T 29 MET cc_start: 0.7207 (mmt) cc_final: 0.5012 (ptt) REVERT: T 93 ASP cc_start: 0.9013 (m-30) cc_final: 0.8684 (m-30) REVERT: T 96 MET cc_start: 0.8708 (ttt) cc_final: 0.7937 (tpp) REVERT: T 122 LYS cc_start: 0.9419 (tttp) cc_final: 0.9074 (mmmm) REVERT: T 186 LYS cc_start: 0.9370 (ttmt) cc_final: 0.8506 (pmtt) REVERT: T 210 MET cc_start: 0.8930 (mmm) cc_final: 0.7769 (ttp) REVERT: T 295 ARG cc_start: 0.9100 (ttp80) cc_final: 0.8491 (mpt180) REVERT: T 323 GLN cc_start: 0.8560 (mp10) cc_final: 0.7983 (mp10) REVERT: T 331 HIS cc_start: 0.8603 (t-90) cc_final: 0.8152 (t-90) REVERT: T 342 LYS cc_start: 0.9059 (mttt) cc_final: 0.7963 (pptt) REVERT: T 392 MET cc_start: 0.8978 (mtt) cc_final: 0.8699 (mtt) outliers start: 45 outliers final: 20 residues processed: 262 average time/residue: 0.6548 time to fit residues: 194.2062 Evaluate side-chains 246 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 N residue 318 ARG 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 103 LEU 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 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 T residue 25 THR Chi-restraints excluded: chain T residue 259 LEU Chi-restraints excluded: chain T residue 314 MET 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 74 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 141 optimal weight: 0.0570 chunk 59 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 263 optimal weight: 40.0000 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 2.8104 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.092132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.059616 restraints weight = 45364.083| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 2.20 r_work: 0.2541 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22833 Z= 0.159 Angle : 0.520 10.493 30917 Z= 0.278 Chirality : 0.042 0.158 3424 Planarity : 0.004 0.047 4038 Dihedral : 4.462 22.348 3072 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.71 % Allowed : 13.28 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.16), residues: 2881 helix: 1.63 (0.24), residues: 541 sheet: 0.39 (0.17), residues: 906 loop : -0.99 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 125 TYR 0.025 0.001 TYR T 204 PHE 0.013 0.001 PHE N 316 TRP 0.015 0.001 TRP T 378 HIS 0.003 0.001 HIS M 63 Details of bonding type rmsd covalent geometry : bond 0.00378 (22833) covalent geometry : angle 0.51993 (30917) hydrogen bonds : bond 0.04247 ( 734) hydrogen bonds : angle 4.75251 ( 2094) *********************** 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 274 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 0.759 Fit side-chains REVERT: M 277 GLN cc_start: 0.9428 (mt0) cc_final: 0.9223 (mt0) REVERT: N 180 LYS cc_start: 0.9270 (mttt) cc_final: 0.8475 (pptt) REVERT: N 186 LYS cc_start: 0.5726 (OUTLIER) cc_final: 0.4535 (ptpt) REVERT: N 363 GLU cc_start: 0.8678 (tt0) cc_final: 0.8390 (tt0) REVERT: O 7 LEU cc_start: 0.8980 (mm) cc_final: 0.8436 (tm) REVERT: O 8 ARG cc_start: 0.8068 (ttt90) cc_final: 0.6412 (pmt-80) REVERT: O 13 TRP cc_start: 0.9219 (OUTLIER) cc_final: 0.7963 (m-10) REVERT: O 24 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8192 (mm-30) REVERT: O 325 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8945 (mt-10) REVERT: P 13 TRP cc_start: 0.9424 (OUTLIER) cc_final: 0.8740 (m-90) REVERT: P 25 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8849 (p) REVERT: P 30 