Starting phenix.real_space_refine on Sun Sep 29 22:12:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uix_26556/09_2024/7uix_26556_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uix_26556/09_2024/7uix_26556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uix_26556/09_2024/7uix_26556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uix_26556/09_2024/7uix_26556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uix_26556/09_2024/7uix_26556_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uix_26556/09_2024/7uix_26556_neut_trim.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians P 33 5.49 5 Mg 11 5.21 5 S 171 5.16 5 C 23846 2.51 5 N 6722 2.21 5 O 7238 1.98 5 H 38286 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 278 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 76307 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 9101 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 18, 'TRANS': 558} Chain: "B" Number of atoms: 9042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 9042 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 18, 'TRANS': 552} Chain breaks: 2 Chain: "C" Number of atoms: 9140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9140 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain breaks: 1 Chain: "D" Number of atoms: 9152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 9152 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 18, 'TRANS': 562} Chain: "E" Number of atoms: 9123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9123 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "F" Number of atoms: 9022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 9022 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 18, 'TRANS': 552} Chain breaks: 2 Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "I" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "K" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "L" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2977 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "M" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "N" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2978 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain: "S" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 396 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' MG': 3, 'ADP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 29.26, per 1000 atoms: 0.38 Number of scatterers: 76307 At special positions: 0 Unit cell: (150.51, 150.51, 159.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 171 16.00 P 33 15.00 Mg 11 11.99 O 7238 8.00 N 6722 7.00 C 23846 6.00 H 38286 1.00 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: 15.15 Conformation dependent library (CDL) restraints added in 5.1 seconds 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8906 Finding SS restraints... Secondary structure from input PDB file: 236 helices and 46 sheets defined 56.4% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.14 Creating SS restraints... Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.533A pdb=" N ILE A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 261 through 278 Processing helix chain 'A' and resid 286 through 292 removed outlier: 4.048A pdb=" N ILE A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 314 removed outlier: 3.922A pdb=" N LYS A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 323 through 330 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 350 through 361 Processing helix chain 'A' and resid 361 through 370 Processing helix chain 'A' and resid 374 through 389 removed outlier: 3.596A pdb=" N VAL A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 412 removed outlier: 3.896A pdb=" N LYS A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILE A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 435 removed outlier: 3.515A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 451 removed outlier: 3.567A pdb=" N ASN A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 458 removed outlier: 3.622A pdb=" N MET A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 480 removed outlier: 3.870A pdb=" N GLY A 480 " --> pdb=" O MET A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 522 through 525 removed outlier: 3.985A pdb=" N MET A 525 " --> pdb=" O SER A 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 522 through 525' Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.884A pdb=" N SER A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 566 through 569 Processing helix chain 'A' and resid 570 through 584 removed outlier: 4.099A pdb=" N PHE A 574 " --> pdb=" O HIS A 570 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 628 through 636 removed outlier: 3.974A pdb=" N ILE A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 removed outlier: 3.648A pdb=" N ARG A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 644 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 675 Processing helix chain 'A' and resid 683 through 695 Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.598A pdb=" N GLN A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.808A pdb=" N LEU A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN A 718 " --> pdb=" O LYS A 714 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 719 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 728 removed outlier: 4.332A pdb=" N ASP A 727 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY A 728 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 219 through 234 removed outlier: 3.672A pdb=" N ALA B 224 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 261 through 278 removed outlier: 4.048A pdb=" N ASP B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 292 removed outlier: 4.157A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.960A pdb=" N ARG B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 370 removed outlier: 3.671A pdb=" N VAL B 355 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Proline residue: B 363 - end of helix Processing helix chain 'B' and resid 374 through 389 Processing helix chain 'B' and resid 393 through 412 removed outlier: 3.500A pdb=" N ILE B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 435 removed outlier: 3.877A pdb=" N ILE B 426 " --> pdb=" O ASN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 460 Processing helix chain 'B' and resid 463 through 480 removed outlier: 3.641A pdb=" N ILE B 467 " --> pdb=" O GLN B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 513 removed outlier: 3.994A pdb=" N THR B 505 " --> pdb=" O LYS B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 528 No H-bonds generated for 'chain 'B' and resid 526 through 528' Processing helix chain 'B' and resid 529 through 535 removed outlier: 4.076A pdb=" N LEU B 533 " --> pdb=" O THR B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 544 removed outlier: 4.319A pdb=" N ASP B 544 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'B' and resid 566 through 569 Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.789A pdb=" N PHE B 574 " --> pdb=" O HIS B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 removed outlier: 3.511A pdb=" N GLU B 613 " --> pdb=" O VAL B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 636 Processing helix chain 'B' and resid 637 through 644 removed outlier: 3.511A pdb=" N ARG B 643 " --> pdb=" O GLU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 677 removed outlier: 3.728A pdb=" N ASP B 663 " --> pdb=" O HIS B 659 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 675 " --> pdb=" O VAL B 671 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS B 676 " --> pdb=" O GLN B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 695 Processing helix chain 'B' and resid 701 through 712 removed outlier: 3.734A pdb=" N ALA B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 723 Processing helix chain 'B' and resid 724 through 727 removed outlier: 4.015A pdb=" N ASP B 727 " --> pdb=" O SER B 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 724 through 727' Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 191 through 203 Processing helix chain 'C' and resid 219 through 234 removed outlier: 4.496A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 241 Processing helix chain 'C' and resid 249 through 255 removed outlier: 3.533A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 278 Processing helix chain 'C' and resid 287 through 291 Processing helix chain 'C' and resid 302 through 313 Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 324 through 329 removed outlier: 3.566A pdb=" N SER C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN C 329 " --> pdb=" O GLN C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 329' Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.574A pdb=" N ARG C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 370 Proline residue: C 363 - end of helix Processing helix chain 'C' and resid 374 through 389 Processing helix chain 'C' and resid 393 through 412 removed outlier: 4.698A pdb=" N ILE C 399 " --> pdb=" O PRO C 395 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 435 removed outlier: 3.638A pdb=" N ILE C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 451 removed outlier: 3.607A pdb=" N THR C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 Processing helix chain 'C' and resid 463 through 479 removed outlier: 3.522A pdb=" N ILE C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 513 removed outlier: 3.662A pdb=" N VAL C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR C 505 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 506 " --> pdb=" O THR C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 524 No H-bonds generated for 'chain 'C' and resid 522 through 524' Processing helix chain 'C' and resid 526 through 528 No H-bonds generated for 'chain 'C' and resid 526 through 528' Processing helix chain 'C' and resid 529 through 535 removed outlier: 3.758A pdb=" N LEU C 533 " --> pdb=" O THR C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 544 removed outlier: 4.381A pdb=" N ASP C 544 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 Processing helix chain 'C' and resid 566 through 569 Processing helix chain 'C' and resid 575 through 583 removed outlier: 4.565A pdb=" N GLN C 579 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 3.996A pdb=" N THR C 612 " --> pdb=" O GLY C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 636 Processing helix chain 'C' and resid 637 through 642 Processing helix chain 'C' and resid 654 through 675 Processing helix chain 'C' and resid 683 through 695 Processing helix chain 'C' and resid 701 through 712 removed outlier: 3.874A pdb=" N ALA C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 722 Processing helix chain 'D' and resid 176 through 182 removed outlier: 3.697A pdb=" N VAL D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 219 through 234 removed outlier: 3.875A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 262 through 278 Processing helix chain 'D' and resid 287 through 290 Processing helix chain 'D' and resid 302 through 314 Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.611A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 370 removed outlier: 3.574A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Proline residue: D 363 - end of helix Processing helix chain 'D' and resid 374 through 389 Processing helix chain 'D' and resid 393 through 412 Processing helix chain 'D' and resid 422 through 435 removed outlier: 3.630A pdb=" N ILE D 426 " --> pdb=" O ASN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 451 removed outlier: 3.673A pdb=" N ASP D 447 " --> pdb=" O GLN D 443 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 