Starting phenix.real_space_refine on Wed Feb 14 18:19:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mpb_9188/02_2024/6mpb_9188.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mpb_9188/02_2024/6mpb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mpb_9188/02_2024/6mpb_9188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mpb_9188/02_2024/6mpb_9188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mpb_9188/02_2024/6mpb_9188.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mpb_9188/02_2024/6mpb_9188.pdb" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 sd= 0.326 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6498 2.51 5 N 1656 2.21 5 O 1767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 98": "NH1" <-> "NH2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9969 Number of models: 1 Model: "" Number of chains: 6 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.86, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B 602 " - " ASN B 163 " " NAG C 602 " - " ASN C 163 " Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.8 seconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 76.3% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'B' and resid 44 through 52 removed outlier: 3.827A pdb=" N CYS B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 75 removed outlier: 3.568A pdb=" N VAL B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.510A pdb=" N LEU B 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 100 removed outlier: 3.852A pdb=" N SER B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.922A pdb=" N LEU B 96 " --> pdb=" O PRO B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.846A pdb=" N VAL B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N CYS B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 114 " --> pdb=" O CYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 151 removed outlier: 3.673A pdb=" N ARG B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP B 130 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.602A pdb=" N ILE B 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.896A pdb=" N ALA B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 3.786A pdb=" N ALA B 188 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.862A pdb=" N PHE B 201 " --> pdb=" O SER B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 248 removed outlier: 3.801A pdb=" N LEU B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 245 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 292 removed outlier: 4.426A pdb=" N LEU B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 271 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 276 " --> pdb=" O TRP B 272 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.941A pdb=" N MET B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 316 removed outlier: 3.570A pdb=" N ARG B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 removed outlier: 3.566A pdb=" N LEU B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.593A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 356 through 367 removed outlier: 3.945A pdb=" N GLU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 382 removed outlier: 3.612A pdb=" N SER B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE B 377 " --> pdb=" O HIS B 373 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Proline residue: B 380 - end of helix Processing helix chain 'B' and resid 387 through 404 removed outlier: 3.802A pdb=" N CYS B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 428 removed outlier: 3.687A pdb=" N ILE B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL B 426 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 439 through 446 removed outlier: 3.663A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 488 removed outlier: 3.616A pdb=" N SER B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 52 removed outlier: 3.827A pdb=" N CYS C 48 " --> pdb=" O GLN C 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 75 removed outlier: 3.568A pdb=" N VAL C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.509A pdb=" N LEU C 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 3.854A pdb=" N SER C 87 " --> pdb=" O PRO C 83 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Proline residue: C 92 - end of helix removed outlier: 3.922A pdb=" N LEU C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.847A pdb=" N VAL C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N CYS C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 151 removed outlier: 3.673A pdb=" N ARG C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.602A pdb=" N ILE C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.896A pdb=" N ALA C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 191 removed outlier: 3.785A pdb=" N ALA C 188 " --> pdb=" O PHE C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 removed outlier: 3.861A pdb=" N PHE C 201 " --> pdb=" O SER C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 248 removed outlier: 3.802A pdb=" N LEU C 234 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 245 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 292 removed outlier: 4.426A pdb=" N LEU C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 266 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER C 271 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP C 272 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 