Starting phenix.real_space_refine on Thu Mar 14 08:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/03_2024/7tyl_26184_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/03_2024/7tyl_26184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/03_2024/7tyl_26184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/03_2024/7tyl_26184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/03_2024/7tyl_26184_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyl_26184/03_2024/7tyl_26184_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.076 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 63 5.16 5 C 5691 2.51 5 N 1579 2.21 5 O 1645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 204": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8978 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1886 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 274 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} Chain: "R" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2815 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 7, 'ASN:plan1': 3, 'TRP:plan': 3, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 177 Time building chain proxies: 5.09, per 1000 atoms: 0.57 Number of scatterers: 8978 At special positions: 0 Unit cell: (80.464, 100.152, 151.512, 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 63 16.00 O 1645 8.00 N 1579 7.00 C 5691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.04 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.39 Conformation dependent library (CDL) restraints added in 1.9 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 12 sheets defined 36.2% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.598A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.974A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.540A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 3.551A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'P' and resid 5 through 18 removed outlier: 3.685A pdb=" N ALA P 8 " --> pdb=" O ALA P 5 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR P 9 " --> pdb=" O THR P 6 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN P 10 " --> pdb=" O CYS P 7 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG P 11 " --> pdb=" O ALA P 8 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA P 13 " --> pdb=" O GLN P 10 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN P 14 " --> pdb=" O ARG P 11 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL P 17 " --> pdb=" O ASN P 14 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG P 18 " --> pdb=" O PHE P 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 60 removed outlier: 3.674A pdb=" N MET R 49 " --> pdb=" O ARG R 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP R 50 " --> pdb=" O LYS R 46 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP R 57 " --> pdb=" O TYR R 53 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 135 No H-bonds generated for 'chain 'R' and resid 133 through 135' Processing helix chain 'R' and resid 138 through 155 Processing helix chain 'R' and resid 157 through 159 No H-bonds generated for 'chain 'R' and resid 157 through 159' Processing helix chain 'R' and resid 161 through 172 removed outlier: 3.872A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER R 166 " --> pdb=" O THR R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 203 Processing helix chain 'R' and resid 209 through 213 Processing helix chain 'R' and resid 217 through 248 removed outlier: 3.554A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU R 247 " --> pdb=" O TYR R 243 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE R 248 " --> pdb=" O LEU R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 266 Processing helix chain 'R' and resid 269 through 282 Proline residue: R 273 - end of helix removed outlier: 3.602A pdb=" N ILE R 276 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS R 277 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE R 279 " --> pdb=" O ILE R 276 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR R 280 " --> pdb=" O HIS R 277 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA R 282 " --> pdb=" O ILE R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 296 through 329 removed outlier: 3.645A pdb=" N TYR R 299 " --> pdb=" O HIS R 296 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS R 302 " --> pdb=" O TYR R 299 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY R 303 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Proline residue: R 304 - end of helix removed outlier: 3.524A pdb=" N ASN R 312 " --> pdb=" O LEU R 309 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 320 " --> pdb=" O LEU R 317 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR R 325 " --> pdb=" O VAL R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 352 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 358 removed outlier: 4.030A pdb=" N VAL R 358 " --> pdb=" O GLN R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 366 through 391 removed outlier: 4.034A pdb=" N GLN R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLY R 384 " --> pdb=" O ILE R 380 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE R 385 " --> pdb=" O HIS R 381 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE R 386 " --> pdb=" O PHE R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 407 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.425A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 292 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.779A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.509A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 124 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.588A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.325A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.666A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.637A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.567A pdb=" N SER N 7 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 Processing sheet with id= K, first strand: chain 'N' and resid 92 through 98 removed outlier: 3.550A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'R' and resid 92 through 94 348 hydrogen bonds defined for protein. 