460 Processing helix chain 'D' and resid 463 through 480 Processing helix chain 'D' and resid 500 through 513 removed outlier: 3.674A pdb=" N THR D 505 " --> pdb=" O LYS D 501 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 509 " --> pdb=" O THR D 505 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 525 Processing helix chain 'D' and resid 526 through 528 No H-bonds generated for 'chain 'D' and resid 526 through 528' Processing helix chain 'D' and resid 529 through 535 removed outlier: 4.083A pdb=" N LEU D 533 " --> pdb=" O THR D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 556 Processing helix chain 'D' and resid 566 through 569 Processing helix chain 'D' and resid 570 through 574 Processing helix chain 'D' and resid 575 through 583 removed outlier: 4.278A pdb=" N GLN D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL D 580 " --> pdb=" O ILE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 614 Processing helix chain 'D' and resid 624 through 636 removed outlier: 3.933A pdb=" N ALA D 628 " --> pdb=" O ASN D 624 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET D 629 " --> pdb=" O SER D 625 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 642 Processing helix chain 'D' and resid 654 through 677 removed outlier: 3.587A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP D 663 " --> pdb=" O HIS D 659 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN D 675 " --> pdb=" O VAL D 671 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS D 676 " --> pdb=" O GLN D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 695 Processing helix chain 'D' and resid 701 through 712 removed outlier: 3.817A pdb=" N ALA D 705 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 706 " --> pdb=" O ARG D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 723 Processing helix chain 'D' and resid 724 through 727 removed outlier: 4.115A pdb=" N ASP D 727 " --> pdb=" O SER D 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 724 through 727' Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 220 through 234 removed outlier: 4.192A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 261 through 276 Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.568A pdb=" N ILE E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE E 291 " --> pdb=" O HIS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 313 removed outlier: 3.845A pdb=" N LYS E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 324 through 328 Processing helix chain 'E' and resid 334 through 340 removed outlier: 3.552A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 370 removed outlier: 3.588A pdb=" N GLN E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Proline residue: E 363 - end of helix Processing helix chain 'E' and resid 374 through 389 Processing helix chain 'E' and resid 393 through 412 removed outlier: 3.593A pdb=" N LEU E 411 " --> pdb=" O ALA E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 434 Processing helix chain 'E' and resid 443 through 451 removed outlier: 3.787A pdb=" N ASN E 451 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 458 Processing helix chain 'E' and resid 463 through 480 removed outlier: 3.611A pdb=" N ILE E 467 " --> pdb=" O GLN E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 513 removed outlier: 3.807A pdb=" N VAL E 504 " --> pdb=" O GLY E 500 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 524 No H-bonds generated for 'chain 'E' and resid 522 through 524' Processing helix chain 'E' and resid 526 through 529 Processing helix chain 'E' and resid 530 through 535 Processing helix chain 'E' and resid 547 through 556 removed outlier: 3.560A pdb=" N ASP E 551 " --> pdb=" O GLY E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 569 Processing helix chain 'E' and resid 573 through 584 removed outlier: 3.692A pdb=" N LEU E 577 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 613 removed outlier: 3.523A pdb=" N THR E 612 " --> pdb=" O VAL E 609 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU E 613 " --> pdb=" O ARG E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 636 removed outlier: 3.734A pdb=" N LYS E 634 " --> pdb=" O GLU E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 643 removed outlier: 3.543A pdb=" N ARG E 643 " --> pdb=" O GLU E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 677 removed outlier: 3.822A pdb=" N HIS E 659 " --> pdb=" O THR E 655 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS E 676 " --> pdb=" O GLN E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 695 Processing helix chain 'E' and resid 702 through 712 removed outlier: 4.164A pdb=" N ARG E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 722 removed outlier: 4.064A pdb=" N LEU E 716 " --> pdb=" O LEU E 712 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN E 718 " --> pdb=" O LYS E 714 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU E 719 " --> pdb=" O PRO E 715 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 728 removed outlier: 3.977A pdb=" N ASP E 727 " --> pdb=" O SER E 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 183 Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 219 through 234 removed outlier: 3.540A pdb=" N ILE F 223 " --> pdb=" O GLY F 219 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 241 Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 261 through 276 removed outlier: 3.991A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 293 removed outlier: 4.008A pdb=" N ILE F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA F 293 " --> pdb=" O THR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 313 removed outlier: 4.052A pdb=" N LEU F 310 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 330 Processing helix chain 'F' and resid 334 through 340 removed outlier: 3.838A pdb=" N ARG F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 370 Proline residue: F 363 - end of helix Processing helix chain 'F' and resid 374 through 389 Processing helix chain 'F' and resid 393 through 412 removed outlier: 3.709A pdb=" N ILE F 399 " --> pdb=" O PRO F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 435 removed outlier: 3.880A pdb=" N ILE F 426 " --> pdb=" O ASN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 451 removed outlier: 3.592A pdb=" N THR F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN F 451 " --> pdb=" O ASP F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 458 Processing helix chain 'F' and resid 463 through 479 removed outlier: 3.525A pdb=" N ILE F 467 " --> pdb=" O GLN F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 512 removed outlier: 3.877A pdb=" N LYS F 510 " --> pdb=" O VAL F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 525 removed outlier: 4.106A pdb=" N MET F 525 " --> pdb=" O SER F 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 522 through 525' Processing helix chain 'F' and resid 530 through 535 removed outlier: 4.118A pdb=" N ILE F 534 " --> pdb=" O VAL F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 556 Processing helix chain 'F' and resid 566 through 569 Processing helix chain 'F' and resid 570 through 584 Processing helix chain 'F' and resid 630 through 636 Processing helix chain 'F' and resid 637 through 642 Processing helix chain 'F' and resid 654 through 675 removed outlier: 3.678A pdb=" N HIS F 659 " --> pdb=" O THR F 655 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN F 660 " --> pdb=" O ASP F 656 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP F 663 " --> pdb=" O HIS F 659 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS F 664 " --> pdb=" O GLN F 660 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE F 665 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN F 675 " --> pdb=" O VAL F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 695 removed outlier: 3.710A pdb=" N ARG F 687 " --> pdb=" O SER F 683 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TRP F 689 " --> pdb=" O GLU F 685 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 692 " --> pdb=" O ASN F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 711 removed outlier: 4.088A pdb=" N ALA F 705 " --> pdb=" O ALA F 701 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 712 through 722 removed outlier: 4.271A pdb=" N LEU F 716 " --> pdb=" O LEU F 712 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN F 718 " --> pdb=" O LYS F 714 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU F 719 " --> pdb=" O PRO F 715 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 25 Processing helix chain 'H' and resid 36 through 54 removed outlier: 3.776A pdb=" N ASN H 41 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU H 42 " --> pdb=" O HIS H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.573A pdb=" N GLY H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 106 Processing helix chain 'H' and resid 131 through 158 Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 175 through 183 removed outlier: 3.856A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 26 removed outlier: 3.569A pdb=" N LEU I 23 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 54 Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.617A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 105 Processing helix chain 'I' and resid 131 through 158 removed outlier: 3.534A pdb=" N GLU I 141 " --> pdb=" O ILE I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 170 removed outlier: 4.152A pdb=" N ARG I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 183 Processing helix chain 'J' and resid 19 through 26 removed outlier: 3.532A pdb=" N GLU J 26 " --> pdb=" O ARG J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 54 removed outlier: 3.519A pdb=" N LEU J 42 " --> pdb=" O HIS J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 83 removed outlier: 3.804A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 105 Processing helix chain 'J' and resid 131 through 158 Processing helix chain 'J' and resid 160 through 168 Processing helix chain 'J' and resid 176 through 182 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.572A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 54 removed outlier: 3.551A pdb=" N ALA K 52 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.542A pdb=" N GLY K 73 " --> pdb=" O VAL K 69 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 104 Processing helix chain 'K' and resid 131 through 158 removed outlier: 3.543A pdb=" N GLU K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 170 removed outlier: 4.264A pdb=" N ARG K 170 " --> pdb=" O ARG K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 183 removed outlier: 3.748A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 25 Processing helix chain 'L' and resid 36 through 54 Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.788A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 106 Processing helix chain 'L' and resid 131 through 158 Processing helix chain 'L' and resid 160 through 170 removed outlier: 4.265A pdb=" N ARG L 170 " --> pdb=" O ARG L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 183 Processing helix chain 'M' and resid 19 through 26 removed outlier: 3.625A pdb=" N GLU M 26 " --> pdb=" O ARG M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 54 removed outlier: 3.580A pdb=" N ASN M 41 " --> pdb=" O ASP M 37 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU M 42 " --> pdb=" O HIS M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 83 removed outlier: 3.597A pdb=" N SER M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 104 Processing helix chain 'M' and resid 131 through 158 removed outlier: 3.500A pdb=" N HIS M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 170 removed