276 " --> pdb=" O TRP C 272 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 3.940A pdb=" N MET C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C 283 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N MET C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 316 removed outlier: 3.570A pdb=" N ARG C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR C 305 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 330 removed outlier: 3.565A pdb=" N LEU C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 339 removed outlier: 3.592A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 351 Processing helix chain 'C' and resid 356 through 367 removed outlier: 3.945A pdb=" N GLU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 382 removed outlier: 3.613A pdb=" N SER C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 376 " --> pdb=" O LYS C 372 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 377 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 379 " --> pdb=" O SER C 375 " (cutoff:3.500A) Proline residue: C 380 - end of helix Processing helix chain 'C' and resid 387 through 404 removed outlier: 3.801A pdb=" N CYS C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 428 removed outlier: 3.688A pdb=" N ILE C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL C 426 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 438 No H-bonds generated for 'chain 'C' and resid 436 through 438' Processing helix chain 'C' and resid 439 through 446 removed outlier: 3.663A pdb=" N ALA C 445 " --> pdb=" O ILE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 488 removed outlier: 3.615A pdb=" N SER C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 484 " --> pdb=" O GLY C 480 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR C 485 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 removed outlier: 3.827A pdb=" N CYS A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 75 removed outlier: 3.568A pdb=" N VAL A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.510A pdb=" N LEU A 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.852A pdb=" N SER A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Proline residue: A 92 - end of helix removed outlier: 3.922A pdb=" N LEU A 96 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.847A pdb=" N VAL A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N CYS A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 112 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 151 removed outlier: 3.673A pdb=" N ARG A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TRP A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.602A pdb=" N ILE A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.896A pdb=" N ALA A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 191 removed outlier: 3.786A pdb=" N ALA A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 201 removed outlier: 3.861A pdb=" N PHE A 201 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 248 removed outlier: 3.800A pdb=" N LEU A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 245 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 292 removed outlier: 4.426A pdb=" N LEU A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR A 276 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Proline residue: A 278 - end of helix removed outlier: 3.940A pdb=" N MET A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N VAL A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N MET A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.569A pdb=" N ARG A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LYS A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 330 removed outlier: 3.564A pdb=" N LEU A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.592A pdb=" N PHE A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 351 Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.945A pdb=" N GLU A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.613A pdb=" N SER A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 377 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 387 through 404 removed outlier: 3.801A pdb=" N CYS A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 428 removed outlier: 3.688A pdb=" N ILE A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL A 426 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 439 through 446 removed outlier: 3.663A pdb=" N ALA A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 488 removed outlier: 3.616A pdb=" N SER A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN A 484 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AA2, first strand: chain 'C' and resid 207 through 209 Processing sheet with id=AA3, first strand: chain 'A' and resid 207 through 209 519 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 4.17 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: 99.31 - 106.24: 244 106.24 - 113.17: 5591 113.17 - 120.10: 3813 120.10 - 127.03: 4058 127.03 - 133.96: 115 Bond angle restraints: 13821 Sorted by residual: angle pdb=" C VAL B 446 " pdb=" N ASN B 447 " pdb=" CA ASN B 447 " ideal model delta sigma weight residual 122.46 129.79 -7.33 1.41e+00 5.03e-01 2.70e+01 angle pdb=" C VAL C 446 " pdb=" N ASN C 447 " pdb=" CA ASN C 447 " ideal model delta sigma weight residual 122.46 129.77 -7.31 1.41e+00 5.03e-01 2.69e+01 angle pdb=" C VAL A 446 " pdb=" N ASN A 447 " pdb=" CA ASN A 