Starting phenix.real_space_refine on Mon Jul 28 05:26:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mpb_9188/07_2025/6mpb_9188.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mpb_9188/07_2025/6mpb_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6mpb_9188/07_2025/6mpb_9188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mpb_9188/07_2025/6mpb_9188.map" model { file = "/net/cci-nas-00/data/ceres_data/6mpb_9188/07_2025/6mpb_9188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mpb_9188/07_2025/6mpb_9188.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.26, per 1000 atoms: 0.93 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: 5.06 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.00 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: 2.84 Time building geometry restraints manager: 5.53 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 243.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.190 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 283.250 ------------------------------------------------------------------------------- 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 : 3.82 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.005 0.001 TRP C 272 HIS 0.004 0.001 HIS C 316 PHE 0.015 0.001 PHE C 201 TYR 0.008 0.002 TYR C 334 ARG 0.004 0.001 ARG C 217 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 2) link_NAG-ASN : angle 3.40711 ( 6) hydrogen bonds : bond 0.32119 ( 519) hydrogen bonds : angle 9.89672 ( 1512) covalent geometry : bond 0.00498 (10143) covalent geometry : angle 1.08689 (13821) *********************** 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 : 1.389 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: 0.9107 (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: 0.5496 (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: 0.9010 (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: 0.8749 (tp) REVERT: A 130 TRP cc_start: 0.8143 (m100) cc_final: 0.7699 (m100) REVERT: A 184 PHE cc_start: 0.7971 (t80) cc_final: 0.7628 (m-80) REVERT: A 264 GLU cc_start: 0.8866 (tp30) cc_final: 0.8287 (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: 0.8665 (m) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.2511 time to fit residues: 143.6253 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 : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.097275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.079404 restraints weight = 27858.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.081707 restraints weight = 14598.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083316 restraints weight = 9461.972| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10145 Z= 0.146 Angle : 0.741 10.116 13827 Z= 0.354 Chirality : 0.043 0.205 1730 Planarity : 0.005 0.034 1725 Dihedral : 5.185 52.041 1479 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 7.28 % Allowed : 19.35 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.19), residues: 1332 helix: -2.07 (0.14), residues: 909 sheet: -1.67 (0.98), residues: 30 loop : -2.83 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 461 HIS 0.006 0.001 HIS A 452 PHE 0.016 0.001 PHE A 192 TYR 0.018 0.001 TYR B 485 ARG 0.003 0.000 ARG B 465 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 2) link_NAG-ASN : angle 2.12639 ( 6) hydrogen bonds : bond 0.05097 ( 519) hydrogen bonds : angle 5.06836 ( 1512) covalent geometry : bond 0.00313 (10143) covalent geometry : angle 0.73941 (13821) *********************** 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 338 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 262 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9135 (mm) REVERT: B 178 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8711 (ptmm) REVERT: B 225 GLU cc_start: 0.8778 (mp0) cc_final: 0.8467 (mp0) REVERT: B 275 TRP cc_start: 0.8439 (m100) cc_final: 0.8158 (m-10) REVERT: B 302 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8709 (pp) REVERT: B 307 LEU cc_start: 0.9054 (tm) cc_final: 0.8543 (mt) REVERT: B 311 LEU cc_start: 0.9157 (tp) cc_final: 0.8626 (mm) REVERT: B 329 THR cc_start: 0.8057 (p) cc_final: 0.7796 (p) REVERT: B 331 LYS cc_start: 0.8516 (mttp) cc_final: 0.8266 (mttp) REVERT: B 387 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7946 (mmp) REVERT: C 149 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8860 (tm) REVERT: C 313 HIS cc_start: 0.8786 (m90) cc_final: 0.8463 (m-70) REVERT: C 328 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8331 (t80) REVERT: C 334 TYR cc_start: 0.8369 (m-10) cc_final: 0.7818 (t80) REVERT: C 366 GLU cc_start: 0.8437 (tt0) cc_final: 0.8217 (tm-30) REVERT: C 471 ASN cc_start: 0.8636 (t0) cc_final: 0.8377 (t0) REVERT: C 481 LEU cc_start: 0.9094 (tt) cc_final: 0.8714 (mm) REVERT: A 50 ARG cc_start: 0.7703 (mtm180) cc_final: 0.7167 (tpt90) REVERT: A 94 GLU cc_start: 0.8130 (tp30) cc_final: 0.7802 (tp30) REVERT: A 130 TRP cc_start: 0.8212 (m100) cc_final: 0.7625 (m100) REVERT: A 319 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8700 (mp) REVERT: A 332 ASN cc_start: 0.8461 (t0) cc_final: 0.7732 (m-40) REVERT: A 363 CYS cc_start: 0.9121 (m) cc_final: 0.8471 (m) REVERT: A 387 MET cc_start: 0.8021 (mmm) cc_final: 0.7726 (mmm) REVERT: A 464 ASP cc_start: 0.8119 (t70) cc_final: 0.7910 (t70) REVERT: A 465 ARG cc_start: 0.9088 (mmm-85) cc_final: 0.8709 (mtt-85) outliers start: 76 outliers final: 32 residues processed: 311 average time/residue: 0.1945 time to fit residues: 86.9778 Evaluate side-chains 248 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 180 VAL 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 302 LEU Chi-restraints excluded: chain A residue 319 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 78 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.094830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.076714 restraints weight = 28694.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.079004 restraints weight = 15227.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.080551 restraints weight = 9938.829| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10145 Z= 0.153 Angle : 0.735 13.357 13827 Z= 0.344 Chirality : 0.043 0.232 1730 Planarity : 0.004 0.034 1725 Dihedral : 4.797 51.841 1479 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 7.38 % Allowed : 21.07 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.22), residues: 1332 helix: -0.98 (0.16), residues: 927 sheet: -1.30 (1.00), residues: 30 loop : -2.34 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 461 HIS 0.004 0.001 HIS A 316 PHE 0.015 0.001 PHE B 135 TYR 0.011 0.001 TYR B 305 ARG 0.004 0.000 ARG A 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 2) link_NAG-ASN : angle 2.01645 ( 6) hydrogen bonds : bond 0.04112 ( 519) hydrogen bonds : angle 4.50889 ( 1512) covalent geometry : bond 0.00340 (10143) covalent geometry : angle 0.73402 (13821) *********************** 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 304 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 227 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 141 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9138 (mm) REVERT: B 178 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8677 (ptmm) REVERT: B 225 GLU cc_start: 0.8875 (mp0) cc_final: 0.8604 (mp0) REVERT: B 275 TRP cc_start: 0.8469 (m100) cc_final: 0.8174 (m-10) REVERT: B 302 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8579 (pp) REVERT: B 387 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8012 (mmp) REVERT: B 413 LYS cc_start: 0.9152 (mttp) cc_final: 0.8951 (mttm) REVERT: C 149 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8959 (tm) REVERT: C 313 HIS cc_start: 0.8899 (m90) cc_final: 0.8176 (m-70) REVERT: C 328 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8388 (t80) REVERT: C 334 TYR cc_start: 0.8308 (m-10) cc_final: 0.7838 (t80) REVERT: A 50 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7284 (tpt90) REVERT: A 130 TRP cc_start: 0.8267 (m100) cc_final: 0.7730 (m100) REVERT: A 214 THR cc_start: 0.5311 (OUTLIER) cc_final: 0.4601 (t) REVERT: A 229 MET cc_start: 0.8385 (tmm) cc_final: 0.8124 (tmm) REVERT: A 267 MET cc_start: 0.8786 (tpt) cc_final: 0.8453 (mmm) REVERT: A 313 HIS cc_start: 0.8937 (m90) cc_final: 0.8697 (m90) REVERT: A 363 CYS cc_start: 0.9228 (m) cc_final: 0.8461 (m) REVERT: A 387 MET cc_start: 0.8197 (mmm) cc_final: 0.7503 (mmm) REVERT: A 403 GLN cc_start: 0.9037 (tp40) cc_final: 0.8559 (tm-30) REVERT: A 465 ARG cc_start: 0.9086 (mmm-85) cc_final: 0.8327 (mtt-85) REVERT: A 471 ASN cc_start: 0.8742 (t0) cc_final: 0.8095 (t0) outliers start: 77 outliers final: 41 residues processed: 277 average time/residue: 0.1892 time to fit residues: 76.3489 Evaluate side-chains 244 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 178 LYS 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 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 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 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 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 284 LEU 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 61 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 116 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 121 optimal weight: 0.0060 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 A 316 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.096274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.078458 restraints weight = 28538.