Starting phenix.real_space_refine on Mon Aug 25 23:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5y5y_6811/08_2025/5y5y_6811.cif Found real_map, /net/cci-nas-00/data/ceres_data/5y5y_6811/08_2025/5y5y_6811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5y5y_6811/08_2025/5y5y_6811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5y5y_6811/08_2025/5y5y_6811.map" model { file = "/net/cci-nas-00/data/ceres_data/5y5y_6811/08_2025/5y5y_6811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5y5y_6811/08_2025/5y5y_6811.cif" } resolution = 4.7 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= 0.030 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 105 5.16 5 C 20371 2.51 5 N 5636 2.21 5 O 6043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 414 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32159 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "B" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "C" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4472 Classifications: {'peptide': 577} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 541} Chain: "D" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain: "E" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain: "F" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3596 Classifications: {'peptide': 459} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 432} Chain: "G" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain: "H" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 758 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 451 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1043 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 5, 'GLU:plan': 9, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "K" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 451 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1043 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 5, 'GLU:plan': 9, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "M" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2513 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 12, 'TRANS': 307} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.36, per 1000 atoms: 0.23 Number of scatterers: 32159 At special positions: 0 Unit cell: (147, 148.4, 205.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 4 15.00 O 6043 8.00 N 5636 7.00 C 20371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M 267 " - pdb=" SG CYS M 322 " 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 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7624 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 44 sheets defined 46.2% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.671A pdb=" N ILE A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.603A pdb=" N ASP A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 272 removed outlier: 3.712A pdb=" N LEU A 272 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 297 through 317 removed outlier: 4.733A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 removed outlier: 3.703A pdb=" N ILE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 355 through 363 removed outlier: 4.046A pdb=" N ALA A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 411 through 417 removed outlier: 3.651A pdb=" N PHE A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 411 through 417' Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 461 removed outlier: 3.946A pdb=" N ILE A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 removed outlier: 4.518A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 removed outlier: 3.612A pdb=" N VAL A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 533 removed outlier: 3.575A pdb=" N LYS A 517 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 520 " --> pdb=" O MET A 516 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 541 removed outlier: 3.740A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 removed outlier: 4.409A pdb=" N GLU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.532A pdb=" N LYS A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLN A 571 " --> pdb=" O MET A 567 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 572 " --> pdb=" O LYS A 568 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 209 through 216 removed outlier: 3.733A pdb=" N LEU B 215 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 245 removed outlier: 3.971A pdb=" N GLN B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 272 removed outlier: 3.550A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.679A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 4.393A pdb=" N GLU B 332 " --> pdb=" O SER B 328 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 333 " --> pdb=" O ARG B 329 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 334 " --> pdb=" O TRP B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 393 through 403 removed outlier: 3.878A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 401 " --> pdb=" O GLN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.983A pdb=" N ARG B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.861A pdb=" N GLY B 426 " --> pdb=" O ASN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 removed outlier: 4.172A pdb=" N LEU B 435 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 466 removed outlier: 3.650A pdb=" N ARG B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 457 " --> pdb=" O ALA B 453 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 493 removed outlier: 3.571A pdb=" N LEU B 482 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 522 removed outlier: 4.080A pdb=" N GLY B 514 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.573A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.616A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 574 removed outlier: 3.559A pdb=" N ALA B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 569 " --> pdb=" O GLU B 565 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY B 572 " --> pdb=" O LYS B 568 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.662A pdb=" N ILE C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 244 removed outlier: 3.795A pdb=" N GLN C 238 " --> pdb=" O LYS C 234 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLN C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 269 removed outlier: 5.350A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE C 269 " --> pdb=" O VAL C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 280 through 283 removed outlier: 3.543A pdb=" N HIS C 283 " --> pdb=" O PRO C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 297 through 316 removed outlier: 3.971A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY C 306 " --> pdb=" O SER C 302 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 308 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.419A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 364 removed outlier: 3.988A pdb=" N ARG C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA C 360 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 398 removed outlier: 3.902A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.846A pdb=" N ALA C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 410 through 416' Processing helix chain 'C' and resid 435 through 443 removed outlier: 3.751A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 471 removed outlier: 3.636A pdb=" N SER C 455 " --> pdb=" O ARG C 451 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU C 457 " --> pdb=" O ALA C 453 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY C 463 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 493 removed outlier: 3.833A pdb=" N ARG C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU C 482 " --> pdb=" O ASP C 478 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 484 " --> pdb=" O GLU C 480 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG C 491 " --> pdb=" O GLY C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 533 removed outlier: 3.562A pdb=" N MET C 518 " --> pdb=" O GLY C 514 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 519 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 520 " --> pdb=" O MET C 516 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 533 " --> pdb=" O ALA C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 540 removed outlier: 3.518A pdb=" N ILE C 539 " --> pdb=" O ILE C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 555 through 558 Processing helix chain 'C' and resid 559 through 574 removed outlier: 3.729A pdb=" N GLU C 564 " --> pdb=" O PRO C 560 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU C 565 " --> pdb=" O ALA C 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 141 removed outlier: 3.549A pdb=" N MET D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 4.015A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE D 167 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA D 171 " --> pdb=" O ILE D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 185 removed outlier: 3.716A pdb=" N GLU D 184 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU D 185 " --> pdb=" O GLU D 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 181 through 185' Processing helix chain 'D' and resid 199 through 212 removed outlier: 3.860A pdb=" N ILE D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 227 through 250 removed outlier: 3.881A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 233 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.657A pdb=" N ALA D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 245 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU D 248 " --> pdb=" O TYR D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 275 removed outlier: 3.575A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 Processing helix chain 'D' and resid 323 through 333 removed outlier: 4.217A pdb=" N THR D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 347 removed outlier: 3.737A pdb=" N HIS D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.501A pdb=" N ASP D 380 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE D 392 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.592A pdb=" N TYR D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 412 " --> pdb=" O ASP D 408 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN D 413 " --> pdb=" O ARG D 409 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA D 415 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.602A pdb=" N LEU D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 438 " --> pdb=" O GLU D 434 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 439 " --> pdb=" O SER D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 460 removed outlier: 3.923A pdb=" N ILE D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 142 removed outlier: 3.560A pdb=" N ASP E 139 " --> pdb=" O ILE E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 170 removed outlier: 3.697A pdb=" N ARG E 169 " --> pdb=" O ALA E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 185 removed outlier: 3.788A pdb=" N GLU E 184 " --> pdb=" O GLY E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 205 removed outlier: 3.930A pdb=" N PHE E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE E 205 " --> pdb=" O LEU E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 210 removed outlier: 3.776A pdb=" N GLU E 209 " --> pdb=" O ILE E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 233 through 248 removed outlier: 3.973A pdb=" N THR E 240 " --> pdb=" O ARG E 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 272 removed outlier: 4.080A pdb=" N GLU E 269 " --> pdb=" O GLU E 265 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE E 270 " --> pdb=" O ALA E 266 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY E 271 " --> pdb=" O LEU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 295 removed outlier: 3.825A pdb=" N ASP E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR E 293 " --> pdb=" O THR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 333 removed outlier: 3.710A pdb=" N ASP E 327 " --> pdb=" O HIS E 323 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 330 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 5.042A pdb=" N ASP E 380 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN E 381 " --> pdb=" O GLN E 377 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE E 392 " --> pdb=" O ASN E 388 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 423 removed outlier: 3.504A pdb=" N PHE E 422 " --> pdb=" O PHE E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.564A pdb=" N ALA E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 removed outlier: 3.951A pdb=" N GLY E 460 " --> pdb=" O LYS E 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 4.206A pdb=" N ILE F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 210 removed outlier: 3.863A pdb=" N GLU F 207 " --> pdb=" O TYR F 203 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE F 208 " --> pdb=" O PHE F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.623A pdb=" N GLU F 230 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG F 231 " --> pdb=" O THR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 248 removed outlier: 3.613A pdb=" N MET F 237 " --> pdb=" O LEU F 233 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU F 248 " --> pdb=" O TYR F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 275 removed outlier: 3.626A pdb=" N CYS F 264 " --> pdb=" O MET F 260 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU F 265 " --> pdb=" O THR F 261 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 