Starting phenix.real_space_refine on Wed Mar 4 02:07:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mpb_9188/03_2026/6mpb_9188.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mpb_9188/03_2026/6mpb_9188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6mpb_9188/03_2026/6mpb_9188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mpb_9188/03_2026/6mpb_9188.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6mpb_9188/03_2026/6mpb_9188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mpb_9188/03_2026/6mpb_9188.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 sd= 0.326 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 48 5.16 5 C 6498 2.51 5 N 1656 2.21 5 O 1767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9969 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "C" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "A" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.21, per 1000 atoms: 0.22 Number of scatterers: 9969 At special positions: 0 Unit cell: (121.632, 111.858, 119.46, 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 48 16.00 O 1767 8.00 N 1656 7.00 C 6498 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 Links applied NAG-ASN " NAG B 602 " - " ASN B 163 " " NAG C 602 " - " ASN C 163 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 546.3 milliseconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 76.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 44 through 52 removed outlier: 3.827A pdb=" N CYS B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 75 removed outlier: 3.568A pdb=" N VAL B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.510A pdb=" N LEU B 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 100 removed outlier: 3.852A pdb=" N SER B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.922A pdb=" N LEU B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.846A pdb=" N VAL B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 151 removed outlier: 3.673A pdb=" N ARG B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.602A pdb=" N ILE B 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.896A pdb=" N ALA B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.786A pdb=" N ALA B 188 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.862A pdb=" N PHE B 201 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 248 removed outlier: 3.801A pdb=" N LEU B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 292 removed outlier: 4.426A pdb=" N LEU B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 271 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.941A pdb=" N MET B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 316 removed outlier: 3.570A pdb=" N ARG B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 removed outlier: 3.566A pdb=" N LEU B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.593A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 356 through 367 removed outlier: 3.945A pdb=" N GLU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 382 removed outlier: 3.612A pdb=" N SER B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 377 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 404 removed outlier: 3.802A pdb=" N CYS B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 428 removed outlier: 3.687A pdb=" N ILE B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 439 through 446 removed outlier: 3.663A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 488 removed outlier: 3.616A pdb=" N SER B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 52 removed outlier: 3.827A pdb=" N CYS C 48 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 75 removed outlier: 3.568A pdb=" N VAL C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.509A pdb=" N LEU C 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 3.854A pdb=" N SER C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Proline residue: C 92 - end of helix removed outlier: 3.922A pdb=" N LEU C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.847A pdb=" N VAL C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N CYS C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 151 removed outlier: 3.673A pdb=" N ARG C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.602A pdb=" N ILE C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.896A pdb=" N ALA C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 191 removed outlier: 3.785A pdb=" N ALA C 188 " --> pdb=" O PHE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.861A pdb=" N PHE C 201 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 248 removed outlier: 3.802A pdb=" N LEU C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 245 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 292 removed outlier: 4.426A pdb=" N LEU C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 266 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER C 271 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP C 272 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 3.940A pdb=" N MET C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C 283 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 316 removed outlier: 3.570A pdb=" N ARG C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 330 removed outlier: 3.565A pdb=" N LEU C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 339 removed outlier: 3.592A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 351 Processing helix chain 'C' and resid 356 through 367 removed outlier: 3.945A pdb=" N GLU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 382 removed outlier: 3.613A pdb=" N SER C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 376 " --> pdb=" O LYS C 372 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 377 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 379 " --> pdb=" O SER C 375 " (cutoff:3.500A) Proline residue: C 380 - end of helix Processing helix chain 'C' and resid 387 through 404 removed outlier: 3.801A pdb=" N