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080740 restraints weight = 15123.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.082183 restraints weight = 9837.248| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10145 Z= 0.121 Angle : 0.710 12.973 13827 Z= 0.323 Chirality : 0.041 0.195 1730 Planarity : 0.003 0.035 1725 Dihedral : 4.530 52.013 1479 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 6.51 % Allowed : 23.37 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.23), residues: 1332 helix: -0.42 (0.17), residues: 936 sheet: -1.13 (1.02), residues: 30 loop : -2.12 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 461 HIS 0.005 0.001 HIS A 452 PHE 0.013 0.001 PHE C 299 TYR 0.008 0.001 TYR B 305 ARG 0.002 0.000 ARG A 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 2) link_NAG-ASN : angle 1.80243 ( 6) hydrogen bonds : bond 0.03532 ( 519) hydrogen bonds : angle 4.26453 ( 1512) covalent geometry : bond 0.00264 (10143) covalent geometry : angle 0.70912 (13821) *********************** 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 295 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 227 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8815 (tm) REVERT: B 141 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9122 (mm) REVERT: B 178 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8651 (ptmm) REVERT: B 302 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8789 (pp) REVERT: B 311 LEU cc_start: 0.9103 (tp) cc_final: 0.8896 (tp) REVERT: B 363 CYS cc_start: 0.8941 (m) cc_final: 0.8115 (t) REVERT: B 387 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7897 (mmp) REVERT: B 465 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7353 (mtp85) REVERT: C 143 SER cc_start: 0.9199 (p) cc_final: 0.8967 (p) REVERT: C 149 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8973 (tm) REVERT: C 313 HIS cc_start: 0.8949 (m90) cc_final: 0.8711 (m-70) REVERT: C 328 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8167 (t80) REVERT: C 334 TYR cc_start: 0.8164 (m-10) cc_final: 0.7807 (t80) REVERT: C 376 ARG cc_start: 0.8690 (ptm160) cc_final: 0.8469 (mtm-85) REVERT: C 418 LEU cc_start: 0.9021 (tp) cc_final: 0.8628 (mt) REVERT: A 50 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7166 (tpt90) REVERT: A 130 TRP cc_start: 0.8256 (m100) cc_final: 0.7709 (m100) REVERT: A 214 THR cc_start: 0.5653 (OUTLIER) cc_final: 0.5018 (t) REVERT: A 229 MET cc_start: 0.8324 (tmm) cc_final: 0.8071 (tmm) REVERT: A 267 MET cc_start: 0.8778 (tpt) cc_final: 0.8472 (mmm) REVERT: A 292 MET cc_start: 0.7942 (mpp) cc_final: 0.7455 (mmm) REVERT: A 313 HIS cc_start: 0.8787 (m90) cc_final: 0.8443 (m90) REVERT: A 332 ASN cc_start: 0.8394 (t0) cc_final: 0.7669 (m-40) REVERT: A 359 LEU cc_start: 0.9109 (tp) cc_final: 0.7540 (tp) REVERT: A 363 CYS cc_start: 0.9206 (m) cc_final: 0.8498 (m) REVERT: A 387 MET cc_start: 0.8147 (mmm) cc_final: 0.7726 (mmm) REVERT: A 403 GLN cc_start: 0.9016 (tp40) cc_final: 0.8568 (tm-30) REVERT: A 465 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8322 (mtt-85) REVERT: A 471 ASN cc_start: 0.8656 (t0) cc_final: 0.8231 (t0) outliers start: 68 outliers final: 35 residues processed: 267 average time/residue: 0.1853 time to fit residues: 71.8547 Evaluate side-chains 241 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 178 LYS 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 418 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 103 ILE 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 180 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 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 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 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 284 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 67 optimal weight: 0.0050 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 56 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.5972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN A 316 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.078764 restraints weight = 28326.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081016 restraints weight = 15000.