271 " --> pdb=" O LEU F 267 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA F 272 " --> pdb=" O ARG F 268 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 291 removed outlier: 3.516A pdb=" N ASP F 290 " --> pdb=" O TYR F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 297 removed outlier: 4.064A pdb=" N ARG F 297 " --> pdb=" O THR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 removed outlier: 3.717A pdb=" N ASP F 327 " --> pdb=" O HIS F 323 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR F 331 " --> pdb=" O ASP F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 Processing helix chain 'F' and resid 375 through 400 removed outlier: 3.916A pdb=" N ASP F 380 " --> pdb=" O LYS F 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE F 392 " --> pdb=" O ASN F 388 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG F 393 " --> pdb=" O GLY F 389 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS F 394 " --> pdb=" O VAL F 390 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 395 " --> pdb=" O ASP F 391 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 421 removed outlier: 4.079A pdb=" N TYR F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP F 416 " --> pdb=" O LEU F 412 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA F 417 " --> pdb=" O GLN F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 446 removed outlier: 3.656A pdb=" N LEU F 436 " --> pdb=" O ILE F 432 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE F 438 " --> pdb=" O GLU F 434 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 462 removed outlier: 3.518A pdb=" N GLY F 460 " --> pdb=" O LYS F 456 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 462 " --> pdb=" O HIS F 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 46 removed outlier: 3.985A pdb=" N GLN G 13 " --> pdb=" O MET G 9 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU G 18 " --> pdb=" O ARG G 14 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS G 29 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ALA G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE G 40 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU G 42 " --> pdb=" O GLU G 38 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU G 45 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 64 removed outlier: 3.613A pdb=" N ALA G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN G 55 " --> pdb=" O LYS G 51 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 79 Processing helix chain 'G' and resid 120 through 132 removed outlier: 4.262A pdb=" N LEU G 124 " --> pdb=" O PRO G 120 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE G 130 " --> pdb=" O ALA G 126 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 166 removed outlier: 3.675A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N THR G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 206 removed outlier: 3.598A pdb=" N ARG G 177 " --> pdb=" O ARG G 173 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP G 190 " --> pdb=" O ARG G 186 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG G 196 " --> pdb=" O PHE G 192 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE G 197 " --> pdb=" O ARG G 193 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS G 198 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 16 removed outlier: 6.120A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 3.671A pdb=" N THR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG H 39 " --> pdb=" O THR H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 64 Processing helix chain 'H' and resid 82 through 94 removed outlier: 3.756A pdb=" N VAL H 86 " --> pdb=" O GLN H 82 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET H 90 " --> pdb=" O VAL H 86 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL H 94 " --> pdb=" O MET H 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 105 removed outlier: 3.638A pdb=" N LYS I 65 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA I 86 " --> pdb=" O GLU I 82 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 119 removed outlier: 3.801A pdb=" N VAL I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 92 removed outlier: 4.110A pdb=" N ALA J 40 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN J 43 " --> pdb=" O LYS J 39 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU J 49 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA J 56 " --> pdb=" O GLN J 52 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA J 60 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.932A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU J 107 " --> pdb=" O VAL J 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 131 removed outlier: 4.472A pdb=" N HIS J 130 " --> pdb=" O GLU J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 137 Processing helix chain 'J' and resid 167 through 178 removed outlier: 3.593A pdb=" N ARG J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 187 Processing helix chain 'K' and resid 61 through 104 removed outlier: 3.935A pdb=" N GLU K 77 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 119 removed outlier: 4.067A pdb=" N VAL K 111 " --> pdb=" O LEU K 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 93 removed outlier: 4.368A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU L 46 " --> pdb=" O LEU L 42 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU L 49 " --> pdb=" O ARG L 45 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA L 56 " --> pdb=" O GLN L 52 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA L 63 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA L 93 " --> pdb=" O GLU L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 removed outlier: 3.775A pdb=" N VAL L 103 " --> pdb=" O GLU L 99 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG L 105 " --> pdb=" O PRO L 101 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU L 107 " --> pdb=" O VAL L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 131 Processing helix chain 'L' and resid 132 through 137 Processing helix chain 'L' and resid 167 through 179 removed outlier: 3.670A pdb=" N MET L 171 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG L 173 " --> pdb=" O ALA L 169 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET L 178 " --> pdb=" O ALA L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 187 Processing helix chain 'M' and resid 5 through 16 removed outlier: 3.626A pdb=" N ALA M 10 " --> pdb=" O ALA M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 19 No H-bonds generated for 'chain 'M' and resid 17 through 19' Processing helix chain 'M' and resid 21 through 29 removed outlier: 3.813A pdb=" N PHE M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU M 29 " --> pdb=" O PHE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 42 Processing helix chain 'M' and resid 43 through 49 removed outlier: 3.708A pdb=" N GLY M 47 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 69 removed outlier: 3.548A pdb=" N LYS M 67 " --> pdb=" O ARG M 63 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU M 68 " --> pdb=" O THR M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 75 Processing helix chain 'M' and resid 78 through 106 removed outlier: 3.500A pdb=" N LEU M 87 " --> pdb=" O ALA M 83 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN M 91 " --> pdb=" O LEU M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 108 through 112 removed outlier: 3.848A pdb=" N GLU M 111 " --> pdb=" O PRO M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 129 Processing helix chain 'M' and resid 132 through 142 removed outlier: 3.973A pdb=" N VAL M 142 " --> pdb=" O GLN M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 156 removed outlier: 4.111A pdb=" N ARG M 149 " --> pdb=" O HIS M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 182 removed outlier: 3.754A pdb=" N LYS M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY M 182 " --> pdb=" O LYS M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 207 Processing helix chain 'M' and resid 213 through 217 Processing helix chain 'M' and resid 226 through 235 Processing helix chain 'M' and resid 237 through 243 removed outlier: 4.065A pdb=" N VAL M 240 " --> pdb=" O ASP M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 253 removed outlier: 3.786A pdb=" N LEU M 252 " --> pdb=" O PHE M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 275 removed outlier: 3.695A pdb=" N LYS M 275 " --> pdb=" O LYS M 271 " (cutoff:3.500A) Processing helix chain 'M' and resid 283 through 310 Processing helix chain 'M' and resid 313 through 318 removed outlier: 4.216A pdb=" N GLU M 318 " --> pdb=" O ALA M 314 " (cutoff:3.500A) Processing helix chain 'M' and resid 319 through 321 No H-bonds generated for 'chain 'M' and resid 319 through 321' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 9 removed outlier: 5.775A pdb=" N ILE A 6 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LYS A 17 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 29 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE A 2 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75 removed outlier: 3.805A pdb=" N VAL A 73 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP A 187 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 75 " --> pdb=" O HIS A 185 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 118 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.512A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL A 160 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N VAL A 172 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 140 Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 198 removed outlier: 6.092A pdb=" N VAL A 249 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET A 323 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 251 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASP A 325 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 253 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 225 through 226 Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 30 removed outlier: 4.631A pdb=" N ILE B 2 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE B 15 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE B 9 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AB2, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.607A pdb=" N THR B 137 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 157 through 160 removed outlier: 3.845A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 285 through 287 removed outlier: 7.171A pdb=" N VAL B 320 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N VAL B 381 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 322 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ALA B 383 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA B 324 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 376 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 368 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 285 through 287 removed outlier: 7.171A pdb=" N VAL B 320 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N VAL B 381 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 322 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ALA B 383 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ALA B 324 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 13 through 17 removed outlier: 6.899A pdb=" N ALA C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE C 9 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE C 15 " --> pdb=" O GLN C 7 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 50 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'C' and resid 46 through 50 removed outlier: 4.065A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE F 20 " --> pdb=" O THR F 12 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE F 14 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU F 18 " --> pdb=" O ILE F 14 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL F 21 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 72 through 75 removed outlier: 4.390A pdb=" N VAL C 73 " --> pdb=" O TRP C 187 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP C 187 " --> pdb=" O VAL C 73 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 143 through 148 removed outlier: 7.027A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 156 through 160 removed outlier: 4.159A pdb=" N ARG C 156 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N VAL C 172 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 173 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 197 through 198 removed outlier: 3.707A pdb=" N GLY C 376 " --> pdb=" O VAL C 368 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C 320 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 249 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 204 through 205 removed outlier: 4.181A pdb=" N PHE C 205 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL C 218 " --> pdb=" O PHE C 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 225 through 226 Processing sheet with id=AC6, first strand: chain 'C' and resid 406 through 407 removed outlier: 3.707A pdb=" N TYR C 428 " --> pdb=" O PHE C 406 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 14 through 15 removed outlier: 3.725A pdb=" N GLN D 46 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA D 31 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.925A pdb=" N LEU D 82 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AD1, first strand: chain 'D' and resid 124 through 125 removed outlier: 4.181A pdb=" N VAL D 300 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 152 through 154 Processing sheet with id=AD3, first strand: chain 'D' and resid 217 through 218 removed outlier: 8.016A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 217 through 218 Processing sheet with id=AD5, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.563A pdb=" N PHE E 20 " --> pdb=" O THR E 12 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 42 through 45 removed outlier: 6.767A pdb=" N ILE E 32 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 36 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER E 72 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 81 through 84 removed outlier: 4.337A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AD9, first strand: chain 'E' and resid 152 through 154 removed outlier: 6.135A pdb=" N ILE E 152 " --> pdb=" O LEU E 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 187 through 189 Processing sheet with id=AE2, first strand: chain 'F' and resid 44 through 46 removed outlier: 3.540A pdb=" N SER F 74 " --> pdb=" O ASP F 34 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.513A pdb=" N VAL F 84 " --> pdb=" O LYS F 110 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AE5, first strand: chain 'F' and resid 313 through 314 removed outlier: 6.146A pdb=" N ILE F 152 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 217 through 219 removed outlier: 3.573A pdb=" N VAL F 218 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL F 253 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE F 311 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL F 255 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 89 through 92 Processing sheet with id=AE8, first strand: chain 'J' and resid 120 through 122 1222 hydrogen bonds defined for protein. 