930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1463 1.32 - 1.44: 2561 1.44 - 1.57: 5064 1.57 - 1.69: 0 1.69 - 1.82: 88 Bond restraints: 9176 Sorted by residual: bond pdb=" N ASP R 215 " pdb=" CA ASP R 215 " ideal model delta sigma weight residual 1.458 1.492 -0.034 7.40e-03 1.83e+04 2.11e+01 bond pdb=" N THR A 285 " pdb=" CA THR A 285 " ideal model delta sigma weight residual 1.455 1.507 -0.052 1.21e-02 6.83e+03 1.82e+01 bond pdb=" C VAL A 287 " pdb=" O VAL A 287 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.04e-02 9.25e+03 1.62e+01 bond pdb=" CA SER A 286 " pdb=" CB SER A 286 " ideal model delta sigma weight residual 1.529 1.463 0.066 1.65e-02 3.67e+03 1.58e+01 bond pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.28e-02 6.10e+03 1.08e+01 ... (remaining 9171 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.27: 290 107.27 - 114.02: 5125 114.02 - 120.78: 3953 120.78 - 127.54: 2988 127.54 - 134.30: 95 Bond angle restraints: 12451 Sorted by residual: angle pdb=" N LEU R 222 " pdb=" CA LEU R 222 " pdb=" C LEU R 222 " ideal model delta sigma weight residual 112.54 105.16 7.38 1.22e+00 6.72e-01 3.66e+01 angle pdb=" N ARG A 283 " pdb=" CA ARG A 283 " pdb=" C ARG A 283 " ideal model delta sigma weight residual 110.53 102.88 7.65 1.29e+00 6.01e-01 3.52e+01 angle pdb=" CA ARG A 283 " pdb=" C ARG A 283 " pdb=" O ARG A 283 " ideal model delta sigma weight residual 121.94 117.25 4.69 1.15e+00 7.56e-01 1.66e+01 angle pdb=" CA ASP R 215 " pdb=" C ASP R 215 " pdb=" N PRO R 216 " ideal model delta sigma weight residual 118.09 121.28 -3.19 8.20e-01 1.49e+00 1.51e+01 angle pdb=" CA SER A 286 " pdb=" C SER A 286 " pdb=" O SER A 286 " ideal model delta sigma weight residual 121.89 117.44 4.45 1.17e+00 7.31e-01 1.45e+01 ... (remaining 12446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 5021 17.73 - 35.47: 352 35.47 - 53.20: 62 53.20 - 70.94: 14 70.94 - 88.67: 7 Dihedral angle restraints: 5456 sinusoidal: 2093 harmonic: 3363 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -167.34 81.34 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS P 2 " pdb=" SG CYS P 2 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 136.87 -43.87 1 1.00e+01 1.00e-02 2.68e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 131.46 -38.46 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 5453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1282 0.073 - 0.145: 100 0.145 - 0.218: 8 0.218 - 0.290: 2 0.290 - 0.363: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA ARG A 283 " pdb=" N ARG A 283 " pdb=" C ARG A 283 " pdb=" CB ARG A 283 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ARG R 214 " pdb=" N ARG R 214 " pdb=" C ARG R 214 " pdb=" CB ARG R 214 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE R 221 " pdb=" CA ILE R 221 " pdb=" CG1 ILE R 221 " pdb=" CG2 ILE R 221 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1390 not shown) Planarity restraints: 1601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 213 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ARG R 213 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG R 213 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG R 214 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 279 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C ASN A 279 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN A 279 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 280 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 282 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C LEU A 282 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU A 282 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 283 " 0.008 2.00e-02 2.50e+03 ... (remaining 1598 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2211 2.79 - 3.32: 8337 3.32 - 3.84: 14642 3.84 - 4.37: 17352 4.37 - 4.90: 30167 Nonbonded interactions: 72709 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.260 2.440 nonbonded pdb=" O GLN A 236 " pdb=" ND2 ASN A 239 " model vdw 2.262 2.520 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.290 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.309 2.440 nonbonded pdb=" O SER G 8 " pdb=" OG SER G 8 " model vdw 2.316 2.440 ... (remaining 72704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 1.020 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: 5.500 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.230 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -oh -his -flip -keep -allalt -limit120 -pen9999 -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: Processing file: --standard input-- Building His ring NH Hydrogens. Building or keeping OH & SH Hydrogens. Rotating existing OH & SH Hydrogens *WARNING*: Residues MET 60 and THR 204 in chain A appear unbonded and will be treated as a chain break *WARNING*: Residues MET 60 and THR 204 in chain A appear unbonded and will be treated as a chain break *WARNING*: Residues SER 250 and ASN 264 in chain A appear unbonded and will be treated as a chain break *WARNING*: Residues SER 250 and ASN 264 in chain A appear unbonded and will be treated as a chain break VDW dot density = 16/A^2 Orientation penalty scale = 9999 (999900%) Eliminate contacts within 3 bonds. Ignore atoms with |occupancy| <= 0.01 during adjustments. Waters ignored if B-Factor >= 40 or |occupancy| < 0.66 Aromatic rings in amino acids accept hydrogen bonds. Flipping Asn, Gln and His groups. For each flip state, bumps where gap is more than 0.4A are indicated with '!'. Rotating NH3 Hydrogens. Not processing Met methyls. Singles(size 298): A 12 GLN : A 24 LYS NZ : A 25 LYS NZ : A 28 LYS NZ : A 29 GLN : A 31 GLN : A 32 LYS NZ : A 34 LYS NZ : A 35 GLN : A 37 TYR OH : A 40 THR OG1 : A 41 HIS : A 51 SER OG : A 53 LYS NZ : A 54 ASN : A 55 THR OG1 : A 58 LYS NZ : A 59 GLN : A 210 THR OG1 : A 216 LYS NZ : A 236 GLN : A 239 ASN : A 242 THR OG1 : A 250 SER OG : A 264 ASN : A 267 GLN : A 271 LYS NZ : A 275 SER OG : A 278 ASN : A 279 ASN : A 280 LYS NZ : A 285 THR OG1 : A 286 SER OG : A 292 ASN : A 293 LYS NZ : A 294 GLN : A 300 LYS NZ : A 305 LYS NZ : A 306 SER OG : A 307 LYS NZ : A 311 TYR OH : A 318 TYR OH : A 319 THR OG1 : A 320 THR OG1 : A 325 THR OG1 : A 335 THR OG1 : A 338 LYS NZ : A 339 TYR OH : A 350 THR OG1 : A 352 SER OG : A 357 HIS : A 358 TYR OH : A 360 TYR OH : A 362 HIS : A 365 CYS SG : A 366 SER OG : A 369 THR OG1 : A 377 ASN : A 379 CYS SG : A 387 HIS : A 390 GLN : A 391 TYR OH : B 2 SER OG : B 6 GLN : B 9 GLN : B 13 GLN : B 15 LYS NZ : B 16 ASN : B 17 GLN : B 23 LYS NZ : B 25 CYS SG : B 29 THR OG1 : B 31 SER OG : B 32 GLN : B 34 THR OG1 : B 35 ASN : B 36 ASN : B 44 GLN : B 47 