CYS C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 428 removed outlier: 3.688A pdb=" N ILE C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 438 No H-bonds generated for 'chain 'C' and resid 436 through 438' Processing helix chain 'C' and resid 439 through 446 removed outlier: 3.663A pdb=" N ALA C 445 " --> pdb=" O ILE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 488 removed outlier: 3.615A pdb=" N SER C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 484 " --> pdb=" O GLY C 480 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 removed outlier: 3.827A pdb=" N CYS A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.568A pdb=" N VAL A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.510A pdb=" N LEU A 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.852A pdb=" N SER A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Proline residue: A 92 - end of helix removed outlier: 3.922A pdb=" N LEU A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.847A pdb=" N VAL A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 151 removed outlier: 3.673A pdb=" N ARG A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.602A pdb=" N ILE A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.896A pdb=" N ALA A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.786A pdb=" N ALA A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.861A pdb=" N PHE A 201 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 248 removed outlier: 3.800A pdb=" N LEU A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 292 removed outlier: 4.426A pdb=" N LEU A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Proline residue: A 278 - end of helix removed outlier: 3.940A pdb=" N MET A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.569A pdb=" N ARG A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 330 removed outlier: 3.564A pdb=" N LEU A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.592A pdb=" N PHE A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.945A pdb=" N GLU A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.613A pdb=" N SER A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 377 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 387 through 404 removed outlier: 3.801A pdb=" N CYS A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 428 removed outlier: 3.688A pdb=" N ILE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.663A pdb=" N ALA A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 488 removed outlier: 3.616A pdb=" N SER A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AA2, first strand: chain 'C' and resid 207 through 209 Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 209 519 hydrogen bonds defined for protein. 1512 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: 1.53 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3149 1.34 - 1.46: 1456 1.46 - 1.57: 5463 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 10143 Sorted by residual: bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C LEU C 105 " pdb=" N PRO C 106 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.45e+00 bond pdb=" N ASN C 447 " pdb=" CA ASN C 447 " ideal model delta sigma weight residual 1.460 1.484 -0.024 1.54e-02 4.22e+03 2.42e+00 ... (remaining 10138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 13504 3.11 - 6.23: 239 6.23 - 9.34: 72 9.34 - 12.46: 0 12.46 - 15.57: 6 Bond angle restraints: 13821 Sorted by residual: angle pdb=" C VAL B 446 " pdb=" N ASN B 447 " pdb=" CA ASN B 447 " ideal model delta sigma weight residual 122.46 129.79 -7.33 1.41e+00 5.03e-01 2.70e+01 angle pdb=" C VAL C 446 " pdb=" N ASN C 447 " pdb=" CA ASN C 447 " ideal model delta sigma weight residual 122.46 129.77 -7.31 1.41e+00 5.03e-01 2.69e+01 angle pdb=" C VAL A 446 " pdb=" N ASN A 447 " pdb=" CA ASN A 447 " ideal model delta sigma weight residual 122.46 129.73 -7.27 1.41e+00 5.03e-01 2.66e+01 angle pdb=" CA LEU C 409 " pdb=" CB LEU C 409 " pdb=" CG LEU C 409 " ideal model delta sigma weight residual 116.30 131.87 -15.57 3.50e+00 8.16e-02 1.98e+01 angle pdb=" CA LEU B 409 " pdb=" CB LEU B 409 " pdb=" CG LEU B 409 " ideal model delta sigma weight residual 116.30 131.84 -15.54 3.50e+00 8.16e-02 1.97e+01 ... (remaining 13816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 5600 15.01 - 30.01: 330 30.01 - 45.01: 70 45.01 - 60.02: 5 60.02 - 75.02: 7 Dihedral angle restraints: 6012 sinusoidal: 2232 harmonic: 3780 Sorted by residual: dihedral pdb=" CA ARG B 211 " pdb=" C ARG B 211 " pdb=" N ASN B 212 " pdb=" CA ASN B 212 " ideal model delta harmonic sigma weight residual 180.00 -158.05 -21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG A 211 " pdb=" C ARG A 211 " pdb=" N ASN A 212 " pdb=" CA ASN A 212 " ideal model delta harmonic sigma weight residual -180.00 -158.06 -21.94 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ARG C 211 " pdb=" C ARG C 211 " pdb=" N ASN C 212 " pdb=" CA ASN C 212 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 6009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1332 0.062 - 0.123: 322 0.123 - 0.185: 65 0.185 - 0.246: 3 0.246 - 0.307: 8 Chirality restraints: 1730 Sorted by residual: chirality pdb=" CB VAL A 446 " pdb=" CA VAL A 446 " pdb=" CG1 VAL A 446 " pdb=" CG2 VAL A 446 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB VAL B 446 " pdb=" CA VAL B 446 " pdb=" CG1 VAL B 446 " pdb=" CG2 VAL B 446 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB VAL C 446 " pdb=" CA VAL C 446 " pdb=" CG1 VAL C 446 " pdb=" CG2 VAL C 446 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1727 not shown) Planarity restraints: 1727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 211 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C ARG C 211 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG C 211 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN C 212 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 211 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C