outlier: 4.276A pdb=" N ARG M 170 " --> pdb=" O ARG M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.689A pdb=" N GLU M 181 " --> pdb=" O PRO M 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 69 through 83 removed outlier: 3.791A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE N 82 " --> pdb=" O ASP N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 106 removed outlier: 3.599A pdb=" N GLY N 106 " --> pdb=" O LEU N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 158 removed outlier: 4.085A pdb=" N ILE N 137 " --> pdb=" O THR N 133 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU N 143 " --> pdb=" O ALA N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 169 Processing helix chain 'N' and resid 176 through 183 removed outlier: 3.572A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 248 removed outlier: 6.704A pdb=" N TYR A 246 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 321 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR A 322 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU A 212 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ASN A 209 " --> pdb=" O GLN A 342 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE A 344 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU A 211 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 373 removed outlier: 6.672A pdb=" N ARG A 372 " --> pdb=" O VAL A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 516 through 520 removed outlier: 6.182A pdb=" N LEU A 561 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR A 604 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 563 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN A 646 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 492 " --> pdb=" O ASN A 646 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 730 through 736 removed outlier: 3.690A pdb=" N GLN A 747 " --> pdb=" O GLN A 730 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'B' and resid 281 through 284 removed outlier: 6.835A pdb=" N LEU B 282 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N SER B 321 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE B 284 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N THR B 323 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N THR B 322 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B 212 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 211 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE B 346 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 213 " --> pdb=" O ILE B 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 373 removed outlier: 7.099A pdb=" N ARG B 372 " --> pdb=" O VAL B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 516 through 520 removed outlier: 6.118A pdb=" N LEU B 561 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR B 604 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 563 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 491 " --> pdb=" O MET B 603 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR B 605 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE B 493 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 646 " --> pdb=" O SER B 490 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 585 through 587 Processing sheet with id=AB1, first strand: chain 'B' and resid 678 through 682 removed outlier: 6.181A pdb=" N SER B 679 " --> pdb=" O VAL B 731 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL B 733 " --> pdb=" O SER B 679 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU B 681 " --> pdb=" O VAL B 733 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N LEU B 735 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 732 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 741 " --> pdb=" O ASP B 736 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 173 through 175 removed outlier: 5.993A pdb=" N THR C 244 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N PHE C 283 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N TYR C 246 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ASP C 285 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU C 248 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER C 280 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ILE C 319 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 282 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N SER C 321 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE C 284 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N THR C 323 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C 214 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN C 209 " --> pdb=" O GLN C 342 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE C 344 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU C 211 " --> pdb=" O ILE C 344 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 346 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C 213 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 515 through 520 removed outlier: 7.118A pdb=" N GLU C 515 " --> pdb=" O VAL C 560 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU C 562 " --> pdb=" O GLU C 515 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU C 517 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASP C 564 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE C 519 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ALA C 559 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL C 602 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LEU C 561 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR C 604 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU C 563 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN C 646 " --> pdb=" O SER C 490 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 585 through 587 Processing sheet with id=AB5, first strand: chain 'C' and resid 678 through 682 removed outlier: 6.672A pdb=" N SER C 679 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL C 733 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLU C 681 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N LEU C 735 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 732 " --> pdb=" O GLY C 745 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 173 through 175 removed outlier: 4.691A pdb=" N ASP D 285 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ILE D 319 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU D 282 " --> pdb=" O ILE D 319 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N SER D 321 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE D 284 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR D 322 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU D 212 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 489 through 494 removed outlier: 7.381A pdb=" N ALA D 559 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL D 602 " --> pdb=" O ALA D 559 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU D 561 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR D 604 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU D 563 " --> pdb=" O THR D 604 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 680 through 682 removed outlier: 6.632A pdb=" N GLU D 681 " --> pdb=" O VAL D 733 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N LEU D 735 " --> pdb=" O GLU D 681 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 173 through 175 removed outlier: 6.489A pdb=" N THR E 244 " --> pdb=" O ILE E 281 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE E 283 " --> pdb=" O THR E 244 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N TYR E 246 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N SER E 280 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ILE E 319 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU E 282 " --> pdb=" O ILE E 319 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N SER E 321 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE E 284 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N THR E 323 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N THR E 322 " --> pdb=" O PRO E 210 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU E 212 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU E 211 " --> pdb=" O ILE E 344 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 515 through 520 removed outlier: 3.663A pdb=" N ASP E 564 " --> pdb=" O PHE E 519 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY E 489 " --> pdb=" O LEU E 601 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N MET E 603 " --> pdb=" O GLY E 489 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE E 491 " --> pdb=" O MET E 603 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN E 646 " --> pdb=" O SER E 490 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 585 through 587 Processing sheet with id=AC3, first strand: chain 'E' and resid 732 through 736 removed outlier: 4.082A pdb=" N THR E 732 " --> pdb=" O GLY E 745 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY E 745 " --> pdb=" O THR E 732 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU E 741 " --> pdb=" O ASP E 736 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 173 through 175 removed outlier: 6.065A pdb=" N TYR F 246 " --> pdb=" O PHE F 283 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP F 285 " --> pdb=" O TYR F 246 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU F 248 " --> pdb=" O ASP F 285 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU F 282 " --> pdb=" O ILE F 319 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N SER F 321 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ILE F 284 " --> pdb=" O SER F 321 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N THR F 323 " --> pdb=" O ILE F 284 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU F 211 " --> pdb=" O ILE F 344 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 372 through 373 removed outlier: 6.609A pdb=" N ARG F 372 " --> pdb=" O VAL F 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 489 through 494 removed outlier: 6.248A pdb=" N LEU F 561 " --> pdb=" O VAL F 602 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR F 604 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU F 563 " --> pdb=" O THR F 604 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU F 517 " --> pdb=" O LEU F 562 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP F 564 " --> pdb=" O LEU F 517 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE F 519 " --> pdb=" O ASP F 564 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 585 through 587 Processing sheet with id=AC8, first strand: chain 'F' and resid 730 through 736 removed outlier: 3.759A pdb=" N ASP F 736 " --> pdb=" O GLU F 741 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU F 741 " --> pdb=" O ASP F 736 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 28 through 32 removed outlier: 3.526A pdb=" N PHE H 112 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 119 through 121 removed outlier: 3.576A pdb=" N ILE H 121 " --> pdb=" O ARG H 172 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG H 172 " --> pdb=" O ILE H 121 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 7 through 8 removed outlier: 3.819A pdb=" N ARG I 15 " --> pdb=" O GLU I 8 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.770A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N MET I 92 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE I 63 " --> pdb=" O MET I 92 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLN I 94 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG I 118 " --> pdb=" O CYS I 91 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLY I 93 " --> pdb=" O ARG I 118 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N