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8964 (mp0) REVERT: P 41 MET cc_start: 0.9200 (tpp) cc_final: 0.8883 (mmm) REVERT: P 93 ASP cc_start: 0.8968 (m-30) cc_final: 0.8342 (m-30) REVERT: P 186 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5449 (pmtt) REVERT: P 219 GLU cc_start: 0.9186 (tt0) cc_final: 0.8678 (tp30) REVERT: P 270 ASP cc_start: 0.8757 (t0) cc_final: 0.8458 (t70) REVERT: P 344 MET cc_start: 0.9456 (ttp) cc_final: 0.8915 (ttp) REVERT: Q 64 ASN cc_start: 0.9470 (t0) cc_final: 0.9182 (t0) REVERT: Q 93 ASP cc_start: 0.9002 (m-30) cc_final: 0.8709 (m-30) REVERT: Q 122 LYS cc_start: 0.9084 (tptm) cc_final: 0.8647 (tppp) REVERT: Q 177 GLU cc_start: 0.5155 (pp20) cc_final: 0.4381 (pp20) REVERT: Q 186 LYS cc_start: 0.9106 (ttpp) cc_final: 0.8429 (mptt) REVERT: Q 270 ASP cc_start: 0.8686 (p0) cc_final: 0.8339 (t70) REVERT: R 270 ASP cc_start: 0.8724 (t0) cc_final: 0.8293 (t0) REVERT: T 24 GLU cc_start: 0.8792 (mp0) cc_final: 0.8235 (tm-30) REVERT: T 29 MET cc_start: 0.7183 (mmt) cc_final: 0.5014 (ptt) REVERT: T 93 ASP cc_start: 0.9037 (m-30) cc_final: 0.8684 (m-30) REVERT: T 96 MET cc_start: 0.8808 (ttt) cc_final: 0.8103 (tpp) REVERT: T 122 LYS cc_start: 0.9422 (tttp) cc_final: 0.9077 (mmmm) REVERT: T 186 LYS cc_start: 0.9358 (ttmt) cc_final: 0.8523 (pmtt) REVERT: T 210 MET cc_start: 0.8912 (mmm) cc_final: 0.7760 (ttp) REVERT: T 295 ARG cc_start: 0.9104 (ttp80) cc_final: 0.8495 (mpt180) REVERT: T 323 GLN cc_start: 0.8543 (mp10) cc_final: 0.8201 (mp10) REVERT: T 331 HIS cc_start: 0.8579 (t-90) cc_final: 0.8145 (t-90) REVERT: T 342 LYS cc_start: 0.9054 (mttt) cc_final: 0.7958 (pptt) REVERT: T 392 MET cc_start: 0.9050 (mtt) cc_final: 0.8775 (mtt) outliers start: 40 outliers final: 18 residues processed: 260 average time/residue: 0.6945 time to fit residues: 205.1660 Evaluate side-chains 253 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 103 LEU Chi-restraints excluded: chain O residue 160 ARG 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 30 GLU 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 254 LEU Chi-restraints excluded: chain T residue 314 MET Chi-restraints excluded: chain c residue 34 VAL Chi-restraints excluded: chain c residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 177 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 chunk 267 optimal weight: 10.0000 chunk 260 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.090771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.058252 restraints weight = 45653.862| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 2.19 r_work: 0.2510 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2410 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.2235 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= 0.257 Angle : 0.583 11.724 30917 Z= 0.312 Chirality : 0.044 0.174 3424 Planarity : 0.004 0.047 4038 Dihedral : 4.651 21.606 3072 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.96 % Allowed : 13.92 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.15), residues: 2881 helix: 1.50 (0.24), residues: 541 sheet: 0.30 (0.17), residues: 908 loop : -1.04 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 125 TYR 0.026 0.002 TYR T 204 PHE 0.017 0.001 PHE N 316 TRP 0.017 0.001 TRP T 378 HIS 0.004 0.001 HIS N 388 Details of bonding type rmsd covalent geometry : bond 0.00616 (22833) covalent geometry : angle 0.58323 (30917) hydrogen bonds : bond 0.04977 ( 734) hydrogen bonds : angle 4.90662 ( 