3453 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: 6.76 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6487 1.33 - 1.46: 12047 1.46 - 1.59: 14009 1.59 - 1.72: 3 1.72 - 1.86: 196 Bond restraints: 32742 Sorted by residual: bond pdb=" CA LEU A 358 " pdb=" C LEU A 358 " ideal model delta sigma weight residual 1.525 1.392 0.133 1.02e-02 9.61e+03 1.69e+02 bond pdb=" CA GLN B 477 " pdb=" C GLN B 477 " ideal model delta sigma weight residual 1.533 1.466 0.067 5.60e-03 3.19e+04 1.42e+02 bond pdb=" CA GLU C 449 " pdb=" C GLU C 449 " ideal model delta sigma weight residual 1.523 1.438 0.085 8.40e-03 1.42e+04 1.02e+02 bond pdb=" CA ASP F 353 " pdb=" C ASP F 353 " ideal model delta sigma weight residual 1.519 1.423 0.096 9.50e-03 1.11e+04 1.02e+02 bond pdb=" CA ILE D 277 " pdb=" C ILE D 277 " ideal model delta sigma weight residual 1.522 1.452 0.071 7.10e-03 1.98e+04 9.86e+01 ... (remaining 32737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.62: 39640 4.62 - 9.24: 4353 9.24 - 13.87: 350 13.87 - 18.49: 31 18.49 - 23.11: 4 Bond angle restraints: 44378 Sorted by residual: angle pdb=" N ALA G 46 " pdb=" CA ALA G 46 " pdb=" C ALA G 46 " ideal model delta sigma weight residual 111.02 134.13 -23.11 1.22e+00 6.72e-01 3.59e+02 angle pdb=" CA PHE C 415 " pdb=" CB PHE C 415 " pdb=" CG PHE C 415 " ideal model delta sigma weight residual 113.80 100.21 13.59 1.00e+00 1.00e+00 1.85e+02 angle pdb=" CA PHE G 130 " pdb=" CB PHE G 130 " pdb=" CG PHE G 130 " ideal model delta sigma weight residual 113.80 100.52 13.28 1.00e+00 1.00e+00 1.76e+02 angle pdb=" CA PHE F 421 " pdb=" CB PHE F 421 " pdb=" CG PHE F 421 " ideal model delta sigma weight residual 113.80 101.13 12.67 1.00e+00 1.00e+00 1.61e+02 angle pdb=" CA PHE F 247 " pdb=" CB PHE F 247 " pdb=" CG PHE F 247 " ideal model delta sigma weight residual 113.80 101.16 12.64 1.00e+00 1.00e+00 1.60e+02 ... (remaining 44373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.46: 19010 33.46 - 66.92: 781 66.92 - 100.37: 151 100.37 - 133.83: 1 133.83 - 167.29: 3 Dihedral angle restraints: 19946 sinusoidal: 8036 harmonic: 11910 Sorted by residual: dihedral pdb=" CA LYS E 6 " pdb=" C LYS E 6 " pdb=" N GLU E 7 " pdb=" CA GLU E 7 " ideal model delta harmonic sigma weight residual -180.00 -68.89 -111.11 0 5.00e+00 4.00e-02 4.94e+02 dihedral pdb=" CA LYS F 6 " pdb=" C LYS F 6 " pdb=" N GLU F 7 " pdb=" CA GLU F 7 " ideal model delta harmonic sigma weight residual -180.00 -109.99 -70.01 0 5.00e+00 4.00e-02 1.96e+02 dihedral pdb=" CA LYS D 6 " pdb=" C LYS D 6 " pdb=" N GLU D 7 " pdb=" CA GLU D 7 " ideal model delta harmonic sigma weight residual -180.00 -112.69 -67.31 0 5.00e+00 4.00e-02 1.81e+02 ... (remaining 19943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 3577 0.159 - 0.318: 1041 0.318 - 0.477: 287 0.477 - 0.637: 65 0.637 - 0.796: 17 Chirality restraints: 4987 Sorted by residual: chirality pdb=" CA THR C 98 " pdb=" N THR C 98 " pdb=" C THR C 98 " pdb=" CB THR C 98 " both_signs ideal model delta sigma weight residual False 2.53 1.73 0.80 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" CA LEU A 458 " pdb=" N LEU A 458 " pdb=" C LEU A 458 " pdb=" CB LEU A 458 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" CA THR D 234 " pdb=" N THR D 234 " pdb=" C THR D 234 " pdb=" CB THR D 234 " both_signs ideal model delta sigma weight residual False 2.53 1.77 0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 4984 not shown) Planarity restraints: 5831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 252 " -0.432 2.00e-02 2.50e+03 2.36e-01 1.12e+03 pdb=" CG TYR C 252 " 0.097 2.00e-02 2.50e+03 pdb=" CD1 TYR C 252 " 0.206 2.00e-02 2.50e+03 pdb=" CD2 TYR C 252 " 0.191 2.00e-02 2.50e+03 pdb=" CE1 TYR C 252 " 0.145 2.00e-02 2.50e+03 pdb=" CE2 TYR C 252 " 0.144 2.00e-02 2.50e+03 pdb=" CZ TYR C 252 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR C 252 " -0.360 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP C 600 " -0.354 2.00e-02 2.50e+03 1.92e-01 1.01e+03 pdb=" C2 ADP C 600 " 0.110 2.00e-02 2.50e+03 pdb=" C4 ADP C 600 " 0.063 2.00e-02 2.50e+03 pdb=" C5 ADP C 600 " 0.164 2.00e-02 2.50e+03 pdb=" C6 ADP C 600 " -0.006 2.00e-02 2.50e+03 pdb=" C8 ADP C 600 " 0.132 2.00e-02 2.50e+03 pdb=" N1 ADP C 600 " 0.027 2.00e-02 2.50e+03 pdb=" N3 ADP C 600 " 0.038 2.00e-02 2.50e+03 pdb=" N6 ADP C 600 " -0.399 2.00e-02 2.50e+03 pdb=" N7 ADP C 600 " 0.238 2.00e-02 2.50e+03 pdb=" N9 ADP C 600 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 304 " 0.384 2.00e-02 2.50e+03 1.98e-01 7.80e+02 pdb=" CG TYR A 304 " -0.130 2.00e-02 2.50e+03 pdb=" CD1 TYR A 304 " -0.179 2.00e-02 2.50e+03 pdb=" CD2 TYR A 304 " -0.181 2.00e-02 2.50e+03 pdb=" CE1 TYR A 304 " -0.087 2.00e-02 2.50e+03 pdb=" CE2 TYR A 304 " -0.086 2.00e-02 2.50e+03 pdb=" CZ TYR A 304 " 0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 304 " 0.261 2.00e-02 2.50e+03 ... (remaining 5828 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6958 2.78 - 3.31: 35636 3.31 - 3.84: 50984 3.84 - 4.37: 62308 4.37 - 4.90: 94763 Nonbonded interactions: 250649 Sorted by model distance: nonbonded pdb=" N PRO C 420 " pdb=" O PRO C 420 " model vdw 2.246 2.496 nonbonded pdb=" N ILE E 352 " pdb=" O ILE E 352 " model vdw 2.249 2.496 nonbonded pdb=" N PRO F 312 " pdb=" O PRO F 312 " model vdw 2.254 2.496 nonbonded pdb=" N PRO B 227 " pdb=" O PRO B 227 " model vdw 2.259 2.496 nonbonded pdb=" N ASP E 353 " pdb=" O ASP E 353 " model vdw 2.278 2.496 ... (remaining 250644 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 1 through 577) selection = chain 'B' selection = (chain 'C' and resid 1 through 577) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.190 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.027 0.133 32743 Z= 1.969 Angle : 2.875 23.111 44380 Z= 1.865 Chirality : 0.169 0.796 4987 Planarity : 0.032 0.240 5831 Dihedral : 18.506 167.287 12319 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 8.61 % Allowed : 16.33 % Favored : 75.06 % Rotamer: Outliers : 9.44 % Allowed : 11.78 % Favored : 78.78 % Cbeta Deviations : 3.36 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -5.44 (0.10), residues: 4134 helix: -3.50 (0.09), residues: 1587 sheet: -3.44 (0.21), residues: 409 loop : -3.80 (0.11), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG E 146 TYR 0.432 0.050 TYR C 252 PHE 0.203 0.035 PHE F 421 TRP 0.297 0.040 TRP A 424 HIS 0.013 0.003 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.02664 (32742) covalent geometry : angle 2.87482 (44378) SS BOND : bond 0.00660 ( 1) SS BOND : angle 1.85983 ( 2) hydrogen bonds : bond 0.27168 ( 1216) hydrogen bonds : angle 11.18133 ( 3453) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 310 poor density : 1239 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 91 LEU cc_start: 0.8834 (mp) cc_final: 0.8071 (mp) REVERT: A 133 MET cc_start: 0.7860 (mtt) cc_final: 0.7539 (mtp) REVERT: A 134 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8883 (m) REVERT: A 140 GLU cc_start: 0.6537 (tt0) cc_final: 0.6305 (tt0) REVERT: A 159 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6445 (mp0) REVERT: A 189 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8205 (t) REVERT: A 207 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9008 (m) REVERT: A 234 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8448 (ttpt) REVERT: A 262 MET cc_start: 0.8282 (tpp) cc_final: 0.7128 (mmp) REVERT: A 273 THR cc_start: 0.7650 (m) cc_final: 0.7049 (t) REVERT: A 379 THR cc_start: 0.9074 (m) cc_final: 0.8363 (m) REVERT: A 425 ASN cc_start: 0.8774 (m110) cc_final: 0.8311 (t0) REVERT: A 465 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7248 (mm-40) REVERT: A 500 TYR cc_start: 0.7025 (m-80) cc_final: 0.6573 (m-80) REVERT: A 519 ILE cc_start: 0.8934 (pt) cc_final: 0.8685 (mm) REVERT: B 52 TYR cc_start: 0.7845 (m-80) cc_final: 0.6496 (m-10) REVERT: B 62 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7766 (mt-10) REVERT: B 87 ILE cc_start: 0.9285 (pt) cc_final: 0.8637 (mm) REVERT: B 109 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7836 (m-70) REVERT: B 144 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8897 (m) REVERT: B 156 ARG cc_start: 0.6376 (mmp-170) cc_final: 0.5642 (mmm160) REVERT: B 186 THR cc_start: 0.8609 (p) cc_final: 0.8298 (t) REVERT: B 198 LYS cc_start: 0.6029 (ttpt) cc_final: 0.5601 (tttt) REVERT: B 199 LEU cc_start: 0.8508 (mt) cc_final: 0.8064 (tp) REVERT: B 257 GLU cc_start: 0.7440 (tt0) cc_final: 0.7206 (tt0) REVERT: B 322 LEU cc_start: 0.9160 (tt) cc_final: 0.8636 (tt) REVERT: B 367 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7939 (tptm) REVERT: B 368 VAL cc_start: 0.8883 (m) cc_final: 0.8674 (p) REVERT: B 439 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: B 450 LEU cc_start: 0.8445 (mt) cc_final: 0.7823 (mm) REVERT: B 452 ASP cc_start: 0.9084 (p0) cc_final: 0.8621 (p0) REVERT: B 458 LEU cc_start: 0.8346 (pp) cc_final: 0.7924 (pp) REVERT: B 490 ILE cc_start: 0.8982 (mm) cc_final: 0.8414 (mm) REVERT: B 516 MET cc_start: 0.8045 (ptm) cc_final: 0.7667 (ttp) REVERT: B 545 LEU cc_start: 0.8837 (mp) cc_final: 0.8544 (mt) REVERT: C 50 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7322 (tp40) REVERT: C 64 VAL cc_start: 0.8381 (t) cc_final: 0.8093 (t) REVERT: C 119 TRP cc_start: 0.9259 (OUTLIER) cc_final: 0.8543 (t-100) REVERT: C 160 VAL cc_start: 0.9001 (t) cc_final: 0.8788 (p) REVERT: C 184 TYR cc_start: 0.8265 (p90) cc_final: 0.7795 (p90) REVERT: C 205 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8518 (t80) REVERT: C 240 SER cc_start: 0.9219 (m) cc_final: 0.8587 (t) REVERT: C 244 TRP cc_start: 0.8531 (m100) cc_final: 0.7566 (m100) REVERT: C 264 ASP cc_start: 0.8713 (m-30) cc_final: 0.8170 (m-30) REVERT: C 300 GLU cc_start: 0.8527 (tt0) cc_final: 0.8285 (tm-30) REVERT: C 344 MET cc_start: 0.8615 (mmt) cc_final: 0.8232 (mmt) REVERT: C 413 LEU cc_start: 0.9378 (tp) cc_final: 0.8972 (mm) REVERT: C 490 ILE cc_start: 0.8568 (mm) cc_final: 0.8089 (mm) REVERT: C 506 TYR cc_start: 0.8201 (t80) cc_final: 0.7780 (t80) REVERT: C 552 ARG cc_start: 0.8694 (ptt90) cc_final: 0.8180 (ptt90) REVERT: D 18 LEU cc_start: 0.8965 (mt) cc_final: 0.8694 (tp) REVERT: D 61 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: D 81 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.6717 (ppt90) REVERT: D 85 SER cc_start: 0.8036 (OUTLIER) cc_final: 0.7287 (m) REVERT: D 100 ILE cc_start: 0.8495 (mm) cc_final: 0.8194 (tp) REVERT: D 173 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8845 (m) REVERT: D 178 SER cc_start: 0.8650 (m) cc_final: 0.8250 (t) REVERT: D 207 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6910 (tp30) REVERT: D 244 TYR cc_start: 0.7876 (t80) cc_final: 0.7333 (t80) REVERT: D 251 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: D 269 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7273 (mm-30) REVERT: D 388 ASN cc_start: 0.9163 (m-40) cc_final: 0.8850 (t0) REVERT: D 423 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8557 (tp) REVERT: D 436 LEU cc_start: 0.9190 (mt) cc_final: 0.8951 (mt) REVERT: E 59 VAL cc_start: 0.8969 (t) cc_final: 0.8751 (p) REVERT: E 82 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8568 (tp) REVERT: E 93 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6967 (t80) REVERT: E 112 LEU cc_start: 0.8419 (pt) cc_final: 0.8164 (pp) REVERT: E 126 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8104 (tttp) REVERT: E 136 SER cc_start: 0.9467 (p) cc_final: 0.9222 (t) REVERT: E 269 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7752 (mt-10) REVERT: E 278 PRO cc_start: 0.8910 (Cg_exo) cc_final: 0.8637 (Cg_endo) REVERT: E 296 GLU cc_start: 0.7525 (tp30) cc_final: 0.7163 (tp30) REVERT: E 307 SER cc_start: 0.8368 (p) cc_final: 0.8067 (m) REVERT: F 19 LEU cc_start: 0.8784 (tt) cc_final: 0.8484 (tt) REVERT: F 53 