Starting phenix.real_space_refine on Fri Sep 11 15:24:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6mpb_9188/09_2026/6mpb_9188.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mpb_9188/09_2026/6mpb_9188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mpb_9188/09_2026/6mpb_9188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mpb_9188/09_2026/6mpb_9188.map" model { file = "/net/cci-nas-00/data/ceres_data/6mpb_9188/09_2026/6mpb_9188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mpb_9188/09_2026/6mpb_9188.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6mpb_9188/09_2026/6mpb_9188.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6mpb_9188/09_2026/6mpb_9188.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 sd= 0.326 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6498 2.51 5 N 1656 2.21 5 O 1767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9969 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "C" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "A" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3299 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 17, 'TRANS': 428} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen 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 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 chiralities: 1 Time building chain proxies: 2.07, per 1000 atoms: 0.21 Number of scatterers: 9969 At special positions: 0 Unit cell: (121.632, 111.858, 119.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1767 8.00 N 1656 7.00 C 6498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 602 " - " ASN B 163 " " NAG C 602 " - " ASN C 163 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 349.4 milliseconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 76.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 44 through 52 removed outlier: 3.827A pdb=" N CYS B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 75 removed outlier: 3.568A pdb=" N VAL B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.510A pdb=" N LEU B 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 100 removed outlier: 3.852A pdb=" N SER B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.922A pdb=" N LEU B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.846A pdb=" N VAL B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 151 removed outlier: 3.673A pdb=" N ARG B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.602A pdb=" N ILE B 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.896A pdb=" N ALA B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.786A pdb=" N ALA B 188 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.862A pdb=" N PHE B 201 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 248 removed outlier: 3.801A pdb=" N LEU B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 292 removed outlier: 4.426A pdb=" N LEU B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 271 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.941A pdb=" N MET B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 316 removed outlier: 3.570A pdb=" N ARG B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 removed outlier: 3.566A pdb=" N LEU B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.593A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 356 through 367 removed outlier: 3.945A pdb=" N GLU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 382 removed outlier: 3.612A pdb=" N SER B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 377 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 404 removed outlier: 3.802A pdb=" N CYS B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 428 removed outlier: 3.687A pdb=" N ILE B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 439 through 446 removed outlier: 3.663A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 488 removed outlier: 3.616A pdb=" N SER B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 52 removed outlier: 3.827A pdb=" N CYS C 48 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 75 removed outlier: 3.568A pdb=" N VAL C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.509A pdb=" N LEU C 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 3.854A pdb=" N SER C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Proline residue: C 92 - end of helix removed outlier: 3.922A pdb=" N LEU C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.847A pdb=" N VAL C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N CYS C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 151 removed outlier: 3.673A pdb=" N ARG C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.602A pdb=" N ILE C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.896A pdb=" N ALA C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 191 removed outlier: 3.785A pdb=" N ALA C 188 " --> pdb=" O PHE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.861A pdb=" N PHE C 201 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 248 removed outlier: 3.802A pdb=" N LEU C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 245 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 292 removed outlier: 4.426A pdb=" N LEU C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 266 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER C 271 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP C 272 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 3.940A pdb=" N MET C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C 283 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 316 removed outlier: 3.570A pdb=" N ARG C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 330 removed outlier: 3.565A pdb=" N LEU C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 339 removed outlier: 3.592A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 351 Processing helix chain 'C' and resid 356 through 367 removed outlier: 3.945A pdb=" N GLU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 382 removed outlier: 3.613A pdb=" N SER C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 376 " --> pdb=" O LYS C 372 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 