2094) *********************** 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 267 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 221 time to evaluate : 0.788 Fit side-chains REVERT: N 180 LYS cc_start: 0.9306 (mttt) cc_final: 0.8495 (pptt) REVERT: N 186 LYS cc_start: 0.5448 (OUTLIER) cc_final: 0.4207 (ptpt) REVERT: N 363 GLU cc_start: 0.8691 (tt0) cc_final: 0.8402 (tt0) REVERT: O 8 ARG cc_start: 0.8096 (ttt90) cc_final: 0.6529 (pmt-80) REVERT: O 13 TRP cc_start: 0.9252 (OUTLIER) cc_final: 0.7912 (m-10) REVERT: O 24 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8278 (mm-30) REVERT: P 13 TRP cc_start: 0.9445 (OUTLIER) cc_final: 0.8772 (m-90) REVERT: P 25 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8882 (p) REVERT: P 30 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9010 (mp0) REVERT: P 93 ASP cc_start: 0.8964 (m-30) cc_final: 0.8336 (m-30) REVERT: P 186 LYS cc_start: 0.6142 (OUTLIER) cc_final: 0.5792 (pmtt) REVERT: P 219 GLU cc_start: 0.9158 (tt0) cc_final: 0.8667 (tp30) REVERT: P 270 ASP cc_start: 0.8788 (t0) cc_final: 0.8453 (t70) REVERT: P 344 MET cc_start: 0.9487 (ttp) cc_final: 0.8949 (ttp) REVERT: Q 93 ASP cc_start: 0.9013 (m-30) cc_final: 0.8725 (m-30) REVERT: Q 122 LYS cc_start: 0.9087 (tptm) cc_final: 0.8492 (tppp) REVERT: Q 177 GLU cc_start: 0.5401 (pp20) cc_final: 0.4465 (pp20) REVERT: Q 186 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8368 (mptt) REVERT: Q 270 ASP cc_start: 0.8670 (p0) cc_final: 0.8317 (t70) REVERT: R 270 ASP cc_start: 0.8767 (t0) cc_final: 0.8282 (t0) REVERT: T 24 GLU cc_start: 0.8830 (mp0) cc_final: 0.8227 (tm-30) REVERT: T 93 ASP cc_start: 0.9011 (m-30) cc_final: 0.8639 (m-30) REVERT: T 96 MET cc_start: 0.8788 (ttt) cc_final: 0.8113 (tpp) REVERT: T 122 LYS cc_start: 0.9416 (tttp) cc_final: 0.9062 (mmmm) REVERT: T 186 LYS cc_start: 0.9353 (ttmt) cc_final: 0.8472 (pmtt) REVERT: T 210 MET cc_start: 0.8898 (mmm) cc_final: 0.7743 (ttp) REVERT: T 295 ARG cc_start: 0.9087 (ttp80) cc_final: 0.8500 (mpt180) REVERT: T 305 ASP cc_start: 0.7676 (p0) cc_final: 0.7470 (p0) REVERT: T 323 GLN cc_start: 0.8645 (mp10) cc_final: 0.8210 (mp10) REVERT: T 331 HIS cc_start: 0.8645 (t-90) cc_final: 0.8224 (t-90) REVERT: T 342 LYS cc_start: 0.8932 (mttt) cc_final: 0.7825 (pptt) REVERT: T 392 MET cc_start: 0.9047 (mtt) cc_final: 0.8772 (mtt) outliers start: 46 outliers final: 22 residues processed: 252 average time/residue: 0.6518 time to fit residues: 186.6037 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 : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 103 LEU Chi-restraints excluded: chain O residue 160 ARG 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 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 T residue 123 VAL Chi-restraints excluded: chain T residue 254 LEU 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 268 optimal weight: 20.0000 chunk 188 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 206 optimal weight: 5.9990 chunk 274 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 275 optimal weight: 50.