Starting phenix.real_space_refine on Thu Feb 5 03:16:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pkz_71708/02_2026/9pkz_71708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pkz_71708/02_2026/9pkz_71708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pkz_71708/02_2026/9pkz_71708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pkz_71708/02_2026/9pkz_71708.map" model { file = "/net/cci-nas-00/data/ceres_data/9pkz_71708/02_2026/9pkz_71708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pkz_71708/02_2026/9pkz_71708.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 89 5.16 5 C 9468 2.51 5 N 2285 2.21 5 O 2587 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14429 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2829 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain breaks: 1 Chain: "D" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2790 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Chain: "C" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2827 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain breaks: 1 Chain: "B" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2809 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} Chain breaks: 1 Chain: "E" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2669 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 163 Unusual residues: {'IVM': 2, 'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {'IVM': 1, 'NAG': 1, 'SY9': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'IVM': 1, 'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'IVM': 1, 'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.05, per 1000 atoms: 0.21 Number of scatterers: 14429 At special positions: 0 Unit cell: (93.24, 94.92, 135.24, 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 89 16.00 O 2587 8.00 N 2285 7.00 C 9468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 222 " - pdb=" SG CYS A 233 " distance=2.03 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 242 " - pdb=" SG CYS E 254 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 62 " " NAG B 502 " - " ASN B 62 " " NAG C 501 " - " ASN C 62 " " NAG D 501 " - " ASN D 62 " " NAG E 601 " - " ASN E 241 " Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 542.2 milliseconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3292 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 24 sheets defined 36.9% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 110 through 117 removed outlier: 3.595A pdb=" N LEU A 114 " --> pdb=" O PRO A 111 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ASP A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE A 117 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.619A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.555A pdb=" N ILE A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TRP A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 272 through 295 removed outlier: 3.521A pdb=" N THR A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 334 removed outlier: 3.561A pdb=" N ILE A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP A 310 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 336 No H-bonds generated for 'chain 'A' and resid 335 through 336' Processing helix chain 'A' and resid 400 through 400 No H-bonds generated for 'chain 'A' and resid 400 through 400' Processing helix chain 'A' and resid 401 through 439 removed outlier: 4.281A pdb=" N SER A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.513A pdb=" N ILE A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 437 " --> pdb=" O TYR A 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 41 removed outlier: 3.617A pdb=" N LEU D 38 " --> pdb=" O PRO D 34 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.927A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 264 removed outlier: 3.535A pdb=" N VAL D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 272 through 295 removed outlier: 3.540A pdb=" N THR D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 294 " --> pdb=" O GLN D 290 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 333 removed outlier: 3.546A pdb=" N ARG D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 435 removed outlier: 3.535A pdb=" N ARG D 406 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP D 411 " --> pdb=" O ALA D 407 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 418 " --> pdb=" O SER D 414 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.775A pdb=" N ILE D 431 " --> pdb=" O ILE D 427 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR D 433 " --> pdb=" O TYR D 429 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 435 " --> pdb=" O ILE D 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 41 removed outlier: 3.668A pdb=" N LEU C 38 " --> pdb=" O PRO C 34 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 41 " --> pdb=" O PHE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 117 removed outlier: 4.938A pdb=" N ASP C 115 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 251 through 263 removed outlier: 3.618A pdb=" N SER C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 272 through 295 removed outlier: 3.535A pdb=" N MET C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 333 removed outlier: 3.533A pdb=" N LEU C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 323 " --> pdb=" O PHE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 