377 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 379 " --> pdb=" O SER C 375 " (cutoff:3.500A) Proline residue: C 380 - end of helix Processing helix chain 'C' and resid 387 through 404 removed outlier: 3.801A pdb=" N CYS C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 428 removed outlier: 3.688A pdb=" N ILE C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 438 No H-bonds generated for 'chain 'C' and resid 436 through 438' Processing helix chain 'C' and resid 439 through 446 removed outlier: 3.663A pdb=" N ALA C 445 " --> pdb=" O ILE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 488 removed outlier: 3.615A pdb=" N SER C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 484 " --> pdb=" O GLY C 480 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 removed outlier: 3.827A pdb=" N CYS A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.568A pdb=" N VAL A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.510A pdb=" N LEU A 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.852A pdb=" N SER A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Proline residue: A 92 - end of helix removed outlier: 3.922A pdb=" N LEU A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.847A pdb=" N VAL A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 151 removed outlier: 3.673A pdb=" N ARG A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.602A pdb=" N ILE A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.896A pdb=" N ALA A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.786A pdb=" N ALA A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.861A pdb=" N PHE A 201 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 248 removed outlier: 3.800A pdb=" N LEU A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 292 removed outlier: 4.426A pdb=" N LEU A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Proline residue: A 278 - end of helix removed outlier: 3.940A pdb=" N MET A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.569A pdb=" N ARG A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 330 removed outlier: 3.564A pdb=" N LEU A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.592A pdb=" N PHE A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.945A pdb=" N GLU A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.613A pdb=" N SER A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 377 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 387 through 404 removed outlier: 3.801A pdb=" N CYS A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 428 removed outlier: 3.688A pdb=" N ILE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.663A pdb=" N ALA A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 488 removed outlier: 3.616A pdb=" N SER A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AA2, first strand: chain 'C' and resid 207 through 209 Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 209 519 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.23 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: 5543 15.01 - 30.01: 328 30.01 - 45.01: 68 45.01 - 60.02: 3 60.02 - 75.02: 7 Dihedral angle restraints: 5949 sinusoidal: 2169 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 5946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1332 0.062 - 0.123: 322 0.123 - 0.185: 65 0.185 - 0.246: 3 0.246 - 0.307: 8 Chirality restraints: 1730 Sorted by residual: chirality pdb=" CB VAL A 446 " pdb=" CA VAL A 446 " pdb=" CG1 VAL A 446 " pdb=" CG2 VAL A 446 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB VAL B 446 " pdb=" CA VAL B 446 " pdb=" CG1 VAL B 446 " pdb=" CG2 VAL B 446 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB VAL C 446 " pdb=" CA VAL C 446 " pdb=" CG1 VAL C 446 " pdb=" CG2 VAL C 446 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1727 not shown) Planarity restraints: 1727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 211 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C ARG C 211 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG C 211 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN C 212 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 211 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C ARG B 211 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG B 211 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 212 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 211 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C ARG A 211 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG A 211 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 212 " -0.012 2.00e-02 2.50e+03 ... (remaining 1724 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3232 2.85 - 3.36: 10038 3.36 - 3.88: 15549 3.88 - 4.39: 17580 4.39 - 4.90: 29128 Nonbonded interactions: 75527 Sorted by model distance: nonbonded pdb=" OG SER A 352 " pdb=" O GLY A 430 " model vdw 2.338 3.040 nonbonded pdb=" OG SER C 352 " pdb=" O GLY C 430 " model vdw 2.339 3.040 nonbonded pdb=" OG SER B 352 " pdb=" O GLY B 430 " model vdw 2.339 3.040 nonbonded pdb=" NE2 GLN C 394 " pdb=" OG1 THR C 438 " model vdw 2.378 3.120 nonbonded pdb=" NE2 GLN B 394 " pdb=" OG1 THR B 438 " model vdw 2.378 3.120 ... (remaining 75522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.480 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 10.517 75.024 3525 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.90 (0.15), residues: 1332 helix: -4.15 (0.09), residues: 846 sheet: None (None), residues: 0 loop : -3.10 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 217 TYR 0.008 0.002 TYR C 334 PHE 0.015 0.001 PHE C 201 TRP 0.005 0.001 TRP C 272 HIS 0.004 0.001 HIS C 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.22 (10143) covalent geometry : angle 1.08689 / 0.51 (13821) hydrogen bonds : bond 0.32119 / 21.52 ( 519) hydrogen bonds : angle 9.89672 / 6.74 ( 1512) link_NAG-ASN : bond 0.00409 / 0.21 ( 2) link_NAG-ASN : angle 3.40711 / 1.