Starting phenix.real_space_refine on Sun Sep 29 23:33:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiz_26558/09_2024/7uiz_26558_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiz_26558/09_2024/7uiz_26558.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/7uiz_26558/09_2024/7uiz_26558.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiz_26558/09_2024/7uiz_26558.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiz_26558/09_2024/7uiz_26558_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uiz_26558/09_2024/7uiz_26558_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 10 5.21 5 S 171 5.16 5 C 23909 2.51 5 N 6743 2.21 5 O 7265 1.98 5 H 38390 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 278 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 76521 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 9098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 9098 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 18, 'TRANS': 558} Chain: "B" Number of atoms: 9141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9141 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "C" 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: "D" Number of atoms: 9144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9144 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "E" Number of atoms: 9138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 9138 Classifications: {'peptide': 580} Link IDs: {'PTRANS': 18, 'TRANS': 561} Chain: "F" Number of atoms: 9122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 9122 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 18, 'TRANS': 560} 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: "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: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 3001 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 7, 'TRANS': 183} Chain: "M" 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: "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: "A" 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: "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: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 55 Unusual residues: {' MG': 1, 'ADP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {' MG': 1, 'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 28.50, per 1000 atoms: 0.37 Number of scatterers: 76521 At special positions: 0 Unit cell: (147.9, 152.25, 166.17, 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 10 11.99 O 7265 8.00 N 6743 7.00 C 23909 6.00 H 38390 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: 15.50 Conformation dependent library (CDL) restraints added in 4.8 seconds 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8934 Finding SS restraints... Secondary structure from input PDB file: 231 helices and 51 sheets defined 56.8% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.20 Creating SS restraints... Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.901A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 261 through 275 Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.897A pdb=" N ILE A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 287 through 292' Processing helix chain 'A' and resid 302 through 314 Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.665A pdb=" N GLU A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 350 through 370 removed outlier: 3.608A pdb=" N GLN A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Proline residue: A 363 - end of helix Processing helix chain 'A' and resid 374 through 389 removed outlier: 3.569A pdb=" N ARG A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 412 removed outlier: 3.702A pdb=" N ILE A 399 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 435 removed outlier: 3.752A pdb=" N ILE A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 451 removed outlier: 3.602A pdb=" N LEU A 449 " --> pdb=" O ASP A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.702A pdb=" N ARG A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 480 removed outlier: 3.531A pdb=" N ALA A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.528A pdb=" N SER A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 4.113A pdb=" N ARG A 532 " --> pdb=" O HIS A 528 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU A 533 " --> pdb=" O THR A 529 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 566 through 570 removed outlier: 5.564A pdb=" N HIS A 570 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 584 removed outlier: 3.852A pdb=" N ASN A 575 " --> pdb=" O PRO A 571 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 removed outlier: 3.506A pdb=" N VAL A 609 " --> pdb=" O ASN A 606 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 610 " --> pdb=" O ALA A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 610' Processing helix chain 'A' and resid 629 through 636 removed outlier: 3.927A pdb=" N LYS A 634 " --> pdb=" O GLU A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing helix chain 'A' and resid 654 through 675 removed outlier: 3.726A pdb=" N HIS A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 695 removed outlier: 3.563A pdb=" N GLY A 694 " --> pdb=" O LEU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 712 removed outlier: 3.928A pdb=" N ALA A 705 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 722 Processing helix chain 'A' and resid 723 through 727 removed outlier: 3.651A pdb=" N VAL A 726 " --> pdb=" O GLY A 723 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 727 " --> pdb=" O SER A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 723 through 727' Processing helix chain 'B' and resid 175 through 182 removed outlier: 3.887A pdb=" N VAL B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 219 through 234 removed outlier: 4.178A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.569A pdb=" N GLN B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 302 through 314 Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.659A pdb=" N ARG B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 370 removed outlier: 4.089A 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 removed outlier: 3.622A pdb=" N