447 " ideal model delta sigma weight residual 122.46 129.73 -7.27 1.41e+00 5.03e-01 2.66e+01 angle pdb=" CA LEU C 409 " pdb=" CB LEU C 409 " pdb=" CG LEU C 409 " ideal model delta sigma weight residual 116.30 131.87 -15.57 3.50e+00 8.16e-02 1.98e+01 angle pdb=" CA LEU B 409 " pdb=" CB LEU B 409 " pdb=" CG LEU B 409 " ideal model delta sigma weight residual 116.30 131.84 -15.54 3.50e+00 8.16e-02 1.97e+01 ... (remaining 13816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.01: 5600 15.01 - 30.01: 330 30.01 - 45.01: 70 45.01 - 60.02: 5 60.02 - 75.02: 7 Dihedral angle restraints: 6012 sinusoidal: 2232 harmonic: 3780 Sorted by residual: dihedral pdb=" CA ARG B 211 " pdb=" C ARG B 211 " pdb=" N ASN B 212 " pdb=" CA ASN B 212 " ideal model delta harmonic sigma weight residual 180.00 -158.05 -21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG A 211 " pdb=" C ARG A 211 " pdb=" N ASN A 212 " pdb=" CA ASN A 212 " ideal model delta harmonic sigma weight residual -180.00 -158.06 -21.94 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ARG C 211 " pdb=" C ARG C 211 " pdb=" N ASN C 212 " pdb=" CA ASN C 212 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 6009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1332 0.062 - 0.123: 322 0.123 - 0.185: 65 0.185 - 0.246: 3 0.246 - 0.307: 8 Chirality restraints: 1730 Sorted by residual: chirality pdb=" CB VAL A 446 " pdb=" CA VAL A 446 " pdb=" CG1 VAL A 446 " pdb=" CG2 VAL A 446 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB VAL B 446 " pdb=" CA VAL B 446 " pdb=" CG1 VAL B 446 " pdb=" CG2 VAL B 446 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB VAL C 446 " pdb=" CA VAL C 446 " pdb=" CG1 VAL C 446 " pdb=" CG2 VAL C 446 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1727 not shown) Planarity restraints: 1727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 211 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C ARG C 211 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG C 211 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN C 212 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 211 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C ARG B 211 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG B 211 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 212 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 211 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C ARG A 211 " 0.035 2.00e-02 2.50e+03 pdb=" O ARG A 211 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 212 " -0.012 2.00e-02 2.50e+03 ... (remaining 1724 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3232 2.85 - 3.36: 10038 3.36 - 3.88: 15549 3.88 - 4.39: 17580 4.39 - 4.90: 29128 Nonbonded interactions: 75527 Sorted by model distance: nonbonded pdb=" OG SER A 352 " pdb=" O GLY A 430 " model vdw 2.338 2.440 nonbonded pdb=" OG SER C 352 " pdb=" O GLY C 430 " model vdw 2.339 2.440 nonbonded pdb=" OG SER B 352 " pdb=" O GLY B 430 " model vdw 2.339 2.440 nonbonded pdb=" NE2 GLN C 394 " pdb=" OG1 THR C 438 " model vdw 2.378 2.520 nonbonded pdb=" NE2 GLN B 394 " pdb=" OG1 THR B 438 " model vdw 2.378 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.880 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 28.780 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10143 Z= 0.323 Angle : 1.087 15.570 13821 Z= 0.510 Chirality : 0.058 0.307 1730 Planarity : 0.006 0.049 1725 Dihedral : 10.552 75.024 3588 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.90 (0.15), residues: 1332 helix: -4.15 (0.09), residues: 846 sheet: None (None), residues: 0 loop : -3.10 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 272 HIS 0.004 0.001 HIS C 316 PHE 0.015 0.001 PHE C 201 TYR 0.008 0.002 TYR C 334 ARG 0.004 0.001 ARG C 217 *********************** 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 fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 THR cc_start: 0.9006 (p) cc_final: 0.8736 (p) REVERT: B 307 LEU cc_start: 0.9225 (tm) cc_final: 0.8724 (mt) REVERT: B 311 LEU cc_start: 0.9256 (tp) cc_final: 0.9013 (tp) REVERT: B 318 LEU cc_start: 0.9328 (tm) cc_final: 0.9107 (mm) REVERT: B 394 GLN cc_start: 0.8394 (mt0) cc_final: 0.8192 (mt0) REVERT: B 403 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8611 (mm-40) REVERT: C 149 LEU cc_start: 0.9002 (tm) cc_final: 0.8758 (tm) REVERT: C 210 GLU cc_start: 0.5826 (mp0) cc_final: 0.5496 (mm-30) REVERT: C 253 GLU cc_start: 0.7631 (tp30) cc_final: 0.7295 (tp30) REVERT: C 267 MET cc_start: 0.8461 (tpp) cc_final: 0.7502 (tpp) REVERT: C 313 HIS cc_start: 0.8809 (m90) cc_final: 0.8422 (m-70) REVERT: C 353 SER cc_start: 0.9010 (t) cc_final: 0.8686 (p) REVERT: C 366 GLU cc_start: 0.8478 (tt0) cc_final: 0.8176 (tm-30) REVERT: C 388 ASP cc_start: 0.8674 (p0) cc_final: 0.8216 (p0) REVERT: C 462 LEU cc_start: 0.8976 (tp) cc_final: 0.8749 (tp) REVERT: A 130 TRP cc_start: 0.8143 (m100) cc_final: 0.7699 (m100) REVERT: A 184 PHE cc_start: 0.7971 (t80) cc_final: 0.7628 (m-80) REVERT: A 264 GLU cc_start: 0.8866 (tp30) cc_final: 0.8287 (tp30) REVERT: A 348 PHE cc_start: 0.8835 (t80) cc_final: 0.8472 (t80) REVERT: A 363 CYS cc_start: 0.9042 (m) cc_final: 0.8665 (m) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.2101 time to fit residues: 119.4210 Evaluate side-chains 218 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 55 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 119 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 