ARG B 211 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG B 211 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 212 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 211 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C ARG A 211 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG A 211 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 212 " -0.012 2.00e-02 2.50e+03 ... (remaining 1724 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3232 2.85 - 3.36: 10038 3.36 - 3.88: 15549 3.88 - 4.39: 17580 4.39 - 4.90: 29128 Nonbonded interactions: 75527 Sorted by model distance: nonbonded pdb=" OG SER A 352 " pdb=" O GLY A 430 " model vdw 2.338 3.040 nonbonded pdb=" OG SER C 352 " pdb=" O GLY C 430 " model vdw 2.339 3.040 nonbonded pdb=" OG SER B 352 " pdb=" O GLY B 430 " model vdw 2.339 3.040 nonbonded pdb=" NE2 GLN C 394 " pdb=" OG1 THR C 438 " model vdw 2.378 3.120 nonbonded pdb=" NE2 GLN B 394 " pdb=" OG1 THR B 438 " model vdw 2.378 3.120 ... (remaining 75522 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.620 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.005 0.059 10145 Z= 0.220 Angle : 1.089 15.570 13827 Z= 0.511 Chirality : 0.058 0.307 1730 Planarity : 0.006 0.049 1725 Dihedral : 10.552 75.024 3588 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.90 (0.15), residues: 1332 helix: -4.15 (0.09), residues: 846 sheet: None (None), residues: 0 loop : -3.10 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 217 TYR 0.008 0.002 TYR C 334 PHE 0.015 0.001 PHE C 201 TRP 0.005 0.001 TRP C 272 HIS 0.004 0.001 HIS C 316 Details of bonding type rmsd covalent geometry : bond 0.00498 (10143) covalent geometry : angle 1.08689 (13821) hydrogen bonds : bond 0.32119 ( 519) hydrogen bonds : angle 9.89672 ( 1512) link_NAG-ASN : bond 0.00409 ( 2) link_NAG-ASN : angle 3.40711 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 THR cc_start: 0.9006 (p) cc_final: 0.8736 (p) REVERT: B 307 LEU cc_start: 0.9225 (tm) cc_final: 0.8724 (mt) REVERT: B 311 LEU cc_start: 0.9256 (tp) cc_final: 0.9013 (tp) REVERT: B 318 LEU cc_start: 0.9328 (tm) cc_final: 0.9106 (mm) REVERT: B 394 GLN cc_start: 0.8394 (mt0) cc_final: 0.8192 (mt0) REVERT: B 403 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8611 (mm-40) REVERT: C 149 LEU cc_start: 0.9002 (tm) cc_final: 0.8758 (tm) REVERT: C 210 GLU cc_start: 0.5826 (mp0) cc_final: 0.5497 (mm-30) REVERT: C 253 GLU cc_start: 0.7631 (tp30) cc_final: 0.7295 (tp30) REVERT: C 267 MET cc_start: 0.8461 (tpp) cc_final: 0.7502 (tpp) REVERT: C 313 HIS cc_start: 0.8809 (m90) cc_final: 0.8422 (m-70) REVERT: C 353 SER cc_start: 0.9009 (t) cc_final: 0.8686 (p) REVERT: C 366 GLU cc_start: 0.8478 (tt0) cc_final: 0.8176 (tm-30) REVERT: C 388 ASP cc_start: 0.8674 (p0) cc_final: 0.8216 (p0) REVERT: C 462 LEU cc_start: 0.8976 (tp) cc_final: 0.8750 (tp) REVERT: A 130 TRP cc_start: 0.8143 (m100) cc_final: 0.7699 (m100) REVERT: A 184 PHE cc_start: 0.7972 (t80) cc_final: 0.7628 (m-80) REVERT: A 264 GLU cc_start: 0.8867 (tp30) cc_final: 0.8288 (tp30) REVERT: A 348 PHE cc_start: 0.8835 (t80) cc_final: 0.8472 (t80) REVERT: A 363 CYS cc_start: 0.9042 (m) cc_final: 0.8664 (m) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.0927 time to fit residues: 53.8403 Evaluate side-chains 218 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 483 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 394 GLN C 483 GLN A 163 ASN A 224 GLN A 483 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.079103 restraints weight = 28198.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081500 restraints weight = 14800.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.083109 restraints weight = 9556.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.084063 restraints weight = 7107.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084745 restraints weight = 5888.676| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10145 Z= 0.145 Angle : 0.738 10.227 13827 Z= 0.353 Chirality : 0.043 0.204 1730 Planarity : 0.005 0.035 1725 Dihedral : 5.134 51.983 1479 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 7.66 % Allowed : 19.25 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.19), residues: 1332 helix: -2.06 (0.14), residues: 909 sheet: -1.61 (0.98), residues: 30 loop : -2.84 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 465 TYR 0.019 0.001 TYR B 485 PHE 0.015 0.001 PHE A 192 TRP 0.023 0.001 TRP A 461 HIS 0.006 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00308 (10143) covalent geometry : angle 0.73668 (13821) hydrogen bonds : bond 0.04804 ( 519) hydrogen bonds : angle 5.01235 ( 1512) link_NAG-ASN : bond 0.00429 ( 2) link_NAG-ASN : angle 2.21553 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 265 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.9151 (tm) cc_final: 0.8939 (tt) REVERT: B 141 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9116 (mm) REVERT: B 178 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8659 (ptmm) REVERT: B 225 GLU cc_start: 0.8754 (mp0) cc_final: 0.8415 (mp0) REVERT: B 275 TRP cc_start: 0.8436 (m100) cc_final: 0.8167 (m-10) REVERT: B 302 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8684 (pp) REVERT: B 307 LEU cc_start: 0.9049 (tm) cc_final: 0.8545 (mt) REVERT: B 311 LEU cc_start: 0.9161 (tp) cc_final: 0.8643 (mm) REVERT: B 329 THR cc_start: 0.8005 (p) cc_final: 0.7705 (p) REVERT: B 331 LYS cc_start: 0.8519 (mttp) cc_final: 0.8253 (mttp) REVERT: B 387 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7926 (mmp) REVERT: C 149 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8866 (tm) REVERT: C 313 HIS cc_start: 0.8832 (m90) cc_final: 0.8431 (m-70) REVERT: C 328 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8368 (t80) REVERT: C 334 TYR cc_start: 0.8326 (m-10) cc_final: 0.7793 (t80) REVERT: C 366 GLU cc_start: 0.8317 (tt0) cc_final: 0.8093 (tm-30) REVERT: C 471 ASN cc_start: 0.8627 (t0) cc_final: 0.8341 (t0) REVERT: A 50 ARG cc_start: 0.7676 (mtm180) cc_final: 0.7174 (tpt90) REVERT: A 94 GLU cc_start: 0.8119 (tp30) cc_final: 0.7796 (tp30) REVERT: A 130 TRP cc_start: 0.8185 (m100) cc_final: 0.7629 (m100) REVERT: A 134 PHE cc_start: 0.9178 (t80) cc_final: 0.8977 (t80) REVERT: A 332 ASN cc_start: 0.8408 (t0) cc_final: 0.7689 (m-40) REVERT: A 363 CYS cc_start: 0.9067 (m) cc_final: 0.8443 (m) REVERT: A 387 MET cc_start: 0.7931 (mmm) cc_final: 0.7656 (mmm) REVERT: A 403 GLN cc_start: 0.9035 (tp40) cc_final: 0.8579 (tm-30) REVERT: A 464 ASP cc_start: 0.8052 (t70) cc_final: 0.7834 (t70) REVERT: A 465 ARG cc_start: 0.9061 (mmm-85) cc_final: 0.8615 (mtt-85) outliers start: 80 outliers final: 32 residues processed: 316 average time/residue: 0.0827 time to fit residues: 38.2048 Evaluate side-chains 247 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.079246 restraints weight = 28749.