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082544 restraints weight = 9814.471| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10145 Z= 0.119 Angle : 0.702 12.676 13827 Z= 0.318 Chirality : 0.042 0.272 1730 Planarity : 0.003 0.035 1725 Dihedral : 4.380 51.945 1479 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 7.09 % Allowed : 23.47 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.23), residues: 1332 helix: -0.06 (0.17), residues: 930 sheet: -1.21 (0.99), residues: 30 loop : -1.97 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 461 HIS 0.004 0.001 HIS A 452 PHE 0.033 0.001 PHE B 411 TYR 0.012 0.001 TYR C 325 ARG 0.003 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 2) link_NAG-ASN : angle 1.69493 ( 6) hydrogen bonds : bond 0.03426 ( 519) hydrogen bonds : angle 4.15683 ( 1512) covalent geometry : bond 0.00262 (10143) covalent geometry : angle 0.70139 (13821) *********************** 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 295 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 221 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8784 (tm) REVERT: B 141 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9090 (mm) REVERT: B 302 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8793 (pp) REVERT: B 363 CYS cc_start: 0.8939 (m) cc_final: 0.8243 (t) REVERT: B 431 ILE cc_start: 0.8547 (mt) cc_final: 0.8257 (tt) REVERT: B 465 ARG cc_start: 0.7692 (mtt90) cc_final: 0.7449 (mtp85) REVERT: C 143 SER cc_start: 0.9200 (p) cc_final: 0.8988 (p) REVERT: C 313 HIS cc_start: 0.9045 (m90) cc_final: 0.8478 (m90) REVERT: C 334 TYR cc_start: 0.8124 (m-10) cc_final: 0.7756 (t80) REVERT: C 360 MET cc_start: 0.9402 (tpt) cc_final: 0.9186 (tpp) REVERT: C 418 LEU cc_start: 0.9096 (tp) cc_final: 0.8712 (mt) REVERT: A 50 ARG cc_start: 0.7780 (mtm180) cc_final: 0.7215 (tpt90) REVERT: A 130 TRP cc_start: 0.8317 (m100) cc_final: 0.7741 (m100) REVERT: A 229 MET cc_start: 0.8381 (tmm) cc_final: 0.8056 (tmm) REVERT: A 267 MET cc_start: 0.8800 (tpt) cc_final: 0.8485 (mmm) REVERT: A 292 MET cc_start: 0.7890 (mpp) cc_final: 0.7516 (mmm) REVERT: A 302 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8664 (pp) REVERT: A 359 LEU cc_start: 0.9084 (tp) cc_final: 0.8736 (tt) REVERT: A 363 CYS cc_start: 0.9146 (m) cc_final: 0.8340 (m) REVERT: A 366 GLU cc_start: 0.8204 (tt0) cc_final: 0.7900 (tt0) REVERT: A 387 MET cc_start: 0.8121 (mmm) cc_final: 0.7558 (mmm) REVERT: A 403 GLN cc_start: 0.9113 (tp40) cc_final: 0.8638 (tm-30) REVERT: A 471 ASN cc_start: 0.8641 (t0) cc_final: 0.8318 (t0) outliers start: 74 outliers final: 41 residues processed: 266 average time/residue: 0.1800 time to fit residues: 70.1880 Evaluate side-chains 249 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 236 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 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 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 151 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 302 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 105 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 284 LEU 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 Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 263 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.077995 restraints weight = 28721.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.080263 restraints weight = 15112.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.081700 restraints weight = 9795.249| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10145 Z= 0.133 Angle : 0.736 12.448 13827 Z= 0.334 Chirality : 0.043 0.221 1730 Planarity : 0.003 0.034 1725 Dihedral : 4.374 51.859 1479 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 6.70 % Allowed : 24.81 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1332 helix: 0.13 (0.17), residues: 939 sheet: -1.22 (1.01), residues: 30 loop : -1.92 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 461 HIS 0.004 0.001 HIS A 452 PHE 0.010 0.001 PHE A 134 TYR 0.009 0.001 TYR B 305 ARG 0.003 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 2) link_NAG-ASN : angle 1.64351 ( 6) hydrogen bonds : bond 0.03522 ( 519) hydrogen bonds : angle 4.18645 ( 1512) covalent geometry : bond 0.00303 (10143) covalent geometry : angle 0.73553 (13821) *********************** 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 277 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 207 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8787 (ppp) cc_final: 0.8506 (ppp) REVERT: B 127 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8710 (tm) REVERT: B 141 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9096 (mm) REVERT: B 302 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 363 CYS cc_start: 0.8824 (m) cc_final: 0.8262 (t) REVERT: B 387 MET cc_start: 0.8054 (mmp) cc_final: 0.7452 (mmm) REVERT: B 431 ILE cc_start: 0.8564 (mt) cc_final: 0.8307 (tt) REVERT: B 465 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7541 (mtp85) REVERT: C 180 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.7995 (p) REVERT: C 313 HIS cc_start: 0.9024 (m90) cc_final: 0.8507 (m90) REVERT: C 334 TYR cc_start: 0.8141 (m-10) cc_final: 0.7755 (t80) REVERT: C 418 LEU cc_start: 0.9080 (tp) cc_final: 0.8715 (mt) REVERT: A 50 ARG cc_start: 0.7771 (mtm180) cc_final: 0.7223 (tpt90) REVERT: A 130 TRP cc_start: 0.8300 (m100) cc_final: 0.7736 (m100) REVERT: A 229 MET cc_start: 0.8344 (tmm) cc_final: 0.8034 (tmm) REVERT: A 267 MET cc_start: 0.8828 (tpt) cc_final: 0.8477 (mmm) REVERT: A 292 MET cc_start: 0.7846 (mpp) cc_final: 0.7560 (mmm) REVERT: A 332 ASN cc_start: 0.8371 (t0) cc_final: 0.7653 (m-40) REVERT: A 359 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8787 (tt) REVERT: A 360 MET cc_start: 0.9293 (tpp) cc_final: 0.9022 (tpp) REVERT: A 363 CYS cc_start: 0.9196 (m) cc_final: 0.8297 (m) REVERT: A 366 GLU cc_start: 0.8167 (tt0) cc_final: 0.7931 (tt0) REVERT: A 387 MET cc_start: 0.8226 (mmm) cc_final: 0.7642 (mmm) REVERT: A 403 GLN cc_start: 0.9167 (tp40) cc_final: 0.8602 (tm-30) REVERT: A 471 ASN cc_start: 0.8624 (t0) cc_final: 0.8228 (t0) outliers start: 70 outliers final: 47 residues processed: 250 average time/residue: 0.1793 time to fit residues: 66.4014 Evaluate side-chains 249 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 186 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 299 PHE 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 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 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 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 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 105 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 284 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 359 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 441 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 106 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 overall best weight: 0.7342 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.096067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.078237 restraints weight = 29062.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.080517 restraints weight = 15348.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082023 restraints weight = 9966.581| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10145 Z= 0.124 Angle : 0.722 12.449 13827 Z= 0.329 Chirality : 0.042 0.193 1730 Planarity : 0.003 0.035 1725 Dihedral : 4.314 51.988 1479 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1332 helix: 0.38 (0.17), residues: 918 sheet: -1.16 (1.00), residues: 30 loop : -2.03 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 461 HIS 0.006 0.001 HIS C 452 PHE 0.010 0.001 PHE A 134 TYR 0.010 0.001 TYR C 325 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 2) link_NAG-ASN : angle 1.56175 ( 6) hydrogen bonds : bond 0.03352 ( 519) hydrogen bonds : angle 4.12287 ( 1512) covalent geometry : bond 0.00281 (10143) covalent geometry : angle 0.72173 (13821) *********************** 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 280 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8770 (ppp) cc_final: 0.8488 (ppp) REVERT: B 127 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8620 (tm) REVERT: B 141 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9097 (mm) REVERT: B 282 MET cc_start: 0.8435 (ttt) cc_final: 0.8184 (ttp) REVERT: B 302 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8742 (pp) REVERT: B 363 CYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8262 (t) REVERT: B 387 MET cc_start: 0.8149 (mmp) cc_final: 0.7483 (mmm) REVERT: B 431 ILE cc_start: 0.8583 (mt) cc_final: 0.8357 (tt) REVERT: B 465 ARG cc_start: 0.7721 (mtt90) cc_final: 0.7502 (mtp85) REVERT: C 178 LYS cc_start: 0.8995 (pttt) cc_final: 0.8688 (ptmm) REVERT: C 186 ASP cc_start: 0.8626 (t70) cc_final: 0.8003 (t0) REVERT: C 313 HIS cc_start: 0.8994 (m90) cc_final: 0.8067 (m-70) REVERT: C 328 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8074 (t80) REVERT: C 334 TYR cc_start: 0.8062 (m-10) cc_final: 0.7733 (t80) REVERT: A 50 ARG cc_start: 0.7844 (mtm180) cc_final: 0.7309 (tpt90) REVERT: A 229 MET cc_start: 0.8349 (tmm) cc_final: 0.7926 (tmm) REVERT: A 267 MET cc_start: 0.8805 (tpt) cc_final: 0.8461 (mmm) REVERT: A 292 MET cc_start: 0.7793 (mpp) cc_final: 0.7531 (mmm) REVERT: A 307 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8766 (tp) REVERT: A 332 ASN cc_start: 0.8392 (t0) cc_final: 0.7660 (m-40) REVERT: A 359 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8819 (tt) REVERT: A 363 CYS cc_start: 0.9166 (m) cc_final: 0.8281 (m) REVERT: A 387 MET cc_start: 0.8209 (mmm) cc_final: 0.7914 (tpp) REVERT: A 403 GLN cc_start: 0.9163 (tp40) cc_final: 0.8633 (tm-30) REVERT: A 418 LEU cc_start: 0.9228 (mt) cc_final: 0.8654 (mt) REVERT: A 444 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8318 (tm-30) outliers start: 