THR OG1 : B 50 THR OG1 : B 57 LYS NZ : B 62 HIS : B 65 THR OG1 : B 67 SER OG : B 75 GLN : B 78 LYS NZ : B 84 SER OG : B 85 TYR OH : B 87 THR OG1 : B 91 HIS : B 97 SER OG : B 98 SER OG : B 102 THR OG1 : B 103 CYS SG : B 105 TYR OH : B 111 TYR OH : B 114 CYS SG : B 122 SER OG : B 124 TYR OH : B 127 LYS NZ : B 132 ASN : B 136 SER OG : B 143 THR OG1 : B 145 TYR OH : B 155 ASN : B 156 GLN : B 161 SER OG : B 164 THR OG1 : B 165 THR OG1 : B 166 CYS SG : B 173 THR OG1 : B 175 GLN : B 177 THR OG1 : B 178 THR OG1 : B 183 HIS : B 184 THR OG1 : B 191 SER OG : B 196 THR OG1 : B 201 SER OG : B 204 CYS SG : B 220 GLN : B 223 THR OG1 : B 227 SER OG : B 233 CYS SG : B 237 ASN : B 239 ASN : B 249 THR OG1 : B 250 CYS SG : B 259 GLN : B 263 THR OG1 : B 264 TYR OH : B 265 SER OG : B 271 CYS SG : B 274 THR OG1 : B 275 SER OG : B 277 SER OG : B 279 SER OG : B 280 LYS NZ : B 281 SER OG : B 289 TYR OH : B 293 ASN : B 294 CYS SG : B 295 ASN : B 301 LYS NZ : B 313 ASN : B 316 SER OG : B 317 CYS SG : B 321 THR OG1 : B 331 SER OG : B 334 SER OG : B 337 LYS NZ : G 8 SER OG : G 11 GLN : G 18 GLN : G 20 LYS NZ : G 24 ASN : G 29 LYS NZ : G 31 SER OG : G 32 LYS NZ : G 40 TYR OH : G 41 CYS SG : G 44 HIS : G 46 LYS NZ : G 52 THR OG1 : G 57 SER OG : N 1 GLN : N 1 GLN N : N 5 GLN : N 7 SER OG : N 13 GLN : N 17 SER OG : N 21 SER OG : N 28 THR OG1 : N 32 TYR OH : N 33 LYS NZ : N 35 ASN : N 39 GLN : N 43 LYS NZ : N 49 SER OG : N 54 SER OG : N 57 SER OG : N 59 SER OG : N 60 TYR OH : N 61 THR OG1 : N 63 SER OG : N 65 LYS NZ : N 69 THR OG1 : N 71 SER OG : N 74 ASN : N 77 ASN : N 78 THR OG1 : N 85 SER OG : N 87 LYS NZ : N 91 THR OG1 : N 94 TYR OH : N 95 TYR OH : N 104 THR OG1 : N 111 THR OG1 : N 112 SER OG : N 113 THR OG1 : N 114 THR OG1 : N 115 TYR OH : N 117 TYR OH : N 120 GLN : N 122 THR OG1 : N 123 GLN : N 125 THR OG1 : N 127 SER OG : N 128 SER OG : P 1 LYS N : P 1 LYS NZ : P 3 ASN : P 14 ASN : P 19 SER OG : P 21 ASN : P 22 ASN : P 30 THR OG1 : P 31 ASN : P 34 SER OG : P 35 ASN : P 36 THR OG1 : P 37 TYR OH : R 98 TYR OH : R 121 HIS : R 129 SER OG : R 130 ASN : R 131 TYR OH : R 135 ASN : R 138 THR OG1 : R 141 LYS NZ : R 143 LYS NZ : R 144 ASN : R 149 TYR OH : R 150 TYR OH : R 157 SER OG : R 162 THR OG1 : R 175 SER OG : R 178 CYS SG : R 179 GLN : R 182 THR OG1 : R 184 HIS : R 185 LYS NZ : R 190 THR OG1 : R 191 TYR OH : R 194 ASN : R 201 HIS : R 208 ASN : R 218 SER OG : R 223 HIS : R 226 HIS : R 228 TYR OH : R 232 CYS SG : R 233 ASN : R 234 TYR OH : R 239 CYS SG : R 243 TYR OH : R 245 HIS : R 254 THR OG1 : R 256 LYS NZ : R 274 THR OG1 : R 275 THR OG1 : R 277 HIS : R 280 THR OG1 : R 284 TYR OH : R 288 ASN : R 292 SER OG : R 295 THR OG1 : R 296 HIS : R 299 TYR OH : R 312 ASN : R 318 ASN : R 325 THR OG1 : R 330 THR OG1 : R 331 HIS : R 335 SER OG : R 336 HIS : R 338 TYR OH : R 340 LYS NZ : R 343 LYS NZ : R 345 THR OG1 : R 364 SER OG : R 365 ASN : R 366 LYS NZ : R 370 LYS NZ : R 372 TYR OH : R 374 TYR OH : R 378 SER OG : R 389 THR OG1 : R 391 TYR OH : R 394 CYS SG : R 395 ASN : R 396 ASN : R 399 GLN : R 400 THR OG1 : R 401 THR OG1 : R 403 LYS NZ : R 405 GLN : R 408 GLN Set 1 (size 3): R 381 HIS : R 377 HIS : P 9 THR OG1 Set 2 (size 2): R 383 GLN : R 355 GLN Set 3 (size 2): R 326 LYS NZ : A 384 GLN Set 4 (size 2): R 286 ASN : R 220 LYS NZ Set 5 (size 2): R 263 TYR OH : R 186 ASN Set 6 (size 3): R 262 TYR OH : R 257 GLN : R 246 THR OG1 Set 7 (size 2): R 392 CYS SG : R 166 SER OG Set 8 (size 3): R 195 SER OG : R 159 SER OG : R 156 HIS Set 9 (size 2): R 146 TYR OH : P 20 SER OG Set 10 (size 2): R 227 GLN : P 10 GLN Set 11 (size 3): R 302 HIS : P 6 THR OG1 : P 4 THR OG1 Set 12 (size 2): N 84 ASN : N 82 GLN Set 13 (size 2): N 76 LYS NZ : N 80 TYR OH Set 14 (size 2): N 53 GLN : N 52 SER OG Set 15 (size 2): N 31 ASN : N 30 SER OG Set 16 (size 2): N 25 SER OG : N 3 GLN Set 17 (size 2): G 59 ASN : B 340 ASN Set 18 (size 2): B 329 THR OG1 : B 311 HIS Set 19 (size 2): B 268 ASN : B 266 HIS Set 20 (size 3): B 245 SER OG : B 243 THR OG1 : B 225 HIS Set 21 (size 2): B 221 THR OG1 : B 218 CYS SG Set 22 (size 2): B 209 LYS NZ : B 207 SER OG Set 23 (size 2): G 14 LYS NZ : B 181 THR OG1 Set 24 (size 2): B 179 THR OG1 : B 176 GLN Set 25 (size 2): B 159 THR OG1 : B 142 HIS Set 26 (size 2): B 189 SER OG : B 148 CYS SG Set 27 (size 2): B 160 SER OG : B 147 SER OG Set 28 (size 2): B 128 THR OG1 : B 125 ASN Set 29 (size 2): B 121 CYS SG : B 149 CYS SG Set 30 (size 2): B 110 ASN : B 108 SER OG Set 31 (size 3): B 89 LYS NZ : B 88 ASN : A 23 ASN Set 32 (size 2): A 19 GLN : B 86 THR OG1 Set 33 (size 3): B 74 SER OG : B 72 SER OG : B 54 HIS Set 34 (size 2): A 237 CYS SG : B 59 TYR OH Set 35 (size 2): A 371 ASN : A 364 THR OG1 Set 36 (size 2): A 359 CYS SG : A 349 SER OG Set 37 (size 2): A 233 LYS NZ : B 230 ASN Set 38 (size 2): B 119 ASN : A 227 GLN Set 39 (size 2): A 220 HIS : A 211 LYS NZ Set 40 (size 2): A 213 GLN : A 218 ASN Set 41 (size 2): A 205 SER OG : A 204 THR OG1 Set 42 (size 2): A 14 ASN : A 17 LYS NZ orientation 1: A 12 GLN : amide: bump=-0.207, HB=0.000, total=-0.207 orientation 1: A 24 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 25 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 28 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 29 GLN : amide: bump=-0.704, HB=0.000, total=-0.704 orientation 1: A 31 GLN : amide: bump=-0.854, HB=0.000, total=-0.854 orientation 1: A 32 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 34 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 35 GLN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: A 37 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 40 THR OG1 : rot 100: bump=-0.121, HB=1.478, total=1.357 orientation 1: A 41 HIS : no HD1: bump=-0.146, HB=0.000, total=-0.146 orientation 2: A 51 SER OG : rot -94: bump=0.000, HB=0.724, total=0.724 orientation 3: A 53 LYS NZ :NH3+ 168: bump=-0.046, HB=0.027, total=-0.020 orientation 1: A 54 ASN : amide: bump=-0.106, HB=0.252, total=0.146 orientation 1: A 55 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 58 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 59 GLN : amide: bump=-2.380, HB=0.000, total=-2.380, BADBUMP orientation 1: A 210 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 216 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 236 GLN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: A 239 ASN : amide: bump=-4.529, HB=0.939, total=-3.590, BADBUMP orientation 1: A 242 THR OG1 : rot -130: bump=0.000, HB=0.000, total=0.000 orientation 