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: F 54 TYR cc_start: 0.8539 (p90) cc_final: 0.7820 (p90) REVERT: F 57 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8846 (mt) REVERT: F 58 GLN cc_start: 0.8749 (tt0) cc_final: 0.8476 (tt0) REVERT: F 73 VAL cc_start: 0.8792 (t) cc_final: 0.8552 (t) REVERT: F 89 LEU cc_start: 0.8953 (mt) cc_final: 0.8414 (mt) REVERT: F 139 ASP cc_start: 0.8597 (m-30) cc_final: 0.8295 (m-30) REVERT: F 148 GLN cc_start: 0.8965 (tt0) cc_final: 0.8303 (tt0) REVERT: F 194 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.6401 (mpm) REVERT: F 201 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8926 (tp) REVERT: F 219 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8217 (pp) REVERT: F 239 LEU cc_start: 0.8551 (mt) cc_final: 0.8294 (mm) REVERT: F 316 MET cc_start: 0.9004 (pp-130) cc_final: 0.8553 (ppp) REVERT: F 334 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6515 (mt-10) REVERT: F 357 SER cc_start: 0.7907 (m) cc_final: 0.7634 (p) REVERT: F 377 GLN cc_start: 0.9083 (mt0) cc_final: 0.8804 (mt0) REVERT: F 393 ARG cc_start: 0.8649 (ttm170) cc_final: 0.8137 (ttm-80) REVERT: F 412 LEU cc_start: 0.8758 (tp) cc_final: 0.8401 (tt) REVERT: F 419 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7751 (pt0) REVERT: F 425 GLN cc_start: 0.8449 (tt0) cc_final: 0.8147 (tt0) REVERT: F 450 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6638 (mm-30) REVERT: G 147 LEU cc_start: 0.7946 (tp) cc_final: 0.7397 (tt) REVERT: G 165 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6428 (tp30) REVERT: G 177 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7888 (mtm180) REVERT: G 193 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7686 (ttm110) REVERT: H 28 GLU cc_start: 0.5331 (OUTLIER) cc_final: 0.4441 (pm20) REVERT: I 118 VAL cc_start: 0.6215 (m) cc_final: 0.5978 (p) REVERT: J 79 VAL cc_start: 0.6038 (t) cc_final: 0.5791 (t) REVERT: J 88 ARG cc_start: 0.8117 (mtp180) cc_final: 0.7696 (tpt170) REVERT: J 128 LEU cc_start: 0.6119 (tp) cc_final: 0.5892 (tp) REVERT: J 182 VAL cc_start: 0.8217 (m) cc_final: 0.7442 (t) REVERT: J 186 LEU cc_start: 0.8744 (mt) cc_final: 0.8050 (mt) REVERT: K 108 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.5191 (t70) REVERT: L 53 TYR cc_start: 0.6900 (t80) cc_final: 0.6625 (t80) REVERT: L 88 ARG cc_start: 0.6913 (ttm110) cc_final: 0.6582 (ttm-80) REVERT: L 152 VAL cc_start: 0.7761 (t) cc_final: 0.7259 (p) REVERT: M 97 GLN cc_start: 0.6560 (mt0) cc_final: 0.6243 (tt0) REVERT: M 157 GLU cc_start: 0.4546 (OUTLIER) cc_final: 0.1693 (tm-30) REVERT: M 269 LEU cc_start: 0.8373 (mt) cc_final: 0.8082 (tt) REVERT: M 289 TYR cc_start: 0.6155 (t80) cc_final: 0.5792 (t80) outliers start: 310 outliers final: 112 residues processed: 1429 average time/residue: 0.2065 time to fit residues: 462.5626 Evaluate side-chains 960 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 817 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 260 ASN A 283 HIS ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN B 196 GLN B 283 HIS B 293 ASN ** B 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN C 238 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN D 363 ASN D 424 ASN ** D 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 GLN D 429 ASN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS E 252 HIS F 129 GLN F 148 GLN F 166 GLN ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 ASN L 124 ASN L 184 GLN M 200 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.115717 restraints weight = 65195.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.117273 restraints weight = 41655.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119048 restraints weight = 30426.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120106 restraints weight = 22248.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120535 restraints weight = 19107.995| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 32743 Z= 0.205 Angle : 0.988 11.407 44380 Z= 0.512 Chirality : 0.052 0.291 4987 Planarity : 0.008 0.132 5831 Dihedral : 8.215 152.856 4623 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.97 % Allowed : 10.57 % Favored : 88.46 % Rotamer: Outliers : 0.24 % Allowed : 6.18 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.25 % 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 aren not related in a simple way. whole: -3.65 (0.12), residues: 4134 helix: -1.91 (0.11), residues: 1639 sheet: -2.63 (0.22), residues: 466 loop : -2.81 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 410 TYR 0.041 0.003 TYR F 383 PHE 0.036 0.003 PHE G 70 TRP 0.042 0.003 TRP C 244 HIS 0.011 0.002 HIS B 418 Details of bonding type rmsd covalent geometry : bond 0.00415 (32742) covalent geometry : angle 0.98780 (44378) SS BOND : bond 0.00122 ( 1) SS BOND : angle 0.70892 ( 2) hydrogen bonds : bond 0.07039 ( 1216) hydrogen bonds : angle 6.66506 ( 3453) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 1170 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 29 LYS cc_start: 0.8537 (mptt) cc_final: 0.8318 (mmtm) REVERT: A 79 MET cc_start: 0.7551 (mtp) cc_final: 0.6661 (ttm) REVERT: A 133 MET cc_start: 0.6576 (mtt) cc_final: 0.5248 (mtp) REVERT: A 161 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7845 (ptpp) REVERT: A 182 LYS cc_start: 0.8435 (mptt) cc_final: 0.8186 (mppt) REVERT: A 196 GLN cc_start: 0.8114 (tt0) cc_final: 0.7676 (tm-30) REVERT: A 199 LEU cc_start: 0.8272 (tp) cc_final: 0.7914 (tt) REVERT: A 207 THR cc_start: 0.9058 (t) cc_final: 0.8486 (p) REVERT: A 252 TYR cc_start: 0.9038 (t80) cc_final: 0.8392 (t80) REVERT: A 293 ASN cc_start: 0.8551 (p0) cc_final: 0.8286 (p0) REVERT: A 343 GLU cc_start: 0.7921 (tt0) cc_final: 0.7381 (tt0) REVERT: A 391 MET cc_start: 0.8882 (mmm) cc_final: 0.8625 (mmm) REVERT: A 397 GLN cc_start: 0.8096 (mt0) cc_final: 0.7859 (mt0) REVERT: A 424 TRP cc_start: 0.6975 (p90) cc_final: 0.6536 (p90) REVERT: A 425 ASN cc_start: 0.8667 (m110) cc_final: 0.7611 (t0) REVERT: A 456 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8487 (mt-10) REVERT: A 565 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7708 (tp30) REVERT: B 39 ILE cc_start: 0.7825 (mt) cc_final: 0.7331 (mt) REVERT: B 52 TYR cc_start: 0.7550 (m-80) cc_final: 0.7232 (m-80) REVERT: B 64 VAL cc_start: 0.9449 (t) cc_final: 0.9230 (p) REVERT: B 75 LEU cc_start: 0.8903 (mt) cc_final: 0.8698 (mt) REVERT: B 79 MET cc_start: 0.7938 (tpt) cc_final: 0.7280 (tpt) REVERT: B 87 ILE cc_start: 0.9129 (pt) cc_final: 0.8746 (mm) REVERT: B 130 ARG cc_start: 0.8262 (ptm160) cc_final: 0.7919 (ttp80) REVERT: B 133 MET cc_start: 0.7714 (ttm) cc_final: 0.7122 (ttp) REVERT: B 156 ARG cc_start: 0.7405 (mmp-170) cc_final: 0.6515 (mmm160) REVERT: B 182 LYS cc_start: 0.7537 (mttt) cc_final: 0.7286 (mttt) REVERT: B 186 THR cc_start: 0.8479 (p) cc_final: 0.8218 (t) REVERT: B 244 TRP cc_start: 0.8225 (m100) cc_final: 0.7980 (m100) REVERT: B 257 GLU cc_start: 0.7574 (tt0) cc_final: 0.6849 (tt0) REVERT: B 262 MET cc_start: 0.7407 (tpt) cc_final: 0.7002 (tpt) REVERT: B 268 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7946 (mm-30) REVERT: B 282 MET cc_start: 0.7940 (tpp) cc_final: 0.7715 (tpp) REVERT: B 396 THR cc_start: 0.8570 (m) cc_final: 0.8042 (m) REVERT: B 437 PRO cc_start: 0.8400 (Cg_exo) cc_final: 0.8183 (Cg_endo) REVERT: B 443 VAL cc_start: 0.9165 (t) cc_final: 0.8871 (t) REVERT: B 504 ASP cc_start: 0.7516 (p0) cc_final: 0.7269 (p0) REVERT: C 43 ASP cc_start: 0.7166 (t70) cc_final: 0.6919 (t0) REVERT: C 133 MET cc_start: 0.8090 (tpt) cc_final: 0.7756 (tpt) REVERT: C 165 GLU cc_start: 0.7398 (mp0) cc_final: 0.7018 (mp0) REVERT: C 209 MET cc_start: 0.7296 (ttm) cc_final: 0.7035 (ttp) REVERT: C 240 SER cc_start: 0.9066 (m) cc_final: 0.8774 (t) REVERT: C 249 VAL cc_start: 0.9274 (m) cc_final: 0.8914 (p) REVERT: C 343 GLU cc_start: 0.7962 (tt0) cc_final: 0.7742 (tt0) REVERT: C 413 LEU cc_start: 0.9131 (tp) cc_final: 0.8711 (mm) REVERT: C 493 ASP cc_start: 0.6984 (m-30) cc_final: 0.6744 (m-30) REVERT: D 14 ILE cc_start: 0.9494 (mt) cc_final: 0.9188 (tp) REVERT: D 57 ILE cc_start: 0.8850 (mt) cc_final: 0.8530 (mm) REVERT: D 138 ILE cc_start: 0.8489 (tt) cc_final: 0.8286 (tt) REVERT: D 170 GLN cc_start: 0.7841 (tp40) cc_final: 0.7465 (tp40) REVERT: D 237 MET cc_start: 0.8555 (tpp) cc_final: 0.8341 (tpp) REVERT: D 269 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7252 (mm-30) REVERT: D 319 ASP cc_start: 0.7951 (m-30) cc_final: 0.7709 (t70) REVERT: D 331 TYR cc_start: 0.8424 (m-10) cc_final: 0.8200 (m-10) REVERT: D 342 GLU cc_start: 0.7808 (pt0) cc_final: 0.7329 (pt0) REVERT: D 382 LEU cc_start: 0.8866 (mp) cc_final: 0.8610 (tp) REVERT: D 429 ASN cc_start: 0.8427 (t0) cc_final: 0.8060 (t0) REVERT: D 462 TYR cc_start: 0.6599 (m-80) cc_final: 0.6164 (m-80) REVERT: E 59 VAL cc_start: 0.9181 (t) cc_final: 0.8926 (p) REVERT: E 126 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8198 (tttm) REVERT: E 136 SER cc_start: 0.8123 (p) cc_final: 0.6849 (t) REVERT: E 206 GLN cc_start: 0.8110 (pp30) cc_final: 0.7685 (pp30) REVERT: E 232 ILE cc_start: 0.9142 (mt) cc_final: 0.8874 (mt) REVERT: E 250 ASP cc_start: 0.6539 (m-30) cc_final: 0.6058 (t0) REVERT: E 263 TYR cc_start: 0.8843 (t80) cc_final: 0.8302 (t80) REVERT: E 269 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7650 (mt-10) REVERT: E 307 SER cc_start: 0.9121 (p) cc_final: 0.8729 (m) REVERT: E 308 VAL cc_start: 0.9382 (t) cc_final: 0.9170 (t) REVERT: E 316 MET cc_start: 0.8306 (ptm) cc_final: 0.8090 (ptm) REVERT: E 336 GLN cc_start: 0.8149 (pm20) cc_final: 0.7414 (pm20) REVERT: E 358 LEU cc_start: 0.9152 (tp) cc_final: 0.8463 (tp) REVERT: E 408 ASP cc_start: 0.8550 (m-30) cc_final: 0.8109 (m-30) REVERT: E 435 SER cc_start: 0.9077 (t) cc_final: 0.8503 (t) REVERT: E 445 MET cc_start: 0.8926 (mmp) cc_final: 0.8661 (mmm) REVERT: F 7 GLU cc_start: 0.5441 (mp0) cc_final: 0.4822 (mm-30) REVERT: F 53 GLU cc_start: 0.8290 (pm20) cc_final: 0.7337 (tm-30) REVERT: F 89 LEU cc_start: 0.8948 (mt) cc_final: 0.8727 (mt) REVERT: F 137 THR cc_start: 0.9166 (p) cc_final: 0.8767 (p) REVERT: F 138 ILE cc_start: 0.8553 (mm) cc_final: 0.8227 (mt) REVERT: F 140 VAL cc_start: 0.9395 (t) cc_final: 0.9152 (t) REVERT: F 176 ASP cc_start: 0.8928 (p0) cc_final: 0.8516 (p0) REVERT: F 203 TYR cc_start: 0.9271 (t80) cc_final: 0.8952 (t80) REVERT: F 219 LEU cc_start: 0.8715 (pt) cc_final: 0.8298 (pp) REVERT: F 221 LEU cc_start: 0.8216 (mt) cc_final: 0.7620 (tt) REVERT: F 226 ASP cc_start: 0.9096 (m-30) cc_final: 0.8364 (m-30) REVERT: F 260 MET cc_start: 0.7886 (tpp) cc_final: 0.7624 (tpp) REVERT: F 280 ARG cc_start: 0.8694 (tpp80) cc_final: 0.8184 (ttt90) REVERT: F 334 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6785 (mt-10) REVERT: F 353 ASP cc_start: 0.8996 (m-30) cc_final: 0.8796 (m-30) REVERT: F 360 ARG cc_start: 0.7456 (tpt170) cc_final: 0.7201 (tpt170) REVERT: F 408 ASP cc_start: 0.8095 (m-30) cc_final: 0.7679 (m-30) REVERT: F 461 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8101 (ttmt) REVERT: G 32 ARG cc_start: 0.8127 (mmp80) cc_final: 0.7746 (mmp80) REVERT: G 152 GLU cc_start: 0.8021 (pt0) cc_final: 0.7602 (pp20) REVERT: G 159 ARG cc_start: 0.8774 (ttm110) cc_final: 0.7969 (ttm110) REVERT: G 194 LEU cc_start: 0.9338 (tp) cc_final: 0.9019 (tt) REVERT: H 1 MET cc_start: 0.7079 (mmm) cc_final: 0.6700 (mmt) REVERT: I 89 ARG cc_start: 0.5817 (ttm110) cc_final: 0.4585 (tpt90) REVERT: I 93 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7029 (mt-10) REVERT: J 88 ARG cc_start: 0.7983 (mtp180) cc_final: 0.7176 (tpt170) REVERT: J 182 VAL cc_start: 0.7701 (m) cc_final: 0.7039 (p) REVERT: J 186 LEU cc_start: 0.8895 (mt) cc_final: 0.8477 (mt) REVERT: K 108 ASP cc_start: 0.7916 (m-30) cc_final: 0.7712 (p0) REVERT: L 81 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7792 (pt0) REVERT: L 150 LEU cc_start: 0.7320 (mm) cc_final: 0.6930 (mm) REVERT: L 168 LEU cc_start: 0.8228 (mp) cc_final: 0.7807 (mp) REVERT: M 39 LEU cc_start: 0.5752 (tp) cc_final: 0.5484 (tp) REVERT: M 97 GLN cc_start: 0.7768 (mt0) cc_final: 0.7170 (tt0) REVERT: M 250 SER cc_start: 0.7260 (t) cc_final: 0.6995 (m) REVERT: M 289 TYR cc_start: 0.7582 (t80) cc_final: 0.7292 (t80) REVERT: M 317 GLU cc_start: 0.5598 (pt0) cc_final: 0.4368 (tt0) outliers start: 8 outliers final: 3 residues processed: 1174 average time/residue: 0.1785 time to fit residues: 334.0049 Evaluate side-chains 814 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 811 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 300 optimal weight: 0.4980 chunk 147 optimal weight: 5.9990 chunk 350 optimal weight: 6.9990 chunk 293 optimal weight: 0.9990 chunk 362 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 345 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 HIS B 496 GLN ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 338 GLN ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN M 65 GLN ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 208 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.109352 restraints weight = 66014.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.111442 restraints weight = 43391.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113003 restraints weight = 30036.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113974 restraints weight = 22994.