ARG B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 411 Processing helix chain 'B' and resid 422 through 435 Processing helix chain 'B' and resid 442 through 452 removed outlier: 3.734A pdb=" N THR B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 460 removed outlier: 3.534A pdb=" N LEU B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 480 Processing helix chain 'B' and resid 502 through 513 removed outlier: 3.552A pdb=" N SER B 509 " --> pdb=" O THR B 505 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 525 removed outlier: 3.524A pdb=" N GLU B 523 " --> pdb=" O ASP B 520 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 525 " --> pdb=" O SER B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 529 Processing helix chain 'B' and resid 530 through 535 Processing helix chain 'B' and resid 547 through 556 removed outlier: 3.534A pdb=" N ASP B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 569 Processing helix chain 'B' and resid 570 through 583 removed outlier: 3.801A pdb=" N PHE B 574 " --> pdb=" O HIS B 570 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 580 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 624 through 636 Processing helix chain 'B' and resid 637 through 643 Processing helix chain 'B' and resid 654 through 677 removed outlier: 3.513A pdb=" N HIS B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 3.723A 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: 3.899A pdb=" N ALA B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'C' and resid 176 through 183 Processing helix chain 'C' and resid 191 through 203 Processing helix chain 'C' and resid 219 through 234 removed outlier: 3.885A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.581A pdb=" N LEU C 254 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 278 removed outlier: 3.589A pdb=" N LEU C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 removed outlier: 3.578A pdb=" N ILE C 291 " --> pdb=" O HIS C 288 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY C 292 " --> pdb=" O THR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 323 through 330 Processing helix chain 'C' and resid 331 through 333 No H-bonds generated for 'chain 'C' and resid 331 through 333' Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 350 through 370 removed outlier: 3.647A pdb=" N GLN C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) Proline residue: C 363 - end of helix removed outlier: 3.511A pdb=" N ALA C 367 " --> pdb=" O PRO C 363 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 389 removed outlier: 3.524A pdb=" N ARG C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 412 removed outlier: 3.502A pdb=" N VAL C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 435 removed outlier: 3.670A pdb=" N ILE C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 451 removed outlier: 3.568A 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 480 Processing helix chain 'C' and resid 500 through 513 removed outlier: 4.092A pdb=" N THR C 505 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 511 " --> pdb=" O GLN C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 529 Processing helix chain 'C' and resid 530 through 535 removed outlier: 3.529A pdb=" N ILE C 534 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 544 removed outlier: 4.164A 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 570 through 583 removed outlier: 3.989A pdb=" N PHE C 574 " --> pdb=" O HIS C 570 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN C 575 " --> pdb=" O PRO C 571 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU C 577 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLN C 579 " --> pdb=" O ASN C 575 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL C 580 " --> pdb=" O ILE C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 Processing helix chain 'C' and resid 624 through 636 removed outlier: 4.092A pdb=" N ALA C 628 " --> pdb=" O ASN C 624 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N MET C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C 630 " --> pdb=" O THR C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 644 removed outlier: 3.645A pdb=" N ARG C 643 " --> pdb=" O GLU C 639 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 644 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 677 removed outlier: 3.673A pdb=" N HIS C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN C 660 " --> pdb=" O ASP C 656 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 676 " --> pdb=" O GLN C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 695 Processing helix chain 'C' and resid 701 through 712 removed outlier: 3.608A pdb=" N ALA C 705 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG C 706 " --> pdb=" O ARG C 702 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN C 709 " --> pdb=" O ALA C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 722 Processing helix chain 'C' and resid 723 through 727 removed outlier: 3.780A pdb=" N VAL C 726 " --> pdb=" O GLY C 723 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP C 727 " --> pdb=" O SER C 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 723 through 727' Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.641A pdb=" N ARG D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 219 through 234 removed outlier: 4.047A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.585A 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 261 through 278 removed outlier: 3.576A pdb=" N LYS D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 292 removed outlier: 3.888A pdb=" N ILE D 291 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 292 " --> pdb=" O THR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 313 Proline residue: D 309 - end of helix removed outlier: 3.543A pdb=" N SER D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.663A pdb=" N ARG D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 370 removed outlier: 3.966A pdb=" N GLN D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Proline residue: D 363 - end of helix removed outlier: 3.510A pdb=" N HIS D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 444 through 460 removed