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 THR cc_start: 0.9006 (p) cc_final: 0.8736 (p) REVERT: B 307 LEU cc_start: 0.9225 (tm) cc_final: 0.8724 (mt) REVERT: B 311 LEU cc_start: 0.9256 (tp) cc_final: 0.9013 (tp) REVERT: B 318 LEU cc_start: 0.9328 (tm) cc_final: 0.9106 (mm) REVERT: B 394 GLN cc_start: 0.8394 (mt0) cc_final: 0.8192 (mt0) REVERT: B 403 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8611 (mm-40) REVERT: C 149 LEU cc_start: 0.9002 (tm) cc_final: 0.8758 (tm) REVERT: C 210 GLU cc_start: 0.5826 (mp0) cc_final: 0.5497 (mm-30) REVERT: C 253 GLU cc_start: 0.7631 (tp30) cc_final: 0.7295 (tp30) REVERT: C 267 MET cc_start: 0.8461 (tpp) cc_final: 0.7502 (tpp) REVERT: C 313 HIS cc_start: 0.8809 (m90) cc_final: 0.8422 (m-70) REVERT: C 353 SER cc_start: 0.9009 (t) cc_final: 0.8686 (p) REVERT: C 366 GLU cc_start: 0.8478 (tt0) cc_final: 0.8176 (tm-30) REVERT: C 388 ASP cc_start: 0.8674 (p0) cc_final: 0.8216 (p0) REVERT: C 462 LEU cc_start: 0.8976 (tp) cc_final: 0.8750 (tp) REVERT: A 130 TRP cc_start: 0.8143 (m100) cc_final: 0.7699 (m100) REVERT: A 184 PHE cc_start: 0.7972 (t80) cc_final: 0.7628 (m-80) REVERT: A 264 GLU cc_start: 0.8867 (tp30) cc_final: 0.8288 (tp30) REVERT: A 348 PHE cc_start: 0.8835 (t80) cc_final: 0.8472 (t80) REVERT: A 363 CYS cc_start: 0.9042 (m) cc_final: 0.8664 (m) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.0888 time to fit residues: 51.8766 Evaluate side-chains 218 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 483 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 394 GLN C 483 GLN A 163 ASN A 224 GLN A 483 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.097464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.079559 restraints weight = 28228.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.081957 restraints weight = 14709.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.083440 restraints weight = 9431.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.084522 restraints weight = 7095.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.085141 restraints weight = 5774.349| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3727 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= 0.144 Angle : 0.737 10.043 13827 Z= 0.352 Chirality : 0.043 0.187 1730 Planarity : 0.005 0.034 1725 Dihedral : 4.768 32.088 1416 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 7.38 % Allowed : 19.44 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.19), residues: 1332 helix: -2.07 (0.14), residues: 909 sheet: -1.64 (0.98), residues: 30 loop : -2.83 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 465 TYR 0.018 0.001 TYR B 305 PHE 0.016 0.001 PHE A 192 TRP 0.024 0.002 TRP A 461 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10143) covalent geometry : angle 0.73576 / 0.35 (13821) hydrogen bonds : bond 0.04866 / 3.26 ( 519) hydrogen bonds : angle 5.02677 / 3.43 ( 1512) link_NAG-ASN : bond 0.00393 / 0.20 ( 2) link_NAG-ASN : angle 1.88920 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 265 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9122 (mm) REVERT: B 178 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8675 (ptmm) REVERT: B 225 GLU cc_start: 0.8767 (mp0) cc_final: 0.8443 (mp0) REVERT: B 275 TRP cc_start: 0.8436 (m100) cc_final: 0.8165 (m-10) REVERT: B 302 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8689 (pp) REVERT: B 307 LEU cc_start: 0.9049 (tm) cc_final: 0.8552 (mt) REVERT: B 311 LEU cc_start: 0.9149 (tp) cc_final: 0.8619 (mm) REVERT: B 329 THR cc_start: 0.8003 (p) cc_final: 0.7575 (p) REVERT: B 331 LYS cc_start: 0.8520 (mttp) cc_final: 0.8232 (mttp) REVERT: B 387 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7921 (mmp) REVERT: C 149 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8857 (tm) REVERT: C 328 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8270 (t80) REVERT: C 334 TYR cc_start: 0.8329 (m-10) cc_final: 0.7801 (t80) REVERT: C 366 GLU cc_start: 0.8379 (tt0) cc_final: 0.8136 (tm-30) REVERT: C 387 MET cc_start: 0.8418 (mmm) cc_final: 0.7982 (mmm) REVERT: C 471 ASN cc_start: 0.8617 (t0) cc_final: 0.8130 (t0) REVERT: C 481 LEU cc_start: 0.9109 (tt) cc_final: 0.8733 (mm) REVERT: A 50 ARG cc_start: 0.7673 (mtm180) cc_final: 0.7177 (tpt90) REVERT: A 94 GLU cc_start: 0.8135 (tp30) cc_final: 0.7797 (tp30) REVERT: A 130 TRP cc_start: 0.8189 (m100) cc_final: 0.7625 (m100) REVERT: A 134 PHE cc_start: 0.9182 (t80) cc_final: 0.8967 (t80) REVERT: A 332 ASN cc_start: 0.8401 (t0) cc_final: 0.7689 (m-40) REVERT: A 363 CYS cc_start: 0.9063 (m) cc_final: 0.8429 (m) REVERT: A 387 MET cc_start: 0.7941 (mmm) cc_final: 0.7664 (mmm) REVERT: A 403 GLN cc_start: 0.9022 (tp40) cc_final: 0.8575 (tm-30) REVERT: A 464 ASP cc_start: 0.8040 (t70) cc_final: 0.7821 (t70) REVERT: A 465 ARG cc_start: 0.9069 (mmm-85) cc_final: 0.8696 (mtt-85) outliers start: 77 outliers final: 32 residues processed: 315 average time/residue: 0.0748 time to fit residues: 35.0399 Evaluate side-chains 247 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL 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 219 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 103 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3404 r_free = 0.3404 target = 0.097069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.079112 restraints weight = 28626.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.081440 restraints weight = 15045.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082936 restraints weight = 9753.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.084013 restraints weight = 7308.