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.114381 restraints weight = 19550.335| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32743 Z= 0.211 Angle : 0.840 10.578 44380 Z= 0.431 Chirality : 0.048 0.320 4987 Planarity : 0.007 0.078 5831 Dihedral : 7.035 128.613 4623 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.73 % Allowed : 10.16 % Favored : 89.11 % Rotamer: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.59 (0.12), residues: 4134 helix: -0.83 (0.12), residues: 1652 sheet: -2.00 (0.23), residues: 444 loop : -2.43 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 410 TYR 0.055 0.002 TYR F 383 PHE 0.025 0.003 PHE A 269 TRP 0.023 0.002 TRP B 330 HIS 0.010 0.002 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00422 (32742) covalent geometry : angle 0.83982 (44378) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.32774 ( 2) hydrogen bonds : bond 0.05642 ( 1216) hydrogen bonds : angle 5.81719 ( 3453) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 999 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 133 MET cc_start: 0.6454 (mtt) cc_final: 0.5984 (mtt) REVERT: A 154 ARG cc_start: 0.7461 (tmm160) cc_final: 0.6969 (tmt-80) REVERT: A 161 LYS cc_start: 0.8197 (mmtp) cc_final: 0.7950 (ptpp) REVERT: A 182 LYS cc_start: 0.8783 (mptt) cc_final: 0.8495 (mppt) REVERT: A 199 LEU cc_start: 0.8580 (tp) cc_final: 0.8106 (tt) REVERT: A 207 THR cc_start: 0.9229 (t) cc_final: 0.8700 (p) REVERT: A 220 MET cc_start: 0.8417 (tpt) cc_final: 0.7994 (tpp) REVERT: A 252 TYR cc_start: 0.9067 (t80) cc_final: 0.8674 (t80) REVERT: A 269 PHE cc_start: 0.8284 (m-80) cc_final: 0.7792 (m-80) REVERT: A 282 MET cc_start: 0.8519 (mmm) cc_final: 0.7955 (mmm) REVERT: A 293 ASN cc_start: 0.8794 (p0) cc_final: 0.8442 (p0) REVERT: A 319 SER cc_start: 0.9387 (m) cc_final: 0.9098 (p) REVERT: A 332 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7704 (mt-10) REVERT: A 363 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 379 THR cc_start: 0.9223 (m) cc_final: 0.8675 (m) REVERT: A 391 MET cc_start: 0.8976 (mmm) cc_final: 0.8604 (mmm) REVERT: A 397 GLN cc_start: 0.8122 (mt0) cc_final: 0.7656 (mt0) REVERT: A 425 ASN cc_start: 0.8625 (m110) cc_final: 0.7950 (t0) REVERT: A 429 SER cc_start: 0.9161 (t) cc_final: 0.8865 (m) REVERT: A 450 LEU cc_start: 0.8625 (tt) cc_final: 0.8281 (tt) REVERT: B 38 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6616 (mt-10) REVERT: B 62 GLU cc_start: 0.8143 (pt0) cc_final: 0.7829 (pt0) REVERT: B 79 MET cc_start: 0.7760 (tpt) cc_final: 0.7189 (tpt) REVERT: B 87 ILE cc_start: 0.9061 (pt) cc_final: 0.8799 (mm) REVERT: B 91 LEU cc_start: 0.9282 (mt) cc_final: 0.8988 (mm) REVERT: B 130 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7837 (ttp80) REVERT: B 133 MET cc_start: 0.8037 (ttm) cc_final: 0.7340 (ttp) REVERT: B 156 ARG cc_start: 0.7314 (mmp-170) cc_final: 0.6843 (mmm160) REVERT: B 182 LYS cc_start: 0.7528 (mttt) cc_final: 0.7228 (mttt) REVERT: B 244 TRP cc_start: 0.8330 (m100) cc_final: 0.7952 (m100) REVERT: B 255 CYS cc_start: 0.8689 (p) cc_final: 0.8093 (p) REVERT: B 257 GLU cc_start: 0.8014 (tt0) cc_final: 0.6992 (tt0) REVERT: B 262 MET cc_start: 0.7491 (tpt) cc_final: 0.7079 (tpt) REVERT: B 293 ASN cc_start: 0.8703 (p0) cc_final: 0.8123 (p0) REVERT: B 294 MET cc_start: 0.8922 (mmm) cc_final: 0.8519 (mmm) REVERT: B 323 MET cc_start: 0.8462 (mmp) cc_final: 0.8160 (mmp) REVERT: B 507 CYS cc_start: 0.7939 (t) cc_final: 0.7149 (t) REVERT: B 516 MET cc_start: 0.8937 (ttp) cc_final: 0.8708 (ttp) REVERT: C 2 ILE cc_start: 0.8150 (mm) cc_final: 0.7834 (mm) REVERT: C 39 ILE cc_start: 0.8479 (mp) cc_final: 0.8069 (mm) REVERT: C 165 GLU cc_start: 0.7307 (mp0) cc_final: 0.6934 (mp0) REVERT: C 240 SER cc_start: 0.9124 (m) cc_final: 0.8728 (t) REVERT: C 294 MET cc_start: 0.9229 (mtt) cc_final: 0.8707 (mtt) REVERT: C 367 LYS cc_start: 0.9322 (ttmt) cc_final: 0.8236 (ttpp) REVERT: C 413 LEU cc_start: 0.9159 (tp) cc_final: 0.8922 (mm) REVERT: D 14 ILE cc_start: 0.9534 (mt) cc_final: 0.9142 (tp) REVERT: D 148 GLN cc_start: 0.8177 (tt0) cc_final: 0.7885 (tt0) REVERT: D 176 ASP cc_start: 0.8594 (m-30) cc_final: 0.8370 (t0) REVERT: D 191 PHE cc_start: 0.8753 (t80) cc_final: 0.8150 (t80) REVERT: D 200 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7108 (mt-10) REVERT: D 225 ASP cc_start: 0.7930 (p0) cc_final: 0.7656 (p0) REVERT: D 258 THR cc_start: 0.7612 (p) cc_final: 0.7411 (t) REVERT: D 269 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7274 (mm-30) REVERT: D 300 VAL cc_start: 0.9185 (t) cc_final: 0.8726 (t) REVERT: D 319 ASP cc_start: 0.8124 (m-30) cc_final: 0.7832 (t70) REVERT: D 327 ASP cc_start: 0.8646 (t0) cc_final: 0.8145 (t0) REVERT: D 331 TYR cc_start: 0.8106 (m-10) cc_final: 0.7776 (m-80) REVERT: D 336 GLN cc_start: 0.8459 (mt0) cc_final: 0.8236 (mt0) REVERT: D 435 SER cc_start: 0.9695 (m) cc_final: 0.9313 (p) REVERT: E 52 GLU cc_start: 0.8039 (pt0) cc_final: 0.7808 (pt0) REVERT: E 54 TYR cc_start: 0.8672 (p90) cc_final: 0.8466 (p90) REVERT: E 87 GLU cc_start: 0.7446 (pt0) cc_final: 0.7158 (pt0) REVERT: E 112 LEU cc_start: 0.9016 (pt) cc_final: 0.8773 (pt) REVERT: E 126 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8483 (tttp) REVERT: E 206 GLN cc_start: 0.8089 (pp30) cc_final: 0.7657 (pp30) REVERT: E 281 ARG cc_start: 0.6798 (mtt180) cc_final: 0.6076 (mtt180) REVERT: E 349 TYR cc_start: 0.9128 (t80) cc_final: 0.8851 (t80) REVERT: E 388 ASN cc_start: 0.7649 (m-40) cc_final: 0.7406 (t0) REVERT: E 421 PHE cc_start: 0.7907 (t80) cc_final: 0.7509 (t80) REVERT: E 432 ILE cc_start: 0.9144 (tp) cc_final: 0.8449 (tp) REVERT: E 445 MET cc_start: 0.8946 (mmp) cc_final: 0.8686 (mmm) REVERT: F 35 ILE cc_start: 0.8996 (mt) cc_final: 0.8724 (mp) REVERT: F 36 LYS cc_start: 0.8988 (tptm) cc_final: 0.8585 (tppt) REVERT: F 53 GLU cc_start: 0.8615 (pm20) cc_final: 0.7833 (tm-30) REVERT: F 89 LEU cc_start: 0.8937 (mt) cc_final: 0.8527 (mt) REVERT: F 137 THR cc_start: 0.9194 (p) cc_final: 0.8627 (p) REVERT: F 139 ASP cc_start: 0.8678 (m-30) cc_final: 0.8323 (m-30) REVERT: F 140 VAL cc_start: 0.9433 (t) cc_final: 0.9089 (t) REVERT: F 176 ASP cc_start: 0.8877 (p0) cc_final: 0.8437 (p0) REVERT: F 221 LEU cc_start: 0.8374 (mt) cc_final: 0.7695 (tt) REVERT: F 237 MET cc_start: 0.8300 (tpp) cc_final: 0.8080 (tpp) REVERT: F 280 ARG cc_start: 0.8799 (tpp80) cc_final: 0.8229 (ttt90) REVERT: F 314 LEU cc_start: 0.9433 (tp) cc_final: 0.9230 (tp) REVERT: F 362 MET cc_start: 0.8557 (ttp) cc_final: 0.8320 (ttt) REVERT: G 119 THR cc_start: 0.7086 (t) cc_final: 0.6648 (t) REVERT: G 152 GLU cc_start: 0.7879 (pt0) cc_final: 0.7526 (tp30) REVERT: G 194 LEU cc_start: 0.9259 (tp) cc_final: 0.8818 (tt) REVERT: H 30 GLN cc_start: 0.9136 (mt0) cc_final: 0.8778 (tt0) REVERT: H 81 PHE cc_start: 0.6605 (t80) cc_final: 0.6389 (t80) REVERT: I 93 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7197 (mt-10) REVERT: J 67 LEU cc_start: 0.8540 (mt) cc_final: 0.8239 (tt) REVERT: J 88 ARG cc_start: 0.7906 (mtp180) cc_final: 0.7301 (tpt170) REVERT: J 182 VAL cc_start: 0.7520 (m) cc_final: 0.7228 (p) REVERT: K 78 ARG cc_start: 0.7871 (mmm-85) cc_final: 0.7620 (mmm-85) REVERT: K 80 GLU cc_start: 0.5155 (mt-10) cc_final: 0.4938 (mt-10) REVERT: L 81 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7828 (pt0) REVERT: L 150 LEU cc_start: 0.7426 (mm) cc_final: 0.7022 (mp) REVERT: L 168 LEU cc_start: 0.7998 (mp) cc_final: 0.7703 (mp) REVERT: M 250 SER cc_start: 0.7333 (t) cc_final: 0.7123 (m) REVERT: M 309 PHE cc_start: 0.7225 (m-10) cc_final: 0.6873 (m-10) outliers start: 3 outliers final: 0 residues processed: 1000 average time/residue: 0.1899 time to fit residues: 306.8623 Evaluate side-chains 757 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 757 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 340 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 251 optimal weight: 0.7980 chunk 263 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 383 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 335 optimal weight: 10.0000 chunk 313 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 ASN B 185 HIS ** B 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 ASN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 GLN F 310 GLN ** F 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN J 124 ASN ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 315 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.135695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107516 restraints weight = 67004.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110056 restraints weight = 43234.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111019 restraints weight = 30416.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112712 restraints weight = 24882.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112934 restraints weight = 19451.891| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32743 Z= 0.212 Angle : 0.818 9.862 44380 Z= 0.415 Chirality : 0.047 0.227 4987 Planarity : 0.006 0.078 5831 Dihedral : 6.629 118.142 4623 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.85 % Favored : 89.65 % Rotamer: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -2.16 (0.13), residues: 4134 helix: -0.39 (0.12), residues: 1659 sheet: -1.60 (0.24), residues: 438 loop : -2.31 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 410 TYR 0.050 0.002 TYR F 383 PHE 0.027 0.003 PHE D 204 TRP 0.033 0.002 TRP J 100 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00465 (32742) covalent geometry : angle 0.81775 (44378) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.32050 ( 2) hydrogen bonds : bond 0.05223 ( 1216) hydrogen bonds : angle 5.54250 ( 3453) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 950 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 79 MET cc_start: 0.7749 (mtp) cc_final: 0.6992 (ttm) REVERT: A 117 TRP cc_start: 0.8694 (m100) cc_final: 0.8028 (m100) REVERT: A 161 LYS cc_start: 0.8317 (mmtp) cc_final: 0.8047 (ptpp) REVERT: A 199 LEU cc_start: 0.8553 (tp) cc_final: 0.8189 (tp) REVERT: A 200 ASP cc_start: 0.8947 (p0) cc_final: 0.8731 (t0) REVERT: A 207 THR cc_start: 0.9338 (t) cc_final: 0.8914 (p) REVERT: A 220 MET cc_start: 0.8729 (tpt) cc_final: 0.8221 (tpp) REVERT: A 252 TYR cc_start: 0.9220 (t80) cc_final: 0.8698 (t80) REVERT: A 282 MET cc_start: 0.8607 (mmm) cc_final: 0.8018 (mmm) REVERT: A 293 ASN cc_start: 0.8913 (p0) cc_final: 0.8415 (p0) REVERT: A 363 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8366 (tm-30) REVERT: A 379 THR cc_start: 0.9260 (m) cc_final: 0.8881 (p) REVERT: A 391 MET cc_start: 0.8922 (mmm) cc_final: 0.8580 (mmm) REVERT: A 425 ASN cc_start: 0.9256 (m110) cc_final: 0.8078 (t0) REVERT: A 429 SER cc_start: 0.9053 (t) cc_final: 0.8842 (m) REVERT: A 442 ASN cc_start: 0.9069 (m110) cc_final: 0.8842 (m110) REVERT: A 450 LEU cc_start: 0.8758 (tt) cc_final: 0.8326 (tt) REVERT: A 468 VAL cc_start: 0.8269 (t) cc_final: 0.8052 (t) REVERT: A 482 LEU cc_start: 0.8522 (tp) cc_final: 0.8197 (tt) REVERT: A 490 ILE cc_start: 0.8490 (mt) cc_final: 0.8266 (mt) REVERT: B 38 GLU cc_start: 0.6422 (mt-10) cc_final: 0.5969 (mt-10) REVERT: B 79 MET cc_start: 0.8392 (tpt) cc_final: 0.7795 (tpt) REVERT: B 91 LEU cc_start: 0.9377 (mt) cc_final: 0.9100 (mm) REVERT: B 130 ARG cc_start: 0.8046 (ptm160) cc_final: 0.7721 (ttp80) REVERT: B 133 MET cc_start: 0.8219 (ttm) cc_final: 0.7777 (ttp) REVERT: B 156 ARG cc_start: 0.7378 (mmp-170) cc_final: 0.7039 (mmm160) REVERT: B 186 THR cc_start: 0.8788 (p) cc_final: 0.8331 (t) REVERT: B 193 ARG cc_start: 0.8192 (mtt90) cc_final: 0.6356 (mtt90) REVERT: B 214 VAL cc_start: 0.9079 (t) cc_final: 0.8760 (t) REVERT: B 244 TRP cc_start: 0.8354 (m100) cc_final: 0.7910 (m100) REVERT: B 257 GLU cc_start: 0.8312 (tt0) cc_final: 0.7083 (tt0) REVERT: B 262 MET cc_start: 0.7674 (tpt) cc_final: 0.7317 (tpt) REVERT: B 293 ASN cc_start: 0.8719 (p0) cc_final: 0.8441 (p0) REVERT: B 294 MET cc_start: 0.8754 (mmm) cc_final: 0.8332 (mmm) REVERT: B 307 VAL cc_start: 0.9386 (t) cc_final: 0.9151 (t) REVERT: B 323 MET cc_start: 0.8442 (mmp) cc_final: 0.8031 (mmp) REVERT: B 364 ARG cc_start: 0.8832 (mtp180) cc_final: 0.8420 (mtp180) REVERT: B 393 GLU cc_start: 0.7550 (pm20) cc_final: 0.7204 (pm20) REVERT: B 408 ARG cc_start: 0.8592 (ttt180) cc_final: 0.7760 (ttm170) REVERT: B 507 CYS cc_start: 0.8391 (t) cc_final: 0.7708 (t) REVERT: B 550 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8276 (ttp-170) REVERT: C 26 ASP cc_start: 0.8320 (p0) cc_final: 0.8098 (p0) REVERT: C 39 ILE cc_start: 0.8477 (mp) cc_final: 0.8129 (mm) REVERT: C 165 GLU cc_start: 0.7469 (mp0) cc_final: 0.7049 (mp0) REVERT: C 240 SER cc_start: 0.9264 (m) cc_final: 0.9062 (t) REVERT: C 261 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6635 (mt-10) REVERT: C 290 ASN cc_start: 0.8820 (t0) cc_final: 0.8325 (t0) REVERT: C 294 MET cc_start: 0.9270 (mtt) cc_final: 0.8665 (mtt) REVERT: C 336 GLU cc_start: 0.8511 (tt0) cc_final: 0.8121 (tm-30) REVERT: C 340 ARG cc_start: 0.8511 (mmp80) cc_final: 0.7983 (mmm-85) REVERT: C 367 LYS cc_start: 0.9376 (ttmt) cc_final: 0.8397 (ttpp) REVERT: C 413 LEU cc_start: 0.9139 (tp) cc_final: 0.8878 (mm) REVERT: D 14 ILE cc_start: 0.9511 (mt) cc_final: 0.9122 (tp) REVERT: D 62 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6749 (mm-30) REVERT: D 141 MET cc_start: 0.9409 (pmm) cc_final: 0.9102 (pmm) REVERT: D 170 GLN cc_start: 0.8842 (tt0) cc_final: 0.7947 (tt0) REVERT: D 200 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7516 (mm-30) REVERT: D 260 MET cc_start: 0.8250 (mmp) cc_final: 0.7988 (mmp) REVERT: D 269 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7484 (mm-30) REVERT: D 296 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8428 (mm-30) REVERT: D 300 VAL cc_start: 0.9148 (t) cc_final: 0.8938 (t) REVERT: D 319 ASP cc_start: 0.8262 (m-30) cc_final: 0.7978 (t70) REVERT: D 327 ASP cc_start: 0.8594 (t0) cc_final: 0.8123 (t0) REVERT: D 331 TYR cc_start: 0.8463 (m-10) cc_final: 0.8122 (m-10) REVERT: D 