MET I 120 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA I 95 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 112 through 113 removed outlier: 3.716A pdb=" N CYS I 113 " --> pdb=" O SER I 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'J' and resid 5 through 9 Processing sheet with id=AD6, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.861A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N MET J 92 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE J 63 " --> pdb=" O MET J 92 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N GLN J 94 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER J 65 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG J 118 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY J 93 " --> pdb=" O ARG J 118 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 112 through 113 removed outlier: 3.721A pdb=" N CYS J 113 " --> pdb=" O SER J 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'K' and resid 5 through 8 Processing sheet with id=AD9, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.458A pdb=" N ILE K 29 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN K 64 " --> pdb=" O ILE K 29 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU K 31 " --> pdb=" O ASN K 64 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG K 111 " --> pdb=" O SER K 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'K' and resid 94 through 95 removed outlier: 6.594A pdb=" N ALA K 95 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.533A pdb=" N ARG L 15 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 28 through 32 removed outlier: 6.921A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS L 113 " --> pdb=" O SER L 187 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 118 through 121 Processing sheet with id=AE5, first strand: chain 'M' and resid 5 through 10 Processing sheet with id=AE6, first strand: chain 'M' and resid 28 through 32 removed outlier: 7.012A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 118 through 121 Processing sheet with id=AE8, first strand: chain 'N' and resid 5 through 8 Processing sheet with id=AE9, first strand: chain 'N' and resid 28 through 32 removed outlier: 7.047A pdb=" N ILE N 29 " --> pdb=" O TYR N 62 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ASN N 64 " --> pdb=" O ILE N 29 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU N 31 " --> pdb=" O ASN N 64 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 94 through 95 removed outlier: 5.618A pdb=" N ALA N 95 " --> pdb=" O MET N 120 " (cutoff:3.500A) 1755 hydrogen bonds defined for protein. 5130 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: 32.35 Time building geometry restraints manager: 18.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 38260 1.06 - 1.28: 6537 1.28 - 1.50: 15509 1.50 - 1.73: 16270 1.73 - 1.95: 307 Bond restraints: 76883 Sorted by residual: bond pdb=" C4 ADP A 802 " pdb=" C5 ADP A 802 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP F 801 " pdb=" C5 ADP F 801 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" CA SER E 440 " pdb=" CB SER E 440 " ideal model delta sigma weight residual 1.528 1.457 0.071 1.35e-02 5.49e+03 2.80e+01 bond pdb=" C5 ADP A 802 " pdb=" C6 ADP A 802 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 76878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 138439 2.67 - 5.34: 747 5.34 - 8.01: 106 8.01 - 10.68: 26 10.68 - 13.35: 15 Bond angle restraints: 139333 Sorted by residual: angle pdb=" N GLN E 443 " pdb=" CA GLN E 443 " pdb=" C GLN E 443 " ideal model delta sigma weight residual 113.72 106.34 7.38 1.30e+00 5.92e-01 3.22e+01 angle pdb=" PA AGS E 802 " pdb=" O3A AGS E 802 " pdb=" PB AGS E 802 " ideal model delta sigma weight residual 119.76 133.11 -13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" CA LYS E 439 " pdb=" C LYS E 439 " pdb=" O LYS E 439 " ideal model delta sigma weight residual 121.00 116.44 4.56 1.05e+00 9.07e-01 1.89e+01 angle pdb=" PB AGS D 801 " pdb=" O3B AGS D 801 " pdb=" PG AGS D 801 " ideal model delta sigma weight residual 120.12 132.66 -12.54 3.00e+00 1.11e-01 1.75e+01 angle pdb=" PA ADP A 802 " pdb=" O3A ADP A 802 " pdb=" PB ADP A 802 " ideal model delta sigma weight residual 120.50 132.48 -11.98 3.00e+00 1.11e-01 1.59e+01 ... (remaining 139328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.55: 34157 28.55 - 57.10: 1281 57.10 - 85.64: 160 85.64 - 114.19: 8 114.19 - 142.74: 14 Dihedral angle restraints: 35620 sinusoidal: 20100 harmonic: 15520 Sorted by residual: dihedral pdb=" C5' ADP F 801 " pdb=" O5' ADP F 801 " pdb=" PA ADP F 801 " pdb=" O2A ADP F 801 " ideal model delta sinusoidal sigma weight residual -60.00 82.74 -142.74 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" O2A ADP F 801 " pdb=" O3A ADP F 801 " pdb=" PA ADP F 801 " pdb=" PB ADP F 801 " ideal model delta sinusoidal sigma weight residual 300.00 178.68 121.32 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 60.89 -120.89 1 2.00e+01 2.50e-03 3.63e+01 ... (remaining 35617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4492 0.043 - 0.087: 1119 0.087 - 0.130: 313 0.130 - 0.174: 53 0.174 - 0.217: 8 Chirality restraints: 5985 Sorted by residual: chirality pdb=" C3' ADP A 802 " pdb=" C2' ADP A 802 " pdb=" C4' ADP A 802 " pdb=" O3' ADP A 802 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C3' ADP A 801 " pdb=" C2' ADP A 801 " pdb=" C4' ADP A 801 " pdb=" O3' ADP A 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL E 441 " pdb=" CA VAL E 441 " pdb=" CG1 VAL E 441 " pdb=" CG2 VAL E 441 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 5982 not shown) Planarity restraints: 11358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 702 " 0.060 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO B 703 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO B 703 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 703 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 442 " 0.017 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" N GLN E 443 " -0.053 2.00e-02 2.50e+03 pdb=" CA GLN E 443 " 0.014 2.00e-02 2.50e+03 pdb=" H GLN E 443 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 412 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO C 413 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 413 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 413 " 0.042 5.00e-02 4.00e+02 ... (remaining 11355 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 9733 2.26 - 2.85: 176052 2.85 - 3.43: 199268 3.43 - 4.02: 276732 4.02 - 4.60: 424677 Nonbonded interactions: 1086462 Sorted by model distance: nonbonded pdb=" O LYS F 387 " pdb=" HE2 HIS F 558 " model vdw 1.677 2.450 nonbonded pdb=" HG1 THR C 221 " pdb="MG MG C 803 " model vdw 1.685 1.700 nonbonded pdb=" OE1 GLU C 567 " pdb=" H GLU C 567 " model vdw 1.702 2.450 nonbonded pdb=" O LYS C 387 " pdb="HH12 ARG C 597 " model vdw 1.703 2.450 nonbonded pdb=" OD1 ASN E 175 " pdb=" H GLN E 178 " model vdw 1.705 2.450 ... (remaining 1086457 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 172 through 294 or (resid 295 and (name N or name CA or na \ me C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or re \ sid 305 through 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA )) or (resid 441 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2 or name H or name HA )) o \ r (resid 442 and (name N or name CA or name C or name O or name CB or name OG or \ name H or name HA )) or (resid 443 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name OE1 or name NE2 or name H or name HA )) \ or resid 444 through 501 or (resid 502 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2 or name H or name HA or name HB or name HG2 \ 1 or name HG22 or name HG23)) or resid 503 through 606 or resid 612 through 626 \ or resid 629 through 748)) selection = (chain 'B' and (resid 172 through 220 or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 222 through 439 or (resid 44 \ 0 and (name N or name CA or name C or name O or name CB or name OG or name H or \ name HA )) or (resid 441 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name H or name HA )) or (resid 442 and (name N or name \ CA or name C or name O or name CB or name OG or name H or name HA )) or (resid \ 443 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name OE1 or name NE2 or name H or name HA )) or resid 444 through 606 or resi \ d 612 through 626 or resid 629 through 748)) selection = (chain 'C' and (resid 172 through 220 or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 222 through 294 or (resid 29 \ 5 and (name N or name CA or name C or name O or name CB or name HA or name HB1 o \ r name HB2 or name HB3)) or resid 305 through 439 or (resid 440 and (name N or n \ ame CA or name C or name O or name CB or name OG or name H or name HA )) or (res \ id 441 and (name N or name CA or name C or name O or name CB or name CG1 or name \ CG2 or name H or name HA )) or (resid 442 and (name N or name CA or name C or n \ ame O or name CB or name OG or name H or name HA )) or (resid 443 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e NE2 or name H or name HA )) or resid 444 through 606 or resid 612 through 626 \ or resid 629 through 748)) selection = (chain 'D' and (resid 172 through 294 or (resid 295 and (name N or name CA or na \ me C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or re \ sid 305 through 439 or (resid 440 and (name N or name CA or name C or name O or \ name CB or name OG or name H or name HA )) or (resid 441 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2 or name H or name HA )) o \ r (resid 442 and (name N or name CA or name C or name O or name CB or name OG or \ name H or name HA )) or (resid 443 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name OE1 or name NE2 or name H or name HA )) \ or resid 444 through 606 or resid 612 through 626 or resid 629 through 748)) selection = (chain 'E' and (resid 172 through 294 or (resid 295 and (name N or name CA or na \ me C or name O or name CB or name HA or name HB1 or name HB2 or name HB3)) or re \ sid 305 through 606 or resid 612 through 626 or resid 629 through 748)) selection = (chain 'F' and (resid 172 through 220 or (resid 221 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2 or name H or name HA or name H \ B or name HG21 or name HG22 or name HG23)) or resid 222 through 294 or (resid 29 \ 5 and (name N or name CA or name C or name O or name CB or name HA or name HB1 o \ r name HB2 or name HB3)) or resid 305 through 439 or (resid 440 and (name N or n \ ame CA or name C or name O or name CB or name OG or name H or name HA )) or (res \ id 441 and (name N or name CA or name C or name O or name CB or name CG1 or name \ CG2 or name H or name HA )) or (resid 442 and (name N or name CA or name C or n \ ame O or name CB or name OG or name H or name HA )) or (resid 443 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e NE2 or name H or name HA )) or resid 444 through 501 or (resid 502 and (name N \ or name CA or name C or name O or name CB or name OG1 or name CG2 or name H or \ name HA or name HB or name HG21 or name HG22 or name HG23)) or resid 503 through \ 748)) } ncs_group { reference = (chain 'H' and resid 2 through 191) selection = (chain 'I' and resid 2 through 191) selection = (chain 'J' and resid 2 through 191) selection = (chain 'K' and resid 2 through 191) selection = chain 'L' selection = (chain 'M' and resid 2 through 191) selection = (chain 'N' and (resid 2 through 186 or (resid 187 and (name N or name CA or name \ C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name HG \ )) or resid 188 through 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 1.010 Extract box with map and model: 2.340 Check model and map are aligned: 0.470 Set scattering table: 0.580 Process input model: 132.280 Find NCS groups from input model: 3.140 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 38597 Z= 0.288 Angle : 0.786 13.345 52148 Z= 0.402 Chirality : 0.043 0.217 5985 Planarity : 0.004 0.091 6722 Dihedral : 14.388 142.739 14718 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 0.06 % Favored : 99.92 % Rotamer: Outliers : 0.02 % Allowed : 2.12 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.11), residues: 4782 helix: 0.03 (0.10), residues: 2332 sheet: -1.41 (0.19), residues: 668 loop : -0.72 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 229 HIS 0.008 0.001 HIS D 393 PHE 0.021 0.001 PHE A 263 TYR 0.017 0.001 TYR M 60 ARG 0.005 0.000 ARG E 610 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1418 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1417 time to evaluate : 4.