Starting phenix.real_space_refine on Sun May 3 06:38:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zwl_74911/05_2026/9zwl_74911.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zwl_74911/05_2026/9zwl_74911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zwl_74911/05_2026/9zwl_74911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zwl_74911/05_2026/9zwl_74911.map" model { file = "/net/cci-nas-00/data/ceres_data/9zwl_74911/05_2026/9zwl_74911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zwl_74911/05_2026/9zwl_74911.cif" } resolution = 2.28 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= -0.001 sd= 0.039 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 5 5.49 5 S 61 5.16 5 C 7077 2.51 5 N 1837 2.21 5 O 2114 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-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11097 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "B" Number of atoms: 5060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 5060 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 26, 'TRANS': 654} Chain: "C" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1417 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 13, 'TRANS': 174} Chain: "D" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 216 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 81 Unusual residues: {' K': 1, '9Y0': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'9Y0': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.77, per 1000 atoms: 0.25 Number of scatterers: 11097 At special positions: 0 Unit cell: (135.78, 78.12, 132.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 61 16.00 P 5 15.00 O 2114 8.00 N 1837 7.00 C 7077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 191 " distance=2.03 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 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 511.4 milliseconds 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2648 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 11 sheets defined 65.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 39 through 51 removed outlier: 3.612A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 119 through 123 removed outlier: 3.515A pdb=" N THR A 123 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 132 Processing helix chain 'A' and resid 132 through 157 removed outlier: 3.754A pdb=" N GLN A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.869A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 248 through 275 removed outlier: 4.637A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.503A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 3.936A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 313 removed outlier: 4.262A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 4.172A pdb=" N VAL A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.740A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix removed outlier: 3.634A pdb=" N MET A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 398 removed outlier: 3.677A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 422 Processing helix chain 'A' and resid 422 through 437 Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.618A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 removed outlier: 3.994A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 509 removed outlier: 4.229A pdb=" N VAL A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.867A pdb=" N SER A 509 " --> pdb=" O GLY A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix removed outlier: 3.677A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'B' and resid 10 through 24 Processing helix chain 'B' and resid 26 through 32 removed outlier: 4.126A pdb=" N ARG B 32 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.866A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 95 removed outlier: 3.510A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 199 through 202 removed outlier: 3.591A pdb=" N ARG B 202 " --> pdb=" O PHE B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 202' Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.535A pdb=" N GLY B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 238 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.909A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 285 removed outlier: 4.871A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 297 removed outlier: 3.881A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 removed outlier: 3.539A pdb=" N ASP B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 