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.081444 restraints weight = 15049.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082888 restraints weight = 9751.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083919 restraints weight = 7333.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.084533 restraints weight = 6048.218| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10145 Z= 0.129 Angle : 0.720 13.360 13827 Z= 0.332 Chirality : 0.042 0.235 1730 Planarity : 0.004 0.035 1725 Dihedral : 4.717 52.046 1479 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 7.09 % Allowed : 20.88 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.22), residues: 1332 helix: -1.04 (0.16), residues: 939 sheet: -1.29 (1.00), residues: 30 loop : -2.26 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.011 0.001 TYR B 305 PHE 0.015 0.001 PHE B 135 TRP 0.019 0.001 TRP A 461 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00281 (10143) covalent geometry : angle 0.71936 (13821) hydrogen bonds : bond 0.03937 ( 519) hydrogen bonds : angle 4.45249 ( 1512) link_NAG-ASN : bond 0.00349 ( 2) link_NAG-ASN : angle 1.92778 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 228 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8810 (tm) REVERT: B 141 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9129 (mm) REVERT: B 225 GLU cc_start: 0.8798 (mp0) cc_final: 0.8503 (mp0) REVERT: B 275 TRP cc_start: 0.8433 (m100) cc_final: 0.8161 (m-10) REVERT: B 282 MET cc_start: 0.8654 (ttt) cc_final: 0.8342 (ttp) REVERT: B 302 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8736 (pp) REVERT: B 387 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7833 (mmp) REVERT: B 465 ARG cc_start: 0.7932 (mtt90) cc_final: 0.7565 (mtp85) REVERT: C 149 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8930 (tm) REVERT: C 313 HIS cc_start: 0.8885 (m90) cc_final: 0.8620 (m-70) REVERT: C 328 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8269 (t80) REVERT: C 334 TYR cc_start: 0.8172 (m-10) cc_final: 0.7825 (t80) REVERT: A 50 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7168 (tpt90) REVERT: A 94 GLU cc_start: 0.8278 (tp30) cc_final: 0.8028 (tp30) REVERT: A 130 TRP cc_start: 0.8177 (m100) cc_final: 0.7680 (m100) REVERT: A 214 THR cc_start: 0.5402 (OUTLIER) cc_final: 0.4730 (t) REVERT: A 305 TYR cc_start: 0.9002 (t80) cc_final: 0.8704 (t80) REVERT: A 313 HIS cc_start: 0.8913 (m90) cc_final: 0.8665 (m90) REVERT: A 363 CYS cc_start: 0.9170 (m) cc_final: 0.8419 (m) REVERT: A 387 MET cc_start: 0.7947 (mmm) cc_final: 0.7279 (mmm) REVERT: A 465 ARG cc_start: 0.9075 (mmm-85) cc_final: 0.8350 (mtt-85) REVERT: A 471 ASN cc_start: 0.8704 (t0) cc_final: 0.8119 (t0) outliers start: 74 outliers final: 37 residues processed: 274 average time/residue: 0.0815 time to fit residues: 33.0908 Evaluate side-chains 245 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 89 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 25 optimal weight: 0.0370 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 20 optimal weight: 0.0030 overall best weight: 0.5268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.097414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.079473 restraints weight = 28609.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081783 restraints weight = 15246.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083218 restraints weight = 9936.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.084295 restraints weight = 7562.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.084892 restraints weight = 6203.315| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10145 Z= 0.117 Angle : 0.711 12.759 13827 Z= 0.321 Chirality : 0.041 0.193 1730 Planarity : 0.004 0.035 1725 Dihedral : 4.488 52.046 1479 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 6.99 % Allowed : 22.70 % Favored : 70.31 % 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 are not related in a simple way. whole: -1.53 (0.23), residues: 1332 helix: -0.47 (0.17), residues: 933 sheet: -1.22 (0.99), residues: 30 loop : -2.16 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 101 TYR 0.009 0.001 TYR B 305 PHE 0.013 0.001 PHE C 299 TRP 0.022 0.001 TRP A 461 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00250 (10143) covalent geometry : angle 0.71057 (13821) hydrogen bonds : bond 0.03487 ( 519) hydrogen bonds : angle 4.25441 ( 1512) link_NAG-ASN : bond 0.00395 ( 2) link_NAG-ASN : angle 1.76241 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 230 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8808 (tm) REVERT: B 141 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9105 (mm) REVERT: B 225 GLU cc_start: 0.8787 (mp0) cc_final: 0.8515 (mp0) REVERT: B 275 TRP cc_start: 0.8539 (m100) cc_final: 0.8118 (m-10) REVERT: B 360 MET cc_start: 0.9505 (mmm) cc_final: 0.9304 (tpp) REVERT: B 362 LYS cc_start: 0.8837 (tptt) cc_final: 0.8267 (tppt) REVERT: B 363 CYS cc_start: 0.8930 (m) cc_final: 0.8183 (t) REVERT: B 387 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7867 (mmp) REVERT: B 394 GLN