404 through 435 removed outlier: 3.833A pdb=" N ARG C 409 " --> pdb=" O SER C 405 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 410 " --> pdb=" O ARG C 406 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.584A pdb=" N TYR C 433 " --> pdb=" O TYR C 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.523A pdb=" N LYS B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 removed outlier: 3.554A pdb=" N LEU B 114 " --> pdb=" O PRO B 111 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 117 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 removed outlier: 3.752A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 272 through 294 Processing helix chain 'B' and resid 305 through 332 removed outlier: 3.556A pdb=" N VAL B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 439 removed outlier: 3.502A pdb=" N ARG B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.780A pdb=" N TYR B 433 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE B 436 " --> pdb=" O THR B 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 64 removed outlier: 3.791A pdb=" N LEU E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN E 61 " --> pdb=" O SER E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 265 through 270 removed outlier: 3.637A pdb=" N MET E 270 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 284 Processing helix chain 'E' and resid 285 through 289 Processing helix chain 'E' and resid 293 through 316 Proline residue: E 299 - end of helix removed outlier: 3.876A pdb=" N SER E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 305 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS E 312 " --> pdb=" O LEU E 308 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR E 313 " --> pdb=" O SER E 309 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 315 " --> pdb=" O GLU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 352 removed outlier: 3.727A pdb=" N ALA E 334 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E 343 " --> pdb=" O GLY E 339 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 344 " --> pdb=" O PHE E 340 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N MET E 352 " --> pdb=" O VAL E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 493 removed outlier: 3.949A pdb=" N ALA E 476 " --> pdb=" O LEU E 472 " (cutoff:3.500A) Proline residue: E 479 - end of helix removed outlier: 3.533A pdb=" N TRP E 490 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER E 491 " --> pdb=" O VAL E 487 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 109 removed outlier: 4.548A pdb=" N LEU A 142 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 6.412A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 178 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 178 Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA7, first strand: chain 'D' and resid 61 through 65 removed outlier: 6.035A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 69 removed outlier: 3.679A pdb=" N GLN D 201 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 76 removed outlier: 3.665A pdb=" N SER D 71 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE D 75 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP D 81 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 71 through 76 removed outlier: 3.665A pdb=" N SER D 71 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE D 75 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP D 81 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 122 through 123 removed outlier: 6.427A pdb=" N GLU D 235 " --> pdb=" O ASP D 218 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASP D 218 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG D 237 " --> pdb=" O GLU D 216 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU D 216 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N HIS D 239 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 224 through 226 removed outlier: 3.586A pdb=" N TYR D 226 " --> pdb=" O GLY D 229 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 106 through 108 removed outlier: 4.422A pdb=" N ASN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 156 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP C 81 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 75 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG C 83 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 71 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE C 87 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE C 69 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ARG C 89 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE C 67 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLN C 91 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N CYS C 65 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN C 93 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL C 63 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 127 through 132 removed outlier: 6.213A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 156 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP C 81 " --> pdb=" O ILE C 75 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 75 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG C 83 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 71 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE C 87 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE C 69 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ARG C 89 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE C 67 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLN C 91 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N CYS C 65 " --> pdb=" O GLN C 91 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN C 93 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL C 63 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.648A pdb=" N SER C 182 " --> pdb=" O THR C 232 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THR C 232 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N GLY C 184 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N LYS C 230 " --> pdb=" O GLY C 184 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N HIS C 239 " --> pdb=" O GLU C 216 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLU C 216 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLU C 241 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LYS C 214 " --> pdb=" O GLU C 241 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 122 through 123 removed outlier: 3.648A pdb=" N SER C 182 " --> pdb=" O THR C 232 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THR C 232 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N GLY C 184 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 9.397A pdb=" N LYS C 230 " --> pdb=" O GLY C 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 106 through 109 removed outlier: 4.731A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.716A pdb=" N GLU B 127 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA B 161 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY B 129 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=AC2, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AC3, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AC4, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.781A pdb=" N SER E 149 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG E 102 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER E 93 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN E 104 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE E 91 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N PHE E 106 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASN E 89 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ARG E 108 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE E 87 " --> pdb=" O ARG E 108 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ARG E 110 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASN E 85 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ASN E 112 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N ARG E 83 " --> pdb=" O ASN E 112 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN E 211 " --> pdb=" O VAL E 80 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 160 through 164 removed outlier: 3.949A pdb=" N ARG E 102 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER E 93 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN E 104 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N PHE E 91 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N PHE E 106 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASN E 89 " --> pdb=" O PHE E 106 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ARG E 108 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE E 87 " --> pdb=" O ARG E 108 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ARG E 110 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASN E 85 " --> pdb=" O ARG E 110 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ASN E 112 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N ARG E 83 " --> pdb=" O ASN E 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 142 through 143 removed outlier: 3.571A pdb=" N SER E 202 " --> pdb=" O THR E 253 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR E 253 " --> pdb=" O SER E 202 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLY E 204 " --> pdb=" O TYR E 251 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N TYR E 251 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY E 250 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR E 246 " --> pdb=" O GLY E 250 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3422 1.33 - 1.46: 4540 1.46 - 1.59: 6732 1.59 - 1.72: 0 1.72 - 1.85: 147 Bond restraints: 14841 Sorted by residual: bond pdb=" N VAL E 129 " pdb=" CA VAL E 129 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.14e-02 7.69e+03 1.01e+01 bond pdb=" N LEU E 137 " pdb=" CA LEU E 137 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.15e-02 7.56e+03 9.09e+00 bond pdb=" N PHE E 122 " pdb=" CA PHE E 122 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.17e-02 7.31e+03 7.61e+00 bond pdb=" N LEU E 64 " pdb=" CA LEU E 64 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 7.11e+00 bond pdb=" N ASP E 125 " pdb=" CA ASP E 125 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.10e+00 ... (remaining 14836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 19370 1.64 - 3.28: 696 3.28 - 4.92: 101 4.92 - 6.56: 53 6.56 - 8.20: 7 Bond angle restraints: 20227 Sorted by residual: angle pdb=" CA ASP E 125 " pdb=" CB ASP E 125 " pdb=" CG ASP E 125 " ideal model delta sigma weight residual 112.60 116.82 -4.22 1.00e+00 1.00e+00 1.78e+01 angle pdb=" C ASP E 130 " pdb=" N PRO E 131 " pdb=" CA PRO E 