361 removed outlier: 3.511A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 397 through 408 removed outlier: 3.521A pdb=" N ARG B 402 " --> pdb=" O VAL B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.906A pdb=" N ASP B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 453 through 463 removed outlier: 3.697A pdb=" N PHE B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.687A pdb=" N ILE B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.912A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 582 removed outlier: 3.505A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.669A pdb=" N LYS B 586 " --> pdb=" O ASN B 582 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.815A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 removed outlier: 4.028A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 657 through 679 Proline residue: B 665 - end of helix removed outlier: 3.549A pdb=" N LYS B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 20 Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.671A pdb=" N GLY C 40 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 108 removed outlier: 3.848A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.889A pdb=" N VAL C 121 " --> pdb=" O PRO C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.738A pdb=" N ILE C 171 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY C 172 " --> pdb=" O LYS C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 172' Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 109 removed outlier: 3.628A pdb=" N VAL B 121 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS B 108 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 134 removed outlier: 7.155A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 140 removed outlier: 3.512A pdb=" N ILE B 140 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR B 180 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 153 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 5.907A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU B 512 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 303 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 302 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL B 468 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 470 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR B 467 " --> pdb=" O ASP B 489 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU B 491 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N MET B 469 " --> pdb=" O LEU B 491 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 324 removed outlier: 4.151A pdb=" N GLN B 318 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA B 444 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE B 322 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL B 442 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N LEU B 440 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 433 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 445 " --> pdb=" O THR B 429 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 373 through 375 removed outlier: 4.083A pdb=" N THR B 373 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 388 " --> pdb=" O ARG B 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 373 through 375 removed outlier: 4.083A pdb=" N THR B 373 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 42 through 45 removed outlier: 3.720A pdb=" N GLY C 51 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU C 45 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 131 through 132 removed outlier: 3.537A pdb=" N ILE C 132 " --> pdb=" O VAL C 176 " (cutoff:3.500A) 654 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: 1.65 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1929 1.33 - 1.45: 2639 1.45 - 1.57: 6488 1.57 - 1.69: 9 1.69 - 1.81: 110 Bond restraints: 11175 Sorted by residual: bond pdb=" C ALA B 523 " pdb=" N PRO B 524 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.38e-02 5.25e+03 1.83e+00 bond pdb=" CB PRO B 524 " pdb=" CG PRO B 524 " ideal model delta sigma weight residual 1.492 1.542 -0.050 5.00e-02 4.00e+02 9.89e-01 bond pdb=" N PRO A 218 " pdb=" CA PRO A 218 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.90e-01 bond pdb=" CB LYS C 169 " pdb=" CG LYS C 169 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.40e-01 bond pdb=" CB MET B 206 " pdb=" CG MET B 206 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 7.20e-01 ... (remaining 11170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 15084 2.35 - 4.70: 89 4.70 - 7.05: 16 7.05 - 9.40: 0 9.40 - 11.75: 2 Bond angle restraints: 15191 Sorted by residual: angle pdb=" N VAL A 496 " pdb=" CA VAL A 496 " pdb=" C VAL A 496 " ideal model delta sigma weight residual 112.96 108.14 4.82 1.00e+00 1.00e+00 2.32e+01 angle pdb=" CB MET B 392 " pdb=" CG MET B 392 " pdb=" SD MET B 392 " ideal model delta sigma weight residual 112.70 124.45 -11.75 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CB MET B 206 " pdb=" CG MET B 206 " pdb=" SD MET B 206 " ideal model delta sigma weight residual 112.70 123.38 -10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CA MET B 206 " pdb=" CB MET B 206 " pdb=" CG MET B 206 " ideal model delta sigma weight residual 114.10 120.37 -6.27 2.00e+00 2.50e-01 9.84e+00 angle pdb=" N GLY B 99 " pdb=" CA GLY B 99 " pdb=" C GLY B 99 " ideal model delta sigma weight residual 115.32 111.32 4.00 1.31e+00 5.83e-01 9.33e+00 ... (remaining 15186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 6064 21.10 - 42.21: 463 42.21 - 63.31: 136 63.31 - 84.42: 21 84.42 - 105.52: 7 Dihedral angle restraints: 6691 sinusoidal: 2570 harmonic: 4121 Sorted by residual: dihedral pdb=" CB CYS B 142 " pdb=" SG CYS B 142 " pdb=" SG CYS B 191 " pdb=" CB CYS B 191 " ideal model delta sinusoidal sigma weight residual -86.00 -52.81 -33.19 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" C30 9Y0 D 101 " pdb=" C31 9Y0 D 101 " pdb=" C32 9Y0 D 101 " pdb=" C33 9Y0 D 101 " ideal model delta sinusoidal sigma weight residual -179.92 -74.40 -105.52 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" CA VAL A 372 " pdb=" C VAL A 372 " pdb=" N PHE A 373 " pdb=" CA PHE A 373 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 6688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1186 0.026 - 0.053: 360 0.053 - 0.079: 170 0.079 - 0.106: 78 0.106 - 0.132: 25 Chirality restraints: 1819 Sorted by residual: chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 34 " pdb=" N ILE A 34 " pdb=" C ILE A 34 " pdb=" CB ILE A 34 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA MET B 392 " pdb=" N MET B 392 " pdb=" C MET B 392 " pdb=" CB MET B 392 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 1816 not shown) Planarity restraints: 1916 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 523 " -0.052 5.00e-02 4.00e+02 7.77e-02 9.67e+00 pdb=" N PRO B 524 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 111 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO B 112 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 133 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO C 134 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 134 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 134 " -0.021 5.00e-02 4.00e+02 ... (remaining 1913 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 3385 2.82 - 3.40: 12545 3.40 - 3.98: 22971 3.98 - 4.56: 31744 4.56 - 5.14: 44542 Nonbonded interactions: 115187 Sorted by model distance: nonbonded pdb=" O SER B 341 " pdb=" OG SER B 341 " model vdw 2.239 3.040 nonbonded pdb=" O MET A 130 " pdb=" O HOH A 701 " model vdw 2.242 3.040 nonbonded pdb=" O GLN B 567 " pdb=" OG1 THR B 571 " model vdw 2.255 3.040 nonbonded pdb=" O LYS A 323 " pdb=" NH1 ARG C 68 " model vdw 2.308 3.120 nonbonded pdb=" OD1 ASN B 606 " pdb=" O HOH B 801 " model vdw 2.315 3.040 ... (remaining 115182 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.240 Find NCS groups from input model: 0.030 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.002 0.050 11176 Z= 0.091 Angle : 0.490 11.754 15193 Z= 0.265 Chirality : 0.036 0.132 1819 Planarity : 0.004 0.078 1916 Dihedral : 16.967 105.524 4040 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.49 % Allowed : 17.63 % Favored : 80.88 % 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: 0.63 (0.22), residues: 1447 helix: 1.09 (0.18), residues: 848 sheet: -0.80 (0.58), residues: 91 loop : -0.37 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 213 TYR 0.013 0.001 TYR A 381 PHE 0.006 0.001 PHE B 412 TRP 0.008 0.001 TRP A 176 HIS 0.001 0.000 HIS B 563 Details of bonding type rmsd covalent geometry : bond 0.00180 (11175) covalent geometry : angle 0.48953 (15191) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.41596 ( 2) hydrogen bonds : bond 0.23183 ( 652) hydrogen bonds : angle 7.27867 ( 1902) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.8769 (mtt) cc_final: 0.8546 (mtm) REVERT: B 392 MET cc_start: 0.3535 (ppp) cc_final: 0.3258 (pmm) outliers start: 17 outliers final: 13 residues processed: 138 average time/residue: 0.5880 time to fit