64 outliers final: 43 residues processed: 254 average time/residue: 0.1852 time to fit residues: 68.8460 Evaluate side-chains 259 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 299 PHE Chi-restraints excluded: chain B residue 302 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 363 CYS Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 470 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 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 446 VAL 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 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 284 LEU 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 359 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 441 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 120 optimal weight: 0.0010 chunk 126 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 25 optimal weight: 0.0070 chunk 113 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 403 GLN B 452 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** 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 = 0.3414 r_free = 0.3414 target = 0.097259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.079526 restraints weight = 28653.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081801 restraints weight = 15123.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.083332 restraints weight = 9821.220| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5765 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= 0.122 Angle : 0.740 12.335 13827 Z= 0.335 Chirality : 0.042 0.184 1730 Planarity : 0.003 0.034 1725 Dihedral : 4.245 52.241 1479 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.56 % Allowed : 27.39 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.24), residues: 1332 helix: 0.52 (0.18), residues: 921 sheet: -1.12 (1.00), residues: 30 loop : -1.69 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 461 HIS 0.005 0.001 HIS C 452 PHE 0.010 0.001 PHE A 134 TYR 0.010 0.001 TYR C 325 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 2) link_NAG-ASN : angle 1.51374 ( 6) hydrogen bonds : bond 0.03303 ( 519) hydrogen bonds : angle 4.12611 ( 1512) covalent geometry : bond 0.00269 (10143) covalent geometry : angle 0.73948 (13821) *********************** 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 268 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 210 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8735 (ppp) cc_final: 0.8465 (ppp) REVERT: B 127 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8579 (tm) REVERT: B 141 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9071 (mm) REVERT: B 179 GLU cc_start: 0.8369 (tp30) cc_final: 0.8168 (tm-30) REVERT: B 282 MET cc_start: 0.8451 (ttt) cc_final: 0.8240 (ppp) REVERT: B 302 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8743 (pp) REVERT: B 331 LYS cc_start: 0.8932 (ptpt) cc_final: 0.8666 (ptpp) REVERT: B 363 CYS cc_start: 0.8645 (m) cc_final: 0.8081 (t) REVERT: B 387 MET cc_start: 0.8038 (mmp) cc_final: 0.7332 (mmm) REVERT: B 431 ILE cc_start: 0.8634 (mt) cc_final: 0.8428 (tt) REVERT: C 186 ASP cc_start: 0.8632 (t70) cc_final: 0.8015 (t0) REVERT: C 313 HIS cc_start: 0.8976 (m90) cc_final: 0.8068 (m-70) REVERT: C 328 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8054 (t80) REVERT: C 334 TYR cc_start: 0.8070 (m-10) cc_final: 0.7651 (t80) REVERT: A 50 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7378 (tpt90) REVERT: A 267 MET cc_start: 0.8763 (tpt) cc_final: 0.8325 (mmm) REVERT: A 292 MET cc_start: 0.7728 (mpp) cc_final: 0.7499 (mmm) REVERT: A 302 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8796 (pp) REVERT: A 307 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8748 (tp) REVERT: A 332 ASN cc_start: 0.8295 (t0) cc_final: 0.7658 (m-40) REVERT: A 359 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8877 (tt) REVERT: A 363 CYS cc_start: 0.9090 (m) cc_final: 0.8267 (m) REVERT: A 387 MET cc_start: 0.8129 (mmm) cc_final: 0.7839 (tpp) REVERT: A 403 GLN cc_start: 0.9106 (tp40) cc_final: 0.8606 (tm-30) REVERT: A 418 LEU cc_start: 0.9202 (mt) cc_final: 0.8651 (mt) outliers start: 58 outliers final: 41 residues processed: 244 average time/residue: 0.1940 time to fit residues: 69.1912 Evaluate side-chains 247 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 182 ASP 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 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 448 LEU Chi-restraints excluded: chain B residue 470 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 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 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 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 105 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 284 LEU 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 359 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 95 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 40 optimal weight: 0.0060 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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** C 394 GLN ** A 471 ASN ** 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 = 0.3401 r_free = 0.3401 target = 0.096501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.078736 restraints weight = 28821.