394 GLN A 163 ASN A 224 GLN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10143 Z= 0.216 Angle : 0.734 10.251 13821 Z= 0.351 Chirality : 0.043 0.208 1730 Planarity : 0.005 0.034 1725 Dihedral : 5.107 51.946 1479 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 7.66 % Allowed : 18.87 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.19), residues: 1332 helix: -2.06 (0.14), residues: 909 sheet: -1.64 (0.97), residues: 30 loop : -2.77 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 461 HIS 0.006 0.001 HIS A 452 PHE 0.017 0.001 PHE A 192 TYR 0.020 0.002 TYR B 485 ARG 0.003 0.000 ARG B 465 *********************** 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 336 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 256 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.9096 (tm) cc_final: 0.8873 (tt) REVERT: B 141 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9140 (mm) REVERT: B 178 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8277 (ptmm) REVERT: B 225 GLU cc_start: 0.8699 (mp0) cc_final: 0.8415 (mp0) REVERT: B 275 TRP cc_start: 0.8404 (m100) cc_final: 0.8153 (m-10) REVERT: B 302 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8594 (pp) REVERT: B 307 LEU cc_start: 0.9077 (tm) cc_final: 0.8544 (mt) REVERT: B 311 LEU cc_start: 0.9193 (tp) cc_final: 0.8625 (mm) REVERT: B 329 THR cc_start: 0.7784 (p) cc_final: 0.7517 (p) REVERT: C 149 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8747 (tm) REVERT: C 328 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8036 (t80) REVERT: C 366 GLU cc_start: 0.8142 (tt0) cc_final: 0.7924 (tm-30) REVERT: C 387 MET cc_start: 0.8461 (mmm) cc_final: 0.7989 (mmm) REVERT: C 481 LEU cc_start: 0.9132 (tt) cc_final: 0.8751 (mm) REVERT: A 50 ARG cc_start: 0.7709 (mtm180) cc_final: 0.7209 (tpt90) REVERT: A 94 GLU cc_start: 0.8127 (tp30) cc_final: 0.7750 (tp30) REVERT: A 130 TRP cc_start: 0.8232 (m100) cc_final: 0.7690 (m100) REVERT: A 264 GLU cc_start: 0.8838 (tp30) cc_final: 0.8615 (mm-30) REVERT: A 319 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 363 CYS cc_start: 0.8994 (m) cc_final: 0.8440 (m) REVERT: A 387 MET cc_start: 0.7879 (mmm) cc_final: 0.7609 (mmm) REVERT: A 403 GLN cc_start: 0.8915 (tp40) cc_final: 0.8616 (tm-30) outliers start: 80 outliers final: 31 residues processed: 308 average time/residue: 0.1807 time to fit residues: 80.9854 Evaluate side-chains 239 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 202 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 182 ASP Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 319 LEU 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 120 ASP 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 319 LEU Chi-restraints excluded: chain A residue 416 THR 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 66 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 0.0060 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 0.0970 chunk 106 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 chunk 96 optimal weight: 4.9990 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10143 Z= 0.158 Angle : 0.700 13.664 13821 Z= 0.317 Chirality : 0.041 0.226 1730 Planarity : 0.004 0.034 1725 Dihedral : 4.613 52.157 1479 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 6.32 % Allowed : 20.98 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.22), residues: 1332 helix: -0.97 (0.16), residues: 921 sheet: -1.27 (0.99), residues: 30 loop : -2.19 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 461 HIS 0.003 0.001 HIS A 316 PHE 0.014 0.001 PHE B 135 TYR 0.013 0.001 TYR B 305 ARG 0.002 0.000 ARG B 98 *********************** 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 303 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 237 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8699 (tm) REVERT: B 141 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9086 (mm) REVERT: B 178 LYS cc_start: 0.8370 (ptmt) cc_final: 0.8091 (ptmm) REVERT: B 225 GLU cc_start: 0.8638 (mp0) cc_final: 0.8380 (mp0) REVERT: B 275 TRP cc_start: 0.8434 (m100) cc_final: 0.8133 (m-10) REVERT: B 282 MET cc_start: 0.8636 (ttt) cc_final: 0.8311 (ttp) REVERT: B 302 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8661 (pp) REVERT: B 308 CYS cc_start: 0.9070 (p) cc_final: 0.8854 (p) REVERT: B 363 CYS cc_start: 0.8949 (m) cc_final: 0.8080 (t) REVERT: C 149 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8788 (tm) REVERT: C 328 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8038 (t80) REVERT: C 334 TYR cc_start: 0.8112 (m-10) cc_final: 0.7806 (t80) REVERT: C 387 MET cc_start: 0.8407 (mmm) cc_final: 0.7762 (mmt) REVERT: A 50 ARG cc_start: 0.7773 (mtm180) cc_final: 0.7227 (tpt90) REVERT: A 94 GLU cc_start: 0.8220 (tp30) cc_final: 0.7988 (tp30) REVERT: A 130 TRP cc_start: 0.8192 (m100) cc_final: 0.7676 (m100) REVERT: A 214 THR cc_start: 0.3863 (OUTLIER) cc_final: 0.3025 (t) REVERT: A 229 MET cc_start: 0.8037 (tmm) cc_final: 0.7806 (tmm) REVERT: A 302 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8664 (pp) REVERT: A 305 TYR cc_start: 0.8988 (t80) cc_final: 0.8632 (t80) REVERT: A 313 HIS cc_start: 0.8829 (m90) cc_final: 0.8587 (m90) REVERT: A 363 CYS cc_start: 0.9108 (m) cc_final: 0.8435 (m) REVERT: A 387 MET cc_start: 0.7701 (mmm) cc_final: 0.7389 (mmm) outliers start: 66 outliers final: 30 residues processed: 280 average time/residue: 0.1815 time to