outlier: 3.747A pdb=" N THR D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY D 453 " --> pdb=" O LEU D 449 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP D 454 " --> pdb=" O LYS D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 480 removed outlier: 3.655A pdb=" N ILE D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 513 removed outlier: 3.740A pdb=" N LYS D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 511 " --> pdb=" O GLN D 507 " (cutoff:3.500A) 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: 4.050A 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 565 through 569 Processing helix chain 'D' and resid 570 through 575 removed outlier: 3.546A pdb=" N ASN D 575 " --> pdb=" O ASP D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 582 removed outlier: 4.134A pdb=" N VAL D 580 " --> pdb=" O ILE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 614 removed outlier: 4.664A pdb=" N ARG D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU D 611 " --> pdb=" O ALA D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 636 removed outlier: 3.531A pdb=" N ILE D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 637 through 644 removed outlier: 3.681A pdb=" N ARG D 643 " --> pdb=" O GLU D 639 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 644 " --> pdb=" O PHE D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 677 removed outlier: 3.617A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 675 " --> pdb=" O VAL D 671 " (cutoff:3.500A) removed outlier: 4.010A 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: 3.950A pdb=" N ALA D 705 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG D 706 " --> pdb=" O ARG D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 722 removed outlier: 3.699A pdb=" N ASN D 718 " --> pdb=" O LYS D 714 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 719 " --> pdb=" O PRO D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 727 removed outlier: 3.702A pdb=" N VAL D 726 " --> pdb=" O GLY D 723 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP D 727 " --> pdb=" O SER D 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 723 through 727' Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.536A pdb=" N VAL E 182 " --> pdb=" O GLN E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 221 through 234 removed outlier: 3.676A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 241 Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'E' and resid 261 through 277 Processing helix chain 'E' and resid 287 through 294 removed outlier: 4.107A pdb=" N ILE E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY E 292 " --> pdb=" O HIS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.655A pdb=" N LEU E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Proline residue: E 309 - end of helix Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.553A pdb=" N ASN E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 340 removed outlier: 3.582A pdb=" N ARG E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 370 removed outlier: 3.592A 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 removed outlier: 3.522A pdb=" N VAL E 382 " --> pdb=" O VAL E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 412 removed outlier: 3.579A pdb=" N GLY E 406 " --> pdb=" O ILE E 402 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 411 " --> pdb=" O ALA E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 435 removed outlier: 3.597A pdb=" N ILE E 426 " --> pdb=" O ASN E 422 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER E 428 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 451 Processing helix chain 'E' and resid 451 through 460 Processing helix chain 'E' and resid 463 through 479 removed outlier: 3.663A pdb=" N LEU E 470 " --> pdb=" O ALA E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 513 Processing helix chain 'E' and resid 526 through 528 No H-bonds generated for 'chain 'E' and resid 526 through 528' Processing helix chain 'E' and resid 529 through 535 removed outlier: 4.079A pdb=" N LEU E 533 " --> pdb=" O THR E 529 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 534 " --> pdb=" O VAL E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 556 Processing helix chain 'E' and resid 566 through 569 Processing helix chain 'E' and resid 570 through 584 removed outlier: 3.549A pdb=" N ILE E 576 " --> pdb=" O ASP E 572 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN E 579 " --> pdb=" O ASN E 575 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL E 580 " --> pdb=" O ILE E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 614 Processing helix chain 'E' and resid 626 through 636 removed outlier: 3.595A pdb=" N ILE E 632 " --> pdb=" O ALA E 628 " (cutoff:3.500A) Processing helix chain 'E' and resid 637 through 644 removed outlier: 3.508A pdb=" N LEU E 644 " --> pdb=" O PHE E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 675 removed outlier: 3.700A pdb=" N HIS E 659 " --> pdb=" O THR E 655 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP E 663 " --> pdb=" O HIS E 659 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN E 675 " --> pdb=" O VAL E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 695 removed outlier: 3.531A pdb=" N GLU E 692 " --> pdb=" O ASN E 688 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 712 removed outlier: 4.234A pdb=" N ARG E 706 " --> pdb=" O ARG E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 712 through 722 removed outlier: 3.519A pdb=" N ASN E 718 " --> pdb=" O LYS E 714 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU E 721 " --> pdb=" O ALA E 717 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE E 722 " --> pdb=" O ASN E 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 723 through 727 removed outlier: 3.515A pdb=" N VAL E 726 " --> pdb=" O GLY E 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 183 Processing helix chain 'F' and resid 191 through 203 removed outlier: 3.543A pdb=" N ARG F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 234 Processing helix chain 'F' and resid 249 through 255 removed outlier: 3.631A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 277 removed