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.084645 restraints weight = 5996.834| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10145 Z= 0.126 Angle : 0.714 13.433 13827 Z= 0.330 Chirality : 0.042 0.233 1730 Planarity : 0.004 0.036 1725 Dihedral : 4.321 22.156 1416 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 7.28 % Allowed : 20.11 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.22), residues: 1332 helix: -1.05 (0.16), residues: 939 sheet: -1.29 (1.00), residues: 30 loop : -2.28 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 101 TYR 0.011 0.001 TYR B 305 PHE 0.015 0.001 PHE B 135 TRP 0.019 0.001 TRP A 461 HIS 0.004 0.001 HIS C 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (10143) covalent geometry : angle 0.71343 / 0.33 (13821) hydrogen bonds : bond 0.03955 / 2.62 ( 519) hydrogen bonds : angle 4.43744 / 3.00 ( 1512) link_NAG-ASN : bond 0.00367 / 0.18 ( 2) link_NAG-ASN : angle 1.79287 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 224 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8799 (tm) REVERT: B 141 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9117 (mm) REVERT: B 178 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8699 (ptmm) REVERT: B 225 GLU cc_start: 0.8809 (mp0) cc_final: 0.8509 (mp0) REVERT: B 275 TRP cc_start: 0.8470 (m100) cc_final: 0.8185 (m-10) REVERT: B 302 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8719 (pp) REVERT: B 413 LYS cc_start: 0.9093 (mttp) cc_final: 0.8833 (mttm) REVERT: B 465 ARG cc_start: 0.7963 (mtt90) cc_final: 0.7604 (mtp85) REVERT: C 149 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8901 (tm) REVERT: C 328 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8293 (t80) REVERT: C 334 TYR cc_start: 0.8199 (m-10) cc_final: 0.7841 (t80) REVERT: C 387 MET cc_start: 0.8416 (mmm) cc_final: 0.8006 (mmt) REVERT: A 50 ARG cc_start: 0.7779 (mtm180) cc_final: 0.7169 (tpt90) REVERT: A 94 GLU cc_start: 0.8262 (tp30) cc_final: 0.8015 (tp30) REVERT: A 130 TRP cc_start: 0.8169 (m100) cc_final: 0.7665 (m100) REVERT: A 134 PHE cc_start: 0.9155 (t80) cc_final: 0.8953 (t80) REVERT: A 214 THR cc_start: 0.5360 (OUTLIER) cc_final: 0.4705 (t) REVERT: A 305 TYR cc_start: 0.9017 (t80) cc_final: 0.8724 (t80) REVERT: A 313 HIS cc_start: 0.8893 (m90) cc_final: 0.8634 (m90) REVERT: A 363 CYS cc_start: 0.9170 (m) cc_final: 0.8425 (m) REVERT: A 387 MET cc_start: 0.7899 (mmm) cc_final: 0.7544 (mmm) REVERT: A 465 ARG cc_start: 0.9028 (mmm-85) cc_final: 0.8304 (mtt-85) REVERT: A 471 ASN cc_start: 0.8665 (t0) cc_final: 0.8153 (t0) outliers start: 76 outliers final: 38 residues processed: 273 average time/residue: 0.0758 time to fit residues: 30.8437 Evaluate side-chains 247 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 202 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 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 359 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 361 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 0.1980 chunk 20 optimal weight: 0.0270 overall best weight: 1.4444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3355 r_free = 0.3355 target = 0.094312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.076210 restraints weight = 28779.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.078373 restraints weight = 15406.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.079941 restraints weight = 10187.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.080867 restraints weight = 7654.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.081559 restraints weight = 6385.350| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10145 Z= 0.156 Angle : 0.730 12.573 13827 Z= 0.341 Chirality : 0.043 0.214 1730 Planarity : 0.004 0.035 1725 Dihedral : 4.167 21.421 1416 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 7.18 % Allowed : 22.99 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.23), residues: 1332 helix: -0.50 (0.16), residues: 960 sheet: -1.24 (1.00), residues: 30 loop : -2.18 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 98 TYR 0.006 0.001 TYR C 208 PHE 0.012 0.001 PHE C 299 TRP 0.020 0.001 TRP A 461 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (10143) covalent geometry : angle 0.72911 / 0.34 (13821) hydrogen bonds : bond 0.03851 / 2.56 ( 519) hydrogen bonds : angle 4.35420 / 2.94 ( 1512) link_NAG-ASN : bond 0.00277 / 0.14 ( 2) link_NAG-ASN : angle 1.87340 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 217 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8842 (tm) REVERT: B 141 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9161 (mm) REVERT: B 302 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8775 (pp) REVERT: B 362 LYS cc_start: 0.8944 (tptt) cc_final: 0.8630 (tppt) REVERT: B 363 CYS cc_start: 0.8992 (m) cc_final: 0.8144 (t) REVERT: B 465 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7496 (mtp85) REVERT: C 149 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8963 (tm) REVERT: C 334 TYR cc_start: 0.8102 (m-10) cc_final: 0.7786 (t80) REVERT: C 387 MET cc_start: 0.8527 (mmm) cc_final: 0.8164 (mmt) REVERT: C 418 LEU cc_start: 0.9022 (tp) cc_final: 0.8745 (mt) REVERT: A 50 ARG cc_start: 0.7792 (mtm180) cc_final: 0.7185 (tpt90) REVERT: A 94 GLU cc_start: 0.8388 (tp30) cc_final: 0.8172 (tp30) REVERT: A 130 TRP cc_start: 0.8303 (m100) cc_final: 0.7848 (m100) REVERT: A 292 MET cc_start: 0.7971 (mpp) cc_final: 0.7438 (mmm) REVERT: A 332 ASN cc_start: 0.8403 (t0) cc_final: 0.7652 (m-40) REVERT: A 359 LEU cc_start: 0.9100 (tp) cc_final: 0.8757 (tt) REVERT: A 360 MET cc_start: 0.9163 (tpp) cc_final: 0.8961 (tpp) REVERT: A 363 CYS cc_start: 0.9105 (m) cc_final: 0.8389 (m) REVERT: A 387 MET cc_start: 0.8190 (mmm) cc_final: 0.7449 (mmm) REVERT: A 403 GLN cc_start: 0.9054 (tp40) cc_final: 0.8545 (tm-30) REVERT: A 465 ARG cc_start: 0.9056 (mmm-85) cc_final: 0.8350 (mtt-85) REVERT: A 470 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8530 (tm) REVERT: A 471 ASN cc_start: 0.8775 (t0) cc_final: 0.8211 (t0) outliers start: 75 outliers final: 43 residues processed: 262 average time/residue: 0.0741 time to fit residues: 29.0548 Evaluate side-chains 242 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 178 LYS Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 298 LEU 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 359 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE 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 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 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 470 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 107 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 101 optimal weight: 0.0010 chunk 127 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 GLN B 403 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.078821 restraints weight = 28499.