cc_start: 0.8185 (mt0) cc_final: 0.7981 (mt0) REVERT: B 465 ARG cc_start: 0.7709 (mtt90) cc_final: 0.7376 (mtp85) REVERT: C 94 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8474 (tt0) REVERT: C 143 SER cc_start: 0.9194 (p) cc_final: 0.8973 (p) REVERT: C 149 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8939 (tm) REVERT: C 313 HIS cc_start: 0.8940 (m90) cc_final: 0.8501 (m90) REVERT: C 334 TYR cc_start: 0.8047 (m-10) cc_final: 0.7801 (t80) REVERT: C 376 ARG cc_start: 0.8661 (ptm160) cc_final: 0.8453 (mtm-85) REVERT: C 418 LEU cc_start: 0.9002 (tp) cc_final: 0.8791 (mt) REVERT: A 50 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7171 (tpt90) REVERT: A 94 GLU cc_start: 0.8353 (tp30) cc_final: 0.8062 (tp30) REVERT: A 130 TRP cc_start: 0.8213 (m100) cc_final: 0.7708 (m100) REVERT: A 214 THR cc_start: 0.5520 (OUTLIER) cc_final: 0.4861 (t) REVERT: A 274 MET cc_start: 0.8638 (tpp) cc_final: 0.8307 (tpp) REVERT: A 292 MET cc_start: 0.7920 (mpp) cc_final: 0.7415 (mmm) REVERT: A 302 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8616 (pp) REVERT: A 305 TYR cc_start: 0.9020 (t80) cc_final: 0.8633 (t80) REVERT: A 332 ASN cc_start: 0.8382 (t0) cc_final: 0.7647 (m-40) REVERT: A 359 LEU cc_start: 0.8966 (tp) cc_final: 0.8162 (tp) REVERT: A 363 CYS cc_start: 0.9148 (m) cc_final: 0.8328 (m) REVERT: A 387 MET cc_start: 0.8099 (mmm) cc_final: 0.7671 (mmm) REVERT: A 403 GLN cc_start: 0.8969 (tp40) cc_final: 0.8559 (tm-30) REVERT: A 465 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8493 (mtt-85) REVERT: A 471 ASN cc_start: 0.8662 (t0) cc_final: 0.8238 (t0) outliers start: 73 outliers final: 39 residues processed: 272 average time/residue: 0.0718 time to fit residues: 29.3531 Evaluate side-chains 248 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 26 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.094335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.076455 restraints weight = 28697.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.078691 restraints weight = 15160.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.080161 restraints weight = 9838.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.081074 restraints weight = 7375.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081584 restraints weight = 6135.035| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10145 Z= 0.154 Angle : 0.718 12.368 13827 Z= 0.334 Chirality : 0.043 0.220 1730 Planarity : 0.004 0.034 1725 Dihedral : 4.449 51.559 1479 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 6.99 % Allowed : 24.14 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.23), residues: 1332 helix: -0.18 (0.17), residues: 957 sheet: -1.11 (1.01), residues: 30 loop : -2.06 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 98 TYR 0.011 0.001 TYR C 325 PHE 0.032 0.001 PHE B 411 TRP 0.023 0.001 TRP A 461 HIS 0.004 0.001 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00355 (10143) covalent geometry : angle 0.71685 (13821) hydrogen bonds : bond 0.03773 ( 519) hydrogen bonds : angle 4.31146 ( 1512) link_NAG-ASN : bond 0.00283 ( 2) link_NAG-ASN : angle 1.78474 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 213 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8811 (tm) REVERT: B 141 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9131 (mm) REVERT: B 178 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8597 (ptmm) REVERT: B 362 LYS cc_start: 0.8834 (tptt) cc_final: 0.8622 (tppt) REVERT: B 363 CYS cc_start: 0.8873 (m) cc_final: 0.8192 (t) REVERT: B 431 ILE cc_start: 0.8643 (mt) cc_final: 0.8376 (tt) REVERT: B 465 ARG cc_start: 0.7882 (mtt90) cc_final: 0.7490 (mmm-85) REVERT: C 143 SER cc_start: 0.9164 (p) cc_final: 0.8945 (p) REVERT: C 149 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8988 (tm) REVERT: C 313 HIS cc_start: 0.9027 (m90) cc_final: 0.8383 (m90) REVERT: C 334 TYR cc_start: 0.8236 (m-10) cc_final: 0.7839 (t80) REVERT: C 360 MET cc_start: 0.9416 (tpt) cc_final: 0.9179 (tpp) REVERT: C 418 LEU cc_start: 0.9115 (tp) cc_final: 0.8705 (mt) REVERT: A 50 ARG cc_start: 0.7794 (mtm180) cc_final: 0.7136 (tpt90) REVERT: A 94 GLU cc_start: 0.8398 (tp30) cc_final: 0.8176 (tp30) REVERT: A 130 TRP cc_start: 0.8332 (m100) cc_final: 0.7809 (m100) REVERT: A 274 MET cc_start: 0.8572 (tpp) cc_final: 0.8284 (tpp) REVERT: A 292 MET cc_start: 0.7885 (mpp) cc_final: 0.7511 (mmm) REVERT: A 359 LEU cc_start: 0.9058 (tp) cc_final: 0.8329 (tp) REVERT: A 363 CYS cc_start: 0.9148 (m) cc_final: 0.8278 (m) REVERT: A 387 MET cc_start: 0.8192 (mmm) cc_final: 0.7805 (tpp) REVERT: A 403 GLN cc_start: 0.9193 (tp40) cc_final: 0.8495 (tm-30) REVERT: A 464 ASP cc_start: 0.8079 (t70) cc_final: 0.7788 (t70) REVERT: A 465 ARG cc_start: 0.9071 (mmm-85) cc_final: 0.8398 (mtt-85) REVERT: A 471 ASN cc_start: 0.8666 (t0) cc_final: 0.8255 (t0) outliers start: 73 outliers final: 47 residues processed: 257 average time/residue: 0.0763 time to fit residues: 29.4184 Evaluate side-chains 244 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 193 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 99 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 GLN B 403 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.078560 restraints weight = 28887.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.080867 restraints weight = 15266.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082403 restraints weight = 9905.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.083429 restraints weight = 7378.