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081004 restraints weight = 15213.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.082456 restraints weight = 9880.523| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5873 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= 0.128 Angle : 0.752 12.364 13827 Z= 0.341 Chirality : 0.042 0.194 1730 Planarity : 0.003 0.034 1725 Dihedral : 4.223 51.921 1479 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.36 % Allowed : 27.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1332 helix: 0.68 (0.18), residues: 903 sheet: -1.10 (1.00), residues: 30 loop : -1.84 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 461 HIS 0.005 0.001 HIS C 452 PHE 0.011 0.001 PHE C 192 TYR 0.020 0.001 TYR B 305 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 2) link_NAG-ASN : angle 1.48711 ( 6) hydrogen bonds : bond 0.03371 ( 519) hydrogen bonds : angle 4.15677 ( 1512) covalent geometry : bond 0.00293 (10143) covalent geometry : angle 0.75199 (13821) *********************** 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 268 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8776 (ppp) cc_final: 0.8484 (ppp) REVERT: B 127 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8593 (tm) REVERT: B 141 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9078 (mm) REVERT: B 179 GLU cc_start: 0.8449 (tp30) cc_final: 0.8230 (tm-30) REVERT: B 282 MET cc_start: 0.8557 (ttt) cc_final: 0.8280 (ppp) REVERT: B 302 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8730 (pp) REVERT: B 331 LYS cc_start: 0.8949 (ptpt) cc_final: 0.8694 (ptpp) REVERT: B 363 CYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8121 (t) REVERT: B 387 MET cc_start: 0.8062 (mmp) cc_final: 0.7810 (mmp) REVERT: B 461 TRP cc_start: 0.8706 (p-90) cc_final: 0.8496 (p-90) REVERT: B 465 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7285 (mmm-85) REVERT: C 179 GLU cc_start: 0.8516 (pp20) cc_final: 0.8259 (pm20) REVERT: C 186 ASP cc_start: 0.8653 (t70) cc_final: 0.8023 (t0) REVERT: C 313 HIS cc_start: 0.8967 (m90) cc_final: 0.8062 (m-70) REVERT: C 334 TYR cc_start: 0.7942 (m-10) cc_final: 0.7595 (t80) REVERT: A 50 ARG cc_start: 0.7820 (mtm180) cc_final: 0.7371 (tpt90) REVERT: A 267 MET cc_start: 0.8811 (tpt) cc_final: 0.8421 (mmm) REVERT: A 292 MET cc_start: 0.7721 (mpp) cc_final: 0.7518 (mmm) REVERT: A 307 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8830 (tp) REVERT: A 332 ASN cc_start: 0.8351 (t0) cc_final: 0.7744 (m-40) REVERT: A 359 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8875 (tt) REVERT: A 363 CYS cc_start: 0.9116 (m) cc_final: 0.8231 (m) REVERT: A 387 MET cc_start: 0.8265 (mmm) cc_final: 0.7886 (tpp) REVERT: A 418 LEU cc_start: 0.9219 (mt) cc_final: 0.8677 (mt) outliers start: 56 outliers final: 42 residues processed: 241 average time/residue: 0.1849 time to fit residues: 65.6457 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 : 1.108 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 302 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 363 CYS Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 470 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 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 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 446 VAL 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 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 284 LEU 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 359 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 464 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 68 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 108 optimal weight: 0.0270 chunk 111 optimal weight: 0.0050 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.5252 ------------------------------------------------------------------------------- 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 471 ASN ** 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 = 0.3416 r_free = 0.3416 target = 0.097474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.079736 restraints weight = 28878.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081947 restraints weight = 15305.