fit residues: 74.5636 Evaluate side-chains 245 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 208 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 470 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 149 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 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 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 118 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN C 394 GLN A 316 HIS ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10143 Z= 0.257 Angle : 0.740 12.853 13821 Z= 0.343 Chirality : 0.043 0.259 1730 Planarity : 0.004 0.043 1725 Dihedral : 4.528 51.924 1479 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 7.09 % Allowed : 23.47 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.23), residues: 1332 helix: -0.39 (0.16), residues: 951 sheet: -1.27 (0.99), residues: 30 loop : -2.18 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 461 HIS 0.006 0.001 HIS C 452 PHE 0.013 0.001 PHE A 400 TYR 0.007 0.001 TYR B 305 ARG 0.004 0.000 ARG C 98 *********************** 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 284 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 210 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8773 (tm) REVERT: B 141 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9142 (mm) REVERT: B 328 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7961 (m-10) REVERT: B 331 LYS cc_start: 0.8445 (ptpt) cc_final: 0.8193 (ptpp) REVERT: B 362 LYS cc_start: 0.8967 (tptt) cc_final: 0.8661 (tppt) REVERT: B 461 TRP cc_start: 0.8573 (p-90) cc_final: 0.8323 (p-90) REVERT: C 149 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8892 (tm) REVERT: C 334 TYR cc_start: 0.8089 (m-10) cc_final: 0.7744 (t80) REVERT: C 387 MET cc_start: 0.8586 (mmm) cc_final: 0.8011 (mmt) REVERT: A 50 ARG cc_start: 0.7837 (mtm180) cc_final: 0.7238 (tpt90) REVERT: A 130 TRP cc_start: 0.8344 (m100) cc_final: 0.7839 (m100) REVERT: A 313 HIS cc_start: 0.8823 (m90) cc_final: 0.7938 (m90) REVERT: A 360 MET cc_start: 0.9226 (tpp) cc_final: 0.9004 (tpp) REVERT: A 363 CYS cc_start: 0.9077 (m) cc_final: 0.8452 (m) REVERT: A 387 MET cc_start: 0.8165 (mmm) cc_final: 0.7533 (mmm) REVERT: A 403 GLN cc_start: 0.9085 (tp40) cc_final: 0.8604 (tm-30) REVERT: A 470 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8404 (tm) outliers start: 74 outliers final: 48 residues processed: 254 average time/residue: 0.1795 time to fit residues: 67.3902 Evaluate side-chains 246 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 193 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 186 ASP 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 298 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 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 104 ILE Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain C residue 171 SER 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 236 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 379 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 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 72 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 GLN ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN A 224 GLN A 316 HIS ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10143 Z= 0.172 Angle : 0.705 12.707 13821 Z= 0.318 Chirality : 0.041 0.205 1730 Planarity : 0.003 0.039 1725 Dihedral : 4.347 52.259 1479 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 6.90 % Allowed : 24.04 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1332 helix: -0.02 (0.17), residues: 957 sheet: -1.19 (1.01), residues: 30 loop : -2.20 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 461 HIS 0.004 0.001 HIS C 452 PHE 0.035 0.001 PHE B 411 TYR 0.006 0.001 TYR C 305 ARG 0.003 0.000 ARG C 98 *********************** 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 294 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 222 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8799 (ppp) cc_final: 0.8544 (ppp) REVERT: B 127 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8587 (tm) REVERT: B 141 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9112 (mm) REVERT: B 328 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7986 (m-10) REVERT: B 331 LYS cc_start: 0.8381 (ptpt) cc_final: 0.8131 (ptpp) REVERT: B 362 LYS cc_start: 0.8874 (tptt) cc_final: 0.8631 (tppt) REVERT: B 363 CYS cc_start: 0.8934 (m) cc_final: 0.8317 (t) REVERT: B 387 MET cc_start: 0.8321 (mmp) cc_final: 0.7940 (mmp) REVERT: C 313 HIS cc_start: 0.8871 (m-70) cc_final: 0.8199 (m-70) REVERT: C 328 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8045 (t80) REVERT: C 387 MET cc_start: 0.8360 (mmm) cc_final: 0.7729 (mmt) REVERT: A 50 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7289 (tpt90) REVERT: A 130 TRP cc_start: 0.8377 (m100) cc_final: 0.7816 (m100) REVERT: A 141 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9337 (mp) REVERT: A 292 MET cc_start: 0.8161 (mpp) cc_final: 0.7531 (mmm) REVERT: A 359 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8669 (tp) REVERT: A 363 CYS cc_start: 0.9108 (m) cc_final: 0.8454 (m) REVERT: A 387 MET cc_start: 0.8030 (mmm) cc_final: 0.7514 (mmm) REVERT: A 403 GLN cc_start: 0.9096 (tp40) cc_final: 0.8652 (tm-30) REVERT: A 470 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8276 (tm) REVERT: A 471 ASN cc_start: 0.8512 (t0) cc_final: 0.8058 (t0) outliers