Starting phenix.real_space_refine on Sat Mar 7 09:03:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wlz_21845/03_2026/6wlz_21845.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wlz_21845/03_2026/6wlz_21845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wlz_21845/03_2026/6wlz_21845.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wlz_21845/03_2026/6wlz_21845.map" model { file = "/net/cci-nas-00/data/ceres_data/6wlz_21845/03_2026/6wlz_21845.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wlz_21845/03_2026/6wlz_21845.cif" } resolution = 2.9 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= 0.004 sd= 0.095 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 2 5.49 5 S 214 5.16 5 C 25708 2.51 5 N 7002 2.21 5 O 7731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 302 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40657 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4652 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "C" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "D" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3600 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "E" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3589 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3596 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2110 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2136 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 257} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2105 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 252} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1570 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "M" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 744 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "G" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1713 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1570 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "L" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 744 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "H" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1570 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "K" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 744 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "N" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} 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: 9.35, per 1000 atoms: 0.23 Number of scatterers: 40657 At special positions: 0 Unit cell: (165.24, 179.28, 183.6, 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 214 16.00 P 2 15.00 O 7731 8.00 N 7002 7.00 C 25708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 2.2 seconds 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9628 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 40 sheets defined 50.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.675A pdb=" N SER A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.689A pdb=" N ILE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 291 removed outlier: 3.942A pdb=" N GLU A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.738A pdb=" N GLU A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.567A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.531A pdb=" N ARG A 381 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 426 Processing helix chain 'A' and resid 436 through 442 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.962A pdb=" N LYS A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 494 removed outlier: 3.998A pdb=" N LEU A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 519 removed outlier: 3.873A pdb=" N LEU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 558 removed outlier: 3.557A pdb=" N THR A 558 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 583 through 587 removed outlier: 3.730A pdb=" N PHE A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS A 587 " --> pdb=" O MET A 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 583 through 587' Processing helix chain 'A' and resid 593 through 616 Processing helix chain 'B' and resid 105 through 113 removed outlier: 4.048A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 removed outlier: 4.223A pdb=" N SER B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 291 removed outlier: 3.554A pdb=" N GLU B 286 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 287 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 351 through 365 removed outlier: 3.683A pdb=" N ALA B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.628A pdb=" N TYR B 374 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 387 removed outlier: 3.621A pdb=" N ARG B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 429 Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.626A pdb=" N ALA B 440 " --> pdb=" O ASP B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 472 through 486 Processing helix chain 'B' and resid 489 through 495 removed outlier: 3.737A pdb=" N VAL B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 519 removed outlier: 3.944A pdb=" N LYS B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 558 removed outlier: 3.625A pdb=" N MET B 544 " --> pdb=" O MET B 540 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 555 " --> pdb=" O ALA B 551 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR B 558 " --> pdb=" O ALA B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 574 removed outlier: 3.534A pdb=" N GLU B 572 " --> pdb=" O SER B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 583 Processing helix chain 'B' and resid 584 through 587 removed outlier: 3.559A pdb=" N LYS B 587 " --> pdb=" O MET B 584 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 584 through 587' Processing helix chain 'B' and resid 593 through 614 removed outlier: 3.685A pdb=" N ILE B 597 " --> pdb=" O GLY B 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 113 removed outlier: 4.129A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 267 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 321 through 339 removed outlier: 4.193A pdb=" N ALA C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 365 removed outlier: 3.929A pdb=" N TRP C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 412 through 416 removed outlier: 3.780A pdb=" N ASP C 416 " --> pdb=" O PRO C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 427 removed outlier: 3.696A pdb=" N GLY C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 442 removed outlier: 3.677A pdb=" N ARG C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 472 through 497 removed outlier: 3.685A pdb=" N GLU C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 519 removed outlier: 3.519A pdb=" N GLU C 510 " --> pdb=" O LYS C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 558 removed outlier: 3.737A pdb=" N PHE C 547 " --> pdb=" O ASN C 543 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR C 548 " --> pdb=" O MET C 544 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C 558 " --> pdb=" O ALA C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 575 through 584 removed outlier: 3.930A pdb=" N TYR C 579 " --> pdb=" O GLY C 575 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS C 580 " --> pdb=" O ASP C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 592 through 615 removed outlier: 4.128A pdb=" N LYS C 596 " --> pdb=" O ASP C 592 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 597 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 605 " --> pdb=" O TYR C 601 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 198 through 210 removed outlier: 3.521A pdb=" N ILE D 202 " --> pdb=" O PRO D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 251 removed outlier: 3.709A pdb=" N ASN D 251 " --> pdb=" O ASP D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 268 through 272 removed outlier: 3.584A pdb=" N ILE D 272 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 288 removed outlier: 3.520A pdb=" N LEU D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 313 removed outlier: 3.664A pdb=" N TYR D 303 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 304 " --> pdb=" O MET D 300 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 323 removed outlier: 3.648A pdb=" N GLY D 322 " --> pdb=" O GLY D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 336 removed outlier: 3.743A pdb=" N THR D 333 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 363 through 371 Processing helix chain 'D' and resid 383 through 387 Processing helix chain 'D' and resid 414 through 439 removed outlier: 4.064A pdb=" N MET D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 462 Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.635A pdb=" N THR D 476 " --> pdb=" O THR D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 504 removed outlier: 3.580A pdb=" N GLU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.666A pdb=" N MET E 127 " --> pdb=" O SER E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 198 through 210 Processing helix chain 'E' and resid 237 through 251 Processing helix chain 'E' and resid 269 through 289 Proline residue: E 275 - end of helix Processing helix chain 'E' and resid 299 through 313 removed outlier: 3.657A pdb=" N TYR E 303 " --> pdb=" O ASP E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 323 removed outlier: 3.802A pdb=" N PHE E 323 " --> pdb=" O ARG E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 336 removed outlier: 3.718A pdb=" N ILE E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 360 Processing helix chain 'E' and resid 363 through 371 removed outlier: 3.729A pdb=" N TYR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 Processing helix chain 'E' and resid 401 through 406 removed outlier: 3.619A pdb=" N ALA E 405 " --> pdb=" O LEU E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 440 removed outlier: 3.971A pdb=" N ALA E 437 " --> pdb=" O GLN E 433 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 462 removed outlier: 3.876A pdb=" N GLN E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 485 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 198 through 210 removed outlier: 3.617A pdb=" N ILE F 202 " --> pdb=" O PRO F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 249 Processing helix chain 'F' and resid 268 through 272 removed outlier: 3.629A pdb=" N ILE F 272 " --> pdb=" O ILE F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 299 through 314 removed outlier: 3.664A pdb=" N ARG F 314 " --> pdb=" O VAL F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 323 removed outlier: 3.592A pdb=" N GLY F 322 " --> pdb=" O GLY F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 336 removed outlier: 3.838A pdb=" N THR F 333 " --> pdb=" O THR F 329 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 360 Processing helix chain 'F' and resid 363 through 371 removed outlier: 3.564A pdb=" N TYR F 371 " --> pdb=" O ASP F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 440 removed outlier: 3.558A pdb=" N ALA F 434 " --> pdb=" O LYS F 430 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA F 437 " --> pdb=" O GLN F 433 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 444 removed outlier: 4.151A pdb=" N LEU F 444 " --> pdb=" O GLU F 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 441 through 444' Processing helix chain 'F' and resid 445 through 462 removed outlier: 3.760A pdb=" N LEU F 449 " --> pdb=" O THR F 445 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU F 450 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN F 456 " --> pdb=" O LEU F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 485 Processing helix chain 'F' and resid 496 through 504 removed outlier: 3.890A pdb=" N GLU F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) Processing helix chain 'X' and resid 15 through 37 removed outlier: 3.639A pdb=" N HIS X 19 " --> pdb=" O SER X 15 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL X 23 " --> pdb=" O HIS X 19 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA X 30 " --> pdb=" O ILE X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 49 removed outlier: 3.989A pdb=" N ASP X 48 " --> pdb=" O LYS X 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 58 Processing helix chain 'X' and resid 61 through 71 removed outlier: 3.576A pdb=" N ILE X 65 " --> pdb=" O ARG X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 98 removed outlier: 3.867A pdb=" N LEU X 86 " --> pdb=" O SER X 82 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE X 87 " --> pdb=" O ARG X 83 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU X 88 " --> pdb=" O ARG X 84 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE X 98 " --> pdb=" O LEU X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 104 through 118 removed outlier: 3.711A pdb=" N HIS X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 142 removed outlier: 3.691A pdb=" N VAL X 128 " --> pdb=" O SER X 124 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASN X 142 " --> pdb=" O ASP X 138 " (cutoff:3.500A) Processing helix chain 'X' and resid 146 through 167 removed outlier: 3.584A pdb=" N GLN X 165 " --> pdb=" O MET X 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 173 through 187 removed outlier: 4.077A pdb=" N LYS X 180 " --> pdb=" O ASN X 176 " (cutoff:3.500A) Processing helix chain 'X' and resid 192 through 207 Processing helix chain 'X' and resid 218 through 234 removed outlier: 3.675A pdb=" N GLN X 222 " --> pdb=" O PRO X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 242 through 250 removed outlier: 3.635A pdb=" N SER X 250 " --> pdb=" O LEU X 246 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 270 removed outlier: 3.753A pdb=" N LEU X 260 " --> pdb=" O THR X 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 37 Processing helix chain 'Y' and resid 42 through 49 Processing helix chain 'Y' and resid 49 through 58 removed outlier: 4.744A pdb=" N TRP Y 55 " --> pdb=" O ASP Y 51 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA Y 56 " --> pdb=" O VAL Y 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS Y 58 " --> pdb=" O ILE Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 61 through 72 Processing helix chain 'Y' and resid 77 through 98 removed outlier: 3.911A pdb=" N ILE Y 87 " --> pdb=" O ARG Y 83 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU Y 88 " --> pdb=" O ARG Y 84 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE Y 98 " --> pdb=" O LEU Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 117 removed outlier: 4.076A pdb=" N GLU Y 109 " --> pdb=" O LEU Y 105 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN Y 117 " --> pdb=" O GLU Y 113 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 124 Processing helix chain 'Y' and resid 125 through 140 removed outlier: 3.697A pdb=" N LEU Y 140 " --> pdb=" O LEU Y 136 " (cutoff:3.500A) Processing helix chain 'Y' and resid 146 through 166 Processing helix chain 'Y' and resid 172 through 187 removed outlier: 3.819A pdb=" N ALA Y 187 " --> pdb=" O LEU Y 183 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 206 removed outlier: 3.518A pdb=" N HIS Y 198 " --> pdb=" O ASP Y 194 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE Y 200 " --> pdb=" O GLN Y 196 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP Y 206 " --> pdb=" O GLY Y 202 " (cutoff:3.500A) Processing helix chain 'Y' and resid 218 through 229 removed outlier: 