2: A 250 SER OG : rot 44: bump=-0.426, HB=1.450, total=1.023 orientation 1: A 264 ASN : amide: bump=-0.049, HB=0.360, total=0.311 orientation 1: A 267 GLN : amide: bump=-0.247, HB=0.000, total=-0.247 orientation 1: A 271 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 4: A 275 SER OG : rot -126: bump=-0.017, HB=1.271, total=1.255 orientation 1: A 278 ASN : amide: bump=-0.918, HB=1.430, total=0.512 orientation 1: A 279 ASN : amide: bump=-2.600, HB=0.128, total=-2.473, BADBUMP orientation 1: A 280 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 285 THR OG1 : rot -53: bump=0.000, HB=0.080, total=0.080 orientation 1: A 286 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 292 ASN : amide: bump=-0.991, HB=0.144, total=-0.846 orientation 4: A 293 LYS NZ :NH3+ -121: bump=-0.761, HB=1.588, total=0.827 orientation 1: A 294 GLN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: A 300 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 305 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 306 SER OG : rot 180: bump=-0.003, HB=0.000, total=-0.003 orientation 1: A 307 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 311 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 7: A 318 TYR OH : rot 24: bump=-0.001, HB=1.142, total=1.142 orientation 1: A 319 THR OG1 : rot 180: bump=-0.079, HB=0.000, total=-0.079 orientation 1: A 320 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 3: A 325 THR OG1 : rot 45: bump=-0.015, HB=0.623, total=0.608 orientation 1: A 335 THR OG1 : rot 150: bump=-0.269, HB=0.000, total=-0.269 orientation 4: A 338 LYS NZ :NH3+ -124: bump=-0.157, HB=0.849, total=0.692 orientation 1: A 339 TYR OH : rot 180: bump=-0.384, HB=0.088, total=-0.296 orientation 2: A 350 THR OG1 : rot 86: bump=0.000, HB=0.392, total=0.392 orientation 2: A 352 SER OG : rot 4: bump=-0.119, HB=1.121, total=1.002 orientation 1: A 357 HIS : no HD1: bump=-0.776, HB=0.000, total=-0.776 orientation 5: A 358 TYR OH : rot 15: bump=0.000, HB=0.000, total=0.000 orientation 1: A 360 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 362 HIS : no HD1: bump=-1.525, HB=0.907, total=-0.619, BADBUMP orientation 1: A 365 CYS SG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: A 366 SER OG : rot -72: bump=-0.016, HB=1.365, total=1.349 orientation 1: A 369 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: A 377 ASN : amide: bump=-0.270, HB=0.000, total=-0.270 orientation 2: A 379 CYS SG : rot 83: bump=-0.169, HB=0.068, total=-0.102 orientation 1: A 387 HIS : no HD1: bump=-0.097, HB=0.000, total=-0.097 orientation 1: A 390 GLN : amide: bump=0.000, HB=0.000, total=0.000 orientation 11: A 391 TYR OH : rot -150: bump=-0.061, HB=0.561, total=0.500 orientation 1: B 2 SER OG : rot 83: bump=-0.825, HB=0.195, total=-0.629, BADBUMP orientation 1: B 6 GLN : amide: bump=-1.619, HB=0.000, total=-1.619 orientation 1: B 9 GLN : amide: bump=-0.823, HB=0.000, total=-0.823 orientation 1: B 13 GLN : amide: bump=-0.287, HB=0.083, total=-0.203 orientation 1: B 15 LYS NZ :NH3+ 171: bump=-0.096, HB=0.000, total=-0.096 orientation 1: B 16 ASN : amide: bump=-0.201, HB=0.000, total=-0.201 orientation 1: B 17 GLN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: B 23 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 3: B 25 CYS SG : rot -17: bump=-0.040, HB=0.201, total=0.161 orientation 1: B 29 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 31 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 32 GLN : amide: bump=-0.056, HB=0.000, total=-0.056 orientation 5: B 34 THR OG1 : rot -83: bump=-0.000, HB=1.105, total=1.104 orientation 1: B 35 ASN : amide: bump=-0.189, HB=0.000, total=-0.189 orientation 1: B 36 ASN : amide: bump=-0.010, HB=0.728, total=0.719 orientation 1: B 44 GLN : amide: bump=-0.282, HB=0.000, total=-0.282 orientation 1: B 47 THR OG1 : rot -101: bump=-0.023, HB=0.000, total=-0.023 orientation 1: B 50 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: B 57 LYS NZ :NH3+ -165: bump=-0.152, HB=0.000, total=-0.152 orientation 1: B 62 HIS : no HD1: bump=-0.521, HB=0.000, total=-0.521 orientation 2: B 65 THR OG1 : rot 149: bump=-0.509, HB=1.531, total=1.021 orientation 6: B 67 SER OG : rot 24: bump=-0.565, HB=1.272, total=0.708 orientation 1: B 75 GLN : amide: bump=-1.217, HB=0.042, total=-1.176 orientation 2: B 78 LYS NZ :NH3+ -163: bump=-0.039, HB=0.000, total=-0.039 orientation 6: B 84 SER OG : rot -171: bump=-0.554, HB=1.738, total=1.184 orientation 1: B 85 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 87 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 91 HIS : no HD1: bump=-0.230, HB=0.000, total=-0.230 orientation 1: B 97 SER OG : rot 81: bump=-0.845, HB=0.173, total=-0.672, BADBUMP orientation 1: B 98 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: B 102 THR OG1 : rot -130: bump=-1.128, HB=0.037, total=-1.091 orientation 1: B 103 CYS SG : rot 140: bump=-1.170, HB=0.172, total=-0.998 orientation 1: B 105 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 111 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 114 CYS SG : rot 180: bump=-1.194, HB=0.000, total=-1.194 orientation 1: B 122 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 124 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 127 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 132 ASN : amide: bump=-0.193, HB=0.799, total=0.606 orientation 1: B 136 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 143 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 11: B 145 TYR OH : rot -149: bump=-0.376, HB=0.123, total=-0.253 orientation 1: B 155 ASN : amide: bump=-0.217, HB=0.000, total=-0.217 orientation 1: B 156 GLN : amide: bump=-2.212, HB=0.000, total=-2.212, BADBUMP orientation 3: B 161 SER OG : rot 10: bump=-1.102, HB=1.312, total=0.210 orientation 2: B 164 THR OG1 : rot 30: bump=-0.743, HB=1.293, total=0.550 orientation 6: B 165 THR OG1 : rot -109: bump=-0.035, HB=0.552, total=0.518 orientation 2: B 166 CYS SG : rot 4: bump=0.000, HB=0.426, total=0.426 orientation 3: B 173 THR OG1 : rot -52: bump=-0.212, HB=1.291, total=1.079 orientation 1: B 175 GLN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: B 177 THR OG1 : rot 180: bump=-0.004, HB=0.000, total=-0.004 orientation 1: B 178 THR OG1 : rot 180: bump=-0.246, HB=0.000, total=-0.246 orientation 2: B 183 HIS : no HE2: bump=-0.461, HB=0.445, total=-0.017 orientation 1: B 184 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 191 SER OG : rot 180: bump=-0.174, HB=0.000, total=-0.174 orientation 3: B 196 THR OG1 : rot -47: bump=-0.048, HB=1.167, total=1.119 orientation 1: B 201 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: B 204 CYS SG : rot 74: bump=-0.232, HB=0.076, total=-0.157 orientation 1: B 220 GLN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: B 223 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: B 227 SER OG : rot 98: bump=0.000, HB=0.341, total=0.341 orientation 2: B 233 CYS SG : rot -140: bump=-1.094, HB=0.118, total=-0.976 orientation 1: B 237 ASN : amide: bump=-0.001, HB=0.000, total=-0.001 orientation 1: B 239 ASN : amide: bump=-0.437, HB=0.273, total=-0.164 orientation 5: B 249 THR OG1 : rot -69: bump=-1.211, HB=1.190, total=-0.021 orientation 2: B 250 CYS SG : rot 49: bump=-0.096, HB=0.012, total=-0.083 orientation 1: B 259 GLN : amide: bump=-0.019, HB=0.000, total=-0.019 orientation 1: B 263 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 8: B 264 TYR OH : rot 9: bump=-0.218, HB=1.195, total=0.977 orientation 1: B 265 SER OG : rot 180: bump=-0.357, HB=0.000, total=-0.357 orientation 1: B 271 CYS SG : rot 26: bump=-2.149, HB=0.393, total=-1.756 orientation 3: B 274 THR OG1 : rot -140: bump=-0.054, HB=1.380, total=1.327 orientation 2: B 275 SER OG : rot 23: bump=-0.692, HB=0.614, total=-0.079 orientation 1: B 277 SER OG : rot -159: bump=-0.129, HB=0.000, total=-0.129 orientation 3: B 279 SER OG : rot 141: bump=-1.001, HB=0.683, total=-0.318, BADBUMP orientation 3: B 280 LYS NZ :NH3+ 157: bump=-0.037, HB=0.059, total=0.022 orientation 2: B 281 SER OG : rot -31: bump=-0.283, HB=0.464, total=0.182 orientation 1: B 289 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: B 293 ASN : amide: bump=-0.273, HB=0.000, total=-0.273 orientation 1: B 294 CYS SG : rot 110: bump=-1.223, HB=0.000, total=-1.223 orientation 1: B 295 ASN : amide: bump=-0.843, HB=0.000, total=-0.843 orientation 4: B 301 LYS NZ :NH3+ -104: bump=-0.686, HB=1.508, total=0.822 orientation 1: B 313 ASN : amide: bump=-0.548, HB=0.578, total=0.030 orientation 1: B 316 SER OG : rot 171: bump=-0.411, HB=1.537, total=1.126 orientation 1: B 317 CYS SG : rot 150: bump=-0.790, HB=0.000, total=-0.790 orientation 1: B 321 THR OG1 : rot 137: bump=-0.061, HB=1.363, total=1.302 orientation 1: B 331 SER OG : rot 159: bump=-0.454, HB=0.248, total=-0.206 orientation 4: B 334 SER OG : rot 27: bump=-0.619, HB=1.286, total=0.667 orientation 4: B 337 LYS NZ :NH3+ -123: bump=-2.220, HB=0.000, total=-2.220 orientation 6: G 8 SER OG : rot -60: bump=-0.247, HB=1.386, total=1.139 orientation 1: G 11 GLN : amide: bump=-0.299, HB=0.000, total=-0.299 orientation 1: G 18 GLN : amide: bump=-0.170, HB=0.000, total=-0.170 orientation 3: G 20 LYS NZ :NH3+ 136: bump=-0.101, HB=0.000, total=-0.101 orientation 1: G 24 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 2: G 29 LYS NZ :NH3+ -137: bump=-0.087, HB=0.000, total=-0.087 orientation 1: G 31 SER OG : rot 180: bump=-0.006, HB=0.000, total=-0.006 orientation 2: G 32 LYS NZ :NH3+ -132: bump=-0.701, HB=0.257, total=-0.443 orientation 1: G 40 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: G 41 CYS SG : rot 62: bump=-0.005, HB=0.769, total=0.764 orientation 1: G 44 HIS : no HD1: bump=-1.373, HB=0.000, total=-1.373 orientation 1: G 46 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: G 52 THR OG1 : rot 180: bump=-0.021, HB=0.000, total=-0.021 orientation 1: G 57 SER OG : rot 180: bump=-1.201, HB=0.000, total=-1.201 orientation 1: N 1 GLN : amide: bump=-0.126, HB=0.000, total=-0.126 orientation 1: N 1 GLN N :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: N 5 GLN : amide: bump=-0.148, HB=0.000, total=-0.148 orientation 1: N 7 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: N 13 GLN : amide: bump=-0.621, HB=0.000, total=-0.621 orientation 1: N 17 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 3: N 21 SER OG : rot -68: bump=0.000, HB=0.521, total=0.521 orientation 2: N 28 THR OG1 : rot 44: bump=0.000, HB=0.144, total=0.144 orientation 1: N 32 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 3: N 33 LYS NZ :NH3+ 168: bump=-1.204, HB=1.026, total=-0.177, BADBUMP orientation 1: N 35 ASN : amide: bump=-0.511, HB=0.000, total=-0.511 orientation 1: N 39 GLN : amide: bump=-0.516, HB=0.000, total=-0.516 orientation 2: N 43 LYS NZ :NH3+ -167: bump=-0.038, HB=0.000, total=-0.038 orientation 1: N 49 SER OG : rot 77: bump=-0.000, HB=0.012, total=0.012 orientation 1: N 54 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: N 57 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: N 59 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: N 60 TYR OH : rot 180: bump=-0.103, HB=0.662, total=0.559 orientation 1: N 61 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: N 63 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: N 65 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: N 69 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: N 71 SER OG : rot 180: bump=-0.182, HB=0.000, total=-0.182 orientation 1: N 74 ASN : amide: bump=-0.089, HB=0.000, total=-0.089 orientation 1: N 77 ASN : amide: bump=-0.121, HB=0.000, total=-0.121 orientation 1: N 78 THR OG1 : rot 180: bump=-0.009, HB=0.000, total=-0.009 orientation 1: N 85 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: N 87 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 2: N 91 THR OG1 : rot 62: bump=-0.060, HB=1.162, total=1.102 orientation 5: N 94 TYR OH : rot 126: bump=0.000, HB=0.002, total=0.002 orientation 1: N 95 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 4: N 104 THR OG1 : rot -108: bump=0.000, HB=0.418, total=0.418 orientation 1: N 111 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 3: N 112 SER OG : rot -130: bump=-0.213, HB=0.000, total=-0.213 orientation 1: N 113 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: N 114 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 7: N 115 TYR OH : rot 0: bump=-0.364, HB=0.000, total=-0.364 orientation 4: N 117 TYR OH : rot 120: bump=-0.295, HB=0.551, total=0.256 orientation 1: N 120 GLN : amide: bump=-0.090, HB=0.000, total=-0.090 orientation 1: N 122 THR OG1 : rot 180: bump=-0.118, HB=0.000, total=-0.118 orientation 1: N 123 GLN : amide: bump=-0.053, HB=0.000, total=-0.053 orientation 1: N 125 THR OG1 : rot 180: bump=-0.312, HB=0.000, total=-0.312 orientation 1: N 127 SER OG : rot 180: bump=-0.045, HB=0.000, total=-0.045 orientation 1: N 128 SER OG : rot 180: bump=0.000, HB=0.014, total=0.014 orientation 4: P 1 LYS N :NH3+ -130: bump=0.000, HB=0.945, total=0.945 orientation 1: P 1 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: P 3 ASN : amide: bump=-0.141, HB=0.000, total=-0.141 orientation 1: P 14 ASN : amide: bump=-2.790, HB=0.000, total=-2.790, BADBUMP orientation 1: P 19 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: P 21 ASN : amide: bump=-0.042, HB=0.000, total=-0.042 orientation 1: P 22 ASN : amide: bump=-3.252, HB=0.000, total=-3.252, BADBUMP orientation 1: P 30 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: P 31 ASN : amide: bump=-0.065, HB=0.513, total=0.448 orientation 1: P 34 SER OG : rot 180: bump=0.000, HB=0.015, total=0.015 orientation 1: P 35 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: P 36 THR OG1 : rot 159: bump=-1.322, HB=1.402, total=0.080, BADBUMP orientation 1: P 37 TYR OH : rot 180: bump=-0.008, HB=0.000, total=-0.008 orientation 1: R 98 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: R 121 HIS : no HE2: bump=-1.279, HB=0.017, total=-1.262 orientation 1: R 129 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 130 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: R 131 TYR OH : rot 180: bump=-0.010, HB=0.000, total=-0.010 orientation 1: R 135 ASN : amide: bump=-0.092, HB=0.277, total=0.185 orientation 2: R 138 THR OG1 : rot -159: bump=0.000, HB=0.211, total=0.211 orientation 1: R 141 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 143 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 144 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 6: R 149 TYR OH : rot 0: bump=0.000, HB=1.250, total=1.250 orientation 1: R 150 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: R 157 SER OG : rot 96: bump=0.000, HB=0.773, total=0.773 orientation 1: R 162 THR OG1 : rot -145: bump=0.000, HB=0.002, total=0.002 orientation 1: R 175 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 178 CYS SG : rot 180: bump=-0.646, HB=0.024, total=-0.622 orientation 1: R 179 GLN : amide: bump=-1.629, HB=0.000, total=-1.629, BADBUMP orientation 3: R 182 THR OG1 : rot 86: bump=-0.159, HB=1.485, total=1.326 orientation 1: R 184 HIS : no HD1: bump=-0.174, HB=0.000, total=-0.174 orientation 1: R 185 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 3: R 190 THR OG1 : rot -12: bump=-0.266, HB=1.289, total=1.023 orientation 9: R 191 TYR OH : rot -110: bump=-0.269, HB=0.000, total=-0.269 orientation 1: R 194 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: R 201 HIS : no HD1: bump=-1.044, HB=0.000, total=-1.044 orientation 1: R 208 ASN : amide: bump=0.000, HB=0.000, total=0.000 orientation 1: R 218 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 223 HIS : no HD1: bump=-0.103, HB=0.000, total=-0.103 orientation 1: R 226 HIS : no HD1: bump=-0.339, HB=0.000, total=-0.339 orientation 8: R 228 TYR OH : rot -29: bump=0.000, HB=0.142, total=0.142 orientation 2: R 232 CYS SG : rot 150: bump=0.000, HB=0.580, total=0.580 orientation 1: R 233 ASN : amide: bump=-0.685, HB=0.134, total=-0.551 orientation 10: R 234 TYR OH : rot -60: bump=0.000, HB=1.015, total=1.015 orientation 3: R 239 CYS SG : rot -139: bump=-0.256, HB=0.431, total=0.175 orientation 1: R 243 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 245 HIS : no HD1: bump=0.000, HB=0.000, total=0.000 orientation 6: R 254 THR OG1 : rot -59: bump=-0.554, HB=1.375, total=0.821 orientation 3: R 256 LYS NZ :NH3+ 173: bump=0.000, HB=0.000, total=0.000 orientation 3: R 274 THR OG1 : rot -90: bump=-0.003, HB=0.573, total=0.569 orientation 1: R 275 THR OG1 : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 277 HIS : no HD1: bump=-2.491, HB=0.000, total=-2.491 orientation 5: R 280 THR OG1 : rot -86: bump=-0.334, HB=1.442, total=1.108 orientation 1: R 284 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 288 ASN : amide: bump=-0.590, HB=0.713, total=0.123 orientation 5: R 292 SER OG : rot -176: bump=-0.317, HB=0.469, total=0.152 orientation 1: R 295 THR OG1 : rot 180: bump=0.000, HB=0.007, total=0.007 orientation 1: R 296 HIS : no HD1: bump=0.000, HB=0.000, total=0.000 orientation 1: R 299 TYR OH : rot 180: bump=-0.266, HB=0.000, total=-0.266 orientation 1: R 312 ASN : amide: bump=-1.452, HB=0.000, total=-1.452 orientation 1: R 318 ASN : amide: bump=-0.003, HB=0.000, total=-0.003 orientation 2: R 325 THR OG1 : rot -34: bump=-0.133, HB=0.137, total=0.004 orientation 3: R 330 THR OG1 : rot -37: bump=0.000, HB=0.019, total=0.019 orientation 1: R 331 HIS : no HD1: bump=-0.004, HB=0.000, total=-0.004 orientation 1: R 335 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: R 336 HIS : no HE2: bump=-0.743, HB=1.077, total=0.335 orientation 6: R 338 TYR OH : rot 68: bump=0.000, HB=1.298, total=1.298 orientation 3: R 340 LYS NZ :NH3+ 134: bump=-0.013, HB=0.000, total=-0.013 orientation 2: R 343 LYS NZ :NH3+ -168: bump=-0.049, HB=0.000, total=-0.049 orientation 2: R 345 THR OG1 : rot 92: bump=0.000, HB=1.273, total=1.273 orientation 1: R 364 SER OG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 365 ASN : amide: bump=-0.568, HB=0.382, total=-0.186 orientation 1: R 366 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 370 LYS NZ :NH3+ 172: bump=-0.142, HB=0.000, total=-0.142 orientation 6: R 372 TYR OH : rot -2: bump=0.000, HB=0.089, total=0.089 orientation 1: R 374 TYR OH : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 2: R 378 SER OG : rot 96: bump=-0.003, HB=0.083, total=0.080 orientation 2: R 389 THR OG1 : rot 75: bump=0.000, HB=0.798, total=0.798 orientation 2: R 391 TYR OH : rot 158: bump=-0.103, HB=1.381, total=1.279 orientation 1: R 394 CYS SG : rot 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 395 ASN : amide: bump=-0.789, HB=0.000, total=-0.789 orientation 1: R 396 ASN : amide: bump=-0.015, HB=0.000, total=-0.015 orientation 1: R 399 GLN : amide: bump=-0.025, HB=0.000, total=-0.025 orientation 2: R 400 THR OG1 : rot -5: bump=-0.106, HB=0.282, total=0.177 orientation 2: R 401 THR OG1 : rot 79: bump=-0.074, HB=1.206, total=1.132 orientation 1: R 403 LYS NZ :NH3+ 180: bump=0.000, HB=0.000, total=0.000 orientation 1: R 405 GLN : amide: bump=-0.194, HB=0.000, total=-0.194 orientation 1: R 408 GLN : amide: bump=0.000, HB=0.000, total=0.000 Processing set: R 381 HIS [6]: R 377 HIS [6]: P 9 THR OG1 [2] permutations: 72 Computing dot scores Num optimizations problems to be solved for this clique: 6 