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.084036 restraints weight = 6081.669| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10145 Z= 0.120 Angle : 0.700 12.330 13827 Z= 0.319 Chirality : 0.042 0.218 1730 Planarity : 0.003 0.034 1725 Dihedral : 4.317 52.243 1479 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 6.99 % Allowed : 24.23 % Favored : 68.77 % 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 are not related in a simple way. whole: -0.80 (0.24), residues: 1332 helix: 0.10 (0.17), residues: 939 sheet: -1.17 (0.99), residues: 30 loop : -1.95 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 98 TYR 0.008 0.001 TYR C 325 PHE 0.011 0.001 PHE A 134 TRP 0.027 0.001 TRP A 461 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00264 (10143) covalent geometry : angle 0.69893 (13821) hydrogen bonds : bond 0.03382 ( 519) hydrogen bonds : angle 4.15405 ( 1512) link_NAG-ASN : bond 0.00350 ( 2) link_NAG-ASN : angle 1.64653 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 219 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8765 (ppp) cc_final: 0.8466 (ppp) REVERT: B 127 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8645 (tm) REVERT: B 141 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9119 (mm) REVERT: B 362 LYS cc_start: 0.8792 (tptt) cc_final: 0.8588 (tppt) REVERT: B 363 CYS cc_start: 0.8752 (m) cc_final: 0.8194 (t) REVERT: B 387 MET cc_start: 0.7991 (mmp) cc_final: 0.7377 (mmm) REVERT: B 431 ILE cc_start: 0.8603 (mt) cc_final: 0.8356 (tt) REVERT: B 438 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.8773 (t) REVERT: B 465 ARG cc_start: 0.7704 (mtt90) cc_final: 0.7441 (mtp85) REVERT: C 143 SER cc_start: 0.9105 (p) cc_final: 0.8892 (p) REVERT: C 149 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8975 (tm) REVERT: C 274 MET cc_start: 0.8474 (ttm) cc_final: 0.7680 (ttp) REVERT: C 313 HIS cc_start: 0.9012 (m90) cc_final: 0.8462 (m90) REVERT: C 328 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8125 (t80) REVERT: C 334 TYR cc_start: 0.8170 (m-10) cc_final: 0.7743 (t80) REVERT: C 418 LEU cc_start: 0.9100 (tp) cc_final: 0.8711 (mt) REVERT: A 50 ARG cc_start: 0.7754 (mtm180) cc_final: 0.7180 (tpt90) REVERT: A 94 GLU cc_start: 0.8404 (tp30) cc_final: 0.8132 (tp30) REVERT: A 130 TRP cc_start: 0.8207 (m100) cc_final: 0.7728 (m100) REVERT: A 141 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9295 (mp) REVERT: A 274 MET cc_start: 0.8511 (tpp) cc_final: 0.8277 (tpp) REVERT: A 292 MET cc_start: 0.7800 (mpp) cc_final: 0.7514 (mmm) REVERT: A 302 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8607 (pp) REVERT: A 305 TYR cc_start: 0.9084 (t80) cc_final: 0.8864 (t80) REVERT: A 332 ASN cc_start: 0.8317 (t0) cc_final: 0.7605 (m-40) REVERT: A 334 TYR cc_start: 0.7809 (m-10) cc_final: 0.7528 (m-10) REVERT: A 359 LEU cc_start: 0.9009 (tp) cc_final: 0.8225 (tp) REVERT: A 363 CYS cc_start: 0.9145 (m) cc_final: 0.8248 (m) REVERT: A 403 GLN cc_start: 0.9116 (tp40) cc_final: 0.8519 (tm-30) REVERT: A 465 ARG cc_start: 0.8953 (mmm-85) cc_final: 0.8638 (mtt-85) outliers start: 73 outliers final: 46 residues processed: 263 average time/residue: 0.0775 time to fit residues: 29.9079 Evaluate side-chains 258 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 3.9990 chunk 124 optimal weight: 0.0070 chunk 86 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 GLN B 403 GLN B 452 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.096747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.078883 restraints weight = 28407.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081185 restraints weight = 15103.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.082649 restraints weight = 9813.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.083691 restraints weight = 7375.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.084205 restraints weight = 6093.178| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10145 Z= 0.121 Angle : 0.713 12.250 13827 Z= 0.325 Chirality : 0.042 0.194 1730 Planarity : 0.003 0.034 1725 Dihedral : 4.235 51.944 1479 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.13 % Allowed : 26.15 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.24), residues: 1332 helix: 0.29 (0.17), residues: 939 sheet: -1.18 (0.99), residues: 30 loop : -1.88 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 101 TYR 0.009 0.001 TYR C 325 PHE 0.021 0.001 PHE B 411 TRP 0.027 0.001 TRP A 461 HIS 0.006 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00273 (10143) covalent geometry : angle 0.71214 (13821) hydrogen bonds : bond 0.03373 ( 519) hydrogen bonds : angle 4.12031 ( 1512) link_NAG-ASN : bond 0.00339 ( 2) link_NAG-ASN : angle 1.54698 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 212 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8766 (ppp) cc_final: 0.8467 (ppp) REVERT: B 127 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8602 (tm) REVERT: B 141 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9113 (mm) REVERT: B 225 GLU cc_start: 0.8780 (mp0) cc_final: 0.8422 (mp0) REVERT: B 282 MET cc_start: 0.8376 (ttt) cc_final: 0.8134 (ttp) REVERT: B 363 CYS cc_start: 0.8741 (m) cc_final: 0.8035 (t) REVERT: B 387 MET cc_start: 0.8082 (mmp) cc_final: 0.7454 (mmm) REVERT: B 431 ILE cc_start: 0.8629 (mt) cc_final: 0.8410 (tt) REVERT: B 465 ARG cc_start: 0.7695 (mtt90) cc_final: 0.7479 (mtp85) REVERT: C 149 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8988 (tm) REVERT: C 274 MET cc_start: 0.8595 (ttm) cc_final: 0.8047 (ttp) REVERT: C 313 HIS cc_start: 0.9039 (m90) cc_final: 0.8574 (m90) REVERT: C 328 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8055 (t80) REVERT: C 334 TYR cc_start: 0.8022 (m-10) cc_final: 0.7651 (t80) REVERT: C 408 SER cc_start: 0.7061 (m) cc_final: 0.6730 (t) REVERT: C 418 LEU cc_start: 0.9114 (tp) cc_final: 0.8734 (mt) REVERT: A 50 ARG cc_start: 0.7799 (mtm180) cc_final: 0.7274 (tpt90) REVERT: A 94 GLU cc_start: 0.8407 (tp30) cc_final: 0.8104 (tp30) REVERT: A 274 MET cc_start: 0.8495 (tpp) cc_final: 0.8248 (tpp) REVERT: A 292 MET cc_start: 0.7798 (mpp) cc_final: 0.7527 (mmm) REVERT: A 302 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8556 (pp) REVERT: A 305 TYR cc_start: 0.9079 (t80) cc_final: 0.8840 (t80) REVERT: A 332 ASN cc_start: 0.8382 (t0) cc_final: 0.7646 (m-40) REVERT: A 359 LEU cc_start: 0.9009 (tp) cc_final: 0.8222 (tp) REVERT: A 363 CYS cc_start: 0.9110 (m) cc_final: 0.8331 (m) REVERT: A 366 GLU cc_start: 0.8144 (tt0) cc_final: 0.7773 (tt0) REVERT: A 403 GLN cc_start: 0.9108 (tp40) cc_final: 0.8500 (tm-30) REVERT: A 418 LEU cc_start: 0.9225 (mt) cc_final: 0.8667 (mt) REVERT: A 444 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8296 (tm-30) REVERT: A 465 ARG cc_start: 0.8983 (mmm-85) cc_final: 0.8701 (mtt-85) outliers start: 64 outliers final: 43 residues processed: 253 average time/residue: 0.0782 time to fit residues: 29.3476 Evaluate side-chains 252 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 0.0970 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078705 restraints weight = 28520.