4.016A pdb=" N ILE Y 224 " --> pdb=" O GLU Y 220 " (cutoff:3.500A) Processing helix chain 'Y' and resid 240 through 249 removed outlier: 3.828A pdb=" N LEU Y 249 " --> pdb=" O LYS Y 245 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 252 No H-bonds generated for 'chain 'Y' and resid 250 through 252' Processing helix chain 'Y' and resid 256 through 273 removed outlier: 3.742A pdb=" N LYS Y 268 " --> pdb=" O ASP Y 264 " (cutoff:3.500A) Processing helix chain 'Z' and resid 15 through 37 removed outlier: 4.073A pdb=" N VAL Z 23 " --> pdb=" O HIS Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 47 Processing helix chain 'Z' and resid 53 through 58 removed outlier: 3.624A pdb=" N GLU Z 57 " --> pdb=" O LEU Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 72 removed outlier: 3.640A pdb=" N GLU Z 67 " --> pdb=" O GLU Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 98 removed outlier: 3.805A pdb=" N ARG Z 83 " --> pdb=" O ASP Z 79 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE Z 87 " --> pdb=" O ARG Z 83 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU Z 88 " --> pdb=" O ARG Z 84 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE Z 98 " --> pdb=" O LEU Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 117 removed outlier: 3.745A pdb=" N GLN Z 117 " --> pdb=" O GLU Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 120 through 123 Processing helix chain 'Z' and resid 124 through 140 removed outlier: 4.020A pdb=" N VAL Z 128 " --> pdb=" O SER Z 124 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 141 through 143 No H-bonds generated for 'chain 'Z' and resid 141 through 143' Processing helix chain 'Z' and resid 146 through 162 Processing helix chain 'Z' and resid 172 through 188 removed outlier: 3.822A pdb=" N MET Z 188 " --> pdb=" O HIS Z 184 " (cutoff:3.500A) Processing helix chain 'Z' and resid 192 through 206 removed outlier: 3.688A pdb=" N GLN Z 196 " --> pdb=" O LYS Z 192 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR Z 197 " --> pdb=" O ILE Z 193 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS Z 198 " --> pdb=" O ASP Z 194 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS Z 205 " --> pdb=" O LYS Z 201 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP Z 206 " --> pdb=" O GLY Z 202 " (cutoff:3.500A) Processing helix chain 'Z' and resid 218 through 234 removed outlier: 3.821A pdb=" N ALA Z 233 " --> pdb=" O MET Z 229 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET Z 234 " --> pdb=" O ILE Z 230 " (cutoff:3.500A) Processing helix chain 'Z' and resid 239 through 243 Processing helix chain 'Z' and resid 257 through 272 removed outlier: 3.798A pdb=" N ASP Z 261 " --> pdb=" O LYS Z 257 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN Z 270 " --> pdb=" O ILE Z 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 108 removed outlier: 4.117A pdb=" N LYS J 52 " --> pdb=" O THR J 48 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS J 69 " --> pdb=" O GLU J 65 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG J 87 " --> pdb=" O VAL J 83 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP J 108 " --> pdb=" O LYS J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 128 removed outlier: 3.671A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY J 118 " --> pdb=" O VAL J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 139 No H-bonds generated for 'chain 'J' and resid 137 through 139' Processing helix chain 'J' and resid 140 through 160 removed outlier: 3.571A pdb=" N ALA J 146 " --> pdb=" O PRO J 142 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS J 150 " --> pdb=" O ALA J 146 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA J 151 " --> pdb=" O ALA J 147 " (cutoff:3.500A) Proline residue: J 153 - end of helix Processing helix chain 'J' and resid 196 through 207 removed outlier: 3.872A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 207 through 217 Processing helix chain 'M' and resid 29 through 91 removed outlier: 5.251A pdb=" N GLU M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N PHE M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS M 56 " --> pdb=" O GLU M 52 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER M 68 " --> pdb=" O GLY M 64 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU M 76 " --> pdb=" O GLU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 104 Processing helix chain 'G' and resid 14 through 74 removed outlier: 4.008A pdb=" N ASN G 31 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU G 71 " --> pdb=" O PHE G 67 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA G 72 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 86 Processing helix chain 'G' and resid 128 through 175 Processing helix chain 'G' and resid 175 through 216 removed outlier: 3.735A pdb=" N ARG G 179 " --> pdb=" O VAL G 175 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE G 187 " --> pdb=" O THR G 183 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG G 196 " --> pdb=" O ASP G 192 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU G 198 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU G 214 " --> pdb=" O LYS G 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 103 removed outlier: 4.165A pdb=" N ILE I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL I 83 " --> pdb=" O ALA I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 128 removed outlier: 3.745A pdb=" N GLN I 113 " --> pdb=" O THR I 109 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 160 Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 196 through 204 Processing helix chain 'I' and resid 207 through 217 removed outlier: 3.546A pdb=" N GLY I 213 " --> pdb=" O PRO I 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 91 removed outlier: 3.725A pdb=" N SER L 68 " --> pdb=" O GLY L 64 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU L 76 " --> pdb=" O GLU L 72 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN L 78 " --> pdb=" O GLU L 74 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN L 85 " --> pdb=" O MET L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 104 Processing helix chain 'H' and resid 35 through 49 Processing helix chain 'H' and resid 50 through 107 removed outlier: 4.520A pdb=" N MET H 54 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU H 55 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN H 67 " --> pdb=" O GLN H 63 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS H 107 " --> pdb=" O SER H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 128 removed outlier: 3.935A pdb=" N VAL H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU H 121 " --> pdb=" O ASP H 117 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN H 126 " --> pdb=" O GLN H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 158 removed outlier: 3.680A pdb=" N ALA H 146 " --> pdb=" O PRO H 142 " (cutoff:3.500A) Proline residue: H 153 - end of helix removed outlier: 3.614A pdb=" N ALA H 158 " --> pdb=" O MET H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 205 removed outlier: 3.610A pdb=" N GLN H 205 " --> pdb=" O ASP H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 207 through 217 Processing helix chain 'K' and resid 30 through 52 removed outlier: 4.363A pdb=" N ALA K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU K 38 " --> pdb=" O LYS K 34 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN K 41 " --> pdb=" O LYS K 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 90 removed outlier: 4.635A pdb=" N GLY K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER K 68 " --> pdb=" O GLY K 64 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER K 70 " --> pdb=" O ARG K 66 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN K 78 " --> pdb=" O GLU K 74 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN K 90 " --> pdb=" O THR K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 104 removed outlier: 3.670A pdb=" N VAL K 95 " --> pdb=" O ASN K 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 24 Processing helix chain 'N' and resid 44 through 58 Processing helix chain 'N' and resid 68 through 72 Processing helix chain 'N' and resid 74 through 80 Processing sheet with id=AA1, first strand: chain 'D' and resid 50 through 54 removed outlier: 5.846A pdb=" N ILE D 59 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL D 53 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 164 through 167 removed outlier: 4.131A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE D 71 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU D 70 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 45 removed outlier: 4.267A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 18 through 25 removed outlier: 6.389A pdb=" N THR A 30 " --> pdb=" O HIS A 22 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A 24 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 56 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL E 89 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL E 95 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.620A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 28 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL B 24 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR B 30 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU E 45 " --> pdb=" O PHE E 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 90 Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.556A pdb=" N ILE A 272 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL A 312 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR A 274 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 271 " --> pdb=" O HIS A 343 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 273 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A 391 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 219 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 99 removed outlier: 6.556A pdb=" N ILE A 272 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL A 312 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR A 274 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 271 " --> pdb=" O HIS A 343 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 273 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR A 246 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR A 245 " --> pdb=" O VAL A 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 163 through 167 removed outlier: 3.657A pdb=" N GLY A 154 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP A 134 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 146 through 148 removed outlier: 6.611A pdb=" N GLU A 193 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 295 through 298 Processing sheet with id=AB3, first strand: chain 'B' and resid 87 through 90 Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.864A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASP B 349 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 275 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG B 391 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 219 " --> pdb=" O LYS B 393 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.864A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ASP B 349 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 275 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR B 246 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL B 410 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE B 248 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.646A pdb=" N GLY B 154 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASP B 134 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.650A pdb=" N GLU B 193 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 295 through 298 Processing sheet with id=AB9, first strand: chain 'B' and resid 431 through 432 Processing sheet with id=AC1, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.848A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 25 current: chain 'F' and resid 111 through 114 Processing sheet with id=AC2, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.848A pdb=" N ILE F 59 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL F 53 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 81 through 90 current: chain 'C' and resid 42 through 45 removed outlier: 6.425A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 28 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL C 24 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR C 30 " --> pdb=" O HIS C 22 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 25 current: chain 'F' and resid 111 through 114 Processing sheet with id=AC3, first strand: chain 'C' and resid 87 through 90 Processing sheet with id=AC4, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.183A pdb=" N PHE C 99 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 272 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL C 312 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR C 274 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASN C 314 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 276 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 271 " --> pdb=" O HIS C 343 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS C 277 " --> pdb=" O ASP C 349 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 391 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 219 " --> pdb=" O LYS C 393 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 98 through 99 removed outlier: 6.183A pdb=" N PHE C 99 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE C 272 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL C 312 " --> pdb=" O ILE C 272 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR C 274 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ASN C 314 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY C 276 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 271 " --> pdb=" O HIS C 343 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS C 277 " --> pdb=" O ASP C 349 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR C 246 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL C 410 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE C 248 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 245 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 163 through 167 removed outlier: 3.556A pdb=" N GLY C 154 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP C 134 " --> pdb=" O SER C 157 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 146 through 148 removed outlier: 6.469A pdb=" N GLU C 193 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 295 through 297 Processing sheet with id=AC9, first strand: chain 'D' and resid 120 through 123 Processing sheet with id=AD1, first strand: chain 'D' and resid 131 through 133 removed outlier: 6.666A pdb=" N ILE D 229 " --> pdb=" O CYS D 258 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE D 260 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE D 231 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASN D 262 " --> pdb=" O PHE D 231 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA D 233 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA D 228 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE D 296 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL D 230 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR D 298 