131 " ideal model delta sigma weight residual 119.82 123.90 -4.08 9.80e-01 1.04e+00 1.74e+01 angle pdb=" N ARG E 115 " pdb=" CA ARG E 115 " pdb=" C ARG E 115 " ideal model delta sigma weight residual 112.90 107.66 5.24 1.31e+00 5.83e-01 1.60e+01 angle pdb=" C ARG E 115 " pdb=" CA ARG E 115 " pdb=" CB ARG E 115 " ideal model delta sigma weight residual 109.67 117.67 -8.00 2.01e+00 2.48e-01 1.58e+01 angle pdb=" CA ASP E 130 " pdb=" C ASP E 130 " pdb=" O ASP E 130 " ideal model delta sigma weight residual 121.34 117.62 3.72 9.40e-01 1.13e+00 1.57e+01 ... (remaining 20222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 8957 23.96 - 47.93: 521 47.93 - 71.89: 76 71.89 - 95.86: 44 95.86 - 119.82: 20 Dihedral angle restraints: 9618 sinusoidal: 4547 harmonic: 5071 Sorted by residual: dihedral pdb=" CB CYS A 222 " pdb=" SG CYS A 222 " pdb=" SG CYS A 233 " pdb=" CB CYS A 233 " ideal model delta sinusoidal sigma weight residual -86.00 -168.68 82.68 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CA TYR B 102 " pdb=" C TYR B 102 " pdb=" N PRO B 103 " pdb=" CA PRO B 103 " ideal model delta harmonic sigma weight residual -180.00 -154.49 -25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CB CYS E 182 " pdb=" SG CYS E 182 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 52.22 40.78 1 1.00e+01 1.00e-02 2.33e+01 ... (remaining 9615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1798 0.052 - 0.103: 374 0.103 - 0.155: 113 0.155 - 0.206: 39 0.206 - 0.258: 9 Chirality restraints: 2333 Sorted by residual: chirality pdb=" C47 IVM D 503 " pdb=" C39 IVM D 503 " pdb=" C41 IVM D 503 " pdb=" C45 IVM D 503 " both_signs ideal model delta sigma weight residual False 3.13 2.87 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C47 IVM C 502 " pdb=" C39 IVM C 502 " pdb=" C41 IVM C 502 " pdb=" C45 IVM C 502 " both_signs ideal model delta sigma weight residual False 3.13 2.88 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C47 IVM B 503 " pdb=" C39 IVM B 503 " pdb=" C41 IVM B 503 " pdb=" C45 IVM B 503 " both_signs ideal model delta sigma weight residual False 3.13 2.90 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2330 not shown) Planarity restraints: 2461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C34 IVM C 502 " -0.258 2.00e-02 2.50e+03 2.59e-01 6.73e+02 pdb=" C36 IVM C 502 " 0.278 2.00e-02 2.50e+03 pdb=" C37 IVM C 502 " 0.240 2.00e-02 2.50e+03 pdb=" C38 IVM C 502 " -0.260 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C34 IVM A 504 " 0.271 2.00e-02 2.50e+03 2.59e-01 6.71e+02 pdb=" C36 IVM A 504 " -0.404 2.00e-02 2.50e+03 pdb=" C37 IVM A 504 " -0.041 2.00e-02 2.50e+03 pdb=" C38 IVM A 504 " 0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM B 503 " -0.237 2.00e-02 2.50e+03 2.21e-01 6.09e+02 pdb=" C38 IVM B 503 " 0.412 2.00e-02 2.50e+03 pdb=" C39 IVM B 503 " -0.105 2.00e-02 2.50e+03 pdb=" C40 IVM B 503 " -0.082 2.00e-02 2.50e+03 pdb=" C47 IVM B 503 " 0.013 2.00e-02 2.50e+03 ... (remaining 2458 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2524 2.77 - 3.30: 13305 3.30 - 3.84: 23082 3.84 - 4.37: 27606 4.37 - 4.90: 47746 Nonbonded interactions: 114263 Sorted by model distance: nonbonded pdb=" NH1 ARG C 295 " pdb=" OH TYR B 246 " model vdw 2.238 3.120 nonbonded pdb=" NH1 ARG E 195 " pdb=" OG1 THR E 260 " model vdw 2.240 3.120 nonbonded pdb=" OE1 GLU D 193 " pdb=" OH TYR D 221 " model vdw 2.278 3.040 nonbonded pdb=" NH2 ARG D 53 " pdb=" O PHE D 56 " model vdw 2.286 3.120 nonbonded pdb=" OD2 ASP B 110 " pdb=" OG SER B 112 " model vdw 2.317 3.040 ... (remaining 114258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 333 or resid 402 through 443)) selection = (chain 'B' and (resid 33 through 333 or resid 402 through 443)) selection = (chain 'C' and (resid 33 through 333 or resid 402 through 443)) selection = (chain 'D' and (resid 33 through 333 or resid 402 through 443)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.010 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.004 0.044 14849 Z= 0.211 Angle : 0.735 8.198 20248 Z= 0.359 Chirality : 0.053 0.258 2333 Planarity : 0.016 0.259 2456 Dihedral : 16.832 119.820 6317 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.19), residues: 1694 helix: -1.66 (0.18), residues: 527 sheet: -0.51 (0.27), residues: 402 loop : -0.99 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 51 TYR 0.016 0.001 TYR B 102 PHE 0.015 0.001 PHE E 340 TRP 0.010 0.001 TRP B 194 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00396 (14841) covalent geometry : angle 0.72910 (20227) SS BOND : bond 0.00447 ( 3) SS BOND : angle 3.08553 ( 6) hydrogen bonds : bond 0.28480 ( 582) hydrogen bonds : angle 8.72676 ( 1902) link_NAG-ASN : bond 0.00483 ( 5) link_NAG-ASN : angle 3.07977 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.6977 (t80) cc_final: 0.6764 (t80) REVERT: E 95 GLN cc_start: 0.8195 (tp40) cc_final: 0.7865 (tp40) REVERT: E 133 MET cc_start: 0.7100 (mtp) cc_final: 0.6847 (mtm) REVERT: E 135 LYS cc_start: 0.8891 (mttt) cc_final: 0.8424 (pptt) REVERT: E 158 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7646 (mp0) REVERT: E 345 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8478 (tm-30) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.6014 time to fit residues: 143.7635 Evaluate side-chains 147 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 93 ASN A 290 GLN D 225 HIS D 250 GLN C 70 ASN C 174 GLN