residues: 87.4208 Evaluate side-chains 136 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.167294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.094364 restraints weight = 10429.740| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.74 r_work: 0.2884 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11176 Z= 0.155 Angle : 0.553 6.494 15193 Z= 0.294 Chirality : 0.042 0.177 1819 Planarity : 0.005 0.067 1916 Dihedral : 10.801 109.546 1667 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.81 % Allowed : 16.05 % Favored : 81.14 % 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: 0.91 (0.22), residues: 1447 helix: 1.40 (0.18), residues: 853 sheet: -0.71 (0.57), residues: 91 loop : -0.42 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 213 TYR 0.024 0.002 TYR A 381 PHE 0.016 0.002 PHE B 578 TRP 0.012 0.001 TRP B 71 HIS 0.002 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00341 (11175) covalent geometry : angle 0.55333 (15191) SS BOND : bond 0.00137 ( 1) SS BOND : angle 0.55092 ( 2) hydrogen bonds : bond 0.05854 ( 652) hydrogen bonds : angle 4.89850 ( 1902) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ARG cc_start: 0.8052 (ttp-110) cc_final: 0.7812 (ttm110) REVERT: A 412 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7539 (ttt180) REVERT: B 191 CYS cc_start: 0.0725 (OUTLIER) cc_final: 0.0089 (t) REVERT: B 212 ARG cc_start: 0.5728 (OUTLIER) cc_final: 0.4783 (tmm160) REVERT: B 491 LEU cc_start: 0.6723 (tp) cc_final: 0.6520 (tt) REVERT: B 539 THR cc_start: 0.5497 (OUTLIER) cc_final: 0.5143 (p) outliers start: 32 outliers final: 14 residues processed: 153 average time/residue: 0.5936 time to fit residues: 97.7692 Evaluate side-chains 146 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 118 optimal weight: 0.8980 chunk 3 optimal weight: 0.0170 chunk 100 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 192 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.168408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.096028 restraints weight = 10594.035| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.91 r_work: 0.2901 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11176 Z= 0.119 Angle : 0.491 7.460 15193 Z= 0.258 Chirality : 0.039 0.168 1819 Planarity : 0.004 0.053 1916 Dihedral : 10.523 110.968 1656 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.37 % Allowed : 15.88 % Favored : 81.75 % 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: 1.01 (0.22), residues: 1447 helix: 1.53 (0.18), residues: 869 sheet: -0.76 (0.56), residues: 93 loop : -0.54 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.021 0.001 TYR A 381 PHE 0.012 0.001 PHE B 578 TRP 0.011 0.001 TRP B 71 HIS 0.002 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00246 (11175) covalent geometry : angle 0.49051 (15191) SS BOND : bond 0.00132 ( 1) SS BOND : angle 0.47408 ( 2) hydrogen bonds : bond 0.05029 ( 652) hydrogen bonds : angle 4.56780 ( 1902) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7576 (ttt180) REVERT: B 191 CYS cc_start: 0.0534 (OUTLIER) cc_final: -0.0178 (t) REVERT: B 212 ARG cc_start: 0.5705 (OUTLIER) cc_final: 0.4808 (tmm160) REVERT: B 282 MET cc_start: 0.7985 (mmm) cc_final: 0.7519 (tpt) REVERT: B 491 LEU cc_start: 0.6679 (tp) cc_final: 0.6447 (tt) REVERT: B 539 THR cc_start: 0.5526 (OUTLIER) cc_final: 0.5186 (p) REVERT: B 568 MET cc_start: 0.8599 (mtm) cc_final: 0.8343 (mtm) outliers start: 27 outliers final: 12 residues processed: 154 average time/residue: 0.6238 time to fit residues: 103.2878 Evaluate side-chains 143 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 101 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 140 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 192 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN B 528 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.093171 restraints weight = 10514.397| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.68 r_work: 0.2869 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11176 Z= 0.142 Angle : 0.516 7.813 15193 Z= 0.271 Chirality : 0.041 0.169 1819 Planarity : 0.004 0.064 1916 Dihedral : 10.587 112.455 1655 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.37 % Allowed : 15.79 % Favored : 81.84 % 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: 0.99 (0.22), residues: 1447 helix: 1.52 (0.17), residues: 867 sheet: -0.88 (0.52), residues: 105 loop : -0.50 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 143 TYR 0.024 0.002 TYR A 381 PHE 0.014 0.001 PHE B 578 TRP 0.011 0.001 TRP B 71 HIS 0.002 