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA D 232 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 297 " --> pdb=" O ILE D 351 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE D 191 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 163 through 164 removed outlier: 4.586A pdb=" N ARG D 340 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 183 through 184 removed outlier: 4.640A pdb=" N ILE D 183 " --> pdb=" O ILE D 170 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.722A pdb=" N ARG E 130 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET E 234 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE E 191 " --> pdb=" O LEU E 354 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR E 378 " --> pdb=" O PRO E 396 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 163 through 164 removed outlier: 4.535A pdb=" N ARG E 340 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 183 through 184 removed outlier: 4.608A pdb=" N ILE E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 120 through 123 Processing sheet with id=AD9, first strand: chain 'F' and resid 130 through 133 removed outlier: 6.501A pdb=" N ARG F 130 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU F 261 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N PHE F 132 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU F 263 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE F 229 " --> pdb=" O CYS F 258 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N PHE F 260 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE F 231 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASN F 262 " --> pdb=" O PHE F 231 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ALA F 233 " --> pdb=" O ASN F 262 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU F 297 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE F 191 " --> pdb=" O LEU F 354 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 163 through 164 removed outlier: 4.473A pdb=" N ARG F 340 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 183 through 184 removed outlier: 4.488A pdb=" N ILE F 183 " --> pdb=" O ILE F 170 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 95 through 101 Processing sheet with id=AE4, first strand: chain 'N' and resid 7 through 11 removed outlier: 7.398A pdb=" N LEU N 7 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N LEU N 65 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA N 9 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ASN N 67 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE N 11 " --> pdb=" O ASN N 67 " (cutoff:3.500A) 2225 hydrogen bonds defined for protein. 6477 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: 11.31 Time building geometry restraints manager: 4.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13437 1.34 - 1.46: 5623 1.46 - 1.57: 21921 1.57 - 1.69: 3 1.69 - 1.81: 374 Bond restraints: 41358 Sorted by residual: bond pdb=" C ARG D 120 " pdb=" N THR D 121 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.07e-02 2.33e+03 1.01e+01 bond pdb=" N GLN D 156 " pdb=" CA GLN D 156 " ideal model delta sigma weight residual 1.457 1.432 0.024 1.41e-02 5.03e+03 3.02e+00 bond pdb=" CA PRO B 169 " pdb=" C PRO B 169 " ideal model delta sigma weight residual 1.514 1.505 0.009 5.50e-03 3.31e+04 2.63e+00 bond pdb=" C GLN Y 207 " pdb=" O GLN Y 207 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.28e+00 bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.82e+00 ... (remaining 41353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 55125 2.25 - 4.49: 627 4.49 - 6.74: 69 6.74 - 8.98: 14 8.98 - 11.23: 4 Bond angle restraints: 55839 Sorted by residual: angle pdb=" C LYS L 34 " pdb=" N GLN L 35 " pdb=" CA GLN L 35 " ideal model delta sigma weight residual 121.14 113.09 8.05 1.75e+00 3.27e-01 2.12e+01 angle pdb=" CA GLN L 35 " pdb=" CB GLN L 35 " pdb=" CG GLN L 35 " ideal model delta sigma weight residual 114.10 121.34 -7.24 2.00e+00 2.50e-01 1.31e+01 angle pdb=" N ILE C 102 " pdb=" CA ILE C 102 " pdb=" C ILE C 102 " ideal model delta sigma weight residual 112.98 108.87 4.11 1.25e+00 6.40e-01 1.08e+01 angle pdb=" N VAL E 438 " pdb=" CA VAL E 438 " pdb=" C VAL E 438 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.06e+01 angle pdb=" N ILE C 94 " pdb=" CA ILE C 94 " pdb=" C ILE C 94 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.06e+01 ... (remaining 55834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 24297 33.88 - 67.76: 1066 67.76 - 101.65: 96 101.65 - 135.53: 1 135.53 - 169.41: 1 Dihedral angle restraints: 25461 sinusoidal: 10518 harmonic: 14943 Sorted by residual: dihedral pdb=" O2A ADP C 701 " pdb=" O3A ADP C 701 " pdb=" PA ADP C 701 " pdb=" PB ADP C 701 " ideal model delta sinusoidal sigma weight residual 300.00 130.59 169.41 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA LYS M 34 " pdb=" C LYS M 34 " pdb=" N GLN M 35 " pdb=" CA GLN M 35 " ideal model delta harmonic sigma weight residual 180.00 148.52 31.48 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA ASN L 30 " pdb=" C ASN L 30 " pdb=" N ARG L 31 " pdb=" CA ARG L 31 " ideal model delta harmonic sigma weight residual 180.00 148.60 31.40 0 5.00e+00 4.00e-02 3.94e+01 ... (remaining 25458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4726 0.053 - 0.105: 1345 0.105 - 0.158: 199 0.158 - 0.210: 5 0.210 - 0.263: 1 Chirality restraints: 6276 Sorted by residual: chirality pdb=" CB ILE B 327 " pdb=" CA ILE B 327 " pdb=" CG1 ILE B 327 " pdb=" CG2 ILE B 327 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA GLN L 35 " pdb=" N GLN L 35 " pdb=" C GLN L 35 " pdb=" CB GLN L 35 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CA ASN C 397 " pdb=" N ASN C 397 " pdb=" C ASN C 397 " pdb=" CB ASN C 397 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 6273 not shown) Planarity restraints: 7245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR Y 146 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO Y 147 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO Y 147 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO Y 147 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN I 194 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.04e+00 pdb=" C ASN I 194 " 0.039 2.00e-02 2.50e+03 pdb=" O ASN I 194 " -0.015 2.00e-02 2.50e+03 pdb=" N THR I 195 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 363 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO D 364 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 364 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 364 " -0.029 5.00e-02 4.00e+02 ... (remaining 7242 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 936 2.69 - 3.24: 38057 3.24 - 3.79: 61035 3.79 - 4.35: 86115 4.35 - 4.90: 144671 Nonbonded interactions: 330814 Sorted by model distance: nonbonded pdb=" NH2 ARG E 208 " pdb=" O PRO E 467 " model vdw 2.132 3.120 nonbonded pdb=" O ASN E 393 " pdb=" OG SER E 397 " model vdw 2.156 3.040 nonbonded pdb=" OH TYR D 39 " pdb=" OE1 GLU H 210 " model vdw 2.163 3.040 nonbonded pdb=" OE2 GLU B 360 " pdb=" OG1 THR E 329 " model vdw 2.164 3.040 nonbonded pdb=" OG SER F 253 " pdb=" OD1 ASP F 255 " model vdw 2.187 3.040 ... (remaining 330809 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' selection = (chain 'B' and (resid 17 through 497 or (resid 498 through 499 and (name N or na \ me CA or name C or name O or name CB )) or resid 500 through 616)) selection = (chain 'C' and (resid 17 through 497 or (resid 498 through 499 and (name N or na \ me CA or name C or name O or name CB )) or resid 500 through 616)) } ncs_group { reference = (chain 'D' and (resid 39 through 314 or (resid 315 and (name N or name CA or nam \ e C or name O or name CB )) or resid 316 through 434 or (resid 435 and (name N o \ r name CA or name C or name O or name CB )) or resid 436 through 440 or (resid 4 \ 41 through 443 and (name N or name CA or name C or name O or name CB )) or resid \ 444 through 506)) selection = (chain 'E' and (resid 39 through 314 or (resid 315 and (name N or name CA or nam \ e C or name O or name CB )) or resid 316 through 506)) selection = (chain 'F' and (resid 39 through 434 or (resid 435 and (name N or name CA or nam \ e C or name O or name CB )) or resid 436 through 440 or (resid 441 through 443 a \ nd (name N or name CA or name C or name O or name CB )) or resid 444 through 506 \ )) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = (chain 'X' and (resid 14 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or resid 102 through 219 or (resid 220 and (name N o \ r name CA or name C or name O or name CB )) or resid 221 through 222 or (resid 2 \ 23 and (name N or name CA or name C or name O or name CB )) or resid 224 through \ 275)) selection = (chain 'Y' and (resid 14 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or resid 102 through 235 or (resid 236 and (name CA \ or name C or name O or name CB or name CG or name CD or name CE or name NZ )) or \ resid 237 through 275)) selection = (chain 'Z' and (resid 14 through 219 or (resid 220 and (name N or name CA or nam \ e C or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N o \ r name CA or name C or name O or name CB )) or resid 224 through 235 or (resid 2 \ 36 and (name CA or name C or name O or name CB or name CG or name CD or name CE \ or name NZ )) or resid 237 through 275)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.270 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: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 40.710 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.160 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 : 0.006 0.069 41358 Z= 0.258 Angle : 0.661 11.231 55839 Z= 0.368 Chirality : 0.047 0.263 6276 Planarity : 0.005 0.061 7245 Dihedral : 17.767 169.411 15833 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 7.27 % Allowed : 20.45 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.10), residues: 5098 helix: -1.67 (0.09), residues: 2478 sheet: -1.43 (0.19), residues: 632 loop : -2.74 (0.11), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 50 TYR 0.014 0.002 TYR I 56 PHE 0.020 0.002 PHE I 38 TRP 0.015 0.002 TRP A 450 HIS 0.005 0.001 HIS C 444 Details of bonding type rmsd covalent geometry : bond 0.00616 (41358) covalent geometry : angle 0.66137 (55839) hydrogen bonds : bond 0.14066 ( 2059) hydrogen bonds : angle 6.66823 ( 6477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 323 poor density : 550 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7901 (mmt-90) REVERT: A 471 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7173 (pp20) REVERT: A 506 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7590 (mmtp) REVERT: A 578 LEU cc_start: 0.9144 (mt) cc_final: 0.8815 (mt) REVERT: B 161 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8205 (tt) REVERT: B 387 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8313 (tp30) REVERT: B 523 ASN cc_start: 0.7960 (t0) cc_final: 0.7739 (t0) REVERT: B 556 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6634 (pm20) REVERT: B 597 ILE cc_start: 0.7995 (mt) cc_final: 0.7783 (mp) REVERT: C 18 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7287 (t80) REVERT: C 80 LEU cc_start: 0.9031 (tt) cc_final: 0.8776 (tp) REVERT: C 171 ARG cc_start: 0.8167 (mtp180) cc_final: 0.7885 (mtm180) REVERT: C 201 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.5435 (tm-30) REVERT: C 467 LYS cc_start: 0.8734 (tttm) cc_final: 0.8383 (ttmm) REVERT: C 571 ARG cc_start: 0.7512 (tmt-80) cc_final: 0.7293 (tmt-80) REVERT: C 573 HIS cc_start: 0.7357 (t-170) cc_final: 0.6906 (t-170) REVERT: C 574 MET cc_start: 0.8209 (mtm) cc_final: 0.7895 (mtp) REVERT: D 57 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8712 (mt) REVERT: D 238 MET cc_start: 0.8560 (tpp) cc_final: 0.8275 (tpt) REVERT: D 386 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7888 (mtm-85) REVERT: E 169 MET cc_start: 0.9116 (ttt) cc_final: 0.8434 (ttt) REVERT: E 180 MET cc_start: 0.9236 (mtp) cc_final: 0.8995 (mtm) REVERT: E 300 MET cc_start: 0.8479 (mmm) cc_final: 0.8047 (mmm) REVERT: E 342 GLU cc_start: 0.7570 (tt0) cc_final: 0.7308 (pt0) REVERT: E 408 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7917 (tp30) REVERT: E 497 GLN cc_start: 0.7985 (mm-40) cc_final: 0.7406 (tp-100) REVERT: F 137 LYS cc_start: 0.8288 (mttt) cc_final: 0.8054 (mppt) REVERT: F 154 MET cc_start: 0.8239 (mmt) cc_final: 0.7976 (mmm) REVERT: F 237 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8258 (p0) REVERT: F 239 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: F 431 ASP cc_start: 0.7643 (m-30) cc_final: 0.7387 (m-30) REVERT: F 435 MET cc_start: 0.8236 (ttp) cc_final: 0.8036 (ttm) REVERT: X 166 TYR cc_start: 0.7302 (m-80) cc_final: 0.6982 (m-80) REVERT: X 171 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7230 (p0) REVERT: Y 115 MET cc_start: 0.7953 (mtt) cc_final: 0.7667 (mtp) REVERT: Y 244 ASP cc_start: 0.6512 (OUTLIER) cc_final: 0.6133 (p0) REVERT: Z 177 GLN cc_start: 0.6831 (tp40) cc_final: 0.6555 (tp40) REVERT: Z 229 MET cc_start: 0.5280 (tpp) cc_final: 0.5041 (mmm) REVERT: J 54 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.6358 (mtm) REVERT: J 55 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6915 (mt-10) REVERT: J 99 LYS cc_start: 0.8099 (mttt) cc_final: 0.7684 (mtpm) REVERT: J 131 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7700 (ttm-80) REVERT: J 185 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8965 (p0) REVERT: J 198 SER cc_start: 0.8680 (OUTLIER) cc_final: 0.8206 (m) REVERT: J 212 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7962 (ttt-90) REVERT: M 85 GLN cc_start: 0.8432 (mp10) cc_final: 0.8221 (mp-120) REVERT: I 89 ASP cc_start: 0.7463 (m-30) cc_final: 0.7090 (m-30) REVERT: I 131 ARG cc_start: 0.7882 (mtm110) cc_final: 0.7655 (mtp85) REVERT: I 139 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8045 (pm20) REVERT: L 74 GLU cc_start: 0.7295 (tt0) cc_final: 0.6728 (tm-30) REVERT: L 79 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6193 (tm-30) REVERT: L 90 GLN cc_start: 0.8061 (mt0) cc_final: 0.7629 (mm110) REVERT: L 102 PHE cc_start: 0.8353 (m-80) cc_final: 0.8018 (m-80) REVERT: H 54 MET cc_start: 0.6678 (ptp) cc_final: 0.6252 (pmt) REVERT: H 97 GLU cc_start: 0.7708 (tp30) cc_final: 0.7375 (tp30) REVERT: H 183 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8718 (mm) REVERT: H 201 ASP cc_start: 0.8117 (t70) cc_final: 0.7911 (t0) REVERT: K 83 ILE cc_start: 0.8309 (mt) cc_final: 0.8056 (mm) REVERT: N 66 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7568 (mm) outliers start: 323 outliers final: 161 residues processed: 836 average time/residue: 0.8021 time to fit residues: 804.6936 Evaluate side-chains 669 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 486 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 568 SER Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain C residue 599 SER Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 226 ASN Chi-restraints excluded: chain E residue 237 ASN Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 347 SER Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 501 SER Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 188 LYS Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 237 ASN Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 314 ARG Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 404 SER Chi-restraints excluded: chain X residue 51 ASP