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7826 (ttmm) REVERT: A 366 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6482 (mm-30) REVERT: A 465 LYS cc_start: 0.8164 (tttp) cc_final: 0.7854 (tptt) REVERT: A 517 LEU cc_start: 0.8406 (mt) cc_final: 0.8191 (mt) REVERT: A 526 GLU cc_start: 0.6843 (mp0) cc_final: 0.6601 (mp0) REVERT: A 664 LYS cc_start: 0.8649 (tmmt) cc_final: 0.8426 (ttpp) REVERT: A 706 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7245 (ttm-80) REVERT: A 741 GLU cc_start: 0.6582 (mm-30) cc_final: 0.5734 (tm-30) REVERT: B 194 GLU cc_start: 0.7834 (mp0) cc_final: 0.7581 (mp0) REVERT: B 215 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6726 (mm-30) REVERT: B 362 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7786 (ttmm) REVERT: B 376 LYS cc_start: 0.8549 (tttm) cc_final: 0.8325 (mtpp) REVERT: B 582 ASP cc_start: 0.6492 (m-30) cc_final: 0.6264 (m-30) REVERT: B 590 ASN cc_start: 0.7070 (t0) cc_final: 0.6616 (t0) REVERT: B 693 LYS cc_start: 0.7543 (tttp) cc_final: 0.7233 (tttm) REVERT: C 353 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7306 (mt-10) REVERT: C 735 LEU cc_start: 0.8401 (pt) cc_final: 0.8145 (tp) REVERT: D 215 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7853 (mm-30) REVERT: D 345 ASP cc_start: 0.6770 (m-30) cc_final: 0.6506 (m-30) REVERT: D 465 LYS cc_start: 0.8819 (mmpt) cc_final: 0.8534 (mmmm) REVERT: D 623 ASP cc_start: 0.7756 (p0) cc_final: 0.7390 (p0) REVERT: D 668 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6522 (mt-10) REVERT: D 730 GLN cc_start: 0.7268 (pt0) cc_final: 0.7034 (mt0) REVERT: E 250 ILE cc_start: 0.8844 (mm) cc_final: 0.8641 (mm) REVERT: E 370 ASP cc_start: 0.7250 (t0) cc_final: 0.6909 (t0) REVERT: E 408 ARG cc_start: 0.7667 (ttt-90) cc_final: 0.7364 (ptm160) REVERT: E 447 ASP cc_start: 0.6881 (m-30) cc_final: 0.6425 (m-30) REVERT: F 200 GLN cc_start: 0.8388 (tt0) cc_final: 0.8146 (tt0) REVERT: F 215 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6452 (mm-30) REVERT: F 220 LYS cc_start: 0.7735 (mtmt) cc_final: 0.6818 (mtpt) REVERT: F 229 TRP cc_start: 0.7636 (t60) cc_final: 0.7394 (t60) REVERT: F 266 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7771 (mtt90) REVERT: F 267 PHE cc_start: 0.8200 (t80) cc_final: 0.7999 (t80) REVERT: F 277 ASP cc_start: 0.6559 (m-30) cc_final: 0.6348 (m-30) REVERT: F 378 VAL cc_start: 0.9002 (t) cc_final: 0.8583 (p) REVERT: F 478 ARG cc_start: 0.7808 (tpp80) cc_final: 0.7523 (mmt-90) REVERT: F 597 ARG cc_start: 0.7852 (mtm110) cc_final: 0.7576 (mtt90) REVERT: F 659 HIS cc_start: 0.7809 (m170) cc_final: 0.7580 (m90) REVERT: F 664 LYS cc_start: 0.8189 (tmtt) cc_final: 0.7890 (tttt) REVERT: F 690 LEU cc_start: 0.6781 (mt) cc_final: 0.6545 (mt) REVERT: H 43 ILE cc_start: 0.7831 (mt) cc_final: 0.7571 (mt) REVERT: H 120 MET cc_start: 0.5867 (tmm) cc_final: 0.5433 (tpp) REVERT: H 159 GLN cc_start: 0.6930 (mm110) cc_final: 0.6339 (mp10) REVERT: I 5 MET cc_start: 0.7843 (mmt) cc_final: 0.7539 (mmt) REVERT: J 78 ASP cc_start: 0.7675 (m-30) cc_final: 0.7450 (m-30) REVERT: J 108 LYS cc_start: 0.7572 (mmmm) cc_final: 0.7345 (tppt) REVERT: L 86 ASP cc_start: 0.7819 (m-30) cc_final: 0.7588 (m-30) REVERT: L 143 LEU cc_start: 0.8954 (mm) cc_final: 0.8696 (mm) REVERT: M 41 ASN cc_start: 0.7542 (m110) cc_final: 0.7204 (m110) REVERT: M 77 TYR cc_start: 0.8613 (t80) cc_final: 0.8298 (t80) REVERT: M 151 GLU cc_start: 0.7613 (pt0) cc_final: 0.7314 (pt0) REVERT: N 148 ARG cc_start: 0.7159 (tpt-90) cc_final: 0.6862 (tpt-90) outliers start: 1 outliers final: 1 residues processed: 1418 average time/residue: 1.1521 time to fit residues: 2557.9179 Evaluate side-chains 1149 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1148 time to evaluate : 4.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 442 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 9.9990 chunk 363 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 124 optimal weight: 0.4980 chunk 245 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 376 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 280 optimal weight: 9.9990 chunk 435 optimal weight: 9.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 ASN A 642 ASN A 675 GLN A 688 ASN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 ASN B 709 GLN C 359 ASN C 624 ASN D 233 GLN D 273 GLN D 305 ASN E 329 ASN ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 GLN E 672 GLN E 711 ASN F 356 GLN F 675 GLN F 740 ASN H 41 ASN H 159 GLN I 156 HIS I 163 GLN J 41 ASN K 116 ASN M 64 ASN M 116 ASN M 129 GLN N 122 HIS ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 38597 Z= 0.232 Angle : 0.569 7.220 52148 Z= 0.307 Chirality : 0.041 0.158 5985 Planarity : 0.005 0.100 6722 Dihedral : 9.301 152.279 5421 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.96 % Allowed : 10.36 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.11), residues: 4782 helix: 0.88 (0.10), residues: 2410 sheet: -1.30 (0.19), residues: 650 loop : -0.56 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 689 HIS 0.012 0.001 HIS H 191 PHE 0.019 0.001 PHE A 263 TYR 0.012 0.001 TYR B 259 ARG 0.007 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1231 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1192 time to evaluate : 4.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7759 (ttmm) REVERT: A 503 GLU cc_start: 0.7497 (tp30) cc_final: 0.7095 (tp30) REVERT: A 517 LEU cc_start: 0.8418 (mt) cc_final: 0.8177 (mt) REVERT: A 526 GLU cc_start: 0.6851 (mp0) cc_final: 0.6363 (mp0) REVERT: A 583 ASN cc_start: 0.7315 (m-40) cc_final: 0.7034 (m-40) REVERT: A 614 ARG cc_start: 0.8099 (tmm-80) cc_final: 0.7850 (ptt90) REVERT: A 706 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7333 (ttm-80) REVERT: B 215 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6928 (mm-30) REVERT: B 362 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7784 (ttmm) REVERT: B 366 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7085 (mt-10) REVERT: B 590 ASN cc_start: 0.7110 (t0) cc_final: 0.6787 (t0) REVERT: C 520 ASP cc_start: 0.8098 (m-30) cc_final: 0.7758 (m-30) REVERT: C 590 ASN cc_start: 0.8042 (m110) cc_final: 0.7587 (m110) REVERT: C 592 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7840 (mtt-85) REVERT: D 465 LYS cc_start: 0.8819 (mmpt) cc_final: 0.8565 (mmmm) REVERT: D 484 GLU cc_start: 0.6910 (pm20) cc_final: 0.6318 (pm20) REVERT: D 730 GLN cc_start: 0.7575 (pt0) cc_final: 0.7184 (pm20) REVERT: E 370 ASP cc_start: 0.7294 (t0) cc_final: 0.6905 (t0) REVERT: E 447 ASP cc_start: 0.6879 (m-30) cc_final: 0.6403 (m-30) REVERT: E 592 ARG cc_start: 0.8083 (ttt-90) cc_final: 0.7848 (mtp-110) REVERT: E 672 GLN cc_start: 0.7808 (mt0) cc_final: 0.7562 (mt0) REVERT: E 744 TYR cc_start: 0.7714 (m-80) cc_final: 0.7502 (m-80) REVERT: F 200 GLN cc_start: 0.8503 (tt0) cc_final: 0.8232 (tt0) REVERT: F 215 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6453 (mm-30) REVERT: F 220 LYS cc_start: 0.7751 (mtmt) cc_final: 0.6929 (mtpt) REVERT: F 246 TYR cc_start: 0.8391 (m-80) cc_final: 0.8188 (m-80) REVERT: F 266 ARG cc_start: 0.8044 (mtt-85) cc_final: 0.7791 (mtt180) REVERT: F 334 ASP cc_start: 0.6712 (t70) cc_final: 0.6462 (t70) REVERT: F 457 LYS cc_start: 0.7093 (mttt) cc_final: 0.6841 (mttp) REVERT: F 472 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7365 (mm-30) REVERT: F 597 ARG cc_start: 0.7952 (mtm110) cc_final: 0.7642 (mtt90) REVERT: H 92 MET cc_start: 0.6519 (mtt) cc_final: 0.6296 (mtt) REVERT: H 120 MET cc_start: 0.5774 (tmm) cc_final: 0.5382 (tpp) REVERT: H 159 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6461 (mp10) REVERT: I 5 MET cc_start: 0.7881 (mmt) cc_final: 0.7405 (mmt) REVERT: I 122 HIS cc_start: 0.6984 (OUTLIER) cc_final: 0.6486 (p-80) REVERT: J 108 LYS cc_start: 0.7769 (mmmm) cc_final: 0.7550 (tppt) REVERT: J 151 GLU cc_start: 0.7275 (tt0) cc_final: 0.6944 (tt0) REVERT: L 86 ASP cc_start: 0.7852 (m-30) cc_final: 0.7646 (m-30) REVERT: M 34 GLN cc_start: 0.7908 (mm110) cc_final: 0.7701 (mm110) REVERT: M 41 ASN cc_start: 0.7532 (m110) cc_final: 0.7113 (m110) REVERT: M 151 GLU cc_start: 0.7857 (pt0) cc_final: 0.7625 (pt0) REVERT: N 148 ARG cc_start: 0.7236 (tpt-90) cc_final: 0.7020 (tpt-90) outliers start: 39 outliers final: 20 residues processed: 1210 average time/residue: 1.2268 time to fit residues: 2341.8082 Evaluate side-chains 1147 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1126 time to evaluate : 4.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 461 PHE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 442 SER Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 647 ILE Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 509 SER Chi-restraints excluded: chain F residue 740 ASN Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain M residue 129 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 362 optimal weight: 10.0000 chunk 296 optimal weight: 0.0870 chunk 120 optimal weight: 7.9990 chunk 436 optimal weight: 9.9990 chunk 471 optimal weight: 20.0000 chunk 388 optimal weight: 0.0870 chunk 433 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 350 optimal weight: 8.9990 overall best weight: 2.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN E 670 GLN F 356 GLN I 41 ASN K 122 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 38597 Z= 0.205 Angle : 0.516 6.481 52148 Z= 0.272 Chirality : 0.040 0.150 5985 Planarity : 0.004 0.081 6722 Dihedral : 9.126 160.502 5421 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.86 % Allowed : 11.87 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.12), residues: 4782 helix: 1.04 (0.10), residues: 2434 sheet: -1.30 (0.19), residues: 636 loop : -0.51 (0.14), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 689 HIS 0.012 0.001 HIS H 191 PHE 0.020 0.001 PHE E 640 TYR 0.013 0.001 TYR F 744 ARG 0.009 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1217 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1182 time to evaluate : 4.