start: 72 outliers final: 44 residues processed: 264 average time/residue: 0.1740 time to fit residues: 68.4327 Evaluate side-chains 249 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 198 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 328 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 408 SER 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 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 PHE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 359 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 455 LEU 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 114 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 127 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10143 Z= 0.183 Angle : 0.717 12.443 13821 Z= 0.325 Chirality : 0.042 0.220 1730 Planarity : 0.003 0.034 1725 Dihedral : 4.243 52.031 1479 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 6.51 % Allowed : 25.00 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.24), residues: 1332 helix: 0.25 (0.17), residues: 954 sheet: -1.16 (1.01), residues: 30 loop : -2.07 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 461 HIS 0.005 0.001 HIS C 452 PHE 0.010 0.001 PHE A 134 TYR 0.023 0.001 TYR C 334 ARG 0.002 0.000 ARG C 98 *********************** 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 273 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 205 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8568 (tm) REVERT: B 141 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9093 (mm) REVERT: B 331 LYS cc_start: 0.8404 (ptpt) cc_final: 0.8169 (ptpp) REVERT: B 362 LYS cc_start: 0.8784 (tptt) cc_final: 0.8554 (tppt) REVERT: B 363 CYS cc_start: 0.8813 (m) cc_final: 0.8175 (t) REVERT: B 387 MET cc_start: 0.8274 (mmp) cc_final: 0.7864 (mmp) REVERT: C 313 HIS cc_start: 0.8964 (m-70) cc_final: 0.8200 (m-70) REVERT: C 387 MET cc_start: 0.8289 (mmm) cc_final: 0.7696 (mmt) REVERT: A 50 ARG cc_start: 0.7800 (mtm180) cc_final: 0.7270 (tpt90) REVERT: A 130 TRP cc_start: 0.8309 (m100) cc_final: 0.7784 (m100) REVERT: A 141 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9311 (mp) REVERT: A 292 MET cc_start: 0.8087 (mpp) cc_final: 0.7523 (mmm) REVERT: A 359 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8643 (tp) REVERT: A 363 CYS cc_start: 0.9107 (m) cc_final: 0.8418 (m) REVERT: A 387 MET cc_start: 0.8046 (mmm) cc_final: 0.7523 (mmm) REVERT: A 403 GLN cc_start: 0.9107 (tp40) cc_final: 0.8627 (tm-30) REVERT: A 470 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8587 (tm) REVERT: A 471 ASN cc_start: 0.8475 (t0) cc_final: 0.7929 (t0) outliers start: 68 outliers final: 44 residues processed: 242 average time/residue: 0.1757 time to fit residues: 63.4796 Evaluate side-chains 244 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 195 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 299 PHE 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 401 ILE 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 141 LEU 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 308 CYS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 363 CYS 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 141 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 470 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 79 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN C 394 GLN A 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10143 Z= 0.179 Angle : 0.715 12.488 13821 Z= 0.322 Chirality : 0.041 0.225 1730 Planarity : 0.003 0.033 1725 Dihedral : 4.190 52.088 1479 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 6.51 % Allowed : 25.48 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1332 helix: 0.41 (0.17), residues: 951 sheet: -1.31 (0.96), residues: 30 loop : -1.95 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 461 HIS 0.004 0.001 HIS A 316 PHE 0.023 0.001 PHE B 411 TYR 0.014 0.001 TYR C 325 ARG 0.002 0.000 ARG B 246 *********************** 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 274 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 206 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8537 (tm) REVERT: B 141 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9090 (mm) REVERT: B 282 MET cc_start: 0.8506 (ttt) cc_final: 0.8217 (ttp) REVERT: B 331 LYS cc_start: 0.8418 (ptpt) cc_final: 0.8191 (ptpp) REVERT: B 363 CYS cc_start: 0.8835 (m) cc_final: 0.8191 (t) REVERT: B 387 MET cc_start: 0.8247 (mmp) cc_final: 0.7786 (mmp) REVERT: C 313 HIS cc_start: 0.9024 (m-70) cc_final: 0.8296 (m-70) REVERT: C 360 MET cc_start: 0.9515 (tpt) cc_final: 0.9279 (tpp) REVERT: C 387 MET cc_start: 0.8230 (mmm) cc_final: 0.7637 (mmt) REVERT: A 50 ARG cc_start: 0.7871 (mtm180) cc_final: 0.7357 (tpt90) REVERT: A 292 MET cc_start: 0.8009 (mpp) cc_final: 0.7446 (mmm) REVERT: A 302 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8559 (pp) REVERT: A 359 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8818 (tp) REVERT: A 363 CYS cc_start: 0.9096 (m) cc_final: 0.8393 (m) REVERT: A 387 MET cc_start: 0.8159 (mmm) cc_final: 0.7629 (mmt) REVERT: A 418 LEU cc_start: 0.9297 (mt) cc_final: 0.8690 (mt) REVERT: A 444 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8267 (tm-30) REVERT: A 470 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8599 (tm) REVERT: A 471 ASN cc_start: 0.8490 (t0) cc_final: 0.7749 (t0) outliers start: 68 outliers final: 46 residues processed: 245 average time/residue: 