336 GLN cc_start: 0.8427 (mt0) cc_final: 0.8196 (mt0) REVERT: D 383 TYR cc_start: 0.9121 (t80) cc_final: 0.8485 (t80) REVERT: D 429 ASN cc_start: 0.8675 (t0) cc_final: 0.8321 (t0) REVERT: E 49 GLU cc_start: 0.8363 (mp0) cc_final: 0.7851 (mp0) REVERT: E 112 LEU cc_start: 0.8949 (pt) cc_final: 0.8633 (pt) REVERT: E 120 ASN cc_start: 0.8852 (m-40) cc_final: 0.8594 (m110) REVERT: E 126 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8341 (tttp) REVERT: E 206 GLN cc_start: 0.8188 (pp30) cc_final: 0.7634 (pp30) REVERT: E 243 GLU cc_start: 0.8768 (tp30) cc_final: 0.7857 (tp30) REVERT: E 247 PHE cc_start: 0.8432 (m-10) cc_final: 0.8074 (m-80) REVERT: E 250 ASP cc_start: 0.7409 (m-30) cc_final: 0.7108 (t70) REVERT: E 281 ARG cc_start: 0.6773 (mtt180) cc_final: 0.6118 (mtt180) REVERT: E 349 TYR cc_start: 0.9143 (t80) cc_final: 0.8888 (t80) REVERT: E 388 ASN cc_start: 0.8092 (m-40) cc_final: 0.7672 (t0) REVERT: E 404 LEU cc_start: 0.8085 (tp) cc_final: 0.7788 (tp) REVERT: E 432 ILE cc_start: 0.9144 (tp) cc_final: 0.8817 (tp) REVERT: F 35 ILE cc_start: 0.9040 (mt) cc_final: 0.8014 (mt) REVERT: F 36 LYS cc_start: 0.8951 (tptm) cc_final: 0.8596 (tppt) REVERT: F 41 ARG cc_start: 0.7745 (ptm160) cc_final: 0.7368 (ptm160) REVERT: F 53 GLU cc_start: 0.8750 (pm20) cc_final: 0.8091 (tm-30) REVERT: F 89 LEU cc_start: 0.8795 (mt) cc_final: 0.8423 (mt) REVERT: F 139 ASP cc_start: 0.8618 (m-30) cc_final: 0.8065 (p0) REVERT: F 140 VAL cc_start: 0.9503 (t) cc_final: 0.8965 (t) REVERT: F 141 MET cc_start: 0.8750 (mpp) cc_final: 0.8519 (mpp) REVERT: F 170 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8295 (mp10) REVERT: F 176 ASP cc_start: 0.8924 (p0) cc_final: 0.8509 (p0) REVERT: F 221 LEU cc_start: 0.8519 (mt) cc_final: 0.7884 (tt) REVERT: F 269 GLU cc_start: 0.8720 (tp30) cc_final: 0.8436 (mm-30) REVERT: F 280 ARG cc_start: 0.8899 (tpp80) cc_final: 0.8273 (ttt90) REVERT: F 314 LEU cc_start: 0.9436 (tp) cc_final: 0.9132 (tp) REVERT: F 316 MET cc_start: 0.8779 (ptp) cc_final: 0.8509 (ptp) REVERT: F 362 MET cc_start: 0.8521 (ttp) cc_final: 0.8175 (ttt) REVERT: G 119 THR cc_start: 0.6718 (t) cc_final: 0.6375 (t) REVERT: G 191 THR cc_start: 0.9369 (p) cc_final: 0.9165 (t) REVERT: H 30 GLN cc_start: 0.9210 (mt0) cc_final: 0.8809 (tt0) REVERT: I 89 ARG cc_start: 0.5923 (ttm110) cc_final: 0.4771 (tpt90) REVERT: I 95 GLU cc_start: 0.8563 (tm-30) cc_final: 0.7960 (tm-30) REVERT: J 88 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7291 (tpt170) REVERT: J 182 VAL cc_start: 0.7382 (m) cc_final: 0.7129 (p) REVERT: K 80 GLU cc_start: 0.5339 (mt-10) cc_final: 0.4228 (tm-30) REVERT: L 81 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7442 (pt0) REVERT: L 168 LEU cc_start: 0.8041 (mp) cc_final: 0.7734 (mp) REVERT: M 37 LEU cc_start: 0.4863 (mt) cc_final: 0.4601 (mt) REVERT: M 97 GLN cc_start: 0.7764 (mt0) cc_final: 0.6545 (tt0) REVERT: M 243 GLU cc_start: 0.6938 (mm-30) cc_final: 0.5745 (pt0) REVERT: M 250 SER cc_start: 0.7240 (t) cc_final: 0.7020 (m) outliers start: 2 outliers final: 1 residues processed: 952 average time/residue: 0.2011 time to fit residues: 308.4139 Evaluate side-chains 747 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 745 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 90 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 383 optimal weight: 20.0000 chunk 325 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 374 optimal weight: 0.7980 chunk 350 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 HIS B 418 HIS ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 161 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.134607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.106704 restraints weight = 67067.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.109046 restraints weight = 44602.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.109851 restraints weight = 33078.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.111249 restraints weight = 26254.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.111732 restraints weight = 20938.274| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32743 Z= 0.219 Angle : 0.814 10.357 44380 Z= 0.411 Chirality : 0.047 0.243 4987 Planarity : 0.006 0.079 5831 Dihedral : 6.581 136.701 4623 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.92 % Favored : 89.57 % Rotamer: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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 aren not related in a simple way. whole: -1.99 (0.13), residues: 4134 helix: -0.26 (0.13), residues: 1662 sheet: -1.37 (0.25), residues: 428 loop : -2.25 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 360 TYR 0.055 0.002 TYR F 383 PHE 0.026 0.003 PHE B 559 TRP 0.036 0.002 TRP A 424 HIS 0.009 0.002 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00483 (32742) covalent geometry : angle 0.81451 (44378) SS BOND : bond 0.00283 ( 1) SS BOND : angle 0.20151 ( 2) hydrogen bonds : bond 0.05021 ( 1216) hydrogen bonds : angle 5.39762 ( 3453) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 908 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 79 MET cc_start: 0.7890 (mtp) cc_final: 0.6992 (ttm) REVERT: A 85 ASP cc_start: 0.8094 (m-30) cc_final: 0.7733 (m-30) REVERT: A 133 MET cc_start: 0.7097 (mtt) cc_final: 0.6780 (mtt) REVERT: A 161 LYS cc_start: 0.8319 (mmtp) cc_final: 0.8058 (ptpp) REVERT: A 199 LEU cc_start: 0.8845 (tp) cc_final: 0.8549 (tp) REVERT: A 207 THR cc_start: 0.9078 (t) cc_final: 0.8394 (p) REVERT: A 220 MET cc_start: 0.8757 (tpt) cc_final: 0.8352 (tpp) REVERT: A 252 TYR cc_start: 0.9218 (t80) cc_final: 0.8564 (t80) REVERT: A 282 MET cc_start: 0.8609 (mmm) cc_final: 0.8213 (mmm) REVERT: A 291 THR cc_start: 0.9098 (m) cc_final: 0.8765 (m) REVERT: A 293 ASN cc_start: 0.8836 (p0) cc_final: 0.8161 (p0) REVERT: A 344 MET cc_start: 0.8995 (ttp) cc_final: 0.8451 (ptm) REVERT: A 379 THR cc_start: 0.9205 (m) cc_final: 0.8849 (p) REVERT: A 425 ASN cc_start: 0.9367 (m110) cc_final: 0.8173 (t0) REVERT: A 429 SER cc_start: 0.9043 (t) cc_final: 0.8795 (m) REVERT: A 442 ASN cc_start: 0.8999 (m110) cc_final: 0.8749 (m110) REVERT: B 38 GLU cc_start: 0.6320 (mt-10) cc_final: 0.6026 (mt-10) REVERT: B 62 GLU cc_start: 0.8356 (pt0) cc_final: 0.7889 (pt0) REVERT: B 79 MET cc_start: 0.7995 (tpt) cc_final: 0.7378 (tpt) REVERT: B 91 LEU cc_start: 0.9304 (mt) cc_final: 0.8953 (mm) REVERT: B 122 MET cc_start: 0.8729 (mtp) cc_final: 0.8527 (mtp) REVERT: B 130 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7871 (ttp80) REVERT: B 133 MET cc_start: 0.8380 (ttm) cc_final: 0.8160 (ttp) REVERT: B 152 ASP cc_start: 0.8051 (m-30) cc_final: 0.7759 (t0) REVERT: B 186 THR cc_start: 0.8466 (p) cc_final: 0.8252 (t) REVERT: B 193 ARG cc_start: 0.7861 (mtt90) cc_final: 0.7313 (mtt90) REVERT: B 244 TRP cc_start: 0.8332 (m100) cc_final: 0.8070 (m100) REVERT: B 257 GLU cc_start: 0.8223 (tt0) cc_final: 0.7565 (tt0) REVERT: B 293 ASN cc_start: 0.8834 (p0) cc_final: 0.8345 (p0) REVERT: B 294 MET cc_start: 0.8916 (mmm) cc_final: 0.8479 (mmm) REVERT: B 408 ARG cc_start: 0.8748 (ttt180) cc_final: 0.7951 (ttm170) REVERT: B 460 ARG cc_start: 0.8546 (ttm170) cc_final: 0.8309 (ttm-80) REVERT: B 504 ASP cc_start: 0.7659 (p0) cc_final: 0.7435 (p0) REVERT: B 516 MET cc_start: 0.9011 (ttp) cc_final: 0.8620 (ttp) REVERT: B 550 ARG cc_start: 0.8900 (mtt180) cc_final: 0.8302 (ttp-170) REVERT: C 2 ILE cc_start: 0.7964 (mm) cc_final: 0.7704 (mm) REVERT: C 39 ILE cc_start: 0.8483 (mp) cc_final: 0.8147 (mm) REVERT: C 62 GLU cc_start: 0.8596 (mp0) cc_final: 0.8008 (mp0) REVERT: C 122 MET cc_start: 0.8280 (tmm) cc_final: 0.7988 (tmm) REVERT: C 165 GLU cc_start: 0.7496 (mp0) cc_final: 0.7174 (mp0) REVERT: C 261 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7563 (mt-10) REVERT: C 264 ASP cc_start: 0.8696 (m-30) cc_final: 0.8436 (m-30) REVERT: C 290 ASN cc_start: 0.8959 (t0) cc_final: 0.8294 (t0) REVERT: C 294 MET cc_start: 0.9340 (mtt) cc_final: 0.8571 (mtt) REVERT: C 336 GLU cc_start: 0.8647 (tt0) cc_final: 0.8071 (tm-30) REVERT: C 367 LYS cc_start: 0.9398 (ttmt) cc_final: 0.8475 (ttpp) REVERT: C 396 THR cc_start: 0.9108 (m) cc_final: 0.8819 (t) REVERT: C 413 LEU cc_start: 0.9021 (tp) cc_final: 0.8804 (mm) REVERT: C 507 CYS cc_start: 0.8560 (m) cc_final: 0.8264 (m) REVERT: C 567 MET cc_start: 0.8234 (tpt) cc_final: 0.8025 (tpp) REVERT: D 14 ILE cc_start: 0.9497 (mt) cc_final: 0.9099 (tp) REVERT: D 50 VAL cc_start: 0.8975 (m) cc_final: 0.8719 (p) REVERT: D 56 VAL cc_start: 0.8828 (t) cc_final: 0.8452 (t) REVERT: D 141 MET cc_start: 0.9339 (pmm) cc_final: 0.9090 (pmm) REVERT: D 142 ASN cc_start: 0.8936 (p0) cc_final: 0.8585 (p0) REVERT: D 148 GLN cc_start: 0.7627 (tt0) cc_final: 0.7316 (mt0) REVERT: D 200 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7824 (mt-10) REVERT: D 260 MET cc_start: 0.8348 (mmp) cc_final: 0.8025 (mmp) REVERT: D 275 GLU cc_start: 0.8975 (tp30) cc_final: 0.8100 (mp0) REVERT: D 276 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7623 (mm-30) REVERT: D 296 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8517 (mm-30) REVERT: D 319 ASP cc_start: 0.8327 (m-30) cc_final: 0.7940 (t70) REVERT: D 327 ASP cc_start: 0.8594 (t0) cc_final: 0.8222 (t0) REVERT: D 328 LEU cc_start: 0.9411 (mt) cc_final: 0.9130 (tp) REVERT: D 331 TYR cc_start: 0.8544 (m-10) cc_final: 0.8143 (m-80) REVERT: D 383 TYR cc_start: 0.9169 (t80) cc_final: 0.8548 (t80) REVERT: D 429 ASN cc_start: 0.8413 (t0) cc_final: 0.8180 (t0) REVERT: E 7 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7924 (mt-10) REVERT: E 49 GLU cc_start: 0.8341 (mp0) cc_final: 0.8058 (mp0) REVERT: E 52 GLU cc_start: 0.7474 (pt0) cc_final: 0.6848 (pm20) REVERT: E 120 ASN cc_start: 0.8817 (m-40) cc_final: 0.8386 (m110) REVERT: E 126 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8098 (ttpt) REVERT: E 205 ILE cc_start: 0.8823 (mm) cc_final: 0.8537 (tp) REVERT: E 206 GLN cc_start: 0.8211 (pp30) cc_final: 0.7095 (pp30) REVERT: E 207 GLU cc_start: 0.8193 (tp30) cc_final: 0.7540 (tp30) REVERT: E 215 SER cc_start: 0.8628 (p) cc_final: 0.8280 (p) REVERT: E 243 GLU cc_start: 0.8519 (tp30) cc_final: 0.7520 (tp30) REVERT: E 247 PHE cc_start: 0.8258 (m-10) cc_final: 0.7608 (m-80) REVERT: E 250 ASP cc_start: 0.7167 (m-30) cc_final: 0.6543 (t0) REVERT: E 269 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8108 (mt-10) REVERT: E 334 GLU cc_start: 0.9207 (pm20) cc_final: 0.8823 (mp0) REVERT: E 349 TYR cc_start: 0.9135 (t80) cc_final: 0.8917 (t80) REVERT: E 388 ASN cc_start: 0.7934 (m-40) cc_final: 0.7560 (t0) REVERT: E 432 ILE cc_start: 0.9243 (tp) cc_final: 0.8749 (mm) REVERT: F 36 LYS cc_start: 0.8803 (tptm) cc_final: 0.8574 (tppt) REVERT: F 53 GLU cc_start: 0.8847 (pm20) cc_final: 0.8166 (tm-30) REVERT: F 60 PHE cc_start: 0.8768 (m-10) cc_final: 0.7819 (m-80) REVERT: F 89 LEU cc_start: 0.8795 (mt) cc_final: 0.8472 (mt) REVERT: F 139 ASP cc_start: 0.8550 (m-30) cc_final: 0.8257 (m-30) REVERT: F 141 MET cc_start: 0.8880 (mpp) cc_final: 0.8530 (mpp) REVERT: F 221 LEU cc_start: 0.8641 (mt) cc_final: 0.8029 (tt) REVERT: F 269 GLU cc_start: 0.8828 (tp30) cc_final: 0.8605 (tp30) REVERT: F 314 LEU cc_start: 0.9447 (tp) cc_final: 0.9100 (tp) REVERT: F 362 MET cc_start: 0.8701 (ttp) cc_final: 0.8480 (ttp) REVERT: F 410 ARG cc_start: 0.7166 (mpp-170) cc_final: 0.6865 (mtm110) REVERT: G 173 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.7871 (ttp-170) REVERT: H 30 GLN cc_start: 0.9225 (mt0) cc_final: 0.8797 (tt0) REVERT: H 68 LEU cc_start: 0.8110 (mt) cc_final: 0.7768 (pt) REVERT: I 78 ARG cc_start: 0.5845 (ttp-110) cc_final: 0.4691 (ptm-80) REVERT: I 89 ARG cc_start: 0.5788 (ttm110) cc_final: 0.4635 (tpt-90) REVERT: J 57 LEU cc_start: 0.8170 (tp) cc_final: 0.7844 (pp) REVERT: K 80 GLU cc_start: 0.5282 (mt-10) cc_final: 0.4035 (tm-30) REVERT: L 81 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7663 (pt0) REVERT: L 94 LEU cc_start: 0.7696 (tp) cc_final: 0.7140 (mp) REVERT: L 168 LEU cc_start: 0.8115 (mp) cc_final: 0.7873 (mp) REVERT: M 97 GLN cc_start: 0.8141 (mt0) cc_final: 0.6715 (tt0) REVERT: M 309 PHE cc_start: 0.7136 (m-10) cc_final: 0.6852 (m-10) outliers start: 2 outliers final: 0 residues processed: 910 average time/residue: 0.2009 time to fit residues: 295.1948 Evaluate side-chains 713 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 713 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 408 optimal weight: 10.0000 chunk 371 optimal weight: 30.0000 chunk 87 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 289 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 375 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 303 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 290 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN C 239 GLN ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS ** F 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.107325 restraints weight = 66260.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109537 restraints weight = 43904.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110569 restraints weight = 31178.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.111909 restraints weight = 25211.