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.8033 (ttmt) cc_final: 0.7741 (ttmm) REVERT: A 400 ASP cc_start: 0.7147 (t0) cc_final: 0.6891 (t0) REVERT: A 517 LEU cc_start: 0.8431 (mt) cc_final: 0.8193 (mt) REVERT: A 526 GLU cc_start: 0.6926 (mp0) cc_final: 0.6437 (mp0) REVERT: A 583 ASN cc_start: 0.7455 (m-40) cc_final: 0.7220 (m110) REVERT: A 706 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7373 (ttm-80) REVERT: B 362 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7800 (ttmm) REVERT: B 590 ASN cc_start: 0.7168 (t0) cc_final: 0.6721 (t0) REVERT: B 634 LYS cc_start: 0.8327 (ttpt) cc_final: 0.8007 (ttpp) REVERT: C 240 MET cc_start: 0.7977 (ppp) cc_final: 0.7311 (ptp) REVERT: C 326 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7242 (mt-10) REVERT: D 465 LYS cc_start: 0.8871 (mmpt) cc_final: 0.8595 (mmmm) REVERT: D 484 GLU cc_start: 0.7097 (pm20) cc_final: 0.6482 (pm20) REVERT: D 704 MET cc_start: 0.8178 (mmm) cc_final: 0.7808 (mmm) REVERT: D 730 GLN cc_start: 0.7689 (pt0) cc_final: 0.7301 (pm20) REVERT: E 408 ARG cc_start: 0.7978 (ptm160) cc_final: 0.7751 (ptp-170) REVERT: E 447 ASP cc_start: 0.6946 (m-30) cc_final: 0.6422 (m-30) REVERT: E 592 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7910 (mtp-110) REVERT: E 713 LYS cc_start: 0.7490 (mtpt) cc_final: 0.7224 (mtpt) REVERT: F 200 GLN cc_start: 0.8524 (tt0) cc_final: 0.8247 (tt0) REVERT: F 207 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8000 (mppt) REVERT: F 215 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6704 (mm-30) REVERT: F 220 LYS cc_start: 0.7720 (mtmt) cc_final: 0.7406 (mtpp) REVERT: F 266 ARG cc_start: 0.8071 (mtt-85) cc_final: 0.7792 (mtt180) REVERT: F 267 PHE cc_start: 0.8158 (t80) cc_final: 0.7909 (t80) REVERT: F 432 ARG cc_start: 0.8336 (ptm-80) cc_final: 0.8017 (ttp80) REVERT: F 457 LYS cc_start: 0.7136 (mttt) cc_final: 0.6907 (mttp) REVERT: F 597 ARG cc_start: 0.8008 (mtm110) cc_final: 0.7619 (mtt90) REVERT: F 659 HIS cc_start: 0.7841 (m90) cc_final: 0.7637 (m90) REVERT: H 120 MET cc_start: 0.5915 (tmm) cc_final: 0.5513 (tpp) REVERT: H 159 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6473 (mp10) REVERT: I 5 MET cc_start: 0.7918 (mmt) cc_final: 0.7386 (mmt) REVERT: J 108 LYS cc_start: 0.7884 (mmmm) cc_final: 0.7648 (tppt) REVERT: J 140 ARG cc_start: 0.7415 (mtm180) cc_final: 0.7105 (ttp-110) REVERT: J 151 GLU cc_start: 0.7474 (tt0) cc_final: 0.7014 (tt0) REVERT: K 8 GLU cc_start: 0.8189 (tt0) cc_final: 0.7879 (tt0) REVERT: M 32 THR cc_start: 0.8790 (m) cc_final: 0.8529 (p) REVERT: M 34 GLN cc_start: 0.7926 (mm110) cc_final: 0.7704 (mm110) REVERT: M 41 ASN cc_start: 0.7540 (m110) cc_final: 0.7123 (m110) REVERT: M 151 GLU cc_start: 0.7908 (pt0) cc_final: 0.7641 (pt0) REVERT: M 163 GLN cc_start: 0.7670 (tp40) cc_final: 0.7305 (tp40) REVERT: N 148 ARG cc_start: 0.7275 (tpt-90) cc_final: 0.6973 (tpt-90) outliers start: 35 outliers final: 29 residues processed: 1193 average time/residue: 1.1637 time to fit residues: 2173.1775 Evaluate side-chains 1161 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1132 time to evaluate : 4.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 637 THR Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 647 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 505 THR Chi-restraints excluded: chain F residue 509 SER Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 26 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 8.9990 chunk 328 optimal weight: 9.9990 chunk 226 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 438 optimal weight: 7.9990 chunk 463 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 415 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 HIS ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 ASN A 730 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 709 GLN C 485 HIS C 606 ASN C 718 ASN E 463 GLN ** E 558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN E 670 GLN K 46 GLN N 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 38597 Z= 0.378 Angle : 0.581 7.066 52148 Z= 0.308 Chirality : 0.043 0.202 5985 Planarity : 0.004 0.079 6722 Dihedral : 9.314 167.732 5420 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.26 % Allowed : 12.56 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 4782 helix: 0.90 (0.10), residues: 2453 sheet: -1.33 (0.19), residues: 634 loop : -0.60 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 689 HIS 0.011 0.001 HIS F 288 PHE 0.021 0.002 PHE H 112 TYR 0.015 0.002 TYR D 524 ARG 0.008 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1245 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1194 time to evaluate : 4.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ASP cc_start: 0.7201 (t0) cc_final: 0.6915 (t0) REVERT: A 503 GLU cc_start: 0.7591 (tp30) cc_final: 0.7216 (tp30) REVERT: A 517 LEU cc_start: 0.8534 (mt) cc_final: 0.8267 (mt) REVERT: A 526 GLU cc_start: 0.6985 (mp0) cc_final: 0.6433 (mp0) REVERT: A 681 GLU cc_start: 0.7312 (tm-30) cc_final: 0.7101 (tm-30) REVERT: A 744 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.6962 (m-80) REVERT: B 362 LYS cc_start: 0.8249 (ttmt) cc_final: 0.7934 (ttmm) REVERT: B 590 ASN cc_start: 0.7291 (t0) cc_final: 0.6960 (t0) REVERT: B 634 LYS cc_start: 0.8470 (ttpt) cc_final: 0.8190 (ttpp) REVERT: C 240 MET cc_start: 0.8118 (ppp) cc_final: 0.7781 (ptp) REVERT: C 260 ARG cc_start: 0.7394 (mtp-110) cc_final: 0.6993 (ttp80) REVERT: C 272 LYS cc_start: 0.8060 (tttt) cc_final: 0.7627 (ttmm) REVERT: C 326 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7340 (mt-10) REVERT: D 268 LYS cc_start: 0.8911 (tppt) cc_final: 0.8347 (mmtt) REVERT: D 387 LYS cc_start: 0.8555 (ttpp) cc_final: 0.8339 (ttpp) REVERT: E 258 LYS cc_start: 0.8536 (pttm) cc_final: 0.8293 (pttp) REVERT: E 438 GLU cc_start: 0.7897 (pm20) cc_final: 0.7535 (mt-10) REVERT: E 447 ASP cc_start: 0.7006 (m-30) cc_final: 0.6572 (m-30) REVERT: E 592 ARG cc_start: 0.8247 (ttt-90) cc_final: 0.7972 (mtp-110) REVERT: E 709 GLN cc_start: 0.8177 (tt0) cc_final: 0.7923 (tp40) REVERT: E 719 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7265 (tp30) REVERT: F 206 ARG cc_start: 0.8518 (mmt-90) cc_final: 0.7486 (mmt-90) REVERT: F 220 LYS cc_start: 0.7907 (mtmt) cc_final: 0.7121 (mtpt) REVERT: F 455 ARG cc_start: 0.7447 (mtm110) cc_final: 0.7232 (mtm110) REVERT: F 583 ASN cc_start: 0.7338 (t0) cc_final: 0.7048 (t0) REVERT: F 597 ARG cc_start: 0.8052 (mtm110) cc_final: 0.7637 (mtt90) REVERT: H 94 GLN cc_start: 0.8031 (tt0) cc_final: 0.7558 (tt0) REVERT: H 120 MET cc_start: 0.6153 (tmm) cc_final: 0.5818 (tpp) REVERT: I 122 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6646 (p-80) REVERT: I 152 LEU cc_start: 0.8361 (mt) cc_final: 0.8160 (mt) REVERT: J 18 ASP cc_start: 0.8307 (p0) cc_final: 0.8057 (p0) REVERT: J 140 ARG cc_start: 0.7440 (mtm180) cc_final: 0.7092 (ttp-110) REVERT: J 149 MET cc_start: 0.7864 (mmm) cc_final: 0.7626 (mmm) REVERT: J 172 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7402 (ttm110) REVERT: L 37 ASP cc_start: 0.7089 (m-30) cc_final: 0.6760 (m-30) REVERT: M 26 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: M 151 GLU cc_start: 0.7994 (pt0) cc_final: 0.7751 (pt0) REVERT: M 163 GLN cc_start: 0.7750 (tp40) cc_final: 0.7428 (tp40) REVERT: N 80 MET cc_start: 0.5513 (ttp) cc_final: 0.5115 (ttp) outliers start: 51 outliers final: 41 residues processed: 1218 average time/residue: 1.1915 time to fit residues: 2266.1689 Evaluate side-chains 1187 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1143 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 483 HIS Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 647 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 509 SER Chi-restraints excluded: chain H residue 122 HIS Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain J residue 14 GLU Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 26 GLU Chi-restraints excluded: chain M residue 129 GLN Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 185 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 3.9990 chunk 263 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 345 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 395 optimal weight: 5.9990 chunk 320 optimal weight: 20.0000 chunk 0 optimal weight: 40.0000 chunk 236 optimal weight: 6.9990 chunk 416 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN A 660 GLN A 675 GLN B 209 ASN C 606 ASN D 342 GLN E 624 ASN E 670 GLN E 718 ASN I 150 ASN K 122 HIS M 116 ASN M 129 GLN N 81 GLN N 150 ASN N 159 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 38597 Z= 0.307 Angle : 0.545 6.746 52148 Z= 0.288 Chirality : 0.041 0.239 5985 Planarity : 0.004 0.085 6722 Dihedral : 9.255 165.109 5420 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.70 % Allowed : 13.74 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.12), residues: 4782 helix: 0.94 (0.10), residues: 2448 sheet: -1.42 (0.19), residues: 601 loop : -0.63 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 689 HIS 0.006 0.001 HIS K 122 PHE 0.015 0.001 PHE F 493 TYR 0.016 0.001 TYR F 744 ARG 0.008 0.001 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1243 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1174 time to evaluate : 4.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 GLN cc_start: 0.8130 (tp-100) cc_final: 0.7877 (tp40) REVERT: A 400 ASP cc_start: 0.7289 (t0) cc_final: 0.7009 (t0) REVERT: A 503 GLU cc_start: 0.7618 (tp30) cc_final: 0.7256 (tp30) REVERT: A 515 GLU cc_start: 0.6104 (tm-30) cc_final: 0.5900 (tm-30) REVERT: A 517 LEU cc_start: 0.8596 (mt) cc_final: 0.8123 (mt) REVERT: A 526 GLU cc_start: 0.6998 (mp0) cc_final: 0.6423 (mp0) REVERT: A 744 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: B 590 ASN cc_start: 0.7326 (t0) cc_final: 0.6860 (t0) REVERT: B 634 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8245 (ttpp) REVERT: C 240 MET cc_start: 0.7965 (ppp) cc_final: 0.7761 (ptp) REVERT: C 272 LYS cc_start: 0.8159 (tttt) cc_final: 0.7690 (ttmm) REVERT: C 305 ASN cc_start: 0.7878 (m-40) cc_final: 0.7665 (m-40) REVERT: D 268 LYS cc_start: 0.8978 (tppt) cc_final: 0.8539 (mmtt) REVERT: E 258 LYS cc_start: 0.8508 (pttm) cc_final: 0.8220 (pttp) REVERT: E 272 LYS cc_start: 0.8395 (tptt) cc_final: 0.8120 (tptt) REVERT: E 315 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7795 (mtmm) REVERT: E 592 ARG cc_start: 0.8258 (ttt-90) cc_final: 0.7977 (mtp-110) REVERT: E 709 GLN cc_start: 0.8207 (tt0) cc_final: 0.7975 (tp40) REVERT: F 206 ARG cc_start: 0.8550 (mmt-90) cc_final: 0.7476 (mmt-90) REVERT: F 207 LYS cc_start: 0.8850 (mtmm) cc_final: 0.8618 (mtmm) REVERT: F 220 LYS cc_start: 0.7873 (mtmt) cc_final: 0.7242 (mtpt) REVERT: F 266 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.8050 (mtt180) REVERT: F 356 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: F 397 LYS cc_start: 0.8264 (pttt) cc_final: 0.7711 (pttt) REVERT: F 450 LYS cc_start: 0.8232 (tmmt) cc_final: 0.8008 (tmmt) REVERT: F 597 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7693 (mtt90) REVERT: F 702 ARG cc_start: 0.7533 (ttm-80) cc_final: 0.7301 (mtt-85) REVERT: H 22 ARG cc_start: 0.7837 (tpt170) cc_final: 0.7606 (tpt170) REVERT: H 120 MET cc_start: 0.6301 (tmm) cc_final: 0.5868 (tpp) REVERT: I 122 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.6671 (p-80) REVERT: J 18 ASP cc_start: 0.8355 (p0) cc_final: 0.8085 (p0) REVERT: J 149 MET cc_start: 0.7923 (mmm) cc_final: 0.7699 (mmm) REVERT: J 172 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7369 (ttm110) REVERT: K 125 LEU cc_start: 0.5176 (tp) cc_final: 0.4933 (tp) REVERT: M 26 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6796 (mp0) REVERT: M 54 ASN cc_start: 0.6923 (t0) cc_final: 0.6689 (t0) REVERT: M 151 GLU cc_start: 0.8021 (pt0) cc_final: 0.7763 (pt0) REVERT: M 163 GLN cc_start: 0.7785 (tp40) cc_final: 0.7501 (tp40) outliers start: 69 outliers final: 51 residues processed: 1205 average time/residue: 1.1723 time to fit residues: 2230.5287 Evaluate side-chains 1192 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1137 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 461 PHE Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 483 HIS Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 647 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 356 GLN Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 668 GLU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 122 HIS Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 34 GLN Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 26 GLU Chi-restraints excluded: chain M residue 129 GLN Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 9.9990 chunk 417 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 272 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 464 optimal weight: 9.9990 chunk 385 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 243 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 ASN C 606 ASN C 688 ASN E 624 ASN E 670 GLN E 718 ASN I 94 GLN K 41 ASN ** K 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN N 81 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 38597 Z= 0.324 Angle : 0.546 6.766 52148 Z= 0.288 Chirality : 0.041 0.195 5985 Planarity : 0.004 0.071 6722 Dihedral : 9.186 164.566 5420 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.99 % Allowed : 14.16 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 4782 helix: 0.95 (0.10), residues: 2451 sheet: -1.43 (0.20), residues: 592 loop : -0.67 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 689 HIS 0.005 0.001 HIS I 138 PHE 0.018 0.001 PHE L 82 TYR 0.018 0.001 TYR F 744 ARG 0.007 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1242 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1161 time to evaluate : 4.