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.081109 restraints weight = 15132.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.082646 restraints weight = 9835.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.083658 restraints weight = 7336.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084245 restraints weight = 6044.385| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10145 Z= 0.116 Angle : 0.691 12.514 13827 Z= 0.315 Chirality : 0.041 0.204 1730 Planarity : 0.003 0.035 1725 Dihedral : 3.998 25.357 1416 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 6.13 % Allowed : 24.04 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.23), residues: 1332 helix: -0.05 (0.17), residues: 933 sheet: -1.26 (0.99), residues: 30 loop : -1.98 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 98 TYR 0.006 0.001 TYR C 325 PHE 0.010 0.001 PHE B 135 TRP 0.024 0.001 TRP A 461 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (10143) covalent geometry : angle 0.69017 / 0.31 (13821) hydrogen bonds : bond 0.03355 / 2.23 ( 519) hydrogen bonds : angle 4.13191 / 2.76 ( 1512) link_NAG-ASN : bond 0.00357 / 0.18 ( 2) link_NAG-ASN : angle 1.61493 / 0.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 224 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8650 (tm) REVERT: B 141 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9116 (mm) REVERT: B 178 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8602 (ptmm) REVERT: B 302 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8688 (pp) REVERT: B 362 LYS cc_start: 0.8807 (tptt) cc_final: 0.8562 (tppt) REVERT: B 363 CYS cc_start: 0.8893 (m) cc_final: 0.8126 (t) REVERT: B 387 MET cc_start: 0.8111 (mmp) cc_final: 0.7799 (mmp) REVERT: B 438 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.8780 (t) REVERT: B 465 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7267 (mtp85) REVERT: C 149 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8950 (tm) REVERT: C 328 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8035 (t80) REVERT: C 334 TYR cc_start: 0.8092 (m-10) cc_final: 0.7738 (t80) REVERT: C 387 MET cc_start: 0.8270 (mmm) cc_final: 0.7823 (mmt) REVERT: A 50 ARG cc_start: 0.7764 (mtm180) cc_final: 0.7189 (tpt90) REVERT: A 94 GLU cc_start: 0.8403 (tp30) cc_final: 0.8105 (tp30) REVERT: A 130 TRP cc_start: 0.8301 (m100) cc_final: 0.7791 (m100) REVERT: A 292 MET cc_start: 0.7856 (mpp) cc_final: 0.7453 (mmm) REVERT: A 302 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8676 (pp) REVERT: A 332 ASN cc_start: 0.8445 (t0) cc_final: 0.7725 (m-40) REVERT: A 334 TYR cc_start: 0.7921 (m-10) cc_final: 0.7690 (m-10) REVERT: A 359 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8735 (tt) REVERT: A 363 CYS cc_start: 0.9164 (m) cc_final: 0.8300 (m) REVERT: A 366 GLU cc_start: 0.8131 (tt0) cc_final: 0.7810 (tt0) REVERT: A 387 MET cc_start: 0.8082 (mmm) cc_final: 0.7535 (mmm) REVERT: A 403 GLN cc_start: 0.9123 (tp40) cc_final: 0.8577 (tm-30) REVERT: A 470 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8456 (tm) REVERT: A 471 ASN cc_start: 0.8582 (t0) cc_final: 0.8300 (t0) outliers start: 64 outliers final: 32 residues processed: 262 average time/residue: 0.0815 time to fit residues: 31.8101 Evaluate side-chains 242 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 178 LYS 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 401 ILE Chi-restraints excluded: chain B residue 438 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 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 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 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 302 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 470 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 24 optimal weight: 0.0570 chunk 56 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 78 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 99 optimal weight: 0.3980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 GLN B 403 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.079884 restraints weight = 28836.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.082130 restraints weight = 15225.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083679 restraints weight = 9901.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.084718 restraints weight = 7334.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.085259 restraints weight = 6022.990| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10145 Z= 0.117 Angle : 0.707 12.286 13827 Z= 0.321 Chirality : 0.042 0.214 1730 Planarity : 0.003 0.035 1725 Dihedral : 3.881 18.157 1416 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.70 % Allowed : 24.52 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.24), residues: 1332 helix: 0.22 (0.17), residues: 927 sheet: -1.23 (0.98), residues: 30 loop : -1.92 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.009 0.001 TYR C 325 PHE 0.029 0.001 PHE B 411 TRP 0.025 0.001 TRP A 461 HIS 0.005 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (10143) covalent geometry : angle 0.70683 / 0.32 (13821) hydrogen bonds : bond 0.03280 / 2.16 ( 519) hydrogen bonds : angle 4.10846 / 2.75 ( 1512) link_NAG-ASN : bond 0.00379 / 0.19 ( 2) link_NAG-ASN : angle 1.55527 / 0.