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111928 restraints weight = 21449.907| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32743 Z= 0.178 Angle : 0.775 11.172 44380 Z= 0.389 Chirality : 0.046 0.310 4987 Planarity : 0.006 0.135 5831 Dihedral : 6.342 134.948 4623 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.93 % Favored : 90.64 % Rotamer: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.44 % 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 aren not related in a simple way. whole: -1.75 (0.13), residues: 4134 helix: -0.01 (0.13), residues: 1662 sheet: -1.41 (0.25), residues: 428 loop : -2.13 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 258 TYR 0.046 0.002 TYR F 383 PHE 0.032 0.002 PHE C 216 TRP 0.026 0.002 TRP L 175 HIS 0.006 0.001 HIS M 145 Details of bonding type rmsd covalent geometry : bond 0.00391 (32742) covalent geometry : angle 0.77459 (44378) SS BOND : bond 0.00184 ( 1) SS BOND : angle 0.05840 ( 2) hydrogen bonds : bond 0.04672 ( 1216) hydrogen bonds : angle 5.25195 ( 3453) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 893 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 19 MET cc_start: 0.8083 (mmm) cc_final: 0.7189 (mmm) REVERT: A 65 VAL cc_start: 0.9166 (m) cc_final: 0.8945 (p) REVERT: A 79 MET cc_start: 0.7826 (mtp) cc_final: 0.7130 (ttm) REVERT: A 133 MET cc_start: 0.7077 (mtt) cc_final: 0.6841 (mtt) REVERT: A 161 LYS cc_start: 0.8258 (mmtp) cc_final: 0.7729 (ptpp) REVERT: A 199 LEU cc_start: 0.8891 (tp) cc_final: 0.8619 (tp) REVERT: A 207 THR cc_start: 0.9295 (t) cc_final: 0.8297 (p) REVERT: A 220 MET cc_start: 0.8797 (tpt) cc_final: 0.8311 (tpp) REVERT: A 252 TYR cc_start: 0.9263 (t80) cc_final: 0.8478 (t80) REVERT: A 282 MET cc_start: 0.8669 (mmm) cc_final: 0.8330 (mmm) REVERT: A 290 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8000 (t0) REVERT: A 293 ASN cc_start: 0.8496 (p0) cc_final: 0.8003 (p0) REVERT: A 336 GLU cc_start: 0.6974 (tt0) cc_final: 0.6535 (tt0) REVERT: A 363 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8459 (tm-30) REVERT: A 379 THR cc_start: 0.9231 (m) cc_final: 0.8744 (m) REVERT: A 425 ASN cc_start: 0.9309 (m110) cc_final: 0.8171 (t0) REVERT: A 442 ASN cc_start: 0.9051 (m110) cc_final: 0.8753 (m110) REVERT: A 461 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7456 (mm-30) REVERT: B 38 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6358 (mt-10) REVERT: B 52 TYR cc_start: 0.7903 (m-80) cc_final: 0.7564 (m-80) REVERT: B 79 MET cc_start: 0.7844 (tpt) cc_final: 0.7331 (tpt) REVERT: B 91 LEU cc_start: 0.9321 (mt) cc_final: 0.9029 (mm) REVERT: B 133 MET cc_start: 0.8515 (ttm) cc_final: 0.8148 (ttp) REVERT: B 152 ASP cc_start: 0.8085 (m-30) cc_final: 0.7707 (t0) REVERT: B 166 TYR cc_start: 0.8216 (m-80) cc_final: 0.7442 (m-10) REVERT: B 244 TRP cc_start: 0.8282 (m100) cc_final: 0.7924 (m100) REVERT: B 257 GLU cc_start: 0.8256 (tt0) cc_final: 0.7555 (tt0) REVERT: B 293 ASN cc_start: 0.8783 (p0) cc_final: 0.8412 (p0) REVERT: B 294 MET cc_start: 0.8940 (mmm) cc_final: 0.8228 (mmm) REVERT: B 311 GLU cc_start: 0.7379 (pp20) cc_final: 0.6549 (pp20) REVERT: B 318 PHE cc_start: 0.9105 (m-10) cc_final: 0.8305 (m-10) REVERT: B 323 MET cc_start: 0.8240 (mmp) cc_final: 0.8014 (mmp) REVERT: B 408 ARG cc_start: 0.8663 (ttt180) cc_final: 0.7872 (tpp80) REVERT: B 460 ARG cc_start: 0.8575 (ttm170) cc_final: 0.8364 (ttm-80) REVERT: B 507 CYS cc_start: 0.8087 (t) cc_final: 0.7827 (t) REVERT: B 516 MET cc_start: 0.9101 (ttp) cc_final: 0.8872 (ttp) REVERT: B 550 ARG cc_start: 0.8911 (mtt180) cc_final: 0.8116 (ttp-170) REVERT: C 39 ILE cc_start: 0.8532 (mp) cc_final: 0.8168 (mm) REVERT: C 62 GLU cc_start: 0.8566 (mp0) cc_final: 0.7938 (mp0) REVERT: C 84 TYR cc_start: 0.7514 (m-80) cc_final: 0.7076 (m-10) REVERT: C 165 GLU cc_start: 0.7609 (mp0) cc_final: 0.7244 (mp0) REVERT: C 175 LEU cc_start: 0.8805 (mt) cc_final: 0.8383 (tt) REVERT: C 261 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6974 (mt-10) REVERT: C 290 ASN cc_start: 0.8848 (t0) cc_final: 0.8284 (t0) REVERT: C 294 MET cc_start: 0.9271 (mtt) cc_final: 0.8595 (mtt) REVERT: C 336 GLU cc_start: 0.8656 (tt0) cc_final: 0.8016 (tm-30) REVERT: C 367 LYS cc_start: 0.9184 (ttmt) cc_final: 0.8907 (ttpp) REVERT: C 507 CYS cc_start: 0.8436 (m) cc_final: 0.8176 (m) REVERT: C 559 PHE cc_start: 0.8027 (t80) cc_final: 0.7806 (t80) REVERT: C 567 MET cc_start: 0.8191 (tpt) cc_final: 0.7987 (tpp) REVERT: D 14 ILE cc_start: 0.9474 (mt) cc_final: 0.9053 (tp) REVERT: D 50 VAL cc_start: 0.9147 (m) cc_final: 0.8903 (p) REVERT: D 200 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7721 (mt-10) REVERT: D 214 LEU cc_start: 0.7503 (mt) cc_final: 0.7154 (tt) REVERT: D 296 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8302 (mm-30) REVERT: D 327 ASP cc_start: 0.8549 (t0) cc_final: 0.8023 (t0) REVERT: D 331 TYR cc_start: 0.8467 (m-10) cc_final: 0.8077 (m-80) REVERT: D 383 TYR cc_start: 0.9092 (t80) cc_final: 0.8337 (t80) REVERT: D 445 MET cc_start: 0.8742 (mtp) cc_final: 0.8381 (mtp) REVERT: E 49 GLU cc_start: 0.8395 (mp0) cc_final: 0.7999 (mp0) REVERT: E 52 GLU cc_start: 0.7520 (pt0) cc_final: 0.6950 (pm20) REVERT: E 112 LEU cc_start: 0.9001 (pp) cc_final: 0.8587 (tt) REVERT: E 120 ASN cc_start: 0.8977 (m-40) cc_final: 0.8423 (m110) REVERT: E 126 LYS cc_start: 0.8646 (ttpt) cc_final: 0.7953 (ttpt) REVERT: E 205 ILE cc_start: 0.8893 (mm) cc_final: 0.8500 (tp) REVERT: E 206 GLN cc_start: 0.8202 (pp30) cc_final: 0.7430 (pp30) REVERT: E 215 SER cc_start: 0.8584 (p) cc_final: 0.8197 (p) REVERT: E 250 ASP cc_start: 0.7064 (m-30) cc_final: 0.6489 (t0) REVERT: E 269 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8191 (mt-10) REVERT: E 316 MET cc_start: 0.8906 (ptm) cc_final: 0.8670 (ptm) REVERT: E 319 ASP cc_start: 0.7259 (m-30) cc_final: 0.6906 (t0) REVERT: E 334 GLU cc_start: 0.8971 (mp0) cc_final: 0.8660 (mp0) REVERT: E 388 ASN cc_start: 0.8227 (m-40) cc_final: 0.7734 (t0) REVERT: E 429 ASN cc_start: 0.7054 (p0) cc_final: 0.6756 (p0) REVERT: E 432 ILE cc_start: 0.9257 (tp) cc_final: 0.8821 (mm) REVERT: F 36 LYS cc_start: 0.8862 (tptm) cc_final: 0.8575 (tppt) REVERT: F 53 GLU cc_start: 0.8721 (pm20) cc_final: 0.7715 (tm-30) REVERT: F 89 LEU cc_start: 0.8774 (mt) cc_final: 0.8470 (mt) REVERT: F 139 ASP cc_start: 0.8634 (m-30) cc_final: 0.7986 (p0) REVERT: F 141 MET cc_start: 0.8707 (mpp) cc_final: 0.8277 (mpp) REVERT: F 194 MET cc_start: 0.7932 (mpp) cc_final: 0.7676 (mpp) REVERT: F 221 LEU cc_start: 0.8582 (mt) cc_final: 0.8005 (tt) REVERT: F 314 LEU cc_start: 0.9359 (tp) cc_final: 0.9045 (tp) REVERT: F 329 THR cc_start: 0.9456 (m) cc_final: 0.9048 (p) REVERT: G 23 LYS cc_start: 0.7337 (tppt) cc_final: 0.7094 (tppt) REVERT: G 119 THR cc_start: 0.6944 (t) cc_final: 0.6492 (t) REVERT: G 173 ARG cc_start: 0.8907 (mmm-85) cc_final: 0.7874 (ttp-170) REVERT: G 187 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7259 (mt-10) REVERT: G 193 ARG cc_start: 0.8989 (ttm110) cc_final: 0.8631 (ttm170) REVERT: H 30 GLN cc_start: 0.9232 (mt0) cc_final: 0.8812 (tt0) REVERT: H 68 LEU cc_start: 0.8157 (mt) cc_final: 0.7789 (pt) REVERT: I 85 LEU cc_start: 0.7538 (pp) cc_final: 0.7332 (pp) REVERT: I 89 ARG cc_start: 0.5912 (ttm110) cc_final: 0.4676 (tpt-90) REVERT: I 95 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8113 (tm-30) REVERT: K 78 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7566 (mmm-85) REVERT: K 80 GLU cc_start: 0.4468 (mt-10) cc_final: 0.3412 (tm-30) REVERT: L 81 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7857 (pt0) REVERT: L 94 LEU cc_start: 0.7554 (tp) cc_final: 0.7050 (mp) REVERT: L 175 TRP cc_start: 0.8268 (t-100) cc_final: 0.8021 (t-100) outliers start: 2 outliers final: 1 residues processed: 894 average time/residue: 0.1880 time to fit residues: 273.4025 Evaluate side-chains 712 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 710 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 396 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 154 optimal weight: 0.0030 chunk 400 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 328 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 312 optimal weight: 0.7980 overall best weight: 2.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 HIS C 571 GLN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.105983 restraints weight = 66882.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.107763 restraints weight = 45662.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108772 restraints weight = 33023.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.109788 restraints weight = 26931.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.110321 restraints weight = 22572.498| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 32743 Z= 0.204 Angle : 0.801 10.273 44380 Z= 0.403 Chirality : 0.047 0.310 4987 Planarity : 0.006 0.120 5831 Dihedral : 6.270 134.486 4623 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.89 % Favored : 89.62 % Rotamer: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % 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 aren not related in a simple way. whole: -1.70 (0.13), residues: 4134 helix: 0.00 (0.13), residues: 1664 sheet: -1.21 (0.26), residues: 399 loop : -2.10 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 258 TYR 0.054 0.002 TYR F 383 PHE 0.025 0.002 PHE B 559 TRP 0.020 0.002 TRP L 175 HIS 0.007 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00452 (32742) covalent geometry : angle 0.80112 (44378) SS BOND : bond 0.00133 ( 1) SS BOND : angle 0.14372 ( 2) hydrogen bonds : bond 0.04729 ( 1216) hydrogen bonds : angle 5.29939 ( 3453) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 880 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 19 MET cc_start: 0.8394 (mmm) cc_final: 0.7507 (mmm) REVERT: A 79 MET cc_start: 0.7883 (mtp) cc_final: 0.7043 (ttm) REVERT: A 161 LYS cc_start: 0.8305 (mmtp) cc_final: 0.7849 (ptpp) REVERT: A 169 GLU cc_start: 0.8831 (mp0) cc_final: 0.6987 (tp30) REVERT: A 183 MET cc_start: 0.8634 (pmm) cc_final: 0.8321 (pmm) REVERT: A 199 LEU cc_start: 0.8972 (tp) cc_final: 0.8642 (tp) REVERT: A 207 THR cc_start: 0.9461 (t) cc_final: 0.8881 (p) REVERT: A 220 MET cc_start: 0.8759 (tpt) cc_final: 0.8290 (tpp) REVERT: A 252 TYR cc_start: 0.9193 (t80) cc_final: 0.8582 (t80) REVERT: A 282 MET cc_start: 0.8753 (mmm) cc_final: 0.8542 (mmm) REVERT: A 293 ASN cc_start: 0.8600 (p0) cc_final: 0.7894 (p0) REVERT: A 344 MET cc_start: 0.8982 (ttp) cc_final: 0.8438 (ptm) REVERT: A 379 THR cc_start: 0.9226 (m) cc_final: 0.8642 (m) REVERT: A 425 ASN cc_start: 0.9375 (m110) cc_final: 0.8259 (t0) REVERT: A 442 ASN cc_start: 0.9038 (m110) cc_final: 0.8742 (m110) REVERT: A 461 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7470 (mm-30) REVERT: A 468 VAL cc_start: 0.8100 (t) cc_final: 0.7828 (t) REVERT: A 469 GLN cc_start: 0.8818 (tp40) cc_final: 0.8597 (tm-30) REVERT: B 38 GLU cc_start: 0.6485 (mt-10) cc_final: 0.6210 (mt-10) REVERT: B 62 GLU cc_start: 0.8461 (pt0) cc_final: 0.8015 (pt0) REVERT: B 79 MET cc_start: 0.7726 (tpt) cc_final: 0.7260 (tpt) REVERT: B 91 LEU cc_start: 0.9363 (mt) cc_final: 0.9064 (mm) REVERT: B 166 TYR cc_start: 0.7911 (m-80) cc_final: 0.7554 (m-10) REVERT: B 244 TRP cc_start: 0.8318 (m100) cc_final: 0.7907 (m100) REVERT: B 257 GLU cc_start: 0.8278 (tt0) cc_final: 0.7737 (tt0) REVERT: B 293 ASN cc_start: 0.8822 (p0) cc_final: 0.8292 (p0) REVERT: B 294 MET cc_start: 0.8954 (mmm) cc_final: 0.8248 (mmm) REVERT: B 311 GLU cc_start: 0.7590 (pp20) cc_final: 0.6614 (pp20) REVERT: B 340 ARG cc_start: 0.9076 (tpp80) cc_final: 0.8474 (tpp80) REVERT: B 408 ARG cc_start: 0.8775 (ttt180) cc_final: 0.8082 (tpp80) REVERT: B 507 CYS cc_start: 0.8195 (t) cc_final: 0.7951 (t) REVERT: B 550 ARG cc_start: 0.9018 (mtt180) cc_final: 0.8176 (ttp-170) REVERT: C 20 LEU cc_start: 0.8481 (mm) cc_final: 0.8141 (mp) REVERT: C 39 ILE cc_start: 0.8499 (mp) cc_final: 0.8145 (mm) REVERT: C 62 GLU cc_start: 0.8621 (mp0) cc_final: 0.7965 (mp0) REVERT: C 84 TYR cc_start: 0.7667 (m-80) cc_final: 0.7300 (m-10) REVERT: C 122 MET cc_start: 0.8356 (tmm) cc_final: 0.8015 (tmm) REVERT: C 165 GLU cc_start: 0.7699 (mp0) cc_final: 0.7369 (mp0) REVERT: C 175 LEU cc_start: 0.8927 (mt) cc_final: 0.8698 (tt) REVERT: C 248 ASP cc_start: 0.7531 (m-30) cc_final: 0.7280 (m-30) REVERT: C 290 ASN cc_start: 0.8909 (t0) cc_final: 0.8317 (t0) REVERT: C 294 MET cc_start: 0.9282 (mtt) cc_final: 0.8642 (mtt) REVERT: C 336 GLU cc_start: 0.8669 (tt0) cc_final: 0.7772 (tm-30) REVERT: C 340 ARG cc_start: 0.8344 (mmp80) cc_final: 0.7962 (mmm-85) REVERT: C 367 LYS cc_start: 0.9234 (ttmt) cc_final: 0.8880 (ttpp) REVERT: C 507 CYS cc_start: 0.8528 (m) cc_final: 0.8148 (m) REVERT: C 559 PHE cc_start: 0.8113 (t80) cc_final: 0.7772 (t80) REVERT: C 567 MET cc_start: 0.8158 (tpt) cc_final: 0.7902 (tpp) REVERT: D 50 VAL cc_start: 0.9024 (m) cc_final: 0.8721 (p) REVERT: D 200 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7791 (mt-10) REVERT: D 214 LEU cc_start: 0.7478 (mt) cc_final: 0.7084 (tt) REVERT: D 275 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8447 (mp0) REVERT: D 276 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7739 (mm-30) REVERT: D 296 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8243 (mm-30) REVERT: D 327 ASP cc_start: 0.8596 (t0) cc_final: 0.8071 (t0) REVERT: D 331 TYR cc_start: 0.8512 (m-10) cc_final: 0.8104 (m-80) REVERT: D 383 TYR cc_start: 0.9158 (t80) cc_final: 0.8479 (t80) REVERT: D 445 MET cc_start: 0.8788 (mtp) cc_final: 0.8433 (mtp) REVERT: E 49 GLU cc_start: 0.8493 (mp0) cc_final: 0.8113 (mp0) REVERT: E 52 GLU cc_start: 0.7539 (pt0) cc_final: 0.6917 (pm20) REVERT: E 120 ASN cc_start: 0.8941 (m-40) cc_final: 0.8399 (m110) REVERT: E 206 GLN cc_start: 0.8271 (pp30) cc_final: 0.7551 (pp30) REVERT: E 215 SER cc_start: 0.8612 (p) cc_final: 0.8259 (p) REVERT: E 250 ASP cc_start: 0.7236 (m-30) cc_final: 0.6708 (t0) REVERT: E 269 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7942 (mt-10) REVERT: E 280 ARG cc_start: 0.7360 (tpm170) cc_final: 0.6949 (mmm160) REVERT: E 388 ASN cc_start: 0.8358 (m-40) cc_final: 0.7742 (t0) REVERT: E 392 ILE