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7875 (tp40) REVERT: A 400 ASP cc_start: 0.7277 (t0) cc_final: 0.6989 (t0) REVERT: A 503 GLU cc_start: 0.7672 (tp30) cc_final: 0.7335 (tp30) REVERT: A 517 LEU cc_start: 0.8578 (mt) cc_final: 0.8362 (mt) REVERT: A 518 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7736 (mtp-110) REVERT: A 526 GLU cc_start: 0.7006 (mp0) cc_final: 0.6414 (mp0) REVERT: A 681 GLU cc_start: 0.7262 (tm-30) cc_final: 0.7062 (tm-30) REVERT: A 744 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: B 590 ASN cc_start: 0.7316 (t0) cc_final: 0.6852 (t0) REVERT: B 634 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8279 (ttpp) REVERT: C 272 LYS cc_start: 0.8193 (tttt) cc_final: 0.7732 (ttmm) REVERT: E 258 LYS cc_start: 0.8525 (pttm) cc_final: 0.8199 (pttp) REVERT: E 272 LYS cc_start: 0.8398 (tptt) cc_final: 0.8096 (tptt) REVERT: E 334 ASP cc_start: 0.7695 (t70) cc_final: 0.7467 (t0) REVERT: E 709 GLN cc_start: 0.8235 (tt0) cc_final: 0.8032 (tp40) REVERT: E 719 GLU cc_start: 0.7403 (tp30) cc_final: 0.7171 (tp30) REVERT: F 356 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6845 (mp-120) REVERT: F 397 LYS cc_start: 0.8225 (pttt) cc_final: 0.7557 (pttm) REVERT: F 432 ARG cc_start: 0.8251 (ptm-80) cc_final: 0.8033 (ttp80) REVERT: F 472 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7747 (mm-30) REVERT: F 476 MET cc_start: 0.7017 (tpt) cc_final: 0.6748 (tpt) REVERT: F 597 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7652 (mtt90) REVERT: H 120 MET cc_start: 0.6361 (tmm) cc_final: 0.5904 (tpp) REVERT: I 122 HIS cc_start: 0.7083 (OUTLIER) cc_final: 0.6770 (p-80) REVERT: J 18 ASP cc_start: 0.8386 (p0) cc_final: 0.8140 (p0) REVERT: J 149 MET cc_start: 0.7924 (mmm) cc_final: 0.7710 (mmm) REVERT: J 172 ARG cc_start: 0.7736 (ttm110) cc_final: 0.7502 (ttm110) REVERT: K 125 LEU cc_start: 0.5162 (tp) cc_final: 0.4961 (tp) REVERT: L 41 ASN cc_start: 0.8797 (t0) cc_final: 0.8527 (t0) REVERT: L 89 THR cc_start: 0.8200 (p) cc_final: 0.7963 (p) REVERT: M 26 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: M 34 GLN cc_start: 0.7961 (mm110) cc_final: 0.7678 (mm-40) REVERT: M 54 ASN cc_start: 0.6849 (t0) cc_final: 0.6597 (t0) REVERT: M 151 GLU cc_start: 0.8036 (pt0) cc_final: 0.7785 (pt0) REVERT: M 163 GLN cc_start: 0.7817 (tp40) cc_final: 0.7525 (tp40) outliers start: 81 outliers final: 61 residues processed: 1199 average time/residue: 1.1431 time to fit residues: 2155.1823 Evaluate side-chains 1205 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1140 time to evaluate : 4.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 356 GLN Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 668 GLU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 8 GLU Chi-restraints excluded: chain I residue 34 GLN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 26 GLU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 185 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 339 optimal weight: 20.0000 chunk 262 optimal weight: 6.9990 chunk 390 optimal weight: 0.9980 chunk 259 optimal weight: 3.9990 chunk 462 optimal weight: 10.0000 chunk 289 optimal weight: 0.9980 chunk 282 optimal weight: 20.0000 chunk 213 optimal weight: 4.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN C 451 ASN C 463 GLN E 624 ASN E 670 GLN H 116 ASN I 150 ASN K 9 GLN ** K 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN N 150 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38597 Z= 0.214 Angle : 0.514 6.616 52148 Z= 0.269 Chirality : 0.040 0.156 5985 Planarity : 0.004 0.067 6722 Dihedral : 9.092 166.553 5420 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.50 % Allowed : 15.29 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.12), residues: 4782 helix: 1.12 (0.10), residues: 2467 sheet: -1.43 (0.20), residues: 587 loop : -0.56 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 689 HIS 0.006 0.001 HIS F 369 PHE 0.020 0.001 PHE L 82 TYR 0.020 0.001 TYR F 744 ARG 0.013 0.000 ARG L 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1227 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1166 time to evaluate : 4.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ASP cc_start: 0.7233 (t0) cc_final: 0.6891 (t0) REVERT: A 517 LEU cc_start: 0.8632 (mt) cc_final: 0.8401 (mt) REVERT: A 526 GLU cc_start: 0.6964 (mp0) cc_final: 0.6366 (mp0) REVERT: A 741 GLU cc_start: 0.6810 (mm-30) cc_final: 0.5239 (tm-30) REVERT: A 744 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: B 590 ASN cc_start: 0.7244 (t0) cc_final: 0.6798 (t0) REVERT: B 634 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8288 (ttpp) REVERT: C 272 LYS cc_start: 0.8232 (tttt) cc_final: 0.7778 (ttmm) REVERT: C 387 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8472 (tttt) REVERT: C 695 TYR cc_start: 0.8476 (t80) cc_final: 0.8250 (t80) REVERT: D 300 GLN cc_start: 0.7787 (mp10) cc_final: 0.7422 (mp10) REVERT: D 704 MET cc_start: 0.8261 (mmm) cc_final: 0.8056 (mmm) REVERT: E 258 LYS cc_start: 0.8464 (pttm) cc_final: 0.8139 (pttp) REVERT: E 272 LYS cc_start: 0.8375 (tptt) cc_final: 0.8094 (tptt) REVERT: E 334 ASP cc_start: 0.7679 (t70) cc_final: 0.7470 (t0) REVERT: E 709 GLN cc_start: 0.8247 (tt0) cc_final: 0.8041 (tp40) REVERT: F 207 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8640 (mtmt) REVERT: F 397 LYS cc_start: 0.8218 (pttt) cc_final: 0.7519 (pttm) REVERT: F 432 ARG cc_start: 0.8216 (ptm-80) cc_final: 0.8015 (ttp80) REVERT: F 476 MET cc_start: 0.7040 (tpt) cc_final: 0.6759 (tpt) REVERT: F 597 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7642 (mtt90) REVERT: F 687 ARG cc_start: 0.7992 (mtt-85) cc_final: 0.7759 (mtt-85) REVERT: H 120 MET cc_start: 0.6283 (tmm) cc_final: 0.5843 (tpp) REVERT: I 120 MET cc_start: 0.7839 (tmm) cc_final: 0.7082 (tmm) REVERT: I 122 HIS cc_start: 0.7049 (OUTLIER) cc_final: 0.6709 (p-80) REVERT: I 178 GLU cc_start: 0.7180 (mp0) cc_final: 0.6978 (mp0) REVERT: J 18 ASP cc_start: 0.8274 (p0) cc_final: 0.8001 (p0) REVERT: J 149 MET cc_start: 0.7891 (mmm) cc_final: 0.7686 (mmm) REVERT: J 172 ARG cc_start: 0.7729 (ttm110) cc_final: 0.7506 (ttm110) REVERT: L 37 ASP cc_start: 0.7155 (m-30) cc_final: 0.6787 (m-30) REVERT: L 41 ASN cc_start: 0.8778 (t0) cc_final: 0.8515 (t0) REVERT: L 89 THR cc_start: 0.8188 (p) cc_final: 0.7950 (p) REVERT: M 25 LYS cc_start: 0.8370 (tttm) cc_final: 0.8104 (tttt) REVERT: M 26 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: M 34 GLN cc_start: 0.7921 (mm110) cc_final: 0.7642 (mm-40) REVERT: M 151 GLU cc_start: 0.7980 (pt0) cc_final: 0.7712 (pt0) REVERT: M 163 GLN cc_start: 0.7784 (tp40) cc_final: 0.7490 (tp40) outliers start: 61 outliers final: 45 residues processed: 1197 average time/residue: 1.1420 time to fit residues: 2154.2680 Evaluate side-chains 1195 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1146 time to evaluate : 4.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 387 LYS Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 356 GLN Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 668 GLU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 34 GLN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain K residue 140 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 26 GLU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 185 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 294 optimal weight: 0.0770 chunk 315 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 43 optimal weight: 20.0000 chunk 363 optimal weight: 20.0000 overall best weight: 5.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 688 ASN E 624 ASN E 670 GLN L 159 GLN N 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38597 Z= 0.293 Angle : 0.537 8.406 52148 Z= 0.282 Chirality : 0.041 0.149 5985 Planarity : 0.004 0.071 6722 Dihedral : 9.079 165.045 5420 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.58 % Allowed : 15.41 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.12), residues: 4782 helix: 1.09 (0.10), residues: 2476 sheet: -1.46 (0.20), residues: 602 loop : -0.51 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 689 HIS 0.006 0.001 HIS A 556 PHE 0.019 0.001 PHE L 82 TYR 0.021 0.001 TYR F 744 ARG 0.012 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1229 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1165 time to evaluate : 4.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ASP cc_start: 0.7264 (t0) cc_final: 0.6940 (t0) REVERT: A 517 LEU cc_start: 0.8672 (mt) cc_final: 0.8436 (mt) REVERT: A 526 GLU cc_start: 0.6990 (mp0) cc_final: 0.6385 (mp0) REVERT: A 741 GLU cc_start: 0.6830 (mm-30) cc_final: 0.5202 (tm-30) REVERT: A 744 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: B 343 LYS cc_start: 0.7812 (tttt) cc_final: 0.7467 (tttm) REVERT: B 590 ASN cc_start: 0.7286 (t0) cc_final: 0.6833 (t0) REVERT: B 634 LYS cc_start: 0.8588 (ttpt) cc_final: 0.8329 (ttpp) REVERT: C 272 LYS cc_start: 0.8273 (tttt) cc_final: 0.7839 (ttmm) REVERT: D 300 GLN cc_start: 0.7869 (mp10) cc_final: 0.7581 (mp10) REVERT: E 258 LYS cc_start: 0.8479 (pttm) cc_final: 0.8122 (pttp) REVERT: E 272 LYS cc_start: 0.8392 (tptt) cc_final: 0.8092 (tptt) REVERT: F 352 GLU cc_start: 0.6847 (tp30) cc_final: 0.6003 (tp30) REVERT: F 356 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6915 (mp-120) REVERT: F 397 LYS cc_start: 0.8228 (pttt) cc_final: 0.7918 (pttm) REVERT: F 471 THR cc_start: 0.8704 (t) cc_final: 0.8391 (p) REVERT: F 597 ARG cc_start: 0.8080 (mtm110) cc_final: 0.7659 (mtt90) REVERT: F 687 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7771 (mtt-85) REVERT: H 69 VAL cc_start: 0.7903 (p) cc_final: 0.7595 (m) REVERT: H 120 MET cc_start: 0.6383 (tmm) cc_final: 0.5925 (tpp) REVERT: I 122 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6816 (p-80) REVERT: I 153 MET cc_start: 0.7772 (ttm) cc_final: 0.7570 (tpp) REVERT: J 8 GLU cc_start: 0.7058 (tp30) cc_final: 0.6690 (tp30) REVERT: J 9 GLN cc_start: 0.7484 (mm-40) cc_final: 0.6730 (mm-40) REVERT: J 18 ASP cc_start: 0.8349 (p0) cc_final: 0.8104 (p0) REVERT: J 172 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7543 (ttm110) REVERT: L 41 ASN cc_start: 0.8807 (t0) cc_final: 0.8532 (t0) REVERT: L 89 THR cc_start: 0.8236 (p) cc_final: 0.8007 (p) REVERT: M 26 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6769 (mp0) REVERT: M 34 GLN cc_start: 0.7952 (mm110) cc_final: 0.7544 (mm-40) REVERT: M 151 GLU cc_start: 0.8018 (pt0) cc_final: 0.7743 (pt0) outliers start: 64 outliers final: 53 residues processed: 1194 average time/residue: 1.1578 time to fit residues: 2171.0146 Evaluate side-chains 1210 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1153 time to evaluate : 4.