Chi-restraints excluded: chain X residue 126 TYR Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 171 ASP Chi-restraints excluded: chain X residue 250 SER Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 16 GLU Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 40 ASN Chi-restraints excluded: chain Y residue 126 TYR Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 188 MET Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 244 ASP Chi-restraints excluded: chain Y residue 269 GLU Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 87 ILE Chi-restraints excluded: chain Z residue 162 GLN Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 171 SER Chi-restraints excluded: chain J residue 185 ASN Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 198 SER Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain M residue 34 LYS Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 124 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 139 GLN Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 95 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 102 LYS Chi-restraints excluded: chain N residue 105 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 494 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 213 GLN A 261 GLN A 430 GLN A 441 GLN A 444 HIS B 65 GLN B 172 ASN B 261 GLN B 314 ASN B 449 ASN B 521 GLN B 560 GLN C 172 ASN C 261 GLN C 441 GLN C 563 ASN D 97 GLN E 226 ASN E 237 ASN E 350 GLN E 363 HIS E 470 ASN F 54 ASN F 85 GLN F 181 ASN ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN X 40 ASN X 134 ASN X 149 ASN X 150 ASN Y 184 HIS Y 190 ASN Y 196 GLN Y 207 GLN Y 270 ASN Z 76 ASN Z 177 GLN Z 207 GLN J 49 GLN J 71 GLN J 77 ASN J 185 ASN J 219 ASN M 35 GLN M 111 HIS G 31 ASN G 46 GLN G 152 GLN G 206 GLN I 71 GLN I 77 ASN I 78 GLN I 149 GLN I 206 GLN I 219 ASN I 221 ASN L 30 ASN L 41 GLN L 78 GLN L 85 GLN L 91 ASN L 98 ASN H 77 ASN H 100 GLN H 139 GLN H 219 ASN K 35 GLN K 46 GLN K 78 GLN K 90 GLN N 31 ASN N 33 HIS N 67 ASN N 83 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111798 restraints weight = 49320.137| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.82 r_work: 0.3134 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41358 Z= 0.140 Angle : 0.574 11.282 55839 Z= 0.298 Chirality : 0.044 0.184 6276 Planarity : 0.005 0.054 7245 Dihedral : 9.234 166.369 5960 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.18 % Allowed : 23.08 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.11), residues: 5098 helix: -0.32 (0.10), residues: 2501 sheet: -0.93 (0.20), residues: 624 loop : -2.18 (0.12), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 31 TYR 0.020 0.001 TYR X 112 PHE 0.022 0.001 PHE I 38 TRP 0.012 0.001 TRP C 567 HIS 0.004 0.001 HIS C 444 Details of bonding type rmsd covalent geometry : bond 0.00309 (41358) covalent geometry : angle 0.57394 (55839) hydrogen bonds : bond 0.05311 ( 2059) hydrogen bonds : angle 4.93613 ( 6477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 527 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8622 (mp) REVERT: A 120 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8477 (mtm180) REVERT: A 324 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: A 578 LEU cc_start: 0.9103 (mt) cc_final: 0.8764 (mt) REVERT: B 142 ARG cc_start: 0.8231 (ptp90) cc_final: 0.8025 (ptp90) REVERT: B 161 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8566 (tt) REVERT: B 387 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8717 (tp30) REVERT: B 459 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7530 (tpt170) REVERT: B 471 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7549 (pp20) REVERT: B 518 ASP cc_start: 0.8154 (m-30) cc_final: 0.7651 (t0) REVERT: C 80 LEU cc_start: 0.9069 (tt) cc_final: 0.8854 (tp) REVERT: C 104 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8825 (mtp180) REVERT: C 171 ARG cc_start: 0.8803 (mtp180) cc_final: 0.8302 (mtm180) REVERT: C 201 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5868 (tm-30) REVERT: C 467 LYS cc_start: 0.8850 (tttm) cc_final: 0.8416 (ttmm) REVERT: C 571 ARG cc_start: 0.7766 (tmt-80) cc_final: 0.7196 (tpt170) REVERT: C 573 HIS cc_start: 0.7462 (t-170) cc_final: 0.7046 (t-170) REVERT: D 237 ASN cc_start: 0.8603 (p0) cc_final: 0.8297 (p0) REVERT: D 386 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7728 (mtm-85) REVERT: D 435 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.6820 (pp-130) REVERT: E 169 MET cc_start: 0.9064 (ttt) cc_final: 0.8422 (ttt) REVERT: E 180 MET cc_start: 0.9408 (mtp) cc_final: 0.9149 (mtm) REVERT: E 215 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7792 (mmtp) REVERT: E 242 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.8105 (mtm-85) REVERT: E 300 MET cc_start: 0.8743 (mmm) cc_final: 0.8315 (mmm) REVERT: E 342 GLU cc_start: 0.8496 (tt0) cc_final: 0.8141 (pt0) REVERT: E 402 MET cc_start: 0.8722 (ttt) cc_final: 0.8475 (ttt) REVERT: E 431 ASP cc_start: 0.8034 (t70) cc_final: 0.7697 (t0) REVERT: E 497 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7697 (tp-100) REVERT: F 154 MET cc_start: 0.8777 (mmt) cc_final: 0.8574 (mmm) REVERT: F 431 ASP cc_start: 0.8075 (m-30) cc_final: 0.7809 (m-30) REVERT: X 98 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6332 (pp) REVERT: X 161 MET cc_start: 0.6830 (tmm) cc_final: 0.6516 (ttp) REVERT: X 166 TYR cc_start: 0.7218 (m-80) cc_final: 0.6953 (m-80) REVERT: X 181 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7295 (mp) REVERT: X 195 GLU cc_start: 0.5684 (mm-30) cc_final: 0.5359 (tp30) REVERT: X 247 SER cc_start: 0.4454 (OUTLIER) cc_final: 0.4197 (m) REVERT: X 271 GLU cc_start: 0.5977 (OUTLIER) cc_final: 0.5452 (tm-30) REVERT: Y 104 LYS cc_start: 0.6080 (pttm) cc_final: 0.5528 (ptmm) REVERT: Y 113 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7652 (tp30) REVERT: Y 115 MET cc_start: 0.7996 (mtt) cc_final: 0.7676 (mtp) REVERT: Y 139 TYR cc_start: 0.8774 (t80) cc_final: 0.8388 (t80) REVERT: Y 141 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8101 (ttmm) REVERT: Y 161 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7598 (tpt) REVERT: Y 201 LYS cc_start: 0.6387 (ptpt) cc_final: 0.5808 (pttt) REVERT: Z 43 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.6327 (mmtm) REVERT: Z 177 GLN cc_start: 0.6579 (tp-100) cc_final: 0.6325 (tp40) REVERT: J 54 MET cc_start: 0.6546 (mtp) cc_final: 0.6269 (mtm) REVERT: J 55 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7134 (mt-10) REVERT: J 99 LYS cc_start: 0.8136 (mttt) cc_final: 0.7752 (mtpm) REVERT: J 131 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7745 (ttm-80) REVERT: J 184 TYR cc_start: 0.9085 (m-80) cc_final: 0.8583 (m-80) REVERT: M 76 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: M 85 GLN cc_start: 0.8328 (mp10) cc_final: 0.8124 (mp-120) REVERT: M 94 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7352 (pt0) REVERT: G 31 ASN cc_start: 0.8323 (m110) cc_final: 0.7816 (m110) REVERT: G 110 GLU cc_start: 0.5864 (OUTLIER) cc_final: 0.5506 (pp20) REVERT: G 168 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.7943 (ttp-110) REVERT: I 89 ASP cc_start: 0.7836 (m-30) cc_final: 0.7428 (m-30) REVERT: I 131 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7796 (mtp85) REVERT: I 183 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8711 (mm) REVERT: L 74 GLU cc_start: 0.7135 (tt0) cc_final: 0.6537 (tm-30) REVERT: L 102 PHE cc_start: 0.8564 (m-80) cc_final: 0.8253 (m-80) REVERT: H 97 GLU cc_start: 0.8207 (tp30) cc_final: 0.7815 (tp30) REVERT: H 201 ASP cc_start: 0.8623 (t70) cc_final: 0.8383 (t0) REVERT: K 83 ILE cc_start: 0.8198 (mt) cc_final: 0.7975 (mm) REVERT: K 115 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7611 (mtm-85) REVERT: N 66 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7467 (mp) outliers start: 230 outliers final: 88 residues processed: 711 average time/residue: 0.8310 time to fit residues: 704.7523 Evaluate side-chains 596 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 483 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 98 ILE Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 237 LEU Chi-restraints excluded: chain X residue 247 SER Chi-restraints excluded: chain X residue 271 GLU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 79 ASP Chi-restraints excluded: chain Y residue 96 SER Chi-restraints excluded: chain Y residue 113 GLU Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 161 MET Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 269 GLU Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 71 SER Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 184 HIS Chi-restraints excluded: chain Z residue 207 GLN Chi-restraints excluded: chain Z residue 242 LEU Chi-restraints excluded: chain Z residue 246 LEU Chi-restraints excluded: chain Z residue 259 LEU Chi-restraints excluded: chain M residue 76 GLU Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 105 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 436 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 346 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 475 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 402 optimal weight: 3.9990 chunk 488 optimal weight: 0.7980 chunk 499 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 397 ASN C 449 ASN F 54 ASN F 97 GLN ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 207 GLN G 46 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN I 221 ASN L 85 GLN H 77 ASN K 90 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.151864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110583 restraints weight = 49306.614| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.88 r_work: 0.3098 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 41358 Z= 0.196 Angle : 0.592 9.568 55839 Z= 0.304 Chirality : 0.045 0.155 6276 Planarity : 0.005 0.053 7245 Dihedral : 7.763 160.435 5757 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.67 % Allowed : 23.33 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.11), residues: 5098 helix: 0.04 (0.11), residues: 2438 sheet: -0.75 (0.20), residues: 614 loop : -1.85 (0.12), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 171 TYR 0.014 0.001 TYR B 20 PHE 0.022 0.002 PHE I 38 TRP 0.013 0.002 TRP C 567 HIS 0.004 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00472 (41358) covalent geometry : angle 0.59212 (55839) hydrogen bonds : bond 0.05517 ( 2059) hydrogen bonds : angle 4.78456 ( 6477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 498 time to evaluate : 1.309 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: A 42 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8579 (mp) REVERT: A 120 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8498 (mtm180) REVERT: A 347 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8966 (tpp) REVERT: A 463 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: A 578 LEU cc_start: 0.9121 (mt) cc_final: 0.8798 (mt) REVERT: B 161 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8665 (tt) REVERT: B 356 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 387 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8695 (tp30) REVERT: B 459 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7494 (tpt170) REVERT: B 471 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7534 (pp20) REVERT: B 530 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8406 (mtm180) REVERT: B 571 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7535 (ttm170) REVERT: C 68 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: C 80 LEU cc_start: 0.9103 (tt) cc_final: 0.8881 (tp) REVERT: C 104 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8694 (mtp180) REVERT: C 171 ARG cc_start: 0.8832 (mtp180) cc_final: 0.8554 (mpp80) REVERT: C 201 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.5672 (tm-30) REVERT: C 467 LYS cc_start: 0.8857 (tttm) cc_final: 0.8398 (ttmm) REVERT: C 571 ARG cc_start: 0.7755 (tmt-80) cc_final: 0.7380 (tmt-80) REVERT: C 573 HIS cc_start: 0.7378 (t70) cc_final: 0.6898 (t-170) REVERT: D 215 LYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5545 (tppp) REVERT: D 237 ASN cc_start: 0.8700 (p0) cc_final: 0.8392 (p0) REVERT: D 386 ARG cc_start: 0.8490 (mtp85) cc_final: 0.7758 (mtm-85) REVERT: E 169 MET cc_start: 0.9138 (ttt) cc_final: 0.8475 (ttt) REVERT: E 180 MET cc_start: 0.9412 (mtp) cc_final: 0.9085 (mtm) REVERT: E 242 ARG cc_start: 0.8397 (mtm-85) cc_final: 0.8128 (mtm-85) REVERT: E 300 MET cc_start: 0.8754 (mmm) cc_final: 0.8342 (mmm) REVERT: E 342 GLU cc_start: 0.8470 (tt0) cc_final: 0.8129 (pt0) REVERT: E 402 MET cc_start: 0.8835 (ttt) cc_final: 0.8410 (ttt) REVERT: E 431 ASP cc_start: 0.8054 (t70) cc_final: 0.7741 (t0) REVERT: E 497 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7676 (tp-100) REVERT: F 154 MET cc_start: 0.8799 (mmt) cc_final: 0.8567 (mmm) REVERT: F 237 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8243 (p0) REVERT: F 239 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: F 431 ASP cc_start: 0.8120 (m-30) cc_final: 0.7839 (m-30) REVERT: F 435 MET cc_start: 0.8592 (ttm) cc_final: 0.8362 (ttm) REVERT: X 161 MET cc_start: 0.6654 (tmm) cc_final: 0.6244 (ttp) REVERT: X 181 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7304 (mp) REVERT: X 247 SER cc_start: 0.4456 (OUTLIER) cc_final: 0.4211 (m) REVERT: Y 104 LYS cc_start: 0.6228 (pttm) cc_final: 0.5703 (ptmm) REVERT: Y 115 MET cc_start: 0.8023 (mtt) cc_final: 0.7681 (mtp) REVERT: Y 141 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8112 (ttmm) REVERT: Y 161 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7590 (tpt) REVERT: Y 181 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7334 (mp) REVERT: Y 201 LYS cc_start: 0.6414 (ptpt) cc_final: 0.5826 (pttt) REVERT: Z 47 GLU cc_start: 0.7630 (pt0) cc_final: 0.7302 (pp20) REVERT: Z 177 GLN cc_start: 0.6638 (tp-100) cc_final: 0.6270 (tp40) REVERT: J 54 MET cc_start: 0.6545 (mtp) cc_final: 0.6206 (mtm) REVERT: J 55 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7097 (mt-10) REVERT: J 99 LYS cc_start: 0.8117 (mttt) cc_final: 0.7731 (mtpm) REVERT: J 131 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7754 (ttm-80) REVERT: J 184 TYR cc_start: 0.9092 (m-80) cc_final: 0.8618 (m-80) REVERT: M 66 ARG cc_start: 0.5408 (OUTLIER) cc_final: 0.5145 (ptm160) REVERT: M 76 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: M 85 GLN cc_start: 0.8351 (mp10) cc_final: 0.8132 (mp-120) REVERT: M 94 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: M 106 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8862 (mp) REVERT: G 31 ASN cc_start: 0.8359 (m110) cc_final: 0.7809 (m110) REVERT: G 57 LEU cc_start: 0.6217 (OUTLIER) cc_final: 0.5781 (tt) REVERT: G 79 PHE cc_start: 0.3849 (OUTLIER) cc_final: 0.3117 (p90) REVERT: G 110 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5495 (pp20) REVERT: G 168 ARG cc_start: 0.8230 (ttp-110) cc_final: 0.7984 (ttp-110) REVERT: I 89 ASP cc_start: 0.7874 (m-30) cc_final: 0.7459 (m-30) REVERT: I 131 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7804 (mtp85) REVERT: L 74 GLU cc_start: 0.7307 (tt0) cc_final: 0.6747 (tm-30) REVERT: L 97 ASP cc_start: 0.8089 (m-30) cc_final: 0.7744 (m-30) REVERT: L 102 PHE cc_start: 0.8593 (m-80) cc_final: 0.8277 (m-80) REVERT: H 59 LYS cc_start: 0.6681 (OUTLIER) cc_final: 0.6447 (tttp) REVERT: H 97 GLU cc_start: 0.8219 (tp30) cc_final: 0.7851 (tp30) REVERT: H 197 