cc_start: 0.8116 (mt) cc_final: 0.7896 (mm) REVERT: E 429 ASN cc_start: 0.7346 (p0) cc_final: 0.6800 (p0) REVERT: E 432 ILE cc_start: 0.9209 (tp) cc_final: 0.8906 (mm) REVERT: F 36 LYS cc_start: 0.8889 (tptm) cc_final: 0.8561 (tppt) REVERT: F 53 GLU cc_start: 0.8650 (pm20) cc_final: 0.7895 (tm-30) REVERT: F 60 PHE cc_start: 0.8903 (m-10) cc_final: 0.8310 (m-80) REVERT: F 89 LEU cc_start: 0.8717 (mt) cc_final: 0.8459 (mt) REVERT: F 139 ASP cc_start: 0.8598 (m-30) cc_final: 0.8001 (p0) REVERT: F 141 MET cc_start: 0.8581 (mpp) cc_final: 0.8057 (mpp) REVERT: F 194 MET cc_start: 0.8058 (mpp) cc_final: 0.7841 (mpp) REVERT: F 221 LEU cc_start: 0.8590 (mt) cc_final: 0.8005 (tt) REVERT: F 269 GLU cc_start: 0.9021 (tp30) cc_final: 0.8569 (mm-30) REVERT: F 314 LEU cc_start: 0.9371 (tp) cc_final: 0.9038 (tp) REVERT: F 329 THR cc_start: 0.9452 (m) cc_final: 0.9026 (p) REVERT: G 23 LYS cc_start: 0.7163 (tppt) cc_final: 0.6904 (tppt) REVERT: G 119 THR cc_start: 0.7530 (t) cc_final: 0.7070 (t) REVERT: G 173 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.7904 (ttp-170) REVERT: G 187 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7205 (mt-10) REVERT: G 193 ARG cc_start: 0.8933 (ttm110) cc_final: 0.8582 (ttm170) REVERT: H 30 GLN cc_start: 0.9263 (mt0) cc_final: 0.8812 (tt0) REVERT: H 68 LEU cc_start: 0.8045 (mt) cc_final: 0.7418 (pt) REVERT: I 89 ARG cc_start: 0.6117 (ttm110) cc_final: 0.4807 (tpt-90) REVERT: K 80 GLU cc_start: 0.4929 (mt-10) cc_final: 0.3712 (tm-30) REVERT: L 81 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7931 (pt0) REVERT: L 94 LEU cc_start: 0.7568 (tp) cc_final: 0.7052 (mp) REVERT: L 168 LEU cc_start: 0.8207 (mp) cc_final: 0.7885 (mp) REVERT: M 38 ARG cc_start: 0.6752 (mmm160) cc_final: 0.5718 (ptm160) REVERT: M 206 LYS cc_start: 0.8466 (pttt) cc_final: 0.8174 (pptt) outliers start: 1 outliers final: 0 residues processed: 880 average time/residue: 0.1743 time to fit residues: 250.8682 Evaluate side-chains 717 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 717 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 411 random chunks: chunk 38 optimal weight: 3.9990 chunk 408 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 224 optimal weight: 0.9980 chunk 406 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 380 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN B 109 HIS C 418 HIS ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 ASN E 458 HIS F 310 GLN L 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.130381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.102602 restraints weight = 67585.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104900 restraints weight = 46464.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106130 restraints weight = 32305.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.107110 restraints weight = 25798.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.107453 restraints weight = 21607.187| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.7070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 32743 Z= 0.266 Angle : 0.868 10.723 44380 Z= 0.441 Chirality : 0.049 0.294 4987 Planarity : 0.007 0.080 5831 Dihedral : 6.491 129.280 4623 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.89 % Favored : 88.68 % Rotamer: Outliers : 0.03 % Allowed : 1.74 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: -1.86 (0.13), residues: 4134 helix: -0.12 (0.13), residues: 1659 sheet: -1.40 (0.25), residues: 419 loop : -2.18 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 360 TYR 0.054 0.003 TYR F 383 PHE 0.041 0.003 PHE B 269 TRP 0.028 0.002 TRP L 100 HIS 0.008 0.002 HIS F 323 Details of bonding type rmsd covalent geometry : bond 0.00591 (32742) covalent geometry : angle 0.86785 (44378) SS BOND : bond 0.00180 ( 1) SS BOND : angle 0.28436 ( 2) hydrogen bonds : bond 0.04990 ( 1216) hydrogen bonds : angle 5.50366 ( 3453) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 851 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET I 104 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 134 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 178 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET K 104 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 134 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 171 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 178 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS M 322 " (corrupted residue). Skipping it. REVERT: A 19 MET cc_start: 0.8528 (mmm) cc_final: 0.7604 (mmm) REVERT: A 65 VAL cc_start: 0.9165 (m) cc_final: 0.8947 (p) REVERT: A 79 MET cc_start: 0.7909 (mtp) cc_final: 0.7199 (ttm) REVERT: A 117 TRP cc_start: 0.8716 (m100) cc_final: 0.8259 (m100) REVERT: A 133 MET cc_start: 0.7146 (mtt) cc_final: 0.6453 (mtp) REVERT: A 161 LYS cc_start: 0.8489 (mmtp) cc_final: 0.7932 (ptpp) REVERT: A 199 LEU cc_start: 0.8995 (tp) cc_final: 0.8719 (tp) REVERT: A 220 MET cc_start: 0.8809 (tpt) cc_final: 0.8353 (tpp) REVERT: A 238 GLN cc_start: 0.8923 (mp10) cc_final: 0.8636 (mp-120) REVERT: A 252 TYR cc_start: 0.9279 (t80) cc_final: 0.8544 (t80) REVERT: A 293 ASN cc_start: 0.8658 (p0) cc_final: 0.7887 (p0) REVERT: A 344 MET cc_start: 0.8967 (ttp) cc_final: 0.8363 (ptp) REVERT: A 379 THR cc_start: 0.9120 (m) cc_final: 0.8657 (p) REVERT: A 425 ASN cc_start: 0.9320 (m110) cc_final: 0.8354 (t0) REVERT: A 450 LEU cc_start: 0.8887 (tt) cc_final: 0.8638 (tt) REVERT: A 468 VAL cc_start: 0.8192 (t) cc_final: 0.7918 (t) REVERT: A 469 GLN cc_start: 0.8925 (tp40) cc_final: 0.8424 (tm-30) REVERT: B 38 GLU cc_start: 0.6327 (mt-10) cc_final: 0.6024 (mt-10) REVERT: B 52 TYR cc_start: 0.8181 (m-80) cc_final: 0.7531 (m-80) REVERT: B 62 GLU cc_start: 0.8535 (pt0) cc_final: 0.8069 (pt0) REVERT: B 79 MET cc_start: 0.7841 (tpt) cc_final: 0.7611 (tpt) REVERT: B 91 LEU cc_start: 0.9402 (mt) cc_final: 0.8951 (mm) REVERT: B 130 ARG cc_start: 0.8193 (ptm-80) cc_final: 0.7500 (ttp80) REVERT: B 166 TYR cc_start: 0.8008 (m-80) cc_final: 0.7583 (m-10) REVERT: B 193 ARG cc_start: 0.8372 (mtt180) cc_final: 0.7973 (mtt90) REVERT: B 244 TRP cc_start: 0.8488 (m100) cc_final: 0.8047 (m100) REVERT: B 257 GLU cc_start: 0.8448 (tt0) cc_final: 0.7319 (tt0) REVERT: B 293 ASN cc_start: 0.8911 (p0) cc_final: 0.8620 (p0) REVERT: B 294 MET cc_start: 0.8993 (mmm) cc_final: 0.8435 (mmm) REVERT: B 340 ARG cc_start: 0.9174 (tpp80) cc_final: 0.8788 (tpm170) REVERT: B 396 THR cc_start: 0.8383 (m) cc_final: 0.6994 (m) REVERT: B 408 ARG cc_start: 0.8903 (ttt180) cc_final: 0.8284 (tpp80) REVERT: B 507 CYS cc_start: 0.8631 (t) cc_final: 0.8286 (t) REVERT: B 516 MET cc_start: 0.8975 (mtp) cc_final: 0.8626 (mtp) REVERT: B 550 ARG cc_start: 0.9094 (mtt180) cc_final: 0.8382 (ttp-170) REVERT: C 20 LEU cc_start: 0.8622 (mm) cc_final: 0.8233 (mp) REVERT: C 39 ILE cc_start: 0.8550 (mp) cc_final: 0.8286 (mm) REVERT: C 84 TYR cc_start: 0.7821 (m-80) cc_final: 0.7401 (m-10) REVERT: C 122 MET cc_start: 0.8299 (tmm) cc_final: 0.7972 (tmm) REVERT: C 165 GLU cc_start: 0.7789 (mp0) cc_final: 0.7427 (mp0) REVERT: C 206 LEU cc_start: 0.9164 (mm) cc_final: 0.8850 (mm) REVERT: C 248 ASP cc_start: 0.7510 (m-30) cc_final: 0.7235 (m-30) REVERT: C 290 ASN cc_start: 0.8923 (t0) cc_final: 0.8357 (t0) REVERT: C 294 MET cc_start: 0.9382 (mtt) cc_final: 0.8631 (mtt) REVERT: C 336 GLU cc_start: 0.8650 (tt0) cc_final: 0.7913 (tm-30) REVERT: C 367 LYS cc_start: 0.9336 (ttmt) cc_final: 0.9001 (ttpp) REVERT: C 516 MET cc_start: 0.8848 (ttp) cc_final: 0.8534 (ttp) REVERT: C 559 PHE cc_start: 0.8205 (t80) cc_final: 0.7990 (t80) REVERT: D 14 ILE cc_start: 0.9330 (mt) cc_final: 0.9032 (tp) REVERT: D 50 VAL cc_start: 0.9156 (m) cc_final: 0.8859 (p) REVERT: D 56 VAL cc_start: 0.8981 (t) cc_final: 0.8494 (t) REVERT: D 200 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8066 (mt-10) REVERT: D 214 LEU cc_start: 0.7477 (mt) cc_final: 0.6949 (tt) REVERT: D 237 MET cc_start: 0.8314 (ttp) cc_final: 0.7905 (ttp) REVERT: D 275 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8430 (mp0) REVERT: D 276 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7495 (pm20) REVERT: D 277 ILE cc_start: 0.9593 (mm) cc_final: 0.9393 (mm) REVERT: D 296 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8220 (mm-30) REVERT: D 327 ASP cc_start: 0.8402 (t0) cc_final: 0.7844 (t0) REVERT: D 328 LEU cc_start: 0.9517 (mt) cc_final: 0.9031 (mt) REVERT: D 331 TYR cc_start: 0.8571 (m-10) cc_final: 0.7939 (m-80) REVERT: D 383 TYR cc_start: 0.9197 (t80) cc_final: 0.8561 (t80) REVERT: E 120 ASN cc_start: 0.9071 (m-40) cc_final: 0.8617 (m110) REVERT: E 126 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8105 (ttpt) REVERT: E 206 GLN cc_start: 0.8317 (pp30) cc_final: 0.7912 (pp30) REVERT: E 207 GLU cc_start: 0.7627 (tp30) cc_final: 0.7364 (tp30) REVERT: E 215 SER cc_start: 0.8622 (p) cc_final: 0.8367 (p) REVERT: E 250 ASP cc_start: 0.7170 (m-30) cc_final: 0.6887 (t0) REVERT: E 269 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8033 (mt-10) REVERT: E 280 ARG cc_start: 0.7797 (tpm170) cc_final: 0.6883 (mmm160) REVERT: E 316 MET cc_start: 0.8879 (ptm) cc_final: 0.8430 (ttm) REVERT: E 319 ASP cc_start: 0.6977 (m-30) cc_final: 0.6722 (t70) REVERT: E 349 TYR cc_start: 0.9169 (t80) cc_final: 0.8913 (t80) REVERT: E 383 TYR cc_start: 0.8019 (t80) cc_final: 0.7747 (t80) REVERT: E 388 ASN cc_start: 0.8425 (m-40) cc_final: 0.8075 (m110) REVERT: E 429 ASN cc_start: 0.7585 (p0) cc_final: 0.7169 (p0) REVERT: F 36 LYS cc_start: 0.8862 (tptm) cc_final: 0.8515 (tppp) REVERT: F 53 GLU cc_start: 0.8674 (pm20) cc_final: 0.7875 (tm-30) REVERT: F 60 PHE cc_start: 0.8922 (m-10) cc_final: 0.8399 (m-80) REVERT: F 139 ASP cc_start: 0.8532 (m-30) cc_final: 0.8084 (p0) REVERT: F 141 MET cc_start: 0.8504 (mpp) cc_final: 0.8008 (mpp) REVERT: F 162 GLU cc_start: 0.8114 (mp0) cc_final: 0.7893 (mp0) REVERT: F 221 LEU cc_start: 0.8600 (mt) cc_final: 0.8189 (tt) REVERT: F 314 LEU cc_start: 0.9449 (tp) cc_final: 0.9027 (tp) REVERT: F 379 SER cc_start: 0.9708 (t) cc_final: 0.9283 (p) REVERT: G 23 LYS cc_start: 0.7312 (tppt) cc_final: 0.7022 (tppt) REVERT: G 119 THR cc_start: 0.7172 (t) cc_final: 0.6876 (t) REVERT: G 196 ARG cc_start: 0.7229 (mmt90) cc_final: 0.6788 (mmt-90) REVERT: H 30 GLN cc_start: 0.9318 (mt0) cc_final: 0.8808 (tt0) REVERT: H 68 LEU cc_start: 0.7760 (mt) cc_final: 0.7530 (pp) REVERT: H 77 LEU cc_start: 0.6242 (pt) cc_final: 0.5960 (mt) REVERT: I 89 ARG cc_start: 0.6218 (ttm110) cc_final: 0.4989 (tpt-90) REVERT: K 78 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7676 (mmm-85) REVERT: K 80 GLU cc_start: 0.4707 (mt-10) cc_final: 0.3450 (tm-30) REVERT: K 108 ASP cc_start: 0.6520 (p0) cc_final: 0.6282 (p0) REVERT: L 81 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7882 (pt0) REVERT: L 94 LEU cc_start: 0.7723 (tp) cc_final: 0.7189 (mp) REVERT: L 168 LEU cc_start: 0.8312 (mp) cc_final: 0.8079 (mp) REVERT: M 38 ARG cc_start: 0.6715 (mmm160) cc_final: 0.5721 (tmm-80) REVERT: M 206 LYS cc_start: 0.8620 (pttt) cc_final: 0.8267 (tmmt) REVERT: M 317 GLU cc_start: 0.5934 (pt0) cc_final: 0.5336 (pt0) outliers start: 1 outliers final: 0 residues processed: 852 average time/residue: 0.1917 time to fit residues: 266.9223 Evaluate side-chains 680 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 680 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.7533 > 50: distance: 19 - 37: 3.067 distance: 21 - 44: 16.659 distance: 25 - 49: 17.873 distance: 33 - 58: 26.897 distance: 39 - 44: 13.770 distance: 40 - 63: 24.357 distance: 44 - 45: 25.010 distance: 45 - 46: 13.851 distance: 45 - 48: 10.782 distance: 46 - 47: 20.951 distance: 46 - 49: 30.157 distance: 47 - 70: 57.310 distance: 49 - 50: 12.787 distance: 50 - 51: 18.730 distance: 50 - 53: 19.593 distance: 51 - 52: 42.189 distance: 51 - 58: 13.857 distance: 53 - 54: 20.014 distance: 54 - 55: 33.134 distance: 55 - 56: 38.483 distance: 56 - 57: 26.654 distance: 58 - 59: 34.661 distance: 59 - 60: 30.761 distance: 59 - 62: 40.264 distance: 60 - 61: 30.361 distance: 60 - 63: 23.573 distance: 63 - 64: 25.399 distance: 64 - 65: 25.027 distance: 64 - 67: 8.143 distance: 65 - 66: 29.946 distance: 65 - 70: 10.497 distance: 67 - 68: 10.930 distance: 67 - 69: 26.336 distance: 70 - 71: 22.026 distance: 71 - 72: 20.976 distance: 72 - 73: 39.116 distance: 72 - 74: 8.953 distance: 74 - 75: 8.374 distance: 75 - 76: 42.023 distance: 75 - 78: 41.605 distance: 76 - 77: 29.276 distance: 76 - 85: 36.444 distance: 78 - 79: 35.613 distance: 79 - 80: 29.370 distance: 80 - 81: 21.289 distance: 81 - 82: 15.903 distance: 82 - 83: 22.194 distance: 82 - 84: 16.723 distance: 85 - 86: 7.426 distance: 85 - 91: 21.545 distance: 86 - 87: 9.771 distance: 86 - 89: 18.407 distance: 87 - 88: 11.767 distance: 87 - 92: 17.182 distance: 89 - 90: 14.589 distance: 90 - 91: 12.739 distance: 92 - 93: 17.264 distance: 93 - 94: 41.383 distance: 93 - 96: 40.753 distance: 94 - 95: 17.572 distance: 94 - 103: 47.250 distance: 95 - 121: 30.530 distance: 96 - 97: 18.481 distance: 97 - 98: 8.037 distance: 97 - 99: 13.628 distance: 98 - 100: 18.249 distance: 99 - 101: 19.345 distance: 100 - 102: 22.937 distance: 101 - 102: 25.912 distance: 103 - 104: 7.811 distance: 104 - 105: 12.590 distance: 104 - 107: 14.955 distance: 105 - 106: 25.534 distance: 105 - 112: 18.897 distance: 107 - 108: 41.010 distance: 108 - 109: 28.047 distance: 109 - 110: 28.412 distance: 109 - 111: 49.390 distance: 112 - 113: 10.832 distance: 113 - 114: 7.460 distance: 113 - 116: 18.003 distance: 114 - 115: 17.241 distance: 114 - 121: 23.541 distance: 116 - 117: 20.512 distance: 117 - 118: 14.713 distance: 118 - 119: 21.107 distance: 118 - 120: 23.167