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.091132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.058554 restraints weight = 45365.415| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 2.18 r_work: 0.2516 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2415 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9050 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 22833 Z= 0.224 Angle : 0.566 11.394 30917 Z= 0.303 Chirality : 0.044 0.163 3424 Planarity : 0.004 0.051 4038 Dihedral : 4.636 22.039 3072 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.67 % Allowed : 14.39 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.15), residues: 2881 helix: 1.52 (0.24), residues: 539 sheet: 0.28 (0.17), residues: 894 loop : -1.05 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 125 TYR 0.026 0.001 TYR T 204 PHE 0.016 0.001 PHE N 316 TRP 0.015 0.001 TRP T 378 HIS 0.003 0.001 HIS M 63 Details of bonding type rmsd covalent geometry : bond 0.00536 (22833) covalent geometry : angle 0.56623 (30917) hydrogen bonds : bond 0.04759 ( 734) hydrogen bonds : angle 4.85826 ( 2094) *********************** 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 262 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.886 Fit side-chains REVERT: M 277 GLN cc_start: 0.9424 (mt0) cc_final: 0.9207 (mt0) REVERT: N 180 LYS cc_start: 0.9301 (mttt) cc_final: 0.8487 (pptt) REVERT: N 186 LYS cc_start: 0.5455 (OUTLIER) cc_final: 0.4263 (ptpt) REVERT: N 363 GLU cc_start: 0.8696 (tt0) cc_final: 0.8405 (tt0) REVERT: O 8 ARG cc_start: 0.8140 (ttt90) cc_final: 0.6560 (pmt-80) REVERT: O 13 TRP cc_start: 0.9256 (OUTLIER) cc_final: 0.7921 (m-10) REVERT: O 24 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8261 (mm-30) REVERT: P 13 TRP cc_start: 0.9434 (OUTLIER) cc_final: 0.8830 (m-90) REVERT: P 25 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8915 (p) REVERT: P 29 MET cc_start: 0.8816 (ttp) cc_final: 0.8444 (mtm) REVERT: P 30 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.9036 (mp0) REVERT: P 93 ASP cc_start: 0.8967 (m-30) cc_final: 0.8322 (m-30) REVERT: P 113 GLU cc_start: 0.8968 (tp30) cc_final: 0.8729 (tp30) REVERT: P 186 LYS cc_start: 0.6189 (OUTLIER) cc_final: 0.5777 (pmtt) REVERT: P 270 ASP cc_start: 0.8777 (t0) cc_final: 0.8502 (t70) REVERT: P 344 MET cc_start: 0.9490 (ttp) cc_final: 0.8981 (ttp) REVERT: Q 93 ASP cc_start: 0.9015 (m-30) cc_final: 0.8739 (m-30) REVERT: Q 122 LYS cc_start: 0.9084 (tptm) cc_final: 0.8493 (tppp) REVERT: Q 177 GLU cc_start: 0.5292 (pp20) cc_final: 0.4439 (pp20) REVERT: Q 186 LYS cc_start: 0.9109 (ttpp) cc_final: 0.8347 (mptt) REVERT: Q 270 ASP cc_start: 0.8677 (p0) cc_final: 0.8336 (t70) REVERT: R 270 ASP cc_start: 0.8766 (t0) cc_final: 0.8290 (t0) REVERT: T 24 GLU cc_start: 0.8802 (mp0) cc_final: 0.8227 (tm-30) REVERT: T 93 ASP cc_start: 0.9040 (m-30) cc_final: 0.8686 (m-30) REVERT: T 96 MET cc_start: 0.8838 (ttt) cc_final: 0.8143 (tpp) REVERT: T 122 LYS cc_start: 0.9410 (tttp) cc_final: 0.9146 (tptm) REVERT: T 186 LYS cc_start: 0.9367 (ttmt) cc_final: 0.8482 (pmtt) REVERT: T 210 MET cc_start: 0.8885 (mmm) cc_final: 0.7712 (ttp) REVERT: T 295 ARG cc_start: 0.9102 (ttp80) cc_final: 0.8497 (mpt180) REVERT: T 323 GLN cc_start: 0.8905 (mp10) cc_final: 0.8593 (mp10) REVERT: T 331 HIS cc_start: 0.8682 (t-90) cc_final: 0.8250 (t-90) REVERT: T 342 LYS cc_start: 0.9072 (mttt) cc_final: 0.7964 (pptt) REVERT: T 392 MET cc_start: 0.9086 (mtt) cc_final: 0.8824 (mtt) outliers start: 39 outliers final: 24 residues processed: 249 average time/residue: 0.7208 time to fit residues: 203.1865 Evaluate side-chains 251 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 30 GLU 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 T residue 123 VAL Chi-restraints excluded: chain T residue 254 LEU 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 