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: H 201 ASP cc_start: 0.8634 (t70) cc_final: 0.8393 (t0) REVERT: K 83 ILE cc_start: 0.8210 (mt) cc_final: 0.7957 (mm) REVERT: K 106 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8618 (mm) REVERT: K 115 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7648 (mtm-85) outliers start: 252 outliers final: 118 residues processed: 692 average time/residue: 0.8432 time to fit residues: 695.1766 Evaluate side-chains 627 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 478 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 530 ARG Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 571 ARG Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 237 ASN Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 126 TYR Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 238 SER Chi-restraints excluded: chain X residue 247 SER Chi-restraints excluded: chain X residue 271 GLU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 79 ASP Chi-restraints excluded: chain Y residue 96 SER Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Y residue 146 THR Chi-restraints excluded: chain Y residue 161 MET Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 71 SER Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 184 HIS Chi-restraints excluded: chain Z residue 242 LEU Chi-restraints excluded: chain Z residue 246 LEU Chi-restraints excluded: chain Z residue 259 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 76 GLU Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 79 PHE Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain N residue 45 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 155 optimal weight: 0.7980 chunk 421 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 337 optimal weight: 0.8980 chunk 478 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 281 optimal weight: 0.9990 chunk 376 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 377 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN F 54 ASN X 198 HIS ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN I 221 ASN L 85 GLN H 77 ASN K 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111850 restraints weight = 49059.799| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.82 r_work: 0.3120 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41358 Z= 0.144 Angle : 0.548 9.473 55839 Z= 0.281 Chirality : 0.043 0.293 6276 Planarity : 0.004 0.053 7245 Dihedral : 7.232 158.159 5733 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.52 % Allowed : 23.87 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.11), residues: 5098 helix: 0.43 (0.11), residues: 2430 sheet: -0.61 (0.20), residues: 614 loop : -1.67 (0.12), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 89 TYR 0.016 0.001 TYR Z 139 PHE 0.020 0.001 PHE I 38 TRP 0.012 0.001 TRP C 567 HIS 0.004 0.001 HIS C 444 Details of bonding type rmsd covalent geometry : bond 0.00334 (41358) covalent geometry : angle 0.54820 (55839) hydrogen bonds : bond 0.04954 ( 2059) hydrogen bonds : angle 4.56169 ( 6477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 508 time to evaluate : 1.751 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: A 42 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8564 (mp) REVERT: A 103 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.9121 (tt0) REVERT: A 324 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: A 347 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8847 (tpp) REVERT: A 463 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: A 578 LEU cc_start: 0.9057 (mt) cc_final: 0.8775 (mt) REVERT: B 68 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8245 (mt-10) REVERT: B 273 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9003 (mm) REVERT: B 356 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7918 (mm-30) REVERT: B 459 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7517 (tpt170) REVERT: B 471 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7540 (pp20) REVERT: B 518 ASP cc_start: 0.8158 (m-30) cc_final: 0.7663 (t0) REVERT: B 530 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8390 (mtm180) REVERT: B 540 MET cc_start: 0.8215 (mtm) cc_final: 0.7894 (mtp) REVERT: B 574 MET cc_start: 0.7487 (mtm) cc_final: 0.7281 (mpp) REVERT: C 18 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7449 (t80) REVERT: C 68 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: C 80 LEU cc_start: 0.9095 (tt) cc_final: 0.8861 (tp) REVERT: C 104 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8742 (mtp180) REVERT: C 171 ARG cc_start: 0.8860 (mtp180) cc_final: 0.8606 (mpp80) REVERT: C 201 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6026 (tm-30) REVERT: C 467 LYS cc_start: 0.8852 (tttm) cc_final: 0.8416 (ttmm) REVERT: C 478 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8034 (tppt) REVERT: C 571 ARG cc_start: 0.7739 (tmt-80) cc_final: 0.7196 (tpt170) REVERT: C 573 HIS cc_start: 0.7400 (t70) cc_final: 0.6976 (t-170) REVERT: D 161 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8425 (mm110) REVERT: D 215 LYS cc_start: 0.6032 (OUTLIER) cc_final: 0.5532 (tppp) REVERT: D 237 ASN cc_start: 0.8578 (p0) cc_final: 0.8307 (p0) REVERT: D 386 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7758 (mtm-85) REVERT: D 435 MET cc_start: 0.7318 (ptp) cc_final: 0.6766 (pp-130) REVERT: E 161 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8578 (tm-30) REVERT: E 169 MET cc_start: 0.9076 (ttt) cc_final: 0.8384 (ttt) REVERT: E 180 MET cc_start: 0.9352 (mtp) cc_final: 0.9081 (mtm) REVERT: E 242 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8133 (mtm-85) REVERT: E 300 MET cc_start: 0.8725 (mmm) cc_final: 0.8229 (mmm) REVERT: E 342 GLU cc_start: 0.8468 (tt0) cc_final: 0.8111 (pt0) REVERT: E 431 ASP cc_start: 0.8068 (t70) cc_final: 0.7736 (t0) REVERT: E 497 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7686 (tp-100) REVERT: F 54 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.8213 (t0) REVERT: F 154 MET cc_start: 0.8785 (mmt) cc_final: 0.8582 (mmm) REVERT: F 431 ASP cc_start: 0.8128 (m-30) cc_final: 0.7841 (m-30) REVERT: F 435 MET cc_start: 0.8582 (ttm) cc_final: 0.8366 (ttm) REVERT: X 53 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6474 (mt) REVERT: X 161 MET cc_start: 0.6666 (tmm) cc_final: 0.6187 (ttp) REVERT: X 181 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7263 (mp) REVERT: X 247 SER cc_start: 0.4304 (OUTLIER) cc_final: 0.4071 (m) REVERT: Y 115 MET cc_start: 0.8057 (mtt) cc_final: 0.7789 (mtp) REVERT: Y 161 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7634 (tpt) REVERT: Y 181 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7360 (mp) REVERT: Z 47 GLU cc_start: 0.7671 (pt0) cc_final: 0.7412 (pp20) REVERT: Z 207 GLN cc_start: 0.5488 (OUTLIER) cc_final: 0.4746 (pp30) REVERT: J 54 MET cc_start: 0.6544 (mtp) cc_final: 0.6211 (mtm) REVERT: J 55 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7014 (mt-10) REVERT: J 99 LYS cc_start: 0.8136 (mttt) cc_final: 0.7780 (mtpm) REVERT: J 131 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7729 (ttm-80) REVERT: J 184 TYR cc_start: 0.9095 (m-80) cc_final: 0.8657 (m-80) REVERT: M 66 ARG cc_start: 0.5649 (OUTLIER) cc_final: 0.5384 (ptm160) REVERT: M 85 GLN cc_start: 0.8349 (mp10) cc_final: 0.8136 (mp-120) REVERT: M 94 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7419 (pt0) REVERT: G 31 ASN cc_start: 0.8389 (m110) cc_final: 0.7882 (m110) REVERT: G 46 GLN cc_start: 0.7533 (mt0) cc_final: 0.7009 (pt0) REVERT: G 57 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5755 (tt) REVERT: G 110 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5491 (pp20) REVERT: I 89 ASP cc_start: 0.7868 (m-30) cc_final: 0.7406 (m-30) REVERT: I 93 ASP cc_start: 0.7751 (t0) cc_final: 0.7192 (m-30) REVERT: I 131 ARG cc_start: 0.8138 (mtm110) cc_final: 0.7789 (mtp85) REVERT: L 74 GLU cc_start: 0.7233 (tt0) cc_final: 0.6740 (tm-30) REVERT: L 76 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7176 (pm20) REVERT: L 97 ASP cc_start: 0.8123 (m-30) cc_final: 0.7782 (m-30) REVERT: L 102 PHE cc_start: 0.8582 (m-80) cc_final: 0.8270 (m-80) REVERT: H 42 LYS cc_start: 0.0466 (OUTLIER) cc_final: -0.0383 (tppp) REVERT: H 97 GLU cc_start: 0.8228 (tp30) cc_final: 0.7880 (tp30) REVERT: H 197 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: H 201 ASP cc_start: 0.8621 (t70) cc_final: 0.8386 (t0) REVERT: K 83 ILE cc_start: 0.8163 (mt) cc_final: 0.7912 (mm) outliers start: 245 outliers final: 107 residues processed: 699 average time/residue: 0.8238 time to fit residues: 687.5576 Evaluate side-chains 618 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 479 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 530 ARG Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 247 SER Chi-restraints excluded: chain X residue 271 GLU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 79 ASP Chi-restraints excluded: chain Y residue 161 MET Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 252 SER Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 71 SER Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 184 HIS Chi-restraints excluded: chain Z residue 207 GLN Chi-restraints excluded: chain Z residue 242 LEU Chi-restraints excluded: chain Z residue 259 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 66 ARG Chi-restraints excluded: chain M residue 69 CYS Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain N residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 64 optimal weight: 0.9990 chunk 325 optimal weight: 0.0980 chunk 356 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 374 optimal weight: 3.9990 chunk 105 optimal weight: 0.0970 chunk 63 optimal weight: 1.9990 chunk 406 optimal weight: 6.9990 chunk 289 optimal weight: 5.9990 chunk 377 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN X 111 GLN ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 177 GLN ** Z 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN I 221 ASN H 77 ASN K 90 GLN N 81 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.154160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112935 restraints weight = 49015.689| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.77 r_work: 0.3124 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41358 Z= 0.127 Angle : 0.534 8.840 55839 Z= 0.273 Chirality : 0.043 0.214 6276 Planarity : 0.004 0.052 7245 Dihedral : 6.760 153.563 5714 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.84 % Allowed : 24.84 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.12), residues: 5098 helix: 0.75 (0.11), residues: 2426 sheet: -0.51 (0.20), residues: 608 loop : -1.52 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 115 TYR 0.016 0.001 TYR Z 139 PHE 0.020 0.001 PHE I 38 TRP 0.011 0.001 TRP C 567 HIS 0.004 0.001 HIS C 444 Details of bonding type rmsd covalent geometry : bond 0.00289 (41358) covalent geometry : angle 0.53449 (55839) hydrogen bonds : bond 0.04663 ( 2059) hydrogen bonds : angle 4.41013 ( 6477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 502 time to evaluate : 1.594 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: A 42 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 324 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: A 347 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8859 (tpp) REVERT: A 463 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: A 578 LEU cc_start: 0.8939 (mt) cc_final: 0.8680 (mt) REVERT: B 68 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: B 273 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.9009 (mm) REVERT: B 356 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7893 (mm-30) REVERT: B 459 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7464 (tpt170) REVERT: B 471 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7533 (pp20) REVERT: B 518 ASP cc_start: 0.8145 (m-30) cc_final: 0.7652 (t0) REVERT: B 540 MET cc_start: 0.8172 (mtm) cc_final: 0.7844 (mtp) REVERT: B 574 MET cc_start: 0.7653 (mtm) cc_final: 0.7391 (mpp) REVERT: C 18 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7521 (t80) REVERT: C 68 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: C 80 LEU cc_start: 0.9086 (tt) cc_final: 0.8848 (tp) REVERT: C 171 ARG cc_start: 0.8818 (mtp180) cc_final: 0.8572 (mpp80) REVERT: C 467 LYS cc_start: 0.8845 (tttm) cc_final: 0.8391 (ttmm) REVERT: C 478 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.8027 (tppt) REVERT: C 571 ARG cc_start: 0.7720 (tmt-80) cc_final: 0.7203 (tpt170) REVERT: C 573 HIS cc_start: 0.7241 (t70) cc_final: 0.6893 (t-170) REVERT: D 161 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8442 (mm110) REVERT: D 215 LYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5385 (tppp) REVERT: D 237 ASN cc_start: 0.8582 (p0) cc_final: 0.8297 (p0) REVERT: D 330 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8534 (t70) REVERT: D 386 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7729 (mtm-85) REVERT: E 161 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8594 (tm-30) REVERT: E 169 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8504 (ttt) REVERT: E 180 MET cc_start: 0.9301 (mtp) cc_final: 0.9042 (mtm) REVERT: E 201 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8483 (pm20) REVERT: E 242 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8103 (mtm-85) REVERT: E 300 MET cc_start: 0.8723 (mmm) cc_final: 0.8469 (mmp) REVERT: E 342 GLU cc_start: 0.8465 (tt0) cc_final: 0.8095 (pt0) REVERT: E 402 MET cc_start: 0.8837 (ttt) cc_final: 0.8359 (ttt) REVERT: E 431 ASP cc_start: 0.8070 (t70) cc_final: 0.7742 (t0) REVERT: E 497 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7672 (tp-100) REVERT: F 154 MET cc_start: 0.8769 (mmt) cc_final: 0.8568 (mmm) REVERT: F 234 MET cc_start: 0.8827 (mtm) cc_final: 0.8531 (mtm) REVERT: F 239 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: F 431 ASP cc_start: 0.8104 (m-30) cc_final: 0.7798 (m-30) REVERT: F 435 MET cc_start: 0.8548 (ttm) cc_final: 0.8272 (ttm) REVERT: X 37 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.6047 (p0) REVERT: X 161 MET cc_start: 0.6642 (tmm) cc_final: 0.6176 (ttp) REVERT: X 181 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7238 (mp) REVERT: X 209 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: X 247 SER cc_start: 0.4253 (OUTLIER) cc_final: 0.4032 (m) REVERT: Y 115 MET cc_start: 0.8007 (mtt) cc_final: 0.7616 (mtp) REVERT: Y 161 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7099 (ttp) REVERT: Y 181 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7548 (mp) REVERT: Y 260 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6796 (mp) REVERT: Z 47 GLU cc_start: 0.7561 (pt0) cc_final: 0.7339 (pp20) REVERT: Z 173 GLU cc_start: 0.5729 (mp0) cc_final: 0.5334 (mm-30) REVERT: J 54 MET cc_start: 0.6437 (mtp) cc_final: 0.6138 (mtm) REVERT: J 99 LYS cc_start: 0.8062 (mttt) cc_final: 0.7712 (mtpm) REVERT: J 131 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7754 (ttm-80) REVERT: J 184 TYR cc_start: 0.9076 (m-80) cc_final: 0.8635 (m-80) REVERT: M 85 GLN cc_start: 0.8307 (mp10) cc_final: 0.8008 (mp-120) REVERT: M 94 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: M 106 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8865 (mp) REVERT: G 31 ASN cc_start: 0.8301 (m110) cc_final: 0.7838 (m110) REVERT: G 46 GLN cc_start: 0.7688 (mt0) cc_final: 0.6975 (pt0) REVERT: G 57 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.5488 (tt) REVERT: G 97 LYS cc_start: 0.7890 (mttm) cc_final: 0.7443 (mmmt) REVERT: G 110 GLU cc_start: 0.5725 (OUTLIER) cc_final: 0.5427 (pp20) REVERT: I 89 ASP cc_start: 0.7955 (m-30) cc_final: 0.7445 (m-30) REVERT: I 93 ASP cc_start: 0.7717 (t0) cc_final: 0.7156 (m-30) REVERT: I 131 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7822 (mtp85) REVERT: L 74 GLU cc_start: 0.7173 (tt0) cc_final: 0.6705 (tm-30) REVERT: L 87 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7525 (m-80) REVERT: L 97 ASP cc_start: 0.8122 (m-30) cc_final: 0.7776 (m-30) REVERT: H 42 LYS cc_start: 0.0430 (OUTLIER) cc_final: -0.0390 (tppp) REVERT: H 97 GLU cc_start: 0.8213 (tp30) cc_final: 0.7822 (tp30) REVERT: H 197 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: H 201 ASP cc_start: 0.8627 (t70) cc_final: 0.8382 (t0) REVERT: K 83 ILE cc_start: 0.8165 (mt) cc_final: 0.7923 (mm) outliers start: 215 outliers final: 109 residues processed: 671 average time/residue: 0.8323 time to fit residues: 665.7693 Evaluate side-chains 624 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 483 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 126 TYR Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 209 GLU Chi-restraints excluded: chain X residue 220 GLU Chi-restraints excluded: chain X residue 247 SER Chi-restraints excluded: chain X residue 271 GLU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 79 ASP Chi-restraints excluded: chain Y residue 161 MET Chi-restraints excluded: chain Y residue 172 ASN Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 252 SER Chi-restraints excluded: chain Y residue 260 LEU Chi-restraints excluded: chain Y residue 273 LEU Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 71 SER Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 162 GLN Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 184 HIS Chi-restraints excluded: chain Z residue 242 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain N residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 466 optimal weight: 9.9990 chunk 160 optimal weight: 0.5980 chunk 249 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 348 optimal weight: 5.9990 chunk 424 optimal weight: 0.6980 chunk 373 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 488 optimal weight: 3.9990 chunk 505 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN C 112 GLN F 54 ASN ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 177 GLN Z 207 GLN J 71 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN I 221 ASN K 90 GLN N 68 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.153711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112708 restraints weight = 49068.720| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.66 r_work: 0.3110 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41358 Z= 0.151 Angle : 0.545 9.267 55839 Z= 0.278 Chirality : 0.043 0.170 6276 Planarity : 0.004 0.051 7245 Dihedral : 6.567 150.505 5704 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.04 % Allowed : 24.75 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.12), residues: 5098 helix: 0.85 (0.11), residues: 2429 sheet: -0.48 (0.20), residues: 628 loop : -1.48 (0.12), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 89 TYR 0.017 0.001 TYR B 20 PHE 0.020 0.001 PHE I 38 TRP 0.011 0.001 TRP C 567 HIS 0.004 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00357 (41358) covalent geometry : angle 0.54451 (55839) hydrogen bonds : bond 0.04790 ( 2059) hydrogen bonds : angle 4.40209 ( 6477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 493 time to evaluate : 1.759 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: A 42 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 103 GLN cc_start: 0.9446 (OUTLIER) cc_final: 0.9143 (tt0) REVERT: A 324 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: A 347 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8863 (tpp) REVERT: A 463 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: A 578 LEU cc_start: 0.8950 (mt) cc_final: 0.8677 (mt) REVERT: A 588 ASP cc_start: 0.8008 (t0) cc_final: 0.7624 (t0) REVERT: B 68 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: B 273 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9070 (mm) REVERT: B 356 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7923 (mm-30) REVERT: B 459 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7434 (tpt170) REVERT: B 471 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7535 (pp20) REVERT: B 492 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6947 (mt) REVERT: B 518 ASP cc_start: 0.8155 (m-30) cc_final: 0.7635 (t0) REVERT: B 540 MET cc_start: 0.8200 (mtm) cc_final: 0.7854 (mtp) REVERT: B 574 MET cc_start: 0.7580 (mtm) cc_final: 0.7333 (mpp) REVERT: C 18 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7528 (t80) REVERT: C 68 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: C 80 LEU cc_start: 0.9082 (tt) cc_final: 0.8840 (tp) REVERT: C 104 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8680 (mtp180) REVERT: C 171 ARG cc_start: 0.8811 (mtp180) cc_final: 0.8570 (mpp80) REVERT: C 201 GLU cc_start: 0.6112 (tm-30) cc_final: 0.5910 (tm-30) REVERT: C 467 LYS cc_start: 0.8845 (tttm) cc_final: 0.8383 (ttmm) REVERT: C 478 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.8023 (tppt) REVERT: C 544 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8111 (mtt) REVERT: C 571 ARG cc_start: 0.7677 (tmt-80) cc_final: 0.7152 (tpt170) REVERT: C 573 HIS cc_start: 0.7242 (t70) cc_final: 0.6880 (t-170) REVERT: D 161 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8446 (mm110) REVERT: D 215 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5340 (tppp) REVERT: D 237 ASN cc_start: 0.8618 (p0) cc_final: 0.8336 (p0) REVERT: D 330 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8582 (t70) REVERT: D 386 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7712 (mtm-85) REVERT: E 161 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8567 (tm-30) REVERT: E 169 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8386 (ttt) REVERT: E 180 MET cc_start: 0.9326 (mtp) cc_final: 0.8997 (mtm) REVERT: E 201 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8461 (pm20) REVERT: E 242 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.8112 (mtm-85) REVERT: E 300 MET cc_start: 0.8750 (mmm) cc_final: 0.8511 (mmp) REVERT: E 342 GLU cc_start: 0.8472 (tt0) cc_final: 0.8105 (pt0) REVERT: E 402 MET cc_start: 0.8885 (ttt) cc_final: 0.8356 (ttt) REVERT: E 431 ASP cc_start: 0.8086 (t70) cc_final: 0.7757 (t0) REVERT: E 497 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7658 (tp-100) REVERT: F 154 MET cc_start: 0.8783 (mmt) cc_final: 0.8567 (mmm) REVERT: F 239 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: F 431 ASP cc_start: 0.8125 (m-30) cc_final: 0.7815 (m-30) REVERT: F 435 MET cc_start: 0.8540 (ttm) cc_final: 0.8340 (ttm) REVERT: X 161 MET cc_start: 0.6682 (tmm) cc_final: 0.6191 (ttp) REVERT: X 181 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7233 (mp) REVERT: X 247 SER cc_start: 0.4248 (OUTLIER) cc_final: 0.4037 (m) REVERT: Y 115 MET cc_start: 0.7995 (mtt) cc_final: 0.7598 (mtp) REVERT: Y 161 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7000 (ttp) REVERT: Y 181 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7413 (mp) REVERT: Z 43 LYS cc_start: 0.6659 (OUTLIER) cc_final: 0.6385 (mmtm) REVERT: Z 173 GLU cc_start: 0.5806 (mp0) cc_final: 0.5363 (mm-30) REVERT: Z 177 GLN cc_start: 0.6794 (tp-100) cc_final: 0.6529 (tp40) REVERT: J 54 MET cc_start: 0.6455 (mtp) cc_final: 0.6143 (mtm) REVERT: J 99 LYS cc_start: 0.8035 (mttt) cc_final: 0.7680 (mtpm) REVERT: J 131 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7736 (ttm-80) REVERT: J 184 TYR cc_start: 0.9060 (m-80) cc_final: 0.8610 (m-80) REVERT: M 85 GLN cc_start: 0.8260 (mp10) cc_final: 0.7993 (mp-120) REVERT: M 94 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: M 106 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8867 (mp) REVERT: G 31 ASN cc_start: 0.8345 (m110) cc_final: 0.7863 (m110) REVERT: G 46 GLN cc_start: 0.7403 (mt0) cc_final: 0.6968 (pt0) REVERT: G 57 LEU cc_start: 0.5753 (OUTLIER) cc_final: 0.5349 (tt) REVERT: G 97 LYS cc_start: 0.7856 (mttm) cc_final: 0.7453 (mmmt) REVERT: G 110 GLU cc_start: 0.5559 (OUTLIER) cc_final: 0.5295 (pp20) REVERT: I 89 ASP cc_start: 0.7941 (m-30) cc_final: 0.7505 (m-30) REVERT: I 131 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7772 (mtp85) REVERT: I 183 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8647 (mm) REVERT: L 74 GLU cc_start: 0.7174 (tt0) cc_final: 0.6665 (tm-30) REVERT: L 81 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7329 (mtt) REVERT: L 85 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: L 87 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7510 (m-80) REVERT: L 97 ASP cc_start: 0.8054 (m-30) cc_final: 0.7608 (m-30) REVERT: H 42 LYS cc_start: 0.0341 (OUTLIER) cc_final: -0.0450 (tppp) REVERT: H 97 GLU cc_start: 0.8196 (tp30) cc_final: 0.7809 (tp30) REVERT: H 183 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8748 (mm) REVERT: H 197 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: H 201 ASP cc_start: 0.8627 (t70) cc_final: 0.8392 (t0) REVERT: K 83 ILE cc_start: 0.8081 (mt) cc_final: 0.7826 (mm) REVERT: N 68 GLN cc_start: 0.6451 (OUTLIER) cc_final: 0.6174 (tm-30) outliers start: 224 outliers final: 126 residues processed: 664 average time/residue: 0.8483 time to fit residues: 673.3809 Evaluate side-chains 643 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 478 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 126 TYR Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 220 GLU Chi-restraints excluded: chain X residue 247 SER Chi-restraints excluded: chain X residue 271 GLU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 79 ASP Chi-restraints excluded: chain Y residue 161 MET Chi-restraints excluded: chain Y residue 172 ASN Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 252 SER Chi-restraints excluded: chain Y residue 273 LEU Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 162 GLN Chi-restraints excluded: chain Z residue 168 ILE Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 184 HIS Chi-restraints excluded: chain Z residue 207 GLN Chi-restraints excluded: chain Z residue 242 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 81 MET Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 45 ILE Chi-restraints excluded: chain N residue 68 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 143 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 347 optimal weight: 0.2980 chunk 288 optimal weight: 0.5980 chunk 240 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 460 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 363 optimal weight: 5.9990 chunk 503 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN F 54 ASN ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 207 GLN J 71 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 GLN I 221 ASN K 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112049 restraints weight = 49085.725| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.75 r_work: 0.3105 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41358 Z= 0.165 Angle : 0.558 10.157 55839 Z= 0.284 Chirality : 0.044 0.156 6276 Planarity : 0.004 0.054 7245 Dihedral : 6.563 148.963 5702 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.00 % Allowed : 24.93 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.12), residues: 5098 helix: 0.89 (0.11), residues: 2437 sheet: -0.48 (0.20), residues: 635 loop : -1.44 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 89 TYR 0.019 0.001 TYR B 20 PHE 0.020 0.001 PHE I 38 TRP 0.011 0.001 TRP A 450 HIS 0.004 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00394 (41358) covalent geometry : angle 0.55776 (55839) hydrogen bonds : bond 0.04868 ( 2059) hydrogen bonds : angle 4.41070 ( 6477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 497 time to evaluate : 1.676 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: A 42 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8589 (mp) REVERT: A 103 GLN cc_start: 0.9457 (OUTLIER) cc_final: 0.9164 (tt0) REVERT: A 303 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: A 324 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7968 (tt0) REVERT: A 347 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8919 (tpp) REVERT: A 463 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: A 506 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7760 (mttp) REVERT: A 578 LEU cc_start: 0.8976 (mt) cc_final: 0.8702 (mt) REVERT: A 588 ASP cc_start: 0.8037 (t0) cc_final: 0.7687 (t0) REVERT: B 356 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8063 (mm-30) REVERT: B 459 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7440 (tpt170) REVERT: B 471 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7537 (pp20) REVERT: B 492 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.7088 (mt) REVERT: B 518 ASP cc_start: 0.8170 (m-30) cc_final: 0.7655 (t0) REVERT: C 18 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7553 (t80) REVERT: C 68 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: C 80 LEU cc_start: 0.9101 (tt) cc_final: 0.8859 (tp) REVERT: C 104 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8718 (mtp180) REVERT: C 171 ARG cc_start: 0.8815 (mtp180) cc_final: 0.8582 (mpp80) REVERT: C 467 LYS cc_start: 0.8865 (tttm) cc_final: 0.8412 (ttmm) REVERT: C 478 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8081 (tppt) REVERT: C 544 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8156 (mtt) REVERT: C 571 ARG cc_start: 0.7741 (tmt-80) cc_final: 0.7219 (tpt170) REVERT: C 573 HIS cc_start: 0.7275 (t70) cc_final: 0.6914 (t-170) REVERT: D 161 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8470 (mm110) REVERT: D 215 LYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5460 (tppp) REVERT: D 237 ASN cc_start: 0.8666 (p0) cc_final: 0.8398 (p0) REVERT: D 330 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8576 (t70) REVERT: D 386 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.7785 (mtm-85) REVERT: E 161 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8579 (tm-30) REVERT: E 169 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8374 (ttt) REVERT: E 180 MET cc_start: 0.9355 (mtp) cc_final: 0.9083 (mtm) REVERT: E 201 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: E 242 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.8162 (mtm-85) REVERT: E 300 MET cc_start: 0.8759 (mmm) cc_final: 0.8527 (mmp) REVERT: E 342 GLU cc_start: 0.8475 (tt0) cc_final: 0.8127 (pt0) REVERT: E 431 ASP cc_start: 0.8143 (t70) cc_final: 0.7801 (t0) REVERT: E 497 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7700 (tp-100) REVERT: F 239 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: F 431 ASP cc_start: 0.8170 (m-30) cc_final: 0.7878 (m-30) REVERT: X 47 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7774 (tm-30) REVERT: X 60 TYR cc_start: 0.7363 (m-10) cc_final: 0.7082 (m-10) REVERT: X 161 MET cc_start: 0.6738 (tmm) cc_final: 0.6240 (ttp) REVERT: X 181 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7269 (mp) REVERT: X 247 SER cc_start: 0.4298 (OUTLIER) cc_final: 0.3739 (m) REVERT: Y 115 MET cc_start: 0.8031 (mtt) cc_final: 0.7740 (mtp) REVERT: Y 161 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7592 (tpt) REVERT: Y 181 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7466 (mp) REVERT: Y 209 GLU cc_start: 0.7977 (mp0) cc_final: 0.7365 (tm-30) REVERT: Z 43 LYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6455 (mmtm) REVERT: Z 173 GLU cc_start: 0.5766 (mp0) cc_final: 0.5334 (mm-30) REVERT: J 54 MET cc_start: 0.6487 (mtp) cc_final: 0.6178 (mtm) REVERT: J 99 LYS cc_start: 0.8100 (mttt) cc_final: 0.7753 (mtpm) REVERT: J 131 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7774 (ttm-80) REVERT: J 184 TYR cc_start: 0.9079 (m-80) cc_final: 0.8634 (m-80) REVERT: M 85 GLN cc_start: 0.8305 (mp10) cc_final: 0.8040 (mp-120) REVERT: M 94 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7498 (pt0) REVERT: M 106 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8829 (mp) REVERT: G 31 ASN cc_start: 0.8374 (m110) cc_final: 0.7883 (m110) REVERT: G 46 GLN cc_start: 0.7454 (mt0) cc_final: 0.7004 (pt0) REVERT: G 57 LEU cc_start: 0.5777 (OUTLIER) cc_final: 0.5376 (tt) REVERT: G 110 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5424 (pp20) REVERT: I 89 ASP cc_start: 0.8002 (m-30) cc_final: 0.7456 (m-30) REVERT: I 131 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7759 (mtp85) REVERT: I 183 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8648 (mm) REVERT: L 74 GLU cc_start: 0.7252 (tt0) cc_final: 0.6733 (tm-30) REVERT: L 76 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7302 (pm20) REVERT: L 81 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7563 (mtt) REVERT: L 85 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7387 (mp10) REVERT: L 87 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: L 97 ASP cc_start: 0.8087 (m-30) cc_final: 0.7644 (m-30) REVERT: H 42 LYS cc_start: 0.0412 (OUTLIER) cc_final: -0.0400 (tppp) REVERT: H 97 GLU cc_start: 0.8207 (tp30) cc_final: 0.7834 (tp30) REVERT: H 183 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8786 (mm) REVERT: H 197 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: H 201 ASP cc_start: 0.8647 (t70) cc_final: 0.8414 (t0) REVERT: K 83 ILE cc_start: 0.8149 (mt) cc_final: 0.7878 (mm) outliers start: 222 outliers final: 135 residues processed: 669 average time/residue: 0.8434 time to fit residues: 675.2946 Evaluate side-chains 652 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 478 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 120 ARG Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 432 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 54 ASN Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 239 GLU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain X residue 32 CYS Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 146 THR Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 181 LEU Chi-restraints excluded: chain X residue 220 GLU Chi-restraints excluded: chain X residue 247 SER Chi-restraints excluded: chain X residue 271 GLU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 79 ASP Chi-restraints excluded: chain Y residue 96 SER Chi-restraints excluded: chain Y residue 161 MET Chi-restraints excluded: chain Y residue 172 ASN Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 252 SER Chi-restraints excluded: chain Y residue 273 LEU Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 43 LYS Chi-restraints excluded: chain Z residue 71 SER Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 162 GLN Chi-restraints excluded: chain Z residue 168 ILE Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 184 HIS Chi-restraints excluded: chain Z residue 242 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 67 PHE Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 183 ILE Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 197 GLU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 81 MET Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 197 GLU Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 45 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 227 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 285 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 480 optimal weight: 0.6980 chunk 325 optimal weight: 0.9990 chunk 174 optimal weight: 0.4980 chunk 261 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 164 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN X 120 ASN ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 177 GLN Z 207 GLN J 71 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN I 221 ASN K 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113535 restraints weight = 49035.503| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.79 r_work: 0.3134 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41358 Z= 0.117 Angle : 0.527 10.881 55839 Z= 0.268 Chirality : 0.042 0.160 6276 Planarity : 0.004 0.055 7245 Dihedral : 6.310 141.472 5701 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.12 % Allowed : 25.99 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.12), residues: 5098 helix: 1.15 (0.11), residues: 2428 sheet: -0.38 (0.20), residues: 616 loop : -1.33 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 89 TYR 0.018 0.001 TYR Z 139 PHE 0.020 0.001 PHE Y 213 TRP 0.010 0.001 TRP C 567 HIS 0.004 0.001 HIS C 444 Details of bonding type rmsd covalent geometry : bond 0.00262 (41358) covalent geometry : angle 0.52668 (55839) hydrogen bonds : bond 0.04353 ( 2059) hydrogen bonds : angle 4.25710 ( 6477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 515 time to evaluate : 1.663 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: A 42 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8528 (mp) REVERT: A 61 MET cc_start: 0.8252 (mmm) cc_final: 0.7949 (mtm) REVERT: A 103 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.9104 (tt0) REVERT: A 303 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7472 (mt-10) REVERT: A 324 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7973 (tt0) REVERT: A 347 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8920 (tpp) REVERT: A 463 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: A 506 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7607 (mttp) REVERT: A 578 LEU cc_start: 0.8851 (mt) cc_final: 0.8582 (mt) REVERT: A 588 ASP cc_start: 0.7857 (t0) cc_final: 0.7500 (t0) REVERT: B 356 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 459 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7338 (tpt170) REVERT: B 471 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7508 (pp20) REVERT: B 518 ASP cc_start: 0.8146 (m-30) cc_final: 0.7601 (t0) REVERT: B 540 MET cc_start: 0.8101 (mtm) cc_final: 0.7826 (mtp) REVERT: C 18 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7572 (t80) REVERT: C 68 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: C 80 LEU cc_start: 0.9065 (tt) cc_final: 0.8827 (tp) REVERT: C 104 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8664 (mtp180) REVERT: C 171 ARG cc_start: 0.8793 (mtp180) cc_final: 0.8315 (mtm180) REVERT: C 467 LYS cc_start: 0.8838 (tttm) cc_final: 0.8375 (ttmm) REVERT: C 544 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8072 (mtt) REVERT: C 571 ARG cc_start: 0.7666 (tmt-80) cc_final: 0.7140 (tpt170) REVERT: C 573 HIS cc_start: 0.7214 (t70) cc_final: 0.6998 (t70) REVERT: D 161 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8465 (mm110) REVERT: D 215 LYS cc_start: 0.5849 (OUTLIER) cc_final: 0.5354 (tppp) REVERT: D 237 ASN cc_start: 0.8546 (p0) cc_final: 0.8321 (p0) REVERT: D 386 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7677 (mtm-85) REVERT: D 435 MET cc_start: 0.7169 (ptp) cc_final: 0.6719 (pp-130) REVERT: E 133 ASN cc_start: 0.9007 (p0) cc_final: 0.8701 (p0) REVERT: E 169 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8427 (ttt) REVERT: E 180 MET cc_start: 0.9283 (mtp) cc_final: 0.9062 (mtm) REVERT: E 201 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8452 (pm20) REVERT: E 300 MET cc_start: 0.8708 (mmm) cc_final: 0.8485 (mmp) REVERT: E 342 GLU cc_start: 0.8470 (tt0) cc_final: 0.8124 (pt0) REVERT: E 402 MET cc_start: 0.8866 (ttt) cc_final: 0.8333 (ttt) REVERT: E 431 ASP cc_start: 0.8060 (t70) cc_final: 0.7702 (t0) REVERT: E 497 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7671 (tp-100) REVERT: F 354 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8201 (tp) REVERT: F 431 ASP cc_start: 0.8096 (m-30) cc_final: 0.7766 (m-30) REVERT: F 435 MET cc_start: 0.8516 (ttm) cc_final: 0.8226 (ttm) REVERT: X 47 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7713 (tm-30) REVERT: X 60 TYR cc_start: 0.7554 (m-10) cc_final: 0.7217 (m-10) REVERT: X 161 MET cc_start: 0.6758 (tmm) cc_final: 0.6225 (ttp) REVERT: X 247 SER cc_start: 0.4394 (OUTLIER) cc_final: 0.3865 (m) REVERT: Y 115 MET cc_start: 0.7980 (mtt) cc_final: 0.7684 (mtp) REVERT: Y 161 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7026 (ttp) REVERT: Y 181 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7408 (mp) REVERT: Y 209 GLU cc_start: 0.8009 (mp0) cc_final: 0.7234 (tp30) REVERT: Z 155 MET cc_start: 0.5843 (mtm) cc_final: 0.5610 (mpp) REVERT: Z 163 ILE cc_start: 0.7670 (tt) cc_final: 0.7417 (tp) REVERT: Z 173 GLU cc_start: 0.5818 (mp0) cc_final: 0.5400 (mm-30) REVERT: Z 177 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6511 (tp40) REVERT: J 54 MET cc_start: 0.6453 (mtp) cc_final: 0.6158 (mtm) REVERT: J 99 LYS cc_start: 0.7987 (mttt) cc_final: 0.7642 (mtpm) REVERT: J 131 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7716 (ttm-80) REVERT: J 184 TYR cc_start: 0.9027 (m-80) cc_final: 0.8560 (m-80) REVERT: M 85 GLN cc_start: 0.8213 (mp10) cc_final: 0.7876 (mp-120) REVERT: M 94 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: M 106 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8812 (mp) REVERT: G 31 ASN cc_start: 0.8275 (m110) cc_final: 0.7787 (m110) REVERT: G 46 GLN cc_start: 0.7603 (mt0) cc_final: 0.7012 (pt0) REVERT: G 57 LEU cc_start: 0.5738 (OUTLIER) cc_final: 0.5380 (tt) REVERT: G 97 LYS cc_start: 0.7903 (mttm) cc_final: 0.7334 (mmmt) REVERT: G 110 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.5299 (pp20) REVERT: I 89 ASP cc_start: 0.7915 (m-30) cc_final: 0.7366 (m-30) REVERT: I 131 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7559 (mtp85) REVERT: L 74 GLU cc_start: 0.7146 (tt0) cc_final: 0.6674 (tm-30) REVERT: L 76 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: L 79 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6499 (tm-30) REVERT: L 81 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7290 (mtt) REVERT: L 85 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7292 (mp10) REVERT: L 87 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: L 97 ASP cc_start: 0.8020 (m-30) cc_final: 0.7577 (m-30) REVERT: H 42 LYS cc_start: 0.0466 (OUTLIER) cc_final: -0.0275 (tppp) REVERT: H 97 GLU cc_start: 0.8168 (tp30) cc_final: 0.7796 (tp30) REVERT: H 201 ASP cc_start: 0.8573 (t70) cc_final: 0.8333 (t0) REVERT: K 83 ILE cc_start: 0.8074 (mt) cc_final: 0.7837 (mm) outliers start: 183 outliers final: 103 residues processed: 654 average time/residue: 0.8291 time to fit residues: 645.7843 Evaluate side-chains 624 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 489 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 463 GLU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 613 ARG Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 350 GLN Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 220 GLU Chi-restraints excluded: chain X residue 247 SER Chi-restraints excluded: chain X residue 271 GLU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 79 ASP Chi-restraints excluded: chain Y residue 96 SER Chi-restraints excluded: chain Y residue 161 MET Chi-restraints excluded: chain Y residue 172 ASN Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 188 MET Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 252 SER Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 71 SER Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 162 GLN Chi-restraints excluded: chain Z residue 168 ILE Chi-restraints excluded: chain Z residue 177 GLN Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 207 GLN Chi-restraints excluded: chain Z residue 242 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain M residue 83 ILE Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 103 SER Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 81 MET Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 409 optimal weight: 0.6980 chunk 295 optimal weight: 0.6980 chunk 493 optimal weight: 20.0000 chunk 297 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 468 optimal weight: 0.6980 chunk 257 optimal weight: 0.0970 chunk 466 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 414 optimal weight: 0.0070 chunk 46 optimal weight: 3.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 177 GLN Z 207 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 221 ASN K 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.155802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114732 restraints weight = 49228.046| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.81 r_work: 0.3152 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 41358 Z= 0.109 Angle : 0.533 14.540 55839 Z= 0.270 Chirality : 0.042 0.392 6276 Planarity : 0.004 0.060 7245 Dihedral : 5.866 134.139 5686 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.56 % Allowed : 26.71 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.12), residues: 5098 helix: 1.31 (0.11), residues: 2426 sheet: -0.37 (0.20), residues: 635 loop : -1.26 (0.13), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 89 TYR 0.023 0.001 TYR X 139 PHE 0.018 0.001 PHE I 38 TRP 0.016 0.001 TRP Y 55 HIS 0.005 0.001 HIS X 19 Details of bonding type rmsd covalent geometry : bond 0.00235 (41358) covalent geometry : angle 0.53346 (55839) hydrogen bonds : bond 0.04168 ( 2059) hydrogen bonds : angle 4.19867 ( 6477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 508 time to evaluate : 1.714 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: A 42 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8536 (mp) REVERT: A 303 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: A 324 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: A 578 LEU cc_start: 0.8776 (mt) cc_final: 0.8498 (mt) REVERT: A 588 ASP cc_start: 0.7856 (t0) cc_final: 0.7527 (t0) REVERT: B 56 ARG cc_start: 0.8485 (ttm110) cc_final: 0.8274 (ttp80) REVERT: B 203 PHE cc_start: 0.6006 (t80) cc_final: 0.5371 (t80) REVERT: B 356 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7950 (mm-30) REVERT: B 458 MET cc_start: 0.8405 (mtp) cc_final: 0.8200 (mtt) REVERT: B 459 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7258 (tpt170) REVERT: B 471 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7622 (pp20) REVERT: B 518 ASP cc_start: 0.8129 (m-30) cc_final: 0.7563 (t0) REVERT: B 540 MET cc_start: 0.8086 (mtm) cc_final: 0.7832 (mtp) REVERT: C 18 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.7607 (t80) REVERT: C 61 MET cc_start: 0.8583 (mmm) cc_final: 0.8365 (tpp) REVERT: C 68 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: C 80 LEU cc_start: 0.9055 (tt) cc_final: 0.8817 (tp) REVERT: C 104 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8630 (mtp180) REVERT: C 171 ARG cc_start: 0.8778 (mtp180) cc_final: 0.8316 (mtm180) REVERT: C 467 LYS cc_start: 0.8842 (tttm) cc_final: 0.8373 (ttmm) REVERT: C 544 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8013 (mtt) REVERT: C 571 ARG cc_start: 0.7631 (tmt-80) cc_final: 0.7103 (tpt170) REVERT: C 573 HIS cc_start: 0.7209 (t70) cc_final: 0.6992 (t70) REVERT: D 126 ASP cc_start: 0.8627 (m-30) cc_final: 0.8336 (m-30) REVERT: D 161 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8338 (mm110) REVERT: D 330 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8526 (t70) REVERT: D 386 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7687 (mtm-85) REVERT: D 435 MET cc_start: 0.7051 (ptp) cc_final: 0.6648 (pp-130) REVERT: E 169 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8461 (ttt) REVERT: E 180 MET cc_start: 0.9237 (mtp) cc_final: 0.8975 (mtm) REVERT: E 201 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8446 (pm20) REVERT: E 300 MET cc_start: 0.8678 (mmm) cc_final: 0.8465 (mmp) REVERT: E 342 GLU cc_start: 0.8441 (tt0) cc_final: 0.8082 (pt0) REVERT: E 402 MET cc_start: 0.8853 (ttt) cc_final: 0.8309 (ttt) REVERT: E 431 ASP cc_start: 0.8059 (t70) cc_final: 0.7622 (t0) REVERT: E 447 ASP cc_start: 0.8486 (m-30) cc_final: 0.7990 (m-30) REVERT: E 497 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7658 (tp-100) REVERT: F 354 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8220 (tp) REVERT: F 431 ASP cc_start: 0.8076 (m-30) cc_final: 0.7745 (m-30) REVERT: F 435 MET cc_start: 0.8497 (ttm) cc_final: 0.8283 (ttm) REVERT: X 47 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7734 (tm-30) REVERT: X 60 TYR cc_start: 0.7518 (m-10) cc_final: 0.7153 (m-10) REVERT: X 161 MET cc_start: 0.6717 (tmm) cc_final: 0.6219 (ttp) REVERT: Y 115 MET cc_start: 0.7933 (mtt) cc_final: 0.7628 (mtp) REVERT: Y 161 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7036 (ttp) REVERT: Y 181 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7426 (mp) REVERT: Y 209 GLU cc_start: 0.8068 (mp0) cc_final: 0.7180 (tp30) REVERT: Z 163 ILE cc_start: 0.7590 (tt) cc_final: 0.7289 (tp) REVERT: Z 227 LYS cc_start: 0.6139 (tmmt) cc_final: 0.5801 (mtmt) REVERT: J 54 MET cc_start: 0.6330 (mtp) cc_final: 0.6047 (mtm) REVERT: J 99 LYS cc_start: 0.7957 (mttt) cc_final: 0.7602 (mtpm) REVERT: J 131 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7700 (ttm-80) REVERT: J 184 TYR cc_start: 0.9007 (m-80) cc_final: 0.8541 (m-80) REVERT: M 79 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7466 (tm-30) REVERT: M 85 GLN cc_start: 0.8233 (mp10) cc_final: 0.7933 (mp-120) REVERT: M 94 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: M 106 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8805 (mp) REVERT: G 31 ASN cc_start: 0.8161 (m110) cc_final: 0.7673 (m110) REVERT: G 46 GLN cc_start: 0.7516 (mt0) cc_final: 0.6968 (pt0) REVERT: G 57 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5373 (tt) REVERT: G 110 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.5360 (pp20) REVERT: I 89 ASP cc_start: 0.7906 (m-30) cc_final: 0.7421 (m-30) REVERT: I 93 ASP cc_start: 0.7733 (t0) cc_final: 0.7135 (m-30) REVERT: I 131 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7611 (mtp85) REVERT: L 74 GLU cc_start: 0.7038 (tt0) cc_final: 0.6622 (tm-30) REVERT: L 76 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7211 (pm20) REVERT: L 79 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6384 (tm-30) REVERT: L 85 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: L 87 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: L 97 ASP cc_start: 0.8001 (m-30) cc_final: 0.7662 (m-30) REVERT: H 42 LYS cc_start: 0.0328 (OUTLIER) cc_final: -0.0433 (tppp) REVERT: H 97 GLU cc_start: 0.8153 (tp30) cc_final: 0.7792 (tp30) REVERT: H 183 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8687 (mm) REVERT: H 201 ASP cc_start: 0.8568 (t70) cc_final: 0.8338 (t0) REVERT: K 83 ILE cc_start: 0.8049 (mt) cc_final: 0.7807 (mm) REVERT: K 115 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7430 (mtm-85) outliers start: 158 outliers final: 90 residues processed: 629 average time/residue: 0.8589 time to fit residues: 644.8781 Evaluate side-chains 605 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 489 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 220 GLU Chi-restraints excluded: chain X residue 271 GLU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 79 ASP Chi-restraints excluded: chain Y residue 96 SER Chi-restraints excluded: chain Y residue 161 MET Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 252 SER Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 71 SER Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 162 GLN Chi-restraints excluded: chain Z residue 168 ILE Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 242 LEU Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 49 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain L residue 87 TYR Chi-restraints excluded: chain L residue 91 ASN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 338 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 476 optimal weight: 2.9990 chunk 274 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 440 optimal weight: 0.5980 chunk 443 optimal weight: 0.9980 chunk 406 optimal weight: 5.9990 chunk 316 optimal weight: 0.0770 chunk 125 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN C 112 GLN ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 177 GLN Z 207 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN I 221 ASN K 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.155616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114471 restraints weight = 48780.460| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.72 r_work: 0.3194 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 41358 Z= 0.116 Angle : 0.541 12.818 55839 Z= 0.272 Chirality : 0.043 0.409 6276 Planarity : 0.004 0.061 7245 Dihedral : 5.688 126.845 5680 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.08 % Allowed : 27.45 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.12), residues: 5098 helix: 1.40 (0.11), residues: 2428 sheet: -0.30 (0.21), residues: 619 loop : -1.20 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 89 TYR 0.020 0.001 TYR Z 139 PHE 0.018 0.001 PHE I 38 TRP 0.019 0.001 TRP Y 55 HIS 0.004 0.001 HIS X 19 Details of bonding type rmsd covalent geometry : bond 0.00260 (41358) covalent geometry : angle 0.54100 (55839) hydrogen bonds : bond 0.04183 ( 2059) hydrogen bonds : angle 4.17842 ( 6477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10196 Ramachandran restraints generated. 5098 Oldfield, 0 Emsley, 5098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 497 time to evaluate : 1.719 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: A 42 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 61 MET cc_start: 0.8307 (mmm) cc_final: 0.7929 (mtm) REVERT: A 103 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.8953 (tt0) REVERT: A 303 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: A 324 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: A 578 LEU cc_start: 0.8790 (mt) cc_final: 0.8526 (mt) REVERT: A 588 ASP cc_start: 0.7943 (t0) cc_final: 0.7625 (t0) REVERT: B 56 ARG cc_start: 0.8443 (ttm110) cc_final: 0.8215 (ttp80) REVERT: B 203 PHE cc_start: 0.6020 (t80) cc_final: 0.5384 (t80) REVERT: B 356 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7962 (mm-30) REVERT: B 459 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7299 (tpt170) REVERT: B 471 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7619 (pp20) REVERT: B 518 ASP cc_start: 0.8125 (m-30) cc_final: 0.7571 (t0) REVERT: B 540 MET cc_start: 0.8126 (mtm) cc_final: 0.7823 (mtp) REVERT: C 18 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7580 (t80) REVERT: C 61 MET cc_start: 0.8599 (mmm) cc_final: 0.8373 (tpp) REVERT: C 68 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7880 (mt-10) REVERT: C 80 LEU cc_start: 0.9068 (tt) cc_final: 0.8834 (tp) REVERT: C 104 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8788 (mtp180) REVERT: C 171 ARG cc_start: 0.8757 (mtp180) cc_final: 0.8314 (mtm180) REVERT: C 301 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.6614 (pttp) REVERT: C 467 LYS cc_start: 0.8850 (tttm) cc_final: 0.8384 (ttmm) REVERT: C 544 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7986 (mtt) REVERT: C 571 ARG cc_start: 0.7664 (tmt-80) cc_final: 0.7144 (tpt170) REVERT: C 573 HIS cc_start: 0.7262 (t70) cc_final: 0.7043 (t70) REVERT: D 161 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8345 (mm110) REVERT: D 330 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8536 (t70) REVERT: D 386 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7717 (mtm-85) REVERT: D 435 MET cc_start: 0.7023 (ptp) cc_final: 0.6649 (pp-130) REVERT: E 161 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8541 (tm-30) REVERT: E 169 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8435 (ttt) REVERT: E 201 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: E 342 GLU cc_start: 0.8423 (tt0) cc_final: 0.8085 (pt0) REVERT: E 431 ASP cc_start: 0.8078 (t70) cc_final: 0.7644 (t0) REVERT: E 447 ASP cc_start: 0.8484 (m-30) cc_final: 0.7977 (m-30) REVERT: E 497 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7672 (tp-100) REVERT: F 354 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8253 (tp) REVERT: F 431 ASP cc_start: 0.8079 (m-30) cc_final: 0.7737 (m-30) REVERT: F 435 MET cc_start: 0.8501 (ttm) cc_final: 0.8297 (ttm) REVERT: X 47 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7718 (tm-30) REVERT: X 60 TYR cc_start: 0.7486 (m-10) cc_final: 0.7187 (m-10) REVERT: Y 115 MET cc_start: 0.7972 (mtt) cc_final: 0.7676 (mtp) REVERT: Y 161 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7053 (ttp) REVERT: Y 181 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7447 (mp) REVERT: Y 209 GLU cc_start: 0.8076 (mp0) cc_final: 0.7241 (tp30) REVERT: Z 163 ILE cc_start: 0.7626 (tt) cc_final: 0.7309 (tp) REVERT: Z 177 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.6427 (tp40) REVERT: Z 227 LYS cc_start: 0.6151 (tmmt) cc_final: 0.5842 (mppt) REVERT: J 54 MET cc_start: 0.6410 (mtp) cc_final: 0.6162 (mtm) REVERT: J 99 LYS cc_start: 0.7970 (mttt) cc_final: 0.7626 (mtpm) REVERT: J 131 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7750 (ttm-80) REVERT: J 184 TYR cc_start: 0.9029 (m-80) cc_final: 0.8570 (m-80) REVERT: M 85 GLN cc_start: 0.8215 (mp10) cc_final: 0.7911 (mp-120) REVERT: M 94 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: M 106 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8809 (mp) REVERT: G 27 GLN cc_start: 0.7941 (pt0) cc_final: 0.7655 (mt0) REVERT: G 31 ASN cc_start: 0.8249 (m110) cc_final: 0.7756 (m110) REVERT: G 46 GLN cc_start: 0.7537 (mt0) cc_final: 0.7006 (pt0) REVERT: G 57 LEU cc_start: 0.5607 (OUTLIER) cc_final: 0.5376 (tt) REVERT: G 110 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5525 (pp20) REVERT: I 89 ASP cc_start: 0.7924 (m-30) cc_final: 0.7425 (m-30) REVERT: I 93 ASP cc_start: 0.7743 (t0) cc_final: 0.7139 (m-30) REVERT: I 131 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7604 (mtp85) REVERT: L 74 GLU cc_start: 0.7117 (tt0) cc_final: 0.6673 (tm-30) REVERT: L 76 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: L 79 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6513 (tm-30) REVERT: L 85 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: L 97 ASP cc_start: 0.8014 (m-30) cc_final: 0.7691 (m-30) REVERT: H 42 LYS cc_start: 0.0418 (OUTLIER) cc_final: -0.0363 (tppp) REVERT: H 97 GLU cc_start: 0.8212 (tp30) cc_final: 0.7860 (tp30) REVERT: H 183 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8731 (mm) REVERT: H 201 ASP cc_start: 0.8621 (t70) cc_final: 0.8414 (t0) REVERT: K 83 ILE cc_start: 0.8019 (mt) cc_final: 0.7782 (mm) REVERT: K 115 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7419 (mtm-85) outliers start: 137 outliers final: 87 residues processed: 606 average time/residue: 0.8432 time to fit residues: 610.9184 Evaluate side-chains 604 residues out of total 4457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 488 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 599 SER Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 453 SER Chi-restraints excluded: chain C residue 544 MET Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 588 ASP Chi-restraints excluded: chain D residue 93 LYS Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 330 ASP Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain D residue 419 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 201 GLU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 257 VAL Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 403 LYS Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 138 ASP Chi-restraints excluded: chain X residue 220 GLU Chi-restraints excluded: chain X residue 271 GLU Chi-restraints excluded: chain Y residue 14 THR Chi-restraints excluded: chain Y residue 36 ILE Chi-restraints excluded: chain Y residue 79 ASP Chi-restraints excluded: chain Y residue 96 SER Chi-restraints excluded: chain Y residue 161 MET Chi-restraints excluded: chain Y residue 181 LEU Chi-restraints excluded: chain Y residue 252 SER Chi-restraints excluded: chain Z residue 14 THR Chi-restraints excluded: chain Z residue 71 SER Chi-restraints excluded: chain Z residue 74 CYS Chi-restraints excluded: chain Z residue 162 GLN Chi-restraints excluded: chain Z residue 177 GLN Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 181 LEU Chi-restraints excluded: chain Z residue 242 LEU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain M residue 87 TYR Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 110 GLU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 87 ARG Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 41 GLN Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 85 GLN Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 42 LYS Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 79 GLU Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 113 optimal weight: 6.9990 chunk 400 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 360 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 379 optimal weight: 7.9990 chunk 319 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS C 112 GLN ** Y 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 177 GLN Z 207 GLN J 71 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN I 221 ASN L 91 ASN K 90 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.152458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111365 restraints weight = 49033.790| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.68 r_work: 0.3088 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 41358 Z= 0.210 Angle : 0.617 12.840 55839 Z= 0.312 Chirality : 0.046 0.182 6276 Planarity : 0.005 0.067 7245 Dihedral : 6.015 134.523 5675 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.33 % Allowed : 27.20 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.12), residues: 5098 helix: 1.06 (0.11), residues: 2442 sheet: -0.39 (0.20), residues: 623 loop : -1.32 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 89 TYR 0.023 0.002 TYR B 20 PHE 0.020 0.002 PHE I 38 TRP 0.022 0.002 TRP Y 55 HIS 0.007 0.001 HIS E 199 Details of bonding type rmsd covalent geometry : bond 0.00513 (41358) covalent geometry : angle 0.61653 (55839) hydrogen bonds : bond 0.05142 ( 2059) hydrogen bonds : angle 4.43305 ( 6477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18604.88 seconds wall clock time: 316 minutes 11.03 seconds (18971.03 seconds total)