0.001 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00311 (11175) covalent geometry : angle 0.51574 (15191) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.45112 ( 2) hydrogen bonds : bond 0.05291 ( 652) hydrogen bonds : angle 4.56093 ( 1902) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7589 (ttt180) REVERT: B 191 CYS cc_start: 0.0186 (OUTLIER) cc_final: -0.0347 (t) REVERT: B 212 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.4938 (tmm160) REVERT: B 282 MET cc_start: 0.8127 (mmm) cc_final: 0.7796 (tpt) REVERT: B 491 LEU cc_start: 0.6760 (tp) cc_final: 0.6537 (tt) REVERT: B 528 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7231 (tm-30) REVERT: B 539 THR cc_start: 0.5622 (OUTLIER) cc_final: 0.5292 (p) outliers start: 27 outliers final: 16 residues processed: 151 average time/residue: 0.5870 time to fit residues: 95.4820 Evaluate side-chains 148 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 126 optimal weight: 0.0370 chunk 18 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 136 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 130 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.168048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.095460 restraints weight = 10531.550| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.67 r_work: 0.2909 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11176 Z= 0.111 Angle : 0.477 7.509 15193 Z= 0.250 Chirality : 0.039 0.168 1819 Planarity : 0.004 0.046 1916 Dihedral : 10.426 112.751 1655 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.93 % Rotamer: Outliers : 2.28 % Allowed : 16.23 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.22), residues: 1447 helix: 1.69 (0.17), residues: 869 sheet: -0.95 (0.51), residues: 105 loop : -0.47 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 382 TYR 0.022 0.001 TYR A 381 PHE 0.011 0.001 PHE B 578 TRP 0.011 0.001 TRP B 71 HIS 0.001 0.000 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00228 (11175) covalent geometry : angle 0.47684 (15191) SS BOND : bond 0.00123 ( 1) SS BOND : angle 0.43273 ( 2) hydrogen bonds : bond 0.04590 ( 652) hydrogen bonds : angle 4.39105 ( 1902) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 CYS cc_start: 0.0123 (OUTLIER) cc_final: -0.0422 (t) REVERT: B 212 ARG cc_start: 0.5758 (OUTLIER) cc_final: 0.4896 (tmm160) REVERT: B 491 LEU cc_start: 0.6707 (tp) cc_final: 0.6449 (tt) REVERT: B 539 THR cc_start: 0.5644 (OUTLIER) cc_final: 0.5317 (p) outliers start: 26 outliers final: 16 residues processed: 151 average time/residue: 0.6058 time to fit residues: 98.3831 Evaluate side-chains 145 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 138 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 100 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 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 114 ASN A 192 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN B 528 GLN C 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.165835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.093537 restraints weight = 10535.052| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.05 r_work: 0.2826 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11176 Z= 0.154 Angle : 0.521 7.681 15193 Z= 0.274 Chirality : 0.041 0.169 1819 Planarity : 0.005 0.075 1916 Dihedral : 10.590 114.373 1655 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.94 % Favored : 98.00 % Rotamer: Outliers : 2.37 % Allowed : 15.88 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.22), residues: 1447 helix: 1.55 (0.17), residues: 867 sheet: -0.94 (0.52), residues: 105 loop : -0.53 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 504 TYR 0.025 0.002 TYR A 381 PHE 0.014 0.001 PHE B 578 TRP 0.010 0.001 TRP B 71 HIS 0.002 0.000 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00345 (11175) covalent geometry : angle 0.52053 (15191) SS BOND : bond 0.00167 ( 1) SS BOND : angle 0.53458 ( 2) hydrogen bonds : bond 0.05374 ( 652) hydrogen bonds : angle 4.51529 ( 1902) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7697 (ttt180) REVERT: B 191 CYS cc_start: 0.0221 (OUTLIER) cc_final: -0.0361 (t) REVERT: B 212 ARG cc_start: 0.5803 (OUTLIER) cc_final: 0.4956 (tmm160) REVERT: B 491 LEU cc_start: 0.6748 (tp) cc_final: 0.6502 (tt) REVERT: B 528 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: B 539 THR cc_start: 0.5682 (OUTLIER) cc_final: 0.5360 (p) outliers start: 27 outliers final: 17 residues processed: 147 average time/residue: 0.6027 time to fit residues: 95.4757 Evaluate side-chains 