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 220 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8652 (tm) REVERT: B 141 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9089 (mm) REVERT: B 179 GLU cc_start: 0.8538 (tp30) cc_final: 0.8331 (tp30) REVERT: B 302 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8717 (pp) REVERT: B 362 LYS cc_start: 0.8732 (tptt) cc_final: 0.8490 (tppt) REVERT: B 363 CYS cc_start: 0.8726 (m) cc_final: 0.8090 (t) REVERT: B 387 MET cc_start: 0.8111 (mmp) cc_final: 0.7831 (mmp) REVERT: C 334 TYR cc_start: 0.7996 (m-10) cc_final: 0.7687 (t80) REVERT: C 387 MET cc_start: 0.7848 (mmm) cc_final: 0.7547 (mmt) REVERT: A 50 ARG cc_start: 0.7792 (mtm180) cc_final: 0.7209 (tpt90) REVERT: A 94 GLU cc_start: 0.8362 (tp30) cc_final: 0.8038 (tp30) REVERT: A 130 TRP cc_start: 0.8306 (m100) cc_final: 0.7786 (m100) REVERT: A 292 MET cc_start: 0.7806 (mpp) cc_final: 0.7488 (mmm) REVERT: A 302 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8565 (pp) REVERT: A 305 TYR cc_start: 0.9067 (t80) cc_final: 0.8834 (t80) REVERT: A 359 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8817 (tt) REVERT: A 363 CYS cc_start: 0.9171 (m) cc_final: 0.8272 (m) REVERT: A 366 GLU cc_start: 0.8092 (tt0) cc_final: 0.7872 (tt0) REVERT: A 387 MET cc_start: 0.8077 (mmm) cc_final: 0.7532 (mmm) REVERT: A 403 GLN cc_start: 0.9073 (tp40) cc_final: 0.8561 (tm-30) REVERT: A 418 LEU cc_start: 0.9247 (mt) cc_final: 0.8683 (mt) REVERT: A 471 ASN cc_start: 0.8533 (t0) cc_final: 0.8270 (t160) outliers start: 70 outliers final: 41 residues processed: 261 average time/residue: 0.0808 time to fit residues: 31.4759 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 : 0.356 ------------------------------------------------------------------------------- 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 229 MET 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 384 THR 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 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 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 127 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL 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 462 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 23 optimal weight: 2.9990 chunk 124 optimal weight: 0.0570 chunk 86 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 403 GLN C 263 ASN C 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.079402 restraints weight = 28542.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.081684 restraints weight = 15247.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.083130 restraints weight = 9961.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.084180 restraints weight = 7518.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.084704 restraints weight = 6207.674| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5580 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= 0.122 Angle : 0.718 12.308 13827 Z= 0.328 Chirality : 0.042 0.193 1730 Planarity : 0.003 0.035 1725 Dihedral : 3.829 21.277 1416 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 6.23 % Allowed : 25.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.24), residues: 1332 helix: 0.34 (0.17), residues: 933 sheet: -1.19 (0.98), residues: 30 loop : -1.83 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.008 0.001 TYR C 325 PHE 0.010 0.001 PHE A 134 TRP 0.027 0.001 TRP A 461 HIS 0.007 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10143) covalent geometry : angle 0.71701 / 0.33 (13821) hydrogen bonds : bond 0.03275 / 2.16 ( 519) hydrogen bonds : angle 4.11845 / 2.75 ( 1512) link_NAG-ASN : bond 0.00362 / 0.18 ( 2) link_NAG-ASN : angle 1.49305 / 0.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 215 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8729 (tm) REVERT: B 141 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9065 (mm) REVERT: B 179 GLU cc_start: 0.8483 (tp30) cc_final: 0.8221 (tp30) REVERT: B 282 MET cc_start: 0.8443 (ttt) cc_final: 0.8180 (ttp) REVERT: B 302 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8665 (pp) REVERT: B 363 CYS cc_start: 0.8692 (m) cc_final: 0.8205 (t) REVERT: B 387 MET cc_start: 0.8088 (mmp) cc_final: 0.7277 (mmm) REVERT: B 465 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7603 (mtp85) REVERT: C 178 LYS cc_start: 0.8971 (pttt) cc_final: 0.8671 (ptmm) REVERT: C 186 ASP cc_start: 0.8628 (t70) cc_final: 0.7975 (t0) REVERT: C 328 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7947 (t80) REVERT: C 334 TYR cc_start: 0.7980 (m-10) cc_final: 0.7677 (t80) REVERT: C 408 SER cc_start: 0.7032 (m) cc_final: 0.6709 (t) REVERT: C 418 LEU cc_start: 0.9240 (tt) cc_final: 0.8912 (pp) REVERT: A 50 ARG cc_start: 0.7796 (mtm180) cc_final: 0.7276 (tpt90) REVERT: A 94 GLU cc_start: 0.8372 (tp30) cc_final: 0.8090 (tp30) REVERT: A 130 TRP cc_start: 0.8212 (m100) cc_final: 0.7735 (m100) REVERT: A 292 MET cc_start: 0.7784 (mpp) cc_final: 0.7501 (mmm) REVERT: A 302 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8563 (pp) REVERT: A 305 TYR cc_start: 0.9053 (t80) cc_final: 0.8660 (t80) REVERT: A 332 ASN cc_start: 0.8334 (t0) cc_final: 0.7643 (m-40) REVERT: A 359 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8851 (tt) REVERT: A 363 CYS cc_start: 0.9122 (m) cc_final: 0.8257 (m) REVERT: A 387 MET cc_start: 0.8011 (mmm) cc_final: 0.7556 (tpp) REVERT: A 403 GLN cc_start: 0.9079 (tp40) cc_final: 0.8600 (tm-30) REVERT: A 418 LEU cc_start: 0.9238 (mt) cc_final: 0.8680 (mt) REVERT: A 444 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8219 (tm-30) REVERT: A 470 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8568 (tm) REVERT: A 471 ASN cc_start: 0.8546 (t0) cc_final: 0.7928 (t160) outliers start: 65 outliers final: 44 residues processed: 253 average time/residue: 0.0796 time to fit residues: 30.5890 Evaluate side-chains 260 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 208 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 229 MET 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 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 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 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 415 ILE 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 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 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 470 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 126 optimal weight: 0.0470 chunk 51 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 0.0770 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 GLN B 403 GLN B 452 HIS ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.078773 restraints weight = 28602.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.081019 restraints weight = 15249.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.082524 restraints weight = 9963.