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 639 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 356 GLN Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 554 ILE Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 668 GLU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 34 GLN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain K residue 140 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 26 GLU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 185 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 7.9990 chunk 443 optimal weight: 6.9990 chunk 404 optimal weight: 4.9990 chunk 431 optimal weight: 3.9990 chunk 259 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 338 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 chunk 389 optimal weight: 7.9990 chunk 407 optimal weight: 0.7980 chunk 429 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN E 670 GLN E 709 GLN I 41 ASN K 116 ASN N 81 GLN N 150 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38597 Z= 0.203 Angle : 0.515 6.487 52148 Z= 0.268 Chirality : 0.040 0.206 5985 Planarity : 0.004 0.060 6722 Dihedral : 9.013 167.526 5420 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.35 % Allowed : 15.81 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.12), residues: 4782 helix: 1.21 (0.10), residues: 2481 sheet: -1.41 (0.20), residues: 591 loop : -0.45 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 689 HIS 0.005 0.001 HIS K 122 PHE 0.020 0.001 PHE L 17 TYR 0.021 0.001 TYR F 744 ARG 0.010 0.000 ARG A 518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1216 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1161 time to evaluate : 4.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ASP cc_start: 0.7392 (t0) cc_final: 0.7014 (t0) REVERT: A 517 LEU cc_start: 0.8670 (mt) cc_final: 0.8428 (mt) REVERT: A 526 GLU cc_start: 0.6951 (mp0) cc_final: 0.6299 (mp0) REVERT: A 556 HIS cc_start: 0.7719 (m90) cc_final: 0.7507 (m90) REVERT: A 629 MET cc_start: 0.6011 (mmm) cc_final: 0.5486 (tpp) REVERT: A 744 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: B 343 LYS cc_start: 0.7812 (tttt) cc_final: 0.7453 (tttm) REVERT: B 590 ASN cc_start: 0.7234 (t0) cc_final: 0.6798 (t0) REVERT: B 634 LYS cc_start: 0.8589 (ttpt) cc_final: 0.8330 (ttpp) REVERT: C 272 LYS cc_start: 0.8243 (tttt) cc_final: 0.7804 (ttmm) REVERT: C 695 TYR cc_start: 0.8434 (t80) cc_final: 0.8227 (t80) REVERT: D 300 GLN cc_start: 0.7812 (mp10) cc_final: 0.7453 (mp10) REVERT: D 326 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7879 (mt-10) REVERT: E 258 LYS cc_start: 0.8444 (pttm) cc_final: 0.8092 (pttp) REVERT: E 272 LYS cc_start: 0.8371 (tptt) cc_final: 0.8084 (tptt) REVERT: E 689 TRP cc_start: 0.6615 (t60) cc_final: 0.5517 (t60) REVERT: F 397 LYS cc_start: 0.8209 (pttt) cc_final: 0.7885 (pttm) REVERT: F 597 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7654 (mtt90) REVERT: F 687 ARG cc_start: 0.8030 (mtt-85) cc_final: 0.7783 (mtt-85) REVERT: F 713 LYS cc_start: 0.7838 (mttt) cc_final: 0.7383 (mmtp) REVERT: H 69 VAL cc_start: 0.7907 (p) cc_final: 0.7619 (m) REVERT: H 120 MET cc_start: 0.6336 (tmm) cc_final: 0.5881 (tpp) REVERT: I 41 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8379 (m-40) REVERT: I 120 MET cc_start: 0.7894 (tmm) cc_final: 0.7105 (tmm) REVERT: I 122 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6707 (p-80) REVERT: I 153 MET cc_start: 0.7764 (ttm) cc_final: 0.7555 (tpp) REVERT: J 8 GLU cc_start: 0.7117 (tp30) cc_final: 0.6748 (tp30) REVERT: J 9 GLN cc_start: 0.7478 (mm-40) cc_final: 0.6678 (mm-40) REVERT: J 18 ASP cc_start: 0.8275 (p0) cc_final: 0.7992 (p0) REVERT: J 172 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7524 (ttm110) REVERT: L 9 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7603 (mm-40) REVERT: L 37 ASP cc_start: 0.7152 (m-30) cc_final: 0.6818 (m-30) REVERT: L 41 ASN cc_start: 0.8784 (t0) cc_final: 0.8528 (t0) REVERT: L 89 THR cc_start: 0.8218 (p) cc_final: 0.7989 (p) REVERT: M 26 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: M 34 GLN cc_start: 0.7825 (mm110) cc_final: 0.7537 (mm-40) REVERT: M 151 GLU cc_start: 0.8015 (pt0) cc_final: 0.7736 (pt0) outliers start: 55 outliers final: 49 residues processed: 1188 average time/residue: 1.1558 time to fit residues: 2172.8069 Evaluate side-chains 1198 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1145 time to evaluate : 4.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 639 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 356 GLN Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 668 GLU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 156 HIS Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 34 GLN Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain K residue 140 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 26 GLU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 9.9990 chunk 455 optimal weight: 20.0000 chunk 278 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 316 optimal weight: 5.9990 chunk 478 optimal weight: 7.9990 chunk 440 optimal weight: 0.6980 chunk 380 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 624 ASN E 670 GLN E 709 GLN H 94 GLN I 41 ASN I 150 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 38597 Z= 0.302 Angle : 0.542 9.796 52148 Z= 0.284 Chirality : 0.041 0.177 5985 Planarity : 0.004 0.071 6722 Dihedral : 9.025 164.753 5420 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.48 % Allowed : 15.95 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.12), residues: 4782 helix: 1.08 (0.10), residues: 2490 sheet: -1.41 (0.20), residues: 595 loop : -0.47 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 689 HIS 0.005 0.001 HIS A 556 PHE 0.017 0.001 PHE L 82 TYR 0.024 0.001 TYR F 744 ARG 0.013 0.000 ARG F 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9564 Ramachandran restraints generated. 4782 Oldfield, 0 Emsley, 4782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Residue THR 221 is missing expected H atoms. Skipping. Residue SER 440 is missing expected H atoms. Skipping. Residue VAL 441 is missing expected H atoms. Skipping. Residue SER 442 is missing expected H atoms. Skipping. Residue THR 502 is missing expected H atoms. Skipping. Evaluate side-chains 1220 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1160 time to evaluate : 4.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ASP cc_start: 0.7372 (t0) cc_final: 0.7032 (t0) REVERT: A 517 LEU cc_start: 0.8645 (mt) cc_final: 0.8398 (mt) REVERT: A 526 GLU cc_start: 0.6955 (mp0) cc_final: 0.6344 (mp0) REVERT: A 629 MET cc_start: 0.6047 (mmm) cc_final: 0.5521 (tpp) REVERT: A 647 ILE cc_start: 0.8676 (mp) cc_final: 0.8411 (mt) REVERT: A 741 GLU cc_start: 0.6804 (mm-30) cc_final: 0.5195 (tm-30) REVERT: A 744 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: B 343 LYS cc_start: 0.7833 (tttt) cc_final: 0.7497 (tttm) REVERT: B 590 ASN cc_start: 0.7265 (t0) cc_final: 0.6827 (t0) REVERT: B 634 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8347 (ttpp) REVERT: C 272 LYS cc_start: 0.8310 (tttt) cc_final: 0.7871 (ttmm) REVERT: C 695 TYR cc_start: 0.8516 (t80) cc_final: 0.8284 (t80) REVERT: D 300 GLN cc_start: 0.7871 (mp10) cc_final: 0.7568 (mp10) REVERT: D 326 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7913 (mt-10) REVERT: E 258 LYS cc_start: 0.8468 (pttm) cc_final: 0.8100 (pttp) REVERT: E 272 LYS cc_start: 0.8403 (tptt) cc_final: 0.8109 (tptt) REVERT: E 689 TRP cc_start: 0.6665 (t60) cc_final: 0.5568 (t60) REVERT: F 397 LYS cc_start: 0.8225 (pttt) cc_final: 0.7911 (pttm) REVERT: F 471 THR cc_start: 0.8698 (t) cc_final: 0.8391 (p) REVERT: F 597 ARG cc_start: 0.8075 (mtm110) cc_final: 0.7672 (mtt90) REVERT: F 687 ARG cc_start: 0.8016 (mtt-85) cc_final: 0.7782 (mtt-85) REVERT: H 69 VAL cc_start: 0.7901 (p) cc_final: 0.7644 (m) REVERT: H 120 MET cc_start: 0.6397 (tmm) cc_final: 0.5978 (tpp) REVERT: I 122 HIS cc_start: 0.7059 (OUTLIER) cc_final: 0.6759 (p-80) REVERT: J 8 GLU cc_start: 0.7139 (tp30) cc_final: 0.6794 (tp30) REVERT: J 9 GLN cc_start: 0.7507 (mm-40) cc_final: 0.6778 (mm-40) REVERT: J 18 ASP cc_start: 0.8335 (p0) cc_final: 0.8073 (p0) REVERT: J 172 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7534 (ttm110) REVERT: L 9 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7694 (mm-40) REVERT: L 37 ASP cc_start: 0.7178 (m-30) cc_final: 0.6843 (m-30) REVERT: L 41 ASN cc_start: 0.8808 (t0) cc_final: 0.8535 (t0) REVERT: L 89 THR cc_start: 0.8287 (p) cc_final: 0.8057 (p) REVERT: M 26 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: M 34 GLN cc_start: 0.7859 (mm110) cc_final: 0.7582 (mm-40) REVERT: M 151 GLU cc_start: 0.8034 (pt0) cc_final: 0.7760 (pt0) outliers start: 60 outliers final: 55 residues processed: 1193 average time/residue: 1.1128 time to fit residues: 2087.7524 Evaluate side-chains 1213 residues out of total 4062 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1155 time to evaluate : 4.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 393 HIS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain A residue 744 TYR Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 620 ILE Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain C residue 172 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 526 GLU Chi-restraints excluded: chain C residue 564 ASP Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 564 ASP Chi-restraints excluded: chain D residue 678 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 604 THR Chi-restraints excluded: chain E residue 639 GLU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 356 GLN Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 668 GLU Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 34 GLN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 17 PHE Chi-restraints excluded: chain K residue 140 ARG Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain L residue 113 CYS Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 26 GLU Chi-restraints excluded: chain M residue 97 SER Chi-restraints excluded: chain M residue 113 CYS Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 61 LEU Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 75 SER Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 185 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 8.9990 chunk 405 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 351 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 381 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 391 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** A 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 HIS D 747 GLN E 624 ASN E 670 GLN E 709 GLN E 718 ASN ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN M 116 ASN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.155566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.113415 restraints weight = 140396.646| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.00 r_work: 0.2938 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 38597 Z= 0.329 Angle : 0.563 8.915 52148 Z= 0.296 Chirality : 0.042 0.282 5985 Planarity : 0.004 0.067 6722 Dihedral : 9.090 163.739 5420 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.58 % Allowed : 16.08 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.12), residues: 4782 helix: 0.98 (0.10), residues: 2491 sheet: -1.44 (0.20), residues: 597 loop : -0.52 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 689 HIS 0.005 0.001 HIS A 556 PHE 0.018 0.001 PHE D 327 TYR 0.020 0.001 TYR F 744 ARG 0.009 0.000 ARG A 518 =============================================================================== Job complete usr+sys time: 30096.95 seconds wall clock time: 508 minutes 13.55 seconds (30493.55 seconds total)