147 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 118 optimal weight: 0.0040 chunk 76 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.166178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.090279 restraints weight = 10451.709| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.49 r_work: 0.2864 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11176 Z= 0.145 Angle : 0.521 9.733 15193 Z= 0.272 Chirality : 0.041 0.164 1819 Planarity : 0.004 0.064 1916 Dihedral : 10.488 114.789 1651 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.00 % Favored : 97.93 % Rotamer: Outliers : 2.46 % Allowed : 16.58 % Favored : 80.96 % 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: 1.01 (0.22), residues: 1447 helix: 1.56 (0.17), residues: 867 sheet: -0.97 (0.51), residues: 107 loop : -0.51 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 326 TYR 0.024 0.002 TYR A 381 PHE 0.013 0.001 PHE B 578 TRP 0.010 0.001 TRP B 71 HIS 0.002 0.000 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00322 (11175) covalent geometry : angle 0.52055 (15191) SS BOND : bond 0.00218 ( 1) SS BOND : angle 0.73062 ( 2) hydrogen bonds : bond 0.05198 ( 652) hydrogen bonds : angle 4.47829 ( 1902) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 412 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7672 (ttt180) REVERT: B 191 CYS cc_start: 0.0352 (OUTLIER) cc_final: -0.0239 (t) REVERT: B 212 ARG cc_start: 0.5815 (OUTLIER) cc_final: 0.4976 (tmm160) REVERT: B 491 LEU cc_start: 0.6736 (tp) cc_final: 0.6490 (tt) REVERT: B 539 THR cc_start: 0.5705 (OUTLIER) cc_final: 0.5384 (p) outliers start: 28 outliers final: 16 residues processed: 151 average time/residue: 0.5697 time to fit residues: 92.8564 Evaluate side-chains 145 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 67 optimal weight: 0.0370 chunk 122 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.093936 restraints weight = 10428.218| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.84 r_work: 0.2866 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11176 Z= 0.135 Angle : 0.507 7.575 15193 Z= 0.266 Chirality : 0.040 0.158 1819 Planarity : 0.004 0.055 1916 Dihedral : 10.343 115.680 1647 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 2.46 % Allowed : 16.67 % Favored : 80.88 % 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: 1.03 (0.22), residues: 1447 helix: 1.57 (0.17), residues: 867 sheet: -0.94 (0.52), residues: 106 loop : -0.50 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 326 TYR 0.024 0.002 TYR A 381 PHE 0.012 0.001 PHE B 578 TRP 0.011 0.001 TRP B 71 HIS 0.002 0.000 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00296 (11175) covalent geometry : angle 0.50711 (15191) SS BOND : bond 0.00168 ( 1) SS BOND : angle 0.60128 ( 2) hydrogen bonds : bond 0.05031 ( 652) hydrogen bonds : angle 4.43305 ( 1902) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 410 ASP cc_start: 0.7846 (p0) cc_final: 0.7557 (p0) REVERT: A 412 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7698 (ttt180) REVERT: B 131 ILE cc_start: -0.0912 (OUTLIER) cc_final: -0.1131 (mm) REVERT: B 191 CYS cc_start: 0.0232 (OUTLIER) cc_final: -0.0332 (t) REVERT: B 212 ARG cc_start: 0.5807 (OUTLIER) cc_final: 0.4938 (tmm160) REVERT: B 491 LEU cc_start: 0.6715 (tp) cc_final: 0.6465 (tt) REVERT: B 539 THR cc_start: 0.5729 (OUTLIER) cc_final: 0.5411 (p) outliers start: 28 outliers final: 17 residues processed: 150 average time/residue: 0.6245 time to fit residues: 100.9731 Evaluate side-chains 149 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 80 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 118 optimal weight: 0.0770 chunk 59 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 104 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 chunk 54 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.168795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.095198 restraints weight = 10472.693| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.43 r_work: 0.2929 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11176 Z= 0.107 Angle : 0.487 8.840 15193 Z= 0.253 Chirality : 0.039 0.157 1819 Planarity : 0.004 0.046 1916 Dihedral : 10.079 116.425 1647 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.94 % Favored : 98.00 % Rotamer: Outliers : 1.84 % Allowed : 17.11 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.28 (0.22), residues: 1447 helix: 1.77 (0.18), residues: 874 sheet: -0.92 (0.52), residues: 106 loop : -0.42 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 365 TYR 