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.083531 restraints weight = 7469.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.084054 restraints weight = 6187.664| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10145 Z= 0.127 Angle : 0.739 12.173 13827 Z= 0.337 Chirality : 0.042 0.187 1730 Planarity : 0.003 0.035 1725 Dihedral : 3.784 18.254 1416 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 6.42 % Allowed : 26.34 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.24), residues: 1332 helix: 0.51 (0.18), residues: 915 sheet: -1.19 (0.98), residues: 30 loop : -1.93 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.008 0.001 TYR C 325 PHE 0.009 0.001 PHE A 134 TRP 0.029 0.001 TRP A 461 HIS 0.006 0.001 HIS C 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (10143) covalent geometry : angle 0.73809 / 0.34 (13821) hydrogen bonds : bond 0.03353 / 2.23 ( 519) hydrogen bonds : angle 4.11922 / 2.75 ( 1512) link_NAG-ASN : bond 0.00338 / 0.17 ( 2) link_NAG-ASN : angle 1.47343 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 210 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8649 (tm) REVERT: B 141 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9065 (mm) REVERT: B 179 GLU cc_start: 0.8504 (tp30) cc_final: 0.8222 (tp30) REVERT: B 282 MET cc_start: 0.8525 (ttt) cc_final: 0.8244 (ppp) REVERT: B 302 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8642 (pp) REVERT: B 363 CYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8171 (t) REVERT: B 387 MET cc_start: 0.8200 (mmp) cc_final: 0.7255 (mmm) REVERT: C 186 ASP cc_start: 0.8647 (t70) cc_final: 0.7998 (t0) REVERT: C 328 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7960 (t80) REVERT: C 334 TYR cc_start: 0.7973 (m-10) cc_final: 0.7616 (t80) REVERT: C 408 SER cc_start: 0.6984 (m) cc_final: 0.6669 (t) REVERT: C 418 LEU cc_start: 0.9246 (tt) cc_final: 0.8939 (pp) REVERT: A 50 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7370 (tpt90) REVERT: A 94 GLU cc_start: 0.8386 (tp30) cc_final: 0.8111 (tp30) REVERT: A 292 MET cc_start: 0.7788 (mpp) cc_final: 0.7536 (mmm) REVERT: A 302 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8808 (pp) REVERT: A 307 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8816 (tp) REVERT: A 332 ASN cc_start: 0.8375 (t0) cc_final: 0.7697 (m-40) REVERT: A 359 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8849 (tt) REVERT: A 360 MET cc_start: 0.9299 (tpp) cc_final: 0.9099 (tpp) REVERT: A 363 CYS cc_start: 0.9088 (m) cc_final: 0.8241 (m) REVERT: A 387 MET cc_start: 0.8097 (mmm) cc_final: 0.7596 (mmm) REVERT: A 403 GLN cc_start: 0.9082 (tp40) cc_final: 0.8469 (tm-30) REVERT: A 418 LEU cc_start: 0.9227 (mt) cc_final: 0.8675 (mt) REVERT: A 470 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8592 (tm) REVERT: A 471 ASN cc_start: 0.8511 (t0) cc_final: 0.7764 (t160) outliers start: 67 outliers final: 46 residues processed: 245 average time/residue: 0.0808 time to fit residues: 29.8776 Evaluate side-chains 257 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 229 MET 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 363 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 394 GLN 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 218 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 415 ILE 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 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 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 470 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 5 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 111 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 394 GLN B 403 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.092542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.074365 restraints weight = 29165.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.076559 restraints weight = 15543.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.078049 restraints weight = 10201.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.078929 restraints weight = 7684.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.079605 restraints weight = 6455.249| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10145 Z= 0.188 Angle : 0.783 11.504 13827 Z= 0.370 Chirality : 0.044 0.228 1730 Planarity : 0.004 0.034 1725 Dihedral : 4.066 16.850 1416 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 6.32 % Allowed : 26.44 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.24), residues: 1332 helix: 0.55 (0.18), residues: 903 sheet: -1.18 (1.00), residues: 30 loop : -1.69 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 465 TYR 0.009 0.001 TYR C 325 PHE 0.016 0.001 PHE A 400 TRP 0.027 0.002 TRP A 461 HIS 0.006 0.001 HIS C 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (10143) covalent geometry : angle 0.78206 / 0.37 (13821) hydrogen bonds : bond 0.04032 / 2.72 ( 519) hydrogen bonds : angle 4.34970 / 2.93 ( 1512) link_NAG-ASN : bond 0.00197 / 0.10 ( 2) link_NAG-ASN : angle 1.65184 / 0.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 189 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8689 (tm) REVERT: B 141 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9167 (mm) REVERT: B 282 MET cc_start: 0.8589 (ttt) cc_final: 0.8336 (ttp) REVERT: B 331 LYS cc_start: 0.9054 (ptpt) cc_final: 0.8748 (ptpp) REVERT: B 363 CYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8322 (t) REVERT: B 387 MET cc_start: 0.8290 (mmp) cc_final: 0.7798 (mmp) REVERT: B 438 THR cc_start: 0.9301 (p) cc_final: 0.9041 (t) REVERT: C 313 HIS cc_start: 0.9007 (m90) cc_final: 0.8783 (m90) REVERT: C 334 TYR cc_start: 0.8033 (m-10) cc_final: 0.7661 (t80) REVERT: C 418 LEU cc_start: 0.9273 (tt) cc_final: 0.9052 (pp) REVERT: A 50 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7422 (tpt90) REVERT: A 94 GLU cc_start: 0.8408 (tp30) cc_final: 0.8189 (tp30) REVERT: A 307 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8839 (tp) REVERT: A 332 ASN cc_start: 0.8499 (t0) cc_final: 0.7787 (m-40) REVERT: A 334 TYR cc_start: 0.7780 (m-10) cc_final: 0.7552 (m-10) REVERT: A 359 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8903 (tp) REVERT: A 363 CYS cc_start: 0.9141 (m) cc_final: 0.8412 (m) REVERT: A 387 MET cc_start: 0.8265 (mmm) cc_final: 0.7698 (mmt) REVERT: A 403 GLN cc_start: 0.9226 (tp40) cc_final: 0.8542 (tm-30) REVERT: A 470 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8881 (tm) REVERT: A 471 ASN cc_start: 0.8640 (t0) cc_final: 0.7648 (t160) outliers start: 66 outliers final: 41 residues processed: 231 average time/residue: 0.0794 time to fit residues: 27.7357 Evaluate side-chains 228 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 182 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 328 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 363 CYS Chi-restraints excluded: chain B residue 384 THR Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 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 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 408 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 117 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 116 optimal weight: 0.0980 chunk 18 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 403 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 HIS A 224 GLN 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 = 0.095237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.077152 restraints weight = 28700.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.079347 restraints weight = 15335.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080854 restraints weight = 10110.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.081853 restraints weight = 7588.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.082354 restraints weight = 6299.507| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10145 Z= 0.135 Angle : 0.792 11.901 13827 Z= 0.358 Chirality : 0.043 0.346 1730 Planarity : 0.003 0.034 1725 Dihedral : 3.927 20.056 1416 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.69 % Allowed : 28.64 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1332 helix: 0.57 (0.18), residues: 930 sheet: -1.14 (0.98), residues: 30 loop : -1.58 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 465 TYR 0.007 0.001 TYR C 325 PHE 0.010 0.001 PHE C 192 TRP 0.042 0.002 TRP A 461 HIS 0.007 0.001 HIS C 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10143) covalent geometry : angle 0.79138 / 0.36 (13821) hydrogen bonds : bond 0.03559 / 2.37 ( 519) hydrogen bonds : angle 4.21040 / 2.81 ( 1512) link_NAG-ASN : bond 0.00292 / 0.15 ( 2) link_NAG-ASN : angle 1.50020 / 0.77 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8540 (tm) REVERT: B 141 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9146 (mm) REVERT: B 331 LYS cc_start: 0.8966 (ptpt) cc_final: 0.8702 (ptpp) REVERT: B 363 CYS cc_start: 0.8782 (m) cc_final: 0.8099 (t) REVERT: B 387 MET cc_start: 0.8187 (mmp) cc_final: 0.7627 (mmp) REVERT: C 313 HIS cc_start: 0.9000 (m90) cc_final: 0.8489 (m-70) REVERT: C 334 TYR cc_start: 0.7921 (m-10) cc_final: 0.7605 (t80) REVERT: C 408 SER cc_start: 0.6558 (m) cc_final: 0.6152 (t) REVERT: A 50 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7415 (tpt90) REVERT: A 94 GLU cc_start: 0.8415 (tp30) cc_final: 0.8162 (tp30) REVERT: A 302 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8729 (pp) REVERT: A 307 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8798 (tp) REVERT: A 332 ASN cc_start: 0.8448 (t0) cc_final: 0.7647 (m-40) REVERT: A 334 TYR cc_start: 0.7781 (m-10) cc_final: 0.7581 (m-10) REVERT: A 359 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8805 (tp) REVERT: A 363 CYS cc_start: 0.9117 (m) cc_final: 0.8362 (m) REVERT: A 387 MET cc_start: 0.8079 (mmm) cc_final: 0.7566 (mmt) REVERT: A 403 GLN cc_start: 0.9155 (tp40) cc_final: 0.8583 (tm-30) REVERT: A 418 LEU cc_start: 0.9271 (mt) cc_final: 0.8692 (mt) REVERT: A 470 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8684 (tm) REVERT: A 471 ASN cc_start: 0.8471 (t0) cc_final: 0.7753 (t160) outliers start: 49 outliers final: 33 residues processed: 238 average time/residue: 0.0764 time to fit residues: 27.5632 Evaluate side-chains 236 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 401 ILE 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 180 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 308 CYS Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 79 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 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 408 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 109 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 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 = 0.3380 r_free = 0.3380 target = 0.095375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.077583 restraints weight = 28770.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.079824 restraints weight = 15249.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.081316 restraints weight = 9946.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.082218 restraints weight = 7457.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.082906 restraints weight = 6235.872| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10145 Z= 0.132 Angle : 0.786 11.971 13827 Z= 0.354 Chirality : 0.043 0.333 1730 Planarity : 0.003 0.036 1725 Dihedral : 3.880 19.364 1416 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.31 % Allowed : 28.45 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.24), residues: 1332 helix: 0.59 (0.18), residues: 930 sheet: -0.98 (0.98), residues: 30 loop : -1.52 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 465 TYR 0.010 0.001 TYR C 325 PHE 0.011 0.001 PHE C 192 TRP 0.039 0.002 TRP A 461 HIS 0.004 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10143) covalent geometry : angle 0.78524 / 0.35 (13821) hydrogen bonds : bond 0.03485 / 2.31 ( 519) hydrogen bonds : angle 4.16331 / 2.77 ( 1512) link_NAG-ASN : bond 0.00327 / 0.17 ( 2) link_NAG-ASN : angle 1.47168 / 0.71 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1690.07 seconds wall clock time: 29 minutes 52.18 seconds (1792.18 seconds total)