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080970 restraints weight = 15187.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.082436 restraints weight = 9898.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083473 restraints weight = 7445.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.084151 restraints weight = 6158.483| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10145 Z= 0.124 Angle : 0.726 12.215 13827 Z= 0.331 Chirality : 0.042 0.192 1730 Planarity : 0.003 0.034 1725 Dihedral : 4.198 52.013 1479 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.75 % Allowed : 27.59 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1332 helix: 0.42 (0.17), residues: 936 sheet: -1.09 (1.00), residues: 30 loop : -1.79 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 217 TYR 0.009 0.001 TYR C 325 PHE 0.009 0.001 PHE A 134 TRP 0.029 0.002 TRP A 461 HIS 0.006 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00283 (10143) covalent geometry : angle 0.72530 (13821) hydrogen bonds : bond 0.03399 ( 519) hydrogen bonds : angle 4.17573 ( 1512) link_NAG-ASN : bond 0.00339 ( 2) link_NAG-ASN : angle 1.50981 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8768 (ppp) cc_final: 0.8460 (ppp) REVERT: B 127 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8586 (tm) REVERT: B 141 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9103 (mm) REVERT: B 225 GLU cc_start: 0.8804 (mp0) cc_final: 0.8407 (mp0) REVERT: B 282 MET cc_start: 0.8462 (ttt) cc_final: 0.8214 (ttp) REVERT: B 362 LYS cc_start: 0.8673 (tptt) cc_final: 0.8434 (tppt) REVERT: B 363 CYS cc_start: 0.8594 (m) cc_final: 0.8150 (t) REVERT: B 387 MET cc_start: 0.8058 (mmp) cc_final: 0.7362 (mmm) REVERT: B 465 ARG cc_start: 0.7698 (mtt90) cc_final: 0.7482 (mtp85) REVERT: C 313 HIS cc_start: 0.8965 (m90) cc_final: 0.8529 (m90) REVERT: C 334 TYR cc_start: 0.7968 (m-10) cc_final: 0.7621 (t80) REVERT: C 361 MET cc_start: 0.9228 (tpp) cc_final: 0.8884 (ttt) REVERT: C 408 SER cc_start: 0.6923 (m) cc_final: 0.6597 (t) REVERT: C 413 LYS cc_start: 0.9086 (ptpp) cc_final: 0.8847 (mtmm) REVERT: C 418 LEU cc_start: 0.9125 (tp) cc_final: 0.8753 (mt) REVERT: A 50 ARG cc_start: 0.7823 (mtm180) cc_final: 0.7322 (tpt90) REVERT: A 94 GLU cc_start: 0.8388 (tp30) cc_final: 0.8129 (tp30) REVERT: A 274 MET cc_start: 0.8503 (tpp) cc_final: 0.8262 (tpp) REVERT: A 302 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8557 (pp) REVERT: A 305 TYR cc_start: 0.9083 (t80) cc_final: 0.8848 (t80) REVERT: A 307 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8787 (tp) REVERT: A 332 ASN cc_start: 0.8380 (t0) cc_final: 0.7691 (m-40) REVERT: A 359 LEU cc_start: 0.9020 (tp) cc_final: 0.8252 (tp) REVERT: A 363 CYS cc_start: 0.9116 (m) cc_final: 0.8335 (m) REVERT: A 366 GLU cc_start: 0.8126 (tt0) cc_final: 0.7840 (tt0) REVERT: A 403 GLN cc_start: 0.9119 (tp40) cc_final: 0.8553 (tm-30) REVERT: A 418 LEU cc_start: 0.9230 (mt) cc_final: 0.8689 (mt) outliers start: 60 outliers final: 42 residues processed: 240 average time/residue: 0.0788 time to fit residues: 28.0518 Evaluate side-chains 245 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 124 optimal weight: 0.0770 chunk 127 optimal weight: 0.0040 overall best weight: 0.7752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 GLN B 403 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.096608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078842 restraints weight = 28671.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.081076 restraints weight = 15196.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.082611 restraints weight = 9944.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083638 restraints weight = 7448.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.084197 restraints weight = 6122.280| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10145 Z= 0.129 Angle : 0.741 12.144 13827 Z= 0.338 Chirality : 0.042 0.193 1730 Planarity : 0.003 0.033 1725 Dihedral : 4.183 52.030 1479 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.84 % Allowed : 27.59 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.24), residues: 1332 helix: 0.51 (0.18), residues: 936 sheet: -1.00 (1.00), residues: 30 loop : -1.73 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 376 TYR 0.018 0.001 TYR B 485 PHE 0.010 0.001 PHE C 192 TRP 0.031 0.002 TRP A 461 HIS 0.005 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00296 (10143) covalent geometry : angle 0.74051 (13821) hydrogen bonds : bond 0.03388 ( 519) hydrogen bonds : angle 4.19045 ( 1512) link_NAG-ASN : bond 0.00327 ( 2) link_NAG-ASN : angle 1.49138 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8772 (ppp) cc_final: 0.8459 (ppp) REVERT: B 127 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8612 (tm) REVERT: B 141 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9100 (mm) REVERT: B 179 GLU cc_start: 0.8541 (tp30) cc_final: 0.8275 (tp30) REVERT: B 225 GLU cc_start: 0.8755 (mp0) cc_final: 0.8328 (mp0) REVERT: B 282 MET cc_start: 0.8471 (ttt) cc_final: 0.8228 (ttp) REVERT: B 362 LYS cc_start: 0.8615 (tptt) cc_final: 0.8398 (tppt) REVERT: B 363 CYS cc_start: 0.8604 (m) cc_final: 0.8156 (t) REVERT: B 387 MET cc_start: 0.8080 (mmp) cc_final: 0.7844 (mmp) REVERT: B 438 THR cc_start: 0.9217 (p) cc_final: 0.8784 (t) REVERT: B 465 ARG cc_start: 