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -1.012 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 > : -1.012 Optimal score following high resolution, local optimization: -1.012 Processing set: R 383 GLN [2]: R 355 GLN [2] permutations: 4 Computing dot scores Num optimizations problems to be solved for this clique: 4 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.066 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following high resolution, local optimization: 0.066 Processing set: R 326 LYS NZ [4]: A 384 GLN [2] permutations: 8 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.700 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -0.937 > : -0.903 > : -0.799 > : -0.775 > : -0.756 > : -0.549 > : -0.532 > : -0.532 > : -0.532 > : -0.532 > : -0.473 > : -0.461 > : -0.448 > : -0.436 > : -0.428 > : -0.424 > : -0.416 > : -0.416 > : -0.416 > : -0.362 > : -0.362 > : -0.362 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 > : -0.347 Optimal score following high resolution, local optimization: -0.347 Processing set: R 286 ASN [2]: R 220 LYS NZ [4] permutations: 8 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.528 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -0.884 > : -0.861 > : -0.838 > : -0.816 > : -0.794 > : -0.772 > : -0.748 > : -0.729 > : -0.705 > : -0.681 > : -0.681 > : -0.681 > : -0.665 > : -0.644 > : -0.572 > : -0.559 > : -0.549 > : -0.542 > : -0.542 > : -0.542 > : -0.542 > : -0.542 > : -0.542 > : -0.539 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 > : -0.528 Optimal score following high resolution, local optimization: -0.528 Processing set: R 263 TYR OH [11]: R 186 ASN [2] permutations: 22 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.003 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 > : -0.003 Optimal score following high resolution, local optimization: -0.003 Processing set: R 262 TYR OH [12]: R 257 GLN [2]: R 246 THR OG1 [6] permutations: 144 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.378 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.378 > : 1.378 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.379 > : 1.381 > : 1.381 > : 1.383 > : 1.383 > : 1.399 > : 1.399 > : 1.399 > : 1.399 > : 1.399 > : 1.399 > : 1.399 > : 1.399 > : 1.399 > : 1.399 > : 1.399 > : 1.399 > : 1.399 > : 1.399 > : 1.399 Optimal score following high resolution, local optimization: 1.399 Processing set: R 392 CYS SG [5]: R 166 SER OG [5] permutations: 25 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 2.368 > : 2.368 > : 2.368 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 > : 2.370 Optimal score following high resolution, local optimization: 2.370 Processing set: R 195 SER OG [3]: R 159 SER OG [7]: R 156 HIS [6] permutations: 126 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.347 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 > : 1.347 Optimal score following high resolution, local optimization: 1.347 Processing set: R 146 TYR OH [11]: P 20 SER OG [2] permutations: 22 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 > : 1.300 Optimal score following high resolution, local optimization: 1.300 Processing set: R 227 GLN [2]: P 10 GLN [2] permutations: 4 Computing dot scores Num optimizations problems to be solved for this clique: 4 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.112 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following high resolution, local optimization: 0.112 Processing set: R 302 HIS [6]: P 6 THR OG1 [3]: P 4 THR OG1 [4] permutations: 72 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.300 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.300 > : 1.300 > : 1.319 > : 1.319 > : 1.334 > : 1.334 > : 1.348 > : 1.348 > : 1.362 > : 1.362 > : 1.375 > : 1.375 > : 1.386 > : 1.386 > : 1.441 > : 1.441 > : 1.445 > : 1.445 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 > : 1.447 Optimal score following high resolution, local optimization: 1.447 Processing set: N 84 ASN [2]: N 82 GLN [2] permutations: 4 Computing dot scores Num optimizations problems to be solved for this clique: 4 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -2.010 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following high resolution, local optimization: -2.010 Processing set: N 76 LYS NZ [4]: N 80 TYR OH [11] permutations: 44 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.689 > : 0.884 > : 0.945 > : 1.007 > : 1.058 > : 1.107 > : 1.156 > : 1.205 > : 1.256 > : 1.299 > : 1.339 > : 1.377 > : 1.413 > : 1.447 > : 1.479 > : 1.508 > : 1.533 > : 1.556 > : 1.575 > : 1.593 > : 1.608 > : 1.622 > : 1.634 > : 1.644 > : 1.651 > : 1.663 > : 1.671 > : 1.680 > : 1.686 > : 1.689 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 > : 1.690 Optimal score following high resolution, local optimization: 1.690 Processing set: N 53 GLN [2]: N 52 SER OG [2] permutations: 4 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.626 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 > : 0.626 Optimal score following high resolution, local optimization: 0.626 Processing set: N 31 ASN [2]: N 30 SER OG [4] permutations: 8 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.384 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.384 > : 1.392 > : 1.392 > : 1.398 > : 1.398 > : 1.401 > : 1.401 > : 1.402 > : 1.402 > : 1.402 > : 1.402 > : 1.402 > : 1.402 > : 1.402 > : 1.402 > : 1.402 > : 1.402 > : 1.402 > : 1.402 > : 1.402 Optimal score following high resolution, local optimization: 1.402 Processing set: N 25 SER OG [3]: N 3 GLN [2] permutations: 6 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.009 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 > : -0.009 Optimal score following high resolution, local optimization: -0.009 Processing set: G 59 ASN [2]: B 340 ASN [2] permutations: 4 Computing dot scores Num optimizations problems to be solved for this clique: 4 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.782 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following high resolution, local optimization: -0.782 Processing set: B 329 THR OG1 [7]: B 311 HIS [6] permutations: 42 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.398 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 > : 0.398 Optimal score following high resolution, local optimization: 0.398 Processing set: B 268 ASN [2]: B 266 HIS [6] permutations: 12 Computing dot scores Num optimizations problems to be solved for this clique: 6 