C 250 GLN B 126 ASN E 54 ASN E 89 ASN ** E 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.086136 restraints weight = 24516.322| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.68 r_work: 0.3036 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14849 Z= 0.162 Angle : 0.688 8.715 20248 Z= 0.332 Chirality : 0.046 0.246 2333 Planarity : 0.004 0.033 2456 Dihedral : 9.769 91.250 2969 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.27 % Allowed : 9.90 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.20), residues: 1694 helix: 0.30 (0.21), residues: 548 sheet: -0.31 (0.27), residues: 401 loop : -0.75 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 117 TYR 0.018 0.001 TYR D 325 PHE 0.027 0.002 PHE C 425 TRP 0.010 0.001 TRP E 331 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00360 (14841) covalent geometry : angle 0.68386 (20227) SS BOND : bond 0.00474 ( 3) SS BOND : angle 1.52316 ( 6) hydrogen bonds : bond 0.05613 ( 582) hydrogen bonds : angle 4.92231 ( 1902) link_NAG-ASN : bond 0.00331 ( 5) link_NAG-ASN : angle 2.66164 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8316 (p90) REVERT: A 333 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6900 (mtm180) REVERT: D 51 ARG cc_start: 0.7904 (mtm110) cc_final: 0.7242 (ttp-110) REVERT: D 316 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8582 (tt) REVERT: D 320 SER cc_start: 0.9017 (t) cc_final: 0.8740 (m) REVERT: C 174 GLN cc_start: 0.7844 (mt0) cc_final: 0.7638 (mm-40) REVERT: C 292 SER cc_start: 0.8317 (m) cc_final: 0.7914 (p) REVERT: E 95 GLN cc_start: 0.8146 (tp40) cc_final: 0.7616 (tp40) REVERT: E 158 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8185 (mp0) REVERT: E 191 MET cc_start: 0.8694 (mpt) cc_final: 0.8492 (mpt) REVERT: E 197 LYS cc_start: 0.8796 (ptpp) cc_final: 0.8081 (mttm) outliers start: 35 outliers final: 9 residues processed: 198 average time/residue: 0.6052 time to fit residues: 130.8117 Evaluate side-chains 165 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 153 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 150 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 0.1980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 210 GLN A 290 GLN D 133 HIS C 250 GLN B 126 ASN E 54 ASN ** E 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.106236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.084948 restraints weight = 24669.472| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.69 r_work: 0.2996 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14849 Z= 0.149 Angle : 0.621 8.191 20248 Z= 0.301 Chirality : 0.044 0.255 2333 Planarity : 0.004 0.030 2456 Dihedral : 7.731 82.562 2969 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.59 % Allowed : 12.94 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.20), residues: 1694 helix: 0.94 (0.22), residues: 544 sheet: -0.27 (0.26), residues: 408 loop : -0.74 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 51 TYR 0.020 0.001 TYR D 325 PHE 0.015 0.001 PHE C 425 TRP 0.010 0.001 TRP B 194 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00348 (14841) covalent geometry : angle 0.61585 (20227) SS BOND : bond 0.00473 ( 3) SS BOND : angle 1.37290 ( 6) hydrogen bonds : bond 0.04947 ( 582) hydrogen bonds : angle 4.48884 ( 1902) link_NAG-ASN : bond 0.00522 ( 5) link_NAG-ASN : angle 2.80161 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8402 (ttm170) REVERT: A 333 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6908 (mtm-85) REVERT: D 316 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8595 (tt) REVERT: D 320 SER cc_start: 0.9061 (t) cc_final: 0.8759 (m) REVERT: C 292 SER cc_start: 0.8343 (m) cc_final: 0.8082 (p) REVERT: E 95 GLN cc_start: 0.8142 (tp40) cc_final: 0.7554 (tp40) REVERT: E 117 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7992 (mmm-85) REVERT: E 158 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8176 (mp0) outliers start: 40 outliers final: 12 residues processed: 187 average time/residue: 0.6484 time to fit residues: 131.7478 Evaluate side-chains 170 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 146 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN C 174 GLN B 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.110799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.088462 restraints weight = 25098.880| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.82 r_work: 0.3029 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14849 Z= 0.115 Angle : 0.573 7.101 20248 Z= 0.279 Chirality : 0.043 0.241 2333 Planarity : 0.003 0.029 2456 Dihedral : 6.765 74.077 2969 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.20 % Allowed : 15.15 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 1694 helix: 1.30 (0.22), residues: 545 sheet: -0.06 (0.26), residues: 408 loop : -0.69 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 295 TYR 0.019 0.001 TYR D 325 PHE 0.015 0.001 PHE C 425 TRP 0.010 0.001 TRP B 194 HIS 0.003 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00258 (14841) covalent geometry : angle 0.56913 (20227) SS BOND : bond 0.00484 ( 3) SS BOND : angle 1.35378 ( 6) hydrogen bonds : bond 0.04106 ( 582) hydrogen bonds : angle 4.14563 ( 1902) link_NAG-ASN : bond 0.00425 ( 5) link_NAG-ASN : angle 2.46358 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7036 (mtm-85) REVERT: D 244 MET cc_start: 0.7887 (tpp) cc_final: 0.7578 (tpp) REVERT: D 316 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8792 (tt) REVERT: D 320 SER cc_start: 0.9222 (t) cc_final: 0.8960 (m) REVERT: C 131 ASN cc_start: 0.8390 (m110) cc_final: 0.8128 (m-40) REVERT: C 292 SER cc_start: 0.8456 (m) cc_final: 0.8251 (p) REVERT: B 102 TYR cc_start: 0.6814 (t80) cc_final: 0.6588 (t80) REVERT: E 95 GLN cc_start: 0.8198 (tp40) cc_final: 0.7606 (tp40) REVERT: E 117 ARG cc_start: 0.8413 (mmm-85) cc_final: 0.8123 (mmm160) REVERT: E 127 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8002 (mm) REVERT: E 158 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8224 (mp0) outliers start: 34 outliers final: 13 residues processed: 188 average time/residue: 0.5924 time to fit residues: 121.4938 Evaluate side-chains 173 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 146 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 125 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 131 ASN A 225 HIS D 250 GLN C 174 GLN B 126 ASN E 95 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.107327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.084683 restraints weight = 25017.286| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.78 r_work: 0.2964 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14849 Z= 0.186 Angle : 0.624 7.021 20248 Z= 0.309 Chirality : 0.045 0.297 2333 Planarity : 0.004 0.033 2456 Dihedral : 6.723 67.471 2969 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.04 % Allowed : 15.66 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1694 helix: 1.28 (0.22), residues: 549 sheet: -0.23 (0.26), residues: 421 loop : -0.65 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 83 TYR 0.023 0.002 TYR B 325 PHE 0.015 0.002 PHE C 123 TRP 0.010 0.001 TRP B 194 HIS 0.005 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00446 (14841) covalent geometry : angle 0.61880 (20227) SS BOND : bond 0.00487 ( 3) SS BOND : angle 1.44145 ( 6) hydrogen bonds : bond 0.04597 ( 582) hydrogen bonds : angle 4.25217 ( 1902) link_NAG-ASN : bond 0.00311 ( 5) link_NAG-ASN : angle 2.99507 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8509 (ttm170) REVERT: A 270 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8276 (ptp) REVERT: A 333 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7045 (mtm-85) REVERT: D 316 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8835 (tt) REVERT: D 320 SER cc_start: 0.9204 (t) cc_final: 0.8923 (m) REVERT: C 117 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8491 (tp) REVERT: B 102 TYR cc_start: 0.6902 (t80) cc_final: 0.6671 (t80) REVERT: E 95 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7851 (tp40) REVERT: E 117 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.8163 (mmm160) REVERT: E 127 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8259 (tm) REVERT: E 158 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8247 (mp0) outliers start: 47 outliers final: 19 residues processed: 190 average time/residue: 0.6304 time to fit residues: 130.7947 Evaluate side-chains 174 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 337 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 49 optimal weight: 0.0770 chunk 160 optimal weight: 0.4980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN D 168 ASN D 250 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.109033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.087198 restraints weight = 24703.353| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.71 r_work: 0.3007 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14849 Z= 0.122 Angle : 0.570 6.999 20248 Z= 0.281 Chirality : 0.043 0.259 2333 Planarity : 0.003 0.037 2456 Dihedral : 6.333 68.446 2969 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.59 % Allowed : 16.57 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1694 helix: 1.48 (0.22), residues: 547 sheet: 0.02 (0.26), residues: 414 loop : -0.66 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG D 295 TYR 0.020 0.001 TYR B 325 PHE 0.015 0.001 PHE C 425 TRP 0.010 0.001 TRP B 194 HIS 0.003 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00279 (14841) covalent geometry : angle 0.56528 (20227) SS BOND : bond 0.00415 ( 3) SS BOND : angle 1.19105 ( 6) hydrogen bonds : bond 0.03990 ( 582) hydrogen bonds : angle 4.01899 ( 1902) link_NAG-ASN : bond 0.00382 ( 5) link_NAG-ASN : angle 2.62881 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8470 (ttm170) REVERT: A 331 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8751 (mp) REVERT: D 187 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8296 (tpp) REVERT: D 316 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8789 (tt) REVERT: D 320 SER cc_start: 0.9230 (t) cc_final: 0.8941 (m) REVERT: C 282 THR cc_start: 0.9239 (m) cc_final: 0.9023 (p) REVERT: B 102 TYR cc_start: 0.6990 (t80) cc_final: 0.6705 (t80) REVERT: E 81 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7058 (mm-30) REVERT: E 95 GLN cc_start: 0.8232 (tp-100) cc_final: 0.7759 (tp40) REVERT: E 117 ARG cc_start: 0.8553 (mmm-85) cc_final: 0.8159 (mmm160) REVERT: E 127 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7932 (mm) REVERT: E 158 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8219 (mp0) REVERT: E 276 THR cc_start: 0.8847 (m) cc_final: 0.8528 (p) outliers start: 40 outliers final: 20 residues processed: 194 average time/residue: 0.6863 time to fit residues: 