0.7703 (mtt90) cc_final: 0.7500 (mtp85) REVERT: C 313 HIS cc_start: 0.8928 (m90) cc_final: 0.8552 (m90) REVERT: C 328 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8107 (t80) REVERT: C 334 TYR cc_start: 0.7971 (m-10) cc_final: 0.7635 (t80) REVERT: C 361 MET cc_start: 0.9223 (tpp) cc_final: 0.8829 (ttt) REVERT: C 408 SER cc_start: 0.6870 (m) cc_final: 0.6544 (t) REVERT: C 413 LYS cc_start: 0.9109 (ptpp) cc_final: 0.8877 (mtmm) REVERT: C 418 LEU cc_start: 0.9134 (tp) cc_final: 0.8767 (mt) REVERT: A 50 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7421 (tpt90) REVERT: A 94 GLU cc_start: 0.8398 (tp30) cc_final: 0.8137 (tp30) REVERT: A 274 MET cc_start: 0.8478 (tpp) cc_final: 0.8241 (tpp) REVERT: A 302 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8560 (pp) REVERT: A 305 TYR cc_start: 0.9114 (t80) cc_final: 0.8905 (t80) REVERT: A 307 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8782 (tp) REVERT: A 332 ASN cc_start: 0.8335 (t0) cc_final: 0.7719 (m-40) REVERT: A 359 LEU cc_start: 0.9053 (tp) cc_final: 0.8276 (tp) REVERT: A 363 CYS cc_start: 0.9120 (m) cc_final: 0.8330 (m) REVERT: A 365 GLU cc_start: 0.8251 (tp30) cc_final: 0.7843 (tp30) REVERT: A 366 GLU cc_start: 0.8078 (tt0) cc_final: 0.7780 (tt0) REVERT: A 403 GLN cc_start: 0.9103 (tp40) cc_final: 0.8557 (tm-30) REVERT: A 418 LEU cc_start: 0.9232 (mt) cc_final: 0.8694 (mt) outliers start: 61 outliers final: 44 residues processed: 244 average time/residue: 0.0786 time to fit residues: 28.4629 Evaluate side-chains 250 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.076429 restraints weight = 28680.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.078657 restraints weight = 15234.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.080167 restraints weight = 9969.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.081133 restraints weight = 7497.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.081532 restraints weight = 6226.030| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10145 Z= 0.154 Angle : 0.760 11.503 13827 Z= 0.351 Chirality : 0.044 0.318 1730 Planarity : 0.004 0.033 1725 Dihedral : 4.300 51.479 1479 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.79 % Allowed : 28.45 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.24), residues: 1332 helix: 0.52 (0.17), residues: 936 sheet: -0.92 (1.00), residues: 30 loop : -1.63 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 376 TYR 0.020 0.001 TYR B 485 PHE 0.012 0.001 PHE C 192 TRP 0.032 0.002 TRP A 461 HIS 0.007 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00361 (10143) covalent geometry : angle 0.75956 (13821) hydrogen bonds : bond 0.03669 ( 519) hydrogen bonds : angle 4.27655 ( 1512) link_NAG-ASN : bond 0.00249 ( 2) link_NAG-ASN : angle 1.52876 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8651 (tm) REVERT: B 141 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9142 (mm) REVERT: B 179 GLU cc_start: 0.8645 (tp30) cc_final: 0.8418 (tp30) REVERT: B 282 MET cc_start: 0.8587 (ttt) cc_final: 0.8316 (ttp) REVERT: B 362 LYS cc_start: 0.8641 (tptt) cc_final: 0.8440 (tppt) REVERT: B 363 CYS cc_start: 0.8689 (m) cc_final: 0.8182 (t) REVERT: B 387 MET cc_start: 0.8197 (mmp) cc_final: 0.7317 (mmm) REVERT: B 438 THR cc_start: 0.9206 (p) cc_final: 0.8860 (t) REVERT: C 274 MET cc_start: 0.8635 (ttm) cc_final: 0.8097 (ttp) REVERT: C 313 HIS cc_start: 0.8974 (m90) cc_final: 0.8023 (m-70) REVERT: C 334 TYR cc_start: 0.7920 (m-10) cc_final: 0.7613 (t80) REVERT: C 362 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8634 (ttpt) REVERT: C 408 SER cc_start: 0.6501 (m) cc_final: 0.6090 (t) REVERT: A 50 ARG cc_start: 0.7898 (mtm180) cc_final: 0.7409 (tpt90) REVERT: A 94 GLU cc_start: 0.8437 (tp30) cc_final: 0.8176 (tp30) REVERT: A 274 MET cc_start: 0.8489 (tpp) cc_final: 0.8287 (tpp) REVERT: A 307 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8800 (tp) REVERT: A 332 ASN cc_start: 0.8433 (t0) cc_final: 0.7776 (m-40) REVERT: A 334 TYR cc_start: 0.7790 (m-10) cc_final: 0.7579 (m-10) REVERT: A 359 LEU cc_start: 0.9115 (tp) cc_final: 0.8362 (tp) REVERT: A 363 CYS cc_start: 0.9143 (m) cc_final: 0.8395 (m) REVERT: A 366 GLU cc_start: 0.8105 (tt0) cc_final: 0.7870 (tt0) REVERT: A 403 GLN cc_start: 0.9173 (tp40) cc_final: 0.8595 (tm-30) REVERT: A 418 LEU cc_start: 0.9241 (mt) cc_final: 0.9004 (mt) outliers start: 50 outliers final: 42 residues processed: 228 average time/residue: 0.0756 time to fit residues: 25.6593 Evaluate side-chains 240 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 0.0020 chunk 66 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.078119 restraints weight = 28701.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080389 restraints weight = 15235.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081862 restraints weight = 9901.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082904 restraints weight = 7451.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.083434 restraints weight = 6143.745| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10145 Z= 0.128 Angle : 0.761 11.678 13827 Z= 0.344 Chirality : 0.043 0.325 1730 Planarity : 0.004 0.033 1725 Dihedral : 4.189 52.286 1479 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.50 % Allowed : 29.02 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.24), residues: 1332 helix: 0.60 (0.18), residues: 939 sheet: -0.80 (1.01), residues: 30 loop : -1.64 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 376 TYR 0.019 0.001 TYR B 485 PHE 0.011 0.001 PHE C 192 TRP 0.041 0.002 TRP A 461 HIS 0.009 0.001 HIS C 452 Details of bonding type rmsd covalent geometry : bond 0.00294 (10143) covalent geometry : angle 0.76034 (13821) hydrogen bonds : bond 0.03363 ( 519) hydrogen bonds : angle 4.15242 ( 1512) link_NAG-ASN : bond 0.00310 ( 2) link_NAG-ASN : angle 1.49041 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1650.21 seconds wall clock time: 29 minutes 7.40 seconds (1747.40 seconds total)