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083362 restraints weight = 9983.436| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10145 Z= 0.126 Angle : 0.769 12.340 13827 Z= 0.346 Chirality : 0.043 0.335 1730 Planarity : 0.004 0.037 1725 Dihedral : 4.163 52.275 1479 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.79 % Allowed : 29.02 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.24), residues: 1332 helix: 0.77 (0.18), residues: 900 sheet: -1.06 (1.00), residues: 30 loop : -1.84 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 461 HIS 0.007 0.001 HIS C 452 PHE 0.013 0.001 PHE C 192 TYR 0.020 0.001 TYR B 305 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 2) link_NAG-ASN : angle 1.45560 ( 6) hydrogen bonds : bond 0.03274 ( 519) hydrogen bonds : angle 4.12254 ( 1512) covalent geometry : bond 0.00284 (10143) covalent geometry : angle 0.76856 (13821) ********************** 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 266 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8749 (ppp) cc_final: 0.8472 (ppp) REVERT: B 127 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8546 (tm) REVERT: B 141 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9040 (mm) REVERT: B 282 MET cc_start: 0.8549 (ttt) cc_final: 0.8282 (ppp) REVERT: B 302 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8722 (pp) REVERT: B 331 LYS cc_start: 0.8946 (ptpt) cc_final: 0.8689 (ptpp) REVERT: B 363 CYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8139 (t) REVERT: B 387 MET cc_start: 0.8069 (mmp) cc_final: 0.7801 (mmp) REVERT: B 413 LYS cc_start: 0.9075 (mttp) cc_final: 0.8373 (mttm) REVERT: B 465 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7147 (mtp85) REVERT: C 186 ASP cc_start: 0.8603 (t70) cc_final: 0.7969 (t0) REVERT: C 313 HIS cc_start: 0.8962 (m90) cc_final: 0.8071 (m-70) REVERT: C 328 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8149 (t80) REVERT: C 334 TYR cc_start: 0.7909 (m-10) cc_final: 0.7593 (t80) REVERT: C 418 LEU cc_start: 0.9274 (tt) cc_final: 0.8901 (pp) REVERT: A 50 ARG cc_start: 0.7863 (mtm180) cc_final: 0.7420 (tpt90) REVERT: A 267 MET cc_start: 0.8787 (tpt) cc_final: 0.8463 (mmm) REVERT: A 302 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8784 (pp) REVERT: A 307 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8793 (tp) REVERT: A 332 ASN cc_start: 0.8325 (t0) cc_final: 0.7731 (m-40) REVERT: A 387 MET cc_start: 0.8329 (mmm) cc_final: 0.7921 (tpp) REVERT: A 403 GLN cc_start: 0.8901 (tp40) cc_final: 0.8408 (tm-30) REVERT: A 418 LEU cc_start: 0.9216 (mt) cc_final: 0.8683 (mt) outliers start: 50 outliers final: 38 residues processed: 244 average time/residue: 0.1814 time to fit residues: 65.0312 Evaluate side-chains 248 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 302 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 363 CYS Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 465 ARG Chi-restraints excluded: chain B residue 470 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 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 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 446 VAL 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 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 284 LEU 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 464 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 ASN ** 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 = 0.096511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.078670 restraints weight = 28832.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080914 restraints weight = 15384.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.082349 restraints weight = 10076.794| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.6091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10145 Z= 0.132 Angle : 0.783 12.350 13827 Z= 0.353 Chirality : 0.044 0.336 1730 Planarity : 0.004 0.034 1725 Dihedral : 4.189 52.006 1479 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.50 % Allowed : 29.60 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1332 helix: 0.73 (0.18), residues: 915 sheet: -1.04 (1.00), residues: 30 loop : -1.84 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 461 HIS 0.008 0.001 HIS C 452 PHE 0.014 0.001 PHE C 192 TYR 0.019 0.001 TYR B 305 ARG 0.002 0.000 ARG C 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00324 ( 2) link_NAG-ASN : angle 1.45333 ( 6) hydrogen bonds : bond 0.03312 ( 519) hydrogen bonds : angle 4.13830 ( 1512) covalent geometry : bond 0.00306 (10143) covalent geometry : angle 0.78236 (13821) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4015.73 seconds wall clock time: 71 minutes 0.76 seconds (4260.76 seconds total)