145.2864 Evaluate side-chains 182 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 487 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 110 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN D 85 ASN D 133 HIS D 168 ASN D 250 GLN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.108839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.086374 restraints weight = 24853.778| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.79 r_work: 0.2987 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14849 Z= 0.130 Angle : 0.571 7.316 20248 Z= 0.283 Chirality : 0.043 0.264 2333 Planarity : 0.003 0.033 2456 Dihedral : 6.045 67.735 2969 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.52 % Allowed : 17.09 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.21), residues: 1694 helix: 1.52 (0.22), residues: 549 sheet: -0.01 (0.26), residues: 422 loop : -0.62 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 83 TYR 0.021 0.001 TYR B 325 PHE 0.014 0.001 PHE C 425 TRP 0.010 0.001 TRP B 194 HIS 0.003 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00304 (14841) covalent geometry : angle 0.56624 (20227) SS BOND : bond 0.00450 ( 3) SS BOND : angle 1.23886 ( 6) hydrogen bonds : bond 0.03977 ( 582) hydrogen bonds : angle 3.98657 ( 1902) link_NAG-ASN : bond 0.00353 ( 5) link_NAG-ASN : angle 2.61096 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8513 (ttm170) REVERT: A 331 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8768 (mp) REVERT: D 187 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8360 (tpp) REVERT: D 316 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8811 (tt) REVERT: D 320 SER cc_start: 0.9249 (t) cc_final: 0.8958 (m) REVERT: B 102 TYR cc_start: 0.7006 (t80) cc_final: 0.6684 (t80) REVERT: E 81 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.6927 (mm-30) REVERT: E 95 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7748 (tp40) REVERT: E 117 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8171 (mmm160) REVERT: E 127 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8171 (tm) REVERT: E 158 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8203 (mp0) REVERT: E 213 MET cc_start: 0.8648 (mtp) cc_final: 0.8201 (mtt) outliers start: 39 outliers final: 21 residues processed: 189 average time/residue: 0.6886 time to fit residues: 141.8587 Evaluate side-chains 180 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN D 168 ASN D 243 GLN D 250 GLN B 168 ASN B 250 GLN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.087100 restraints weight = 24691.790| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.79 r_work: 0.2998 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14849 Z= 0.120 Angle : 0.570 7.471 20248 Z= 0.282 Chirality : 0.043 0.255 2333 Planarity : 0.003 0.032 2456 Dihedral : 5.946 67.871 2969 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.52 % Allowed : 17.80 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1694 helix: 1.60 (0.22), residues: 548 sheet: 0.02 (0.26), residues: 424 loop : -0.61 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 295 TYR 0.020 0.001 TYR B 325 PHE 0.014 0.001 PHE C 425 TRP 0.009 0.001 TRP B 194 HIS 0.003 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00277 (14841) covalent geometry : angle 0.56538 (20227) SS BOND : bond 0.00461 ( 3) SS BOND : angle 1.26560 ( 6) hydrogen bonds : bond 0.03854 ( 582) hydrogen bonds : angle 3.92697 ( 1902) link_NAG-ASN : bond 0.00368 ( 5) link_NAG-ASN : angle 2.50126 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8504 (ttm170) REVERT: A 331 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8743 (mp) REVERT: D 187 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8319 (tpp) REVERT: D 316 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8816 (tt) REVERT: D 320 SER cc_start: 0.9243 (t) cc_final: 0.8955 (m) REVERT: C 131 ASN cc_start: 0.8482 (m110) cc_final: 0.8229 (m-40) REVERT: B 102 TYR cc_start: 0.7057 (t80) cc_final: 0.6726 (t80) REVERT: E 95 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7727 (tp40) REVERT: E 117 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8218 (mmm160) REVERT: E 127 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8107 (tm) REVERT: E 158 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8162 (mp0) REVERT: E 213 MET cc_start: 0.8629 (mtp) cc_final: 0.8307 (mtt) REVERT: E 231 ASP cc_start: 0.8905 (t70) cc_final: 0.8516 (t0) REVERT: E 238 GLU cc_start: 0.7288 (mp0) cc_final: 0.6945 (mp0) outliers start: 39 outliers final: 17 residues processed: 193 average time/residue: 0.6683 time to fit residues: 140.4967 Evaluate side-chains 178 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 159 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 157 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN D 168 ASN D 250 GLN B 168 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.106386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.084147 restraints weight = 24313.142| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.89 r_work: 0.2986 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14849 Z= 0.102 Angle : 0.546 7.680 20248 Z= 0.271 Chirality : 0.042 0.233 2333 Planarity : 0.003 0.031 2456 Dihedral : 5.711 67.788 2969 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.68 % Allowed : 18.90 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1694 helix: 1.76 (0.22), residues: 543 sheet: 0.14 (0.26), residues: 423 loop : -0.56 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 295 TYR 0.018 0.001 TYR D 325 PHE 0.013 0.001 PHE C 425 TRP 0.010 0.001 TRP D 263 HIS 0.002 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00224 (14841) covalent geometry : angle 0.54204 (20227) SS BOND : bond 0.00429 ( 3) SS BOND : angle 1.14533 ( 6) hydrogen bonds : bond 0.03562 ( 582) hydrogen bonds : angle 3.80697 ( 1902) link_NAG-ASN : bond 0.00393 ( 5) link_NAG-ASN : angle 2.23884 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ASN cc_start: 0.8331 (m-40) cc_final: 0.7998 (m-40) REVERT: A 331 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8650 (mp) REVERT: D 187 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8182 (tpp) REVERT: D 320 SER cc_start: 0.9144 (t) cc_final: 0.8813 (m) REVERT: B 102 TYR cc_start: 0.7002 (t80) cc_final: 0.6630 (t80) REVERT: E 95 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7586 (tp40) REVERT: E 117 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8210 (mmm160) REVERT: E 127 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8058 (tm) REVERT: E 146 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8182 (p0) REVERT: E 158 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8148 (mp0) REVERT: E 213 MET cc_start: 0.8612 (mtp) cc_final: 0.8270 (mtt) REVERT: E 231 ASP cc_start: 0.8882 (t70) cc_final: 0.8491 (t0) outliers start: 26 outliers final: 12 residues processed: 181 average time/residue: 0.5993 time to fit residues: 118.5758 Evaluate side-chains 171 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 153 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN D 168 ASN D 250 GLN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.105851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.083516 restraints weight = 24177.819| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.89 r_work: 0.2984 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14849 Z= 0.115 Angle : 0.563 7.666 20248 Z= 0.280 Chirality : 0.042 0.240 2333 Planarity : 0.003 0.029 2456 Dihedral : 5.706 67.573 2969 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.55 % Allowed : 19.16 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1694 helix: 1.72 (0.22), residues: 544 sheet: 0.16 (0.26), residues: 423 loop : -0.54 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 195 TYR 0.026 0.001 TYR D 325 PHE 0.014 0.001 PHE C 319 TRP 0.010 0.001 TRP D 263 HIS 0.001 0.000 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00267 (14841) covalent geometry : angle 0.55964 (20227) SS BOND : bond 0.00528 ( 3) SS BOND : angle 1.31824 ( 6) hydrogen bonds : bond 0.03652 ( 582) hydrogen bonds : angle 3.82847 ( 1902) link_NAG-ASN : bond 0.00362 ( 5) link_NAG-ASN : angle 2.32422 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 131 ASN cc_start: 0.8358 (m-40) cc_final: 0.8084 (m-40) REVERT: A 331 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8672 (mp) REVERT: D 187 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8240 (tpp) REVERT: D 320 SER cc_start: 0.9132 (t) cc_final: 0.8785 (m) REVERT: B 102 TYR cc_start: 0.7023 (t80) cc_final: 0.6658 (t80) REVERT: E 81 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: E 95 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7436 (tp40) REVERT: E 117 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.8293 (mmm160) REVERT: E 127 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8063 (tm) REVERT: E 146 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8252 (p0) REVERT: E 158 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8165 (mp0) REVERT: E 166 ARG cc_start: 0.7793 (tpp80) cc_final: 0.7527 (tpp80) REVERT: E 231 ASP cc_start: 0.8892 (t70) cc_final: 0.8501 (t0) REVERT: E 238 GLU cc_start: 0.7265 (mp0) cc_final: 0.6901 (mp0) outliers start: 24 outliers final: 12 residues processed: 169 average time/residue: 0.5877 time to fit residues: 108.3788 Evaluate side-chains 158 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 143 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 0.0270 chunk 83 optimal weight: 3.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN D 168 ASN D 250 GLN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.108251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.086088 restraints weight = 24830.559| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.68 r_work: 0.2991 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14849 Z= 0.145 Angle : 0.591 7.682 20248 Z= 0.295 Chirality : 0.043 0.270 2333 Planarity : 0.003 0.031 2456 Dihedral : 5.900 67.756 2969 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.81 % Allowed : 19.29 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1694 helix: 1.68 (0.22), residues: 544 sheet: 0.13 (0.26), residues: 422 loop : -0.55 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 195 TYR 0.022 0.001 TYR D 325 PHE 0.015 0.001 PHE C 319 TRP 0.008 0.001 TRP E 331 HIS 0.003 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00344 (14841) covalent geometry : angle 0.58600 (20227) SS BOND : bond 0.00566 ( 3) SS BOND : angle 1.41709 ( 6) hydrogen bonds : bond 0.03954 ( 582) hydrogen bonds : angle 3.92625 ( 1902) link_NAG-ASN : bond 0.00348 ( 5) link_NAG-ASN : angle 2.63199 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.00 seconds wall clock time: 62 minutes 37.73 seconds (3757.73 seconds total)