0.1810 time to fit residues: 66.1276 Evaluate side-chains 250 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 199 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 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 467 CYS Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 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 354 SER Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 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 470 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 0.2980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10143 Z= 0.196 Angle : 0.733 12.372 13821 Z= 0.334 Chirality : 0.042 0.240 1730 Planarity : 0.003 0.033 1725 Dihedral : 4.172 51.976 1479 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 6.80 % Allowed : 26.15 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1332 helix: 0.52 (0.17), residues: 945 sheet: -1.31 (0.95), residues: 30 loop : -1.73 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 461 HIS 0.004 0.001 HIS A 316 PHE 0.010 0.001 PHE A 134 TYR 0.007 0.001 TYR C 325 ARG 0.002 0.000 ARG A 465 *********************** 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 fitting. rotamer outliers: 71 poor density : 206 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8498 (tm) REVERT: B 141 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9109 (mm) REVERT: B 282 MET cc_start: 0.8575 (ttt) cc_final: 0.8255 (ttp) REVERT: B 331 LYS cc_start: 0.8439 (ptpt) cc_final: 0.8214 (ptpp) REVERT: B 363 CYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8281 (t) REVERT: B 387 MET cc_start: 0.8272 (mmp) cc_final: 0.7822 (mmp) REVERT: C 313 HIS cc_start: 0.9026 (m-70) cc_final: 0.8288 (m-70) REVERT: C 387 MET cc_start: 0.8287 (mmm) cc_final: 0.7683 (mmt) REVERT: C 482 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8571 (tp) REVERT: A 50 ARG cc_start: 0.7947 (mtm180) cc_final: 0.7441 (tpt90) REVERT: A 292 MET cc_start: 0.7981 (mpp) cc_final: 0.7468 (mmm) REVERT: A 359 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8863 (tp) REVERT: A 363 CYS cc_start: 0.9135 (m) cc_final: 0.8403 (m) REVERT: A 387 MET cc_start: 0.8194 (mmm) cc_final: 0.7641 (mmt) REVERT: A 403 GLN cc_start: 0.9116 (tp40) cc_final: 0.8671 (tm-30) REVERT: A 418 LEU cc_start: 0.9301 (mt) cc_final: 0.8721 (mt) REVERT: A 470 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8614 (tm) REVERT: A 471 ASN cc_start: 0.8489 (t0) cc_final: 0.7696 (t0) outliers start: 71 outliers final: 50 residues processed: 245 average time/residue: 0.1762 time to fit residues: 64.1669 Evaluate side-chains 252 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 196 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 147 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 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 401 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 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 323 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 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 408 SER Chi-restraints excluded: chain A residue 416 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 118 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 77 optimal weight: 0.0870 chunk 125 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10143 Z= 0.174 Angle : 0.742 12.391 13821 Z= 0.330 Chirality : 0.042 0.246 1730 Planarity : 0.003 0.034 1725 Dihedral : 4.114 52.405 1479 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.46 % Allowed : 27.87 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1332 helix: 0.70 (0.18), residues: 927 sheet: -1.20 (0.96), residues: 30 loop : -1.67 (0.35), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 461 HIS 0.003 0.001 HIS C 313 PHE 0.010 0.001 PHE C 192 TYR 0.010 0.001 TYR C 325 ARG 0.002 0.000 ARG A 465 *********************** 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 271 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 214 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8859 (ppp) cc_final: 0.8582 (ppp) REVERT: B 127 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8480 (tm) REVERT: B 141 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9071 (mm) REVERT: B 282 MET cc_start: 0.8529 (ttt) cc_final: 0.8222 (ttp) REVERT: B 360 MET cc_start: 0.9551 (mmm) cc_final: 0.9255 (tpp) REVERT: B 361 MET cc_start: 0.8931 (mtp) cc_final: 0.8700 (mtt) REVERT: B 363 CYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8248 (t) REVERT: B 387 MET cc_start: 0.8248 (mmp) cc_final: 0.7803 (mmp) REVERT: C 313 HIS cc_start: 0.9022 (m-70) cc_final: 0.8253 (m-70) REVERT: C 360 MET cc_start: 0.9500 (tpp) cc_final: 0.9289 (tpp) REVERT: C 482 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8599 (tp) REVERT: A 50 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7479 (tpt90) REVERT: A 292 MET cc_start: 0.7973 (mpp) cc_final: 0.7489 (mmm) REVERT: A 302 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8553 (pp) REVERT: A 307 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8837 (tp) REVERT: A 359 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8804 (tp) REVERT: A 363 CYS cc_start: 0.9067 (m) cc_final: 0.8376 (m) REVERT: A 387 MET cc_start: 0.8080 (mmm) cc_final: 0.7651 (mmm) REVERT: A 403 GLN cc_start: 0.9066 (tp40) cc_final: 0.8563 (tm-30) REVERT: A 418 LEU cc_start: 0.9293 (mt) cc_final: 0.8706 (mt) REVERT: A 470 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8525 (tm) outliers start: 57 outliers final: 42 residues processed: 243 average time/residue: 0.1779 time to fit residues: 64.4610 Evaluate side-chains 253 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 133 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 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 401 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 475 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 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 354 SER Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 395 CYS Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 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 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 59 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 121 optimal weight: 0.0020 chunk 104 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 83 optimal weight: 0.0030 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 0.0030 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10143 Z= 0.169 Angle : 0.756 11.943 13821 Z= 0.333 Chirality : 0.042 0.312 1730 Planarity : 0.003 0.035 1725 Dihedral : 4.083 52.455 1479 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.89 % Allowed : 28.83 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1332 helix: 0.85 (0.18), residues: 921 sheet: -1.22 (0.94), residues: 30 loop : -1.71 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 461 HIS 0.003 0.001 HIS C 313 PHE 0.011 0.001 PHE C 192 TYR 0.005 0.001 TYR C 334 ARG 0.002 0.000 ARG A 465 ********************** 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 278 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 227 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 MET cc_start: 0.8833 (ppp) cc_final: 0.8562 (ppp) REVERT: B 127 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8434 (tm) REVERT: B 141 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9031 (mm) REVERT: B 282 MET cc_start: 0.8576 (ttt) cc_final: 0.8296 (ttp) REVERT: B 360 MET cc_start: 0.9550 (mmm) cc_final: 0.9297 (tpp) REVERT: B 363 CYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8226 (t) REVERT: B 387 MET cc_start: 0.8259 (mmp) cc_final: 0.7886 (mmp) REVERT: C 282 MET cc_start: 0.8811 (ttt) cc_final: 0.8258 (tmm) REVERT: C 313 HIS cc_start: 0.9025 (m-70) cc_final: 0.8277 (m-70) REVERT: C 361 MET cc_start: 0.9281 (tpp) cc_final: 0.8988 (ttt) REVERT: C 408 SER cc_start: 0.6026 (m) cc_final: 0.5773 (t) REVERT: C 413 LYS cc_start: 0.8950 (ptpp) cc_final: 0.8731 (mtmm) REVERT: C 418 LEU cc_start: 0.9113 (tt) cc_final: 0.8729 (pp) REVERT: C 455 LEU cc_start: 0.9158 (mm) cc_final: 0.8822 (tp) REVERT: A 50 ARG cc_start: 0.7811 (mtm180) cc_final: 0.7490 (tpt90) REVERT: A 102 MET cc_start: 0.8726 (ppp) cc_final: 0.8453 (ppp) REVERT: A 292 MET cc_start: 0.7950 (mpp) cc_final: 0.7504 (mmm) REVERT: A 302 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8532 (pp) REVERT: A 307 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8789 (tp) REVERT: A 359 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8854 (tp) REVERT: A 360 MET cc_start: 0.9402 (tpp) cc_final: 0.8828 (tpp) REVERT: A 363 CYS cc_start: 0.9051 (m) cc_final: 0.8344 (m) REVERT: A 387 MET cc_start: 0.8018 (mmm) cc_final: 0.7611 (mmm) REVERT: A 403 GLN cc_start: 0.8997 (tp40) cc_final: 0.8698 (tm-30) REVERT: A 418 LEU cc_start: 0.9283 (mt) cc_final: 0.8698 (mt) REVERT: A 470 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8521 (tm) outliers start: 51 outliers final: 38 residues processed: 251 average time/residue: 0.1691 time to fit residues: 63.6148 Evaluate side-chains 257 residues out of total 1044 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 212 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 133 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 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 401 ILE Chi-restraints excluded: chain B residue 467 CYS 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 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 342 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 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 302 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 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 96 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.0370 chunk 104 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 373 HIS ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.097004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.079241 restraints weight = 28670.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.081495 restraints weight = 15278.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.083016 restraints weight = 9978.248| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10143 Z= 0.183 Angle : 0.761 11.836 13821 Z= 0.338 Chirality : 0.043 0.315 1730 Planarity : 0.003 0.032 1725 Dihedral : 4.075 52.129 1479 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.79 % Allowed : 29.50 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1332 helix: 0.82 (0.18), residues: 936 sheet: -1.33 (0.93), residues: 30 loop : -1.76 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 461 HIS 0.002 0.001 HIS C 313 PHE 0.025 0.001 PHE A 134 TYR 0.014 0.001 TYR B 485 ARG 0.002 0.000 ARG A 465 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.74 seconds wall clock time: 40 minutes 2.34 seconds (2402.34 seconds total)