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.138 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following high resolution, local optimization: -0.138 Processing set: B 245 SER OG [12]: B 243 THR OG1 [7]: B 225 HIS [6] permutations: 504 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.679 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 0.679 > : 0.679 > : 0.679 > : 0.679 > : 0.679 > : 0.679 > : 0.696 > : 0.696 > : 0.787 > : 0.787 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 > : 0.847 Optimal score following high resolution, local optimization: 0.847 Processing set: B 221 THR OG1 [7]: B 218 CYS SG [3] permutations: 21 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.014 > : 0.014 > : 0.014 > : 0.014 > : 0.014 > : 0.014 > : 0.014 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 > : 0.054 Optimal score following high resolution, local optimization: 0.054 Processing set: B 209 LYS NZ [4]: B 207 SER OG [7] permutations: 28 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.159 > : 1.029 > : 1.045 > : 1.059 > : 1.074 > : 1.090 > : 1.105 > : 1.118 > : 1.131 > : 1.139 > : 1.145 > : 1.150 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.159 > : 1.180 > : 1.180 > : 1.209 > : 1.209 > : 1.247 > : 1.247 > : 1.301 > : 1.301 > : 1.325 > : 1.325 > : 1.349 > : 1.349 > : 1.349 > : 1.349 > : 1.349 > : 1.349 > : 1.349 > : 1.349 Optimal score following high resolution, local optimization: 1.349 Processing set: G 14 LYS NZ [4]: B 181 THR OG1 [4] permutations: 16 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.938 > : 0.939 > : 0.939 > : 0.939 > : 0.939 > : 0.939 > : 0.939 > : 0.939 > : 0.939 > : 0.939 > : 0.939 > : 0.939 > : 1.041 > : 1.041 > : 1.096 > : 1.096 > : 1.096 > : 1.096 > : 1.096 Optimal score following high resolution, local optimization: 1.096 Processing set: B 179 THR OG1 [2]: B 176 GLN [2] permutations: 4 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.043 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.043 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 > : 1.044 Optimal score following high resolution, local optimization: 1.044 Processing set: B 159 THR OG1 [9]: B 142 HIS [6] permutations: 54 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 1.698 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 > : 1.698 Optimal score following high resolution, local optimization: 1.698 Processing set: B 189 SER OG [2]: B 148 CYS SG [2] permutations: 4 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 > : 0.127 Optimal score following high resolution, local optimization: 0.127 Processing set: B 160 SER OG [4]: B 147 SER OG [8] permutations: 32 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.456 > : 0.456 > : 0.481 > : 0.481 > : 0.483 > : 0.483 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.487 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.514 > : 0.564 > : 0.564 Optimal score following high resolution, local optimization: 0.564 Processing set: B 128 THR OG1 [4]: B 125 ASN [2] permutations: 8 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.009 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 > : 0.009 Optimal score following high resolution, local optimization: 0.009 Processing set: B 121 CYS SG [1]: B 149 CYS SG [2] permutations: 2 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 > : -0.128 Optimal score following high resolution, local optimization: -0.128 Processing set: B 110 ASN [2]: B 108 SER OG [4] permutations: 8 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 2.132 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 > : 2.132 Optimal score following high resolution, local optimization: 2.132 Processing set: B 89 LYS NZ [4]: B 88 ASN [2]: A 23 ASN [2] permutations: 16 Computing dot scores Num optimizations problems to be solved for this clique: 4 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.198 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -0.352 > : -0.330 > : -0.307 > : -0.285 > : -0.263 > : -0.243 > : -0.224 > : -0.224 > : -0.224 > : -0.224 > : -0.213 > : -0.200 > : -0.187 > : -0.175 > : -0.143 > : -0.133 > : -0.117 > : -0.116 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 > : -0.115 Optimal score following high resolution, local optimization: -0.115 Processing set: A 19 GLN [2]: B 86 THR OG1 [7] permutations: 14 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 2.694 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 2.694 > : 2.694 > : 2.704 > : 2.739 > : 2.739 > : 2.739 > : 2.739 > : 2.739 > : 2.739 > : 2.739 > : 2.739 > : 2.739 > : 2.739 > : 2.739 > : 2.746 > : 2.746 > : 2.746 > : 2.746 > : 2.746 > : 2.746 Optimal score following high resolution, local optimization: 2.746 Processing set: B 74 SER OG [12]: B 72 SER OG [7]: B 54 HIS [6] permutations: 504 Computing dot scores Num optimizations problems to be solved for this clique: 5 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.053 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : 0.053 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 > : 0.124 Optimal score following high resolution, local optimization: 0.124 Processing set: A 237 CYS SG [3]: B 59 TYR OH [13] permutations: 39 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 > : -0.736 Optimal score following high resolution, local optimization: -0.736 Processing set: A 371 ASN [2]: A 364 THR OG1 [4] permutations: 8 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -0.376 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 > : -0.376 Optimal score following high resolution, local optimization: -0.376 Processing set: A 359 CYS SG [3]: A 349 SER OG [4] permutations: 12 Computing dot scores Num optimizations problems to be solved for this clique: 1 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.604 > : 0.612 > : 0.612 > : 0.621 > : 0.621 > : 0.628 > : 0.628 > : 0.635 > : 0.635 > : 0.641 > : 0.641 > : 0.645 > : 0.645 > : 0.649 > : 0.649 > : 0.652 > : 0.652 > : 0.653 > : 0.653 > : 0.654 Optimal score following high resolution, local optimization: 0.654 Processing set: A 233 LYS NZ [4]: B 230 ASN [2] permutations: 8 Computing dot scores Num optimizations problems to be solved for this clique: 3 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph Optimal score following low resolution optimization: -1.347 Beginning Optimization Dynamic programming succeeded to fully optimize hypergraph > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 > : -1.347 >