0.020 0.001 TYR A 381 PHE 0.010 0.001 PHE A 109 TRP 0.012 0.001 TRP B 71 HIS 0.002 0.000 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00218 (11175) covalent geometry : angle 0.48721 (15191) SS BOND : bond 0.00138 ( 1) SS BOND : angle 0.56654 ( 2) hydrogen bonds : bond 0.04253 ( 652) hydrogen bonds : angle 4.28444 ( 1902) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: B 191 CYS cc_start: 0.0252 (OUTLIER) cc_final: -0.0299 (t) REVERT: B 212 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.5020 (tmm160) REVERT: B 491 LEU cc_start: 0.6740 (tp) cc_final: 0.6476 (tt) REVERT: B 539 THR cc_start: 0.5680 (OUTLIER) cc_final: 0.5370 (p) REVERT: B 552 ASP cc_start: 0.7203 (m-30) cc_final: 0.6552 (t0) outliers start: 21 outliers final: 13 residues processed: 148 average time/residue: 0.6080 time to fit residues: 97.0874 Evaluate side-chains 142 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 90 optimal weight: 20.0000 chunk 120 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 chunk 21 optimal weight: 0.0470 chunk 35 optimal weight: 3.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.167852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.093487 restraints weight = 10528.340| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.46 r_work: 0.2904 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11176 Z= 0.115 Angle : 0.493 7.568 15193 Z= 0.256 Chirality : 0.039 0.155 1819 Planarity : 0.004 0.046 1916 Dihedral : 10.002 117.894 1646 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.07 % Favored : 97.86 % Rotamer: Outliers : 1.67 % Allowed : 17.02 % Favored : 81.32 % 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: 1.25 (0.22), residues: 1447 helix: 1.78 (0.18), residues: 867 sheet: -0.85 (0.52), residues: 107 loop : -0.49 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 365 TYR 0.023 0.001 TYR A 381 PHE 0.011 0.001 PHE A 494 TRP 0.011 0.001 TRP B 71 HIS 0.002 0.000 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00243 (11175) covalent geometry : angle 0.49272 (15191) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.60628 ( 2) hydrogen bonds : bond 0.04552 ( 652) hydrogen bonds : angle 4.30228 ( 1902) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2894 Ramachandran restraints generated. 1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: B 191 CYS cc_start: -0.0125 (OUTLIER) cc_final: -0.0538 (t) REVERT: B 212 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5027 (tmm160) REVERT: B 491 LEU cc_start: 0.6817 (tp) cc_final: 0.6563 (tt) REVERT: B 539 THR cc_start: 0.5789 (OUTLIER) cc_final: 0.5486 (p) REVERT: B 552 ASP cc_start: 0.7218 (m-30) cc_final: 0.6573 (t0) outliers start: 19 outliers final: 13 residues processed: 147 average time/residue: 0.6174 time to fit residues: 97.6576 Evaluate side-chains 142 residues out of total 1140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain B residue 191 CYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 317 ARG Chi-restraints excluded: chain B residue 352 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 41 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 126 optimal weight: 0.0980 chunk 89 optimal weight: 20.0000 chunk 132 optimal weight: 0.5980 chunk 90 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 GLN B 528 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.167948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094152 restraints weight = 10552.131| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.44 r_work: 0.2905 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11176 Z= 0.115 Angle : 0.493 8.236 15193 Z= 0.256 Chirality : 0.039 0.155 1819 Planarity : 0.004 0.046 1916 Dihedral : 9.957 118.420 1646 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.79 % Rotamer: Outliers : 1.58 % Allowed : 17.19 % Favored : 81.23 % 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: 1.26 (0.22), residues: 1447 helix: 1.79 (0.18), residues: 866 sheet: -0.69 (0.56), residues: 95 loop : -0.53 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 365 TYR 0.022 0.001 TYR A 381 PHE 0.011 0.001 PHE A 494 TRP 0.011 0.001 TRP B 71 HIS 0.001 0.000 HIS A 523 Details of bonding type rmsd covalent geometry : bond 0.00242 (11175) covalent geometry : angle 0.49273 (15191) SS BOND : bond 0.00166 ( 1) SS BOND : angle 0.61825 ( 2) hydrogen bonds : bond 0.04523 ( 652) hydrogen bonds : angle 4.28094 ( 1902) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5636.76 seconds wall clock time: 96 minutes 21.30 seconds (5781.30 seconds total)