97 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 234 optimal weight: 30.0000 chunk 125 optimal weight: 0.0270 chunk 87 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 303 ASN N 303 ASN P 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.060991 restraints weight = 45135.692| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.20 r_work: 0.2572 rms_B_bonded: 2.31 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: 0.9016 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22833 Z= 0.110 Angle : 0.507 9.575 30917 Z= 0.268 Chirality : 0.041 0.156 3424 Planarity : 0.004 0.049 4038 Dihedral : 4.340 22.862 3072 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.37 % Allowed : 14.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.16), residues: 2881 helix: 1.65 (0.24), residues: 542 sheet: 0.36 (0.17), residues: 902 loop : -0.96 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 125 TYR 0.024 0.001 TYR T 204 PHE 0.010 0.001 PHE R 212 TRP 0.018 0.001 TRP T 378 HIS 0.002 0.000 HIS M 63 Details of bonding type rmsd covalent geometry : bond 0.00258 (22833) covalent geometry : angle 0.50740 (30917) hydrogen bonds : bond 0.03666 ( 734) hydrogen bonds : angle 4.60871 ( 2094) *********************** 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 272 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.953 Fit side-chains REVERT: M 29 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7263 (mmt) REVERT: M 277 GLN cc_start: 0.9422 (mt0) cc_final: 0.9196 (mt0) REVERT: N 180 LYS cc_start: 0.9250 (mttt) cc_final: 0.8476 (pptt) REVERT: N 186 LYS cc_start: 0.5780 (OUTLIER) cc_final: 0.4595 (ptpt) REVERT: N 363 GLU cc_start: 0.8673 (tt0) cc_final: 0.8374 (tt0) REVERT: O 7 LEU cc_start: 0.9050 (mm) cc_final: 0.8550 (tm) REVERT: O 8 ARG cc_start: 0.8080 (ttt90) cc_final: 0.6377 (pmt-80) REVERT: O 13 TRP cc_start: 0.9209 (OUTLIER) cc_final: 0.7933 (m-10) REVERT: O 24 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8256 (mm-30) REVERT: P 13 TRP cc_start: 0.9388 (OUTLIER) cc_final: 0.8918 (m-90) REVERT: P 25 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8878 (p) REVERT: P 29 MET cc_start: 0.8700 (ttp) cc_final: 0.8426 (mtm) REVERT: P 30 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8952 (mp0) REVERT: P 82 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8837 (m-30) REVERT: P 93 ASP cc_start: 0.8970 (m-30) cc_final: 0.8324 (m-30) REVERT: P 113 GLU cc_start: 0.8944 (tp30) cc_final: 0.8737 (tp30) REVERT: P 186 LYS cc_start: 0.5974 (OUTLIER) cc_final: 0.5729 (pmtt) REVERT: P 219 GLU cc_start: 0.9165 (tt0) cc_final: 0.8711 (tp30) REVERT: P 270 ASP cc_start: 0.8725 (t0) cc_final: 0.8518 (t70) REVERT: P 344 MET cc_start: 0.9468 (ttp) cc_final: 0.9022 (ttp) REVERT: Q 93 ASP cc_start: 0.9003 (m-30) cc_final: 0.8730 (m-30) REVERT: Q 122 LYS cc_start: 0.9077 (tptm) cc_final: 0.8641 (tppp) REVERT: Q 177 GLU cc_start: 0.5152 (pp20) cc_final: 0.4569 (pp20) REVERT: Q 186 LYS cc_start: 0.9097 (ttpp) cc_final: 0.8371 (mptt) REVERT: Q 270 ASP cc_start: 0.8611 (p0) cc_final: 0.8239 (t70) REVERT: R 270 ASP cc_start: 0.8638 (t0) cc_final: 0.8264 (t0) REVERT: T 24 GLU cc_start: 0.8805 (mp0) cc_final: 0.8248 (tm-30) REVERT: T 93 ASP cc_start: 0.9070 (m-30) cc_final: 0.8710 (m-30) REVERT: T 96 MET cc_start: 0.8826 (ttt) cc_final: 0.8127 (tpp) REVERT: T 122 LYS cc_start: 0.9387 (tttp) cc_final: 0.9134 (tptm) REVERT: T 186 LYS cc_start: 0.9364 (ttmt) cc_final: 0.8492 (pmtt) REVERT: T 210 MET cc_start: 0.8778 (mmm) cc_final: 0.7512 (tmt) REVERT: T 295 ARG cc_start: 0.9103 (ttp80) cc_final: 0.8473 (mpt180) REVERT: T 303 ASN cc_start: 0.8731 (m-40) cc_final: 0.8457 (m-40) REVERT: T 323 GLN cc_start: 0.8543 (mp10) cc_final: 0.8180 (mp10) REVERT: T 331 HIS cc_start: 0.8574 (t-90) cc_final: 0.8195 (t-90) REVERT: T 342 LYS cc_start: 0.9053 (mttt) cc_final: 0.7905 (pptt) REVERT: c 11 MET cc_start: 0.8309 (mmm) cc_final: 0.7761 (mmm) outliers start: 32 outliers final: 16 residues processed: 259 average time/residue: 0.6514 time to fit residues: 191.7060 Evaluate side-chains 253 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 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 30 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 268 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 260 optimal weight: 20.0000 chunk 177 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 267 optimal weight: 10.0000 chunk 205 optimal weight: 1.9990 chunk 136 optimal weight: 0.0030 overall best weight: 1.3594 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.094033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.061680 restraints weight = 45336.877| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.21 r_work: 0.2588 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22833 Z= 0.103 Angle : 0.503 9.419 30917 Z= 0.264 Chirality : 0.041 0.158 3424 Planarity : 0.004 0.053 4038 Dihedral : 4.204 21.695 3072 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 1.11 % Allowed : 15.29 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.16), residues: 2881 helix: 1.79 (0.25), residues: 537 sheet: 0.40 (0.17), residues: 904 loop : -0.89 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 199 TYR 0.024 0.001 TYR T 204 PHE 0.010 0.001 PHE N 316 TRP 0.026 0.001 TRP T 378 HIS 0.002 0.000 HIS M 63 Details of bonding type rmsd covalent geometry : bond 0.00239 (22833) covalent geometry : angle 0.50256 (30917) hydrogen bonds : bond 0.03507 ( 734) hydrogen bonds : angle 4.50839 ( 2094) ********************** 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 272 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 246 time to evaluate : 0.976 Fit side-chains REVERT: M 277 GLN cc_start: 0.9400 (mt0) cc_final: 0.9191 (mt0) REVERT: N 180 LYS cc_start: 0.9238 (mttt) cc_final: 0.8485 (pptt) REVERT: N 186 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.4479 (ptpt) REVERT: N 363 GLU cc_start: 0.8690 (tt0) cc_final: 0.8361 (tt0) REVERT: O 7 LEU cc_start: 0.9064 (mm) cc_final: 0.8519 (tm) REVERT: O 8 ARG cc_start: 0.7981 (ttt90) cc_final: 0.6369 (pmt-80) REVERT: O 13 TRP cc_start: 0.9210 (OUTLIER) cc_final: 0.7965 (m-10) REVERT: O 24 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8239 (mm-30) REVERT: P 13 TRP cc_start: 0.9380 (OUTLIER) cc_final: 0.8970 (m-90) REVERT: P 25 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8881 (p) REVERT: P 29 MET cc_start: 0.8740 (ttp) cc_final: 0.8366 (mtm) REVERT: P 30 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8885 (mp0) REVERT: P 82 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8830 (m-30) REVERT: P 93 ASP cc_start: 0.8953 (m-30) cc_final: 0.8307 (m-30) REVERT: P 113 GLU cc_start: 0.8965 (tp30) cc_final: 0.8746 (tp30) REVERT: P 186 LYS cc_start: 0.5856 (pttt) cc_final: 0.5539 (pmtt) REVERT: P 219 GLU cc_start: 0.9172 (tt0) cc_final: 0.8704 (tp30) REVERT: P 325 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8560 (mt-10) REVERT: P 344 MET cc_start: 0.9428 (ttp) cc_final: 0.8955 (ttp) REVERT: Q 93 ASP cc_start: 0.9005 (m-30) cc_final: 0.8737 (m-30) REVERT: Q 122 LYS cc_start: 0.9074 (tptm) cc_final: 0.8510 (tppp) REVERT: Q 177 GLU cc_start: 0.4940 (pp20) cc_final: 0.4359 (pp20) REVERT: Q 186 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8357 (mptt) REVERT: R 270 ASP cc_start: 0.8646 (t0) cc_final: 0.8331 (t0) REVERT: T 24 GLU cc_start: 0.8827 (mp0) cc_final: 0.8184 (tm-30) REVERT: T 93 ASP cc_start: 0.9063 (m-30) cc_final: 0.8701 (m-30) REVERT: T 96 MET cc_start: 0.8802 (ttt) cc_final: 0.8114 (tpp) REVERT: T 122 LYS cc_start: 0.9388 (tttp) cc_final: 0.9175 (tptm) REVERT: T 186 LYS cc_start: 0.9368 (ttmt) cc_final: 0.8529 (pmtt) REVERT: T 210 MET cc_start: 0.8689 (mmm) cc_final: 0.7457 (ttp) REVERT: T 295 ARG cc_start: 0.9095 (ttp80) cc_final: 0.8448 (mpt180) REVERT: T 303 ASN cc_start: 0.8804 (m-40) cc_final: 0.8553 (m-40) REVERT: T 323 GLN cc_start: 0.8476 (mp10) cc_final: 0.8199 (mp10) REVERT: T 331 HIS cc_start: 0.8522 (t-90) cc_final: 0.8141 (t-90) REVERT: T 342 LYS cc_start: 0.9046 (mttt) cc_final: 0.7954 (pptt) outliers start: 26 outliers final: 14 residues processed: 262 average time/residue: 0.7099 time to fit residues: 211.0125 Evaluate side-chains 252 residues out of total 2342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 186 LYS Chi-restraints excluded: chain O residue 13 TRP Chi-restraints excluded: chain O residue 15 ASN Chi-restraints excluded: chain O residue 139 THR 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 30 GLU Chi-restraints excluded: chain P residue 82 ASP Chi-restraints excluded: chain P residue 346 VAL Chi-restraints excluded: chain P residue 369 VAL 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 254 LEU Chi-restraints excluded: chain T residue 317 THR Chi-restraints excluded: chain c residue 34 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 135 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 257 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 282 optimal weight: 50.0000 chunk 58 optimal weight: 6.9990 chunk 159 optimal weight: 0.0870 chunk 4 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 278 optimal weight: 20.0000 overall best weight: 3.7764 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.091708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.059064 restraints weight = 45711.662| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 2.20 r_work: 0.2532 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22833 Z= 0.208 Angle : 0.576 10.858 30917 Z= 0.304 Chirality : 0.043 0.172 3424 Planarity : 0.004 0.052 4038 Dihedral : 4.488 21.364 3072 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.24 % Allowed : 15.33 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.16), residues: 2881 helix: 1.58 (0.24), residues: 542 sheet: 0.33 (0.17), residues: 893 loop : -0.97 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 125 TYR 0.026 0.001 TYR T 204 PHE 0.016 0.001 PHE N 316 TRP 0.021 0.001 TRP T 378 HIS 0.003 0.001 HIS M 63 Details of bonding type rmsd covalent geometry : bond 0.00498 (22833) covalent geometry : angle 0.57579 (30917) hydrogen bonds : bond 0.04576 ( 734) hydrogen bonds : angle 4.75305 ( 2094) =============================================================================== Job complete usr+sys time: 9281.22 seconds wall clock time: 158 minutes 12.65 seconds (9492.65 seconds total)