outlier: 3.687A pdb=" N ASP F 277 " --> pdb=" O GLN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 291 removed outlier: 4.215A pdb=" N ILE F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.756A pdb=" N ASN F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU F 332 " --> pdb=" O SER F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 340 Processing helix chain 'F' and resid 350 through 370 removed outlier: 3.568A pdb=" N GLN F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Proline residue: F 363 - end of helix Processing helix chain 'F' and resid 374 through 389 removed outlier: 3.679A pdb=" N VAL F 382 " --> pdb=" O VAL F 378 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU F 383 " --> pdb=" O ARG F 379 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS F 387 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 412 Processing helix chain 'F' and resid 422 through 435 removed outlier: 3.762A pdb=" N SER F 428 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE F 433 " --> pdb=" O VAL F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 442 Processing helix chain 'F' and resid 444 through 451 Processing helix chain 'F' and resid 451 through 460 Processing helix chain 'F' and resid 463 through 479 removed outlier: 3.542A pdb=" N GLU F 472 " --> pdb=" O GLU F 468 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 513 removed outlier: 4.007A pdb=" N THR F 505 " --> pdb=" O LYS F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 525 removed outlier: 3.548A 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 526 through 535 removed outlier: 3.998A pdb=" N SER F 531 " --> pdb=" O ARG F 527 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG F 532 " --> pdb=" O HIS F 528 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU F 533 " --> pdb=" O THR F 529 " (cutoff:3.500A) removed outlier: 4.131A 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 570 through 584 removed outlier: 3.813A pdb=" N PHE F 574 " --> pdb=" O HIS F 570 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN F 575 " --> pdb=" O PRO F 571 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE F 576 " --> pdb=" O ASP F 572 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 577 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL F 580 " --> pdb=" O ILE F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 614 Processing helix chain 'F' and resid 627 through 636 removed outlier: 4.175A pdb=" N GLU F 631 " --> pdb=" O ASP F 627 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE F 636 " --> pdb=" O ILE F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 644 Processing helix chain 'F' and resid 654 through 675 removed outlier: 3.595A pdb=" N HIS F 659 " --> pdb=" O THR F 655 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN F 660 " --> pdb=" O ASP F 656 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL F 661 " --> pdb=" O VAL F 657 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 665 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN F 675 " --> pdb=" O VAL F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 695 removed outlier: 3.686A pdb=" N ASN F 688 " --> pdb=" O GLN F 684 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP F 689 " --> pdb=" O GLU F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 712 removed outlier: 4.257A pdb=" N ALA F 705 " --> pdb=" O ALA F 701 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG F 706 " --> pdb=" O ARG F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 712 through 722 removed outlier: 3.638A pdb=" N ASN F 718 " --> pdb=" O LYS F 714 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 727 Processing helix chain 'H' and resid 19 through 26 removed outlier: 3.611A pdb=" N GLU H 26 " --> pdb=" O ARG H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 54 Processing helix chain 'H' and resid 69 through 83 removed outlier: 3.620A pdb=" N GLY H 73 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 105 Processing helix chain 'H' and resid 131 through 158 removed outlier: 3.555A pdb=" N LEU H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS H 144 " --> pdb=" O ARG H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 170 removed outlier: 4.404A pdb=" N ARG H 170 " --> pdb=" O ARG H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.745A pdb=" N VAL H 180 " --> pdb=" O ALA H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.508A pdb=" N GLU I 26 " --> pdb=" O ARG I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 54 removed outlier: 3.715A pdb=" N ALA I 52 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU I 53 " --> pdb=" O PHE I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 83 removed outlier: 3.670A pdb=" N GLY I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER I 75 " --> pdb=" O THR I 71 " (cutoff:3.500A) removed outlier: 3.724A 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: 3.520A pdb=" N LEU I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 169 Processing helix chain 'I' and resid 176 through 183 removed outlier: 3.502A pdb=" N GLU I 181 " --> pdb=" O PRO I 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 25 Processing helix chain 'J' and resid 36 through 54 removed outlier: 3.700A pdb=" N LEU J 42 " --> pdb=" O HIS J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 83 removed outlier: 3.939A pdb=" N SER J 75 " --> pdb=" O THR J 71 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE J 76 " --> pdb=" O ALA J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 104 Processing helix chain 'J' and resid 131 through 158 Processing helix chain 'J' and resid 160 through 169 Processing helix chain 'J' and resid 175 through 182 Processing helix chain 'K' and resid 19 through 26 removed outlier: 3.597A pdb=" N LEU K 23 " --> pdb=" O ILE K 19 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU K 26 " --> pdb=" O ARG K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 54 removed outlier: 3.531A pdb=" N LEU K 42 " --> pdb=" O HIS K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 83 removed outlier: 3.620A pdb=" N SER K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 106 removed outlier: 3.535A pdb=" N LEU K 103 " --> pdb=" O GLY K 99 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY K 106 " --> pdb=" O LEU K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 158 removed outlier: 3.701A pdb=" N ILE K 137 " --> pdb=" O THR K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 168 Processing helix chain 'K' and resid 176 through 183 removed outlier: 3.906A pdb=" N VAL K 180 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU K 181 " --> pdb=" O PRO K 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 26 removed outlier: 3.649A pdb=" N GLU L 26 " --> pdb=" O ARG L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 54 Processing helix chain 'L' and resid 69 through 83 removed outlier: 3.564A pdb=" N GLY L 73 " --> pdb=" O VAL L 69 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER L 75 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR L 77 " --> pdb=" O GLY L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 106 removed outlier: 3.648A pdb=" N GLY L 106 " --> pdb=" O LEU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 158 removed outlier: 3.540A pdb=" N ILE L 137 " --> pdb=" O THR L 133 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU L 141 " --> pdb=" O ILE L 137 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN L 150 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 170 removed outlier: 4.317A 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 Processing helix chain 'M' and resid 36 through 54 removed outlier: 3.875A pdb=" N ASN M 41 " --> pdb=" O ASP M 37 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU M 42 " --> pdb=" O HIS M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 82 removed outlier: 3.567A pdb=" N SER M 75 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE M 76 " --> pdb=" O ALA M 72 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN M 81 " --> pdb=" O TYR M 77 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE M 82 " --> pdb=" O ASP M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 104 Processing helix chain 'M' and resid 131 through 158 removed outlier: 3.625A pdb=" N LEU M 143 " --> pdb=" O ALA M 139 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS M 144 " --> pdb=" O ARG M 140 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 169 Processing helix chain 'M' and resid 176 through 183 Processing helix chain 'N' and resid 19 through 26 removed outlier: 3.500A pdb=" N LYS N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 69 through 83 removed outlier: 3.609A pdb=" N GLY N 73 " --> pdb=" O VAL N 69 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER N 75 " --> pdb=" O THR N 71 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE N 76 " --> pdb=" O ALA N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 106 Processing helix chain 'N' and resid 131 through 158 Processing helix chain 'N' and resid 160 through 169 removed outlier: 3.661A pdb=" N GLU N 169 " --> pdb=" O GLU N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 183 removed outlier: 3.709A pdb=" N VAL N 180 " --> pdb=" O ALA N 176 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU N 181 " --> pdb=" O PRO N 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175 removed outlier: 6.126A pdb=" N THR A 244 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE A 283 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR A 246 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ILE A 319 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU A 282 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N SER A 321 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N THR A 322 " --> pdb=" O PRO A 210 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU A 212 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 372 through 373 removed outlier: 6.934A 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 515 through 520 removed outlier: 3.780A pdb=" N ASP A 564 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLY A 489 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N MET A 603 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE A 491 " --> pdb=" O MET A 603 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N THR A 605 " --> pdb=" O PHE A 491 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE A 493 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A 646 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 492 " --> pdb=" O ASN A 646 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 494 " --> pdb=" O ILE A 648 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AA5, first strand: chain 'A' and resid 679 through 682 removed outlier: 6.680A pdb=" N SER A 679 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL A 733 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLU A 681 " --> pdb=" O VAL A 733 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N LEU A 735 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 741 " --> pdb=" O ASP A 736 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 245 through 247 removed outlier: 6.102A pdb=" N TYR B 246 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASP B 285 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 321 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N THR B 322 " --> pdb=" O PRO B 210 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 212 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASN B 209 " --> pdb=" O GLN B 342 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE B 344 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 211 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 346 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 213 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 516 through 518 removed outlier: 6.802A pdb=" N LEU B 517 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLY B 489 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N MET B 603 " --> pdb=" O GLY B 489 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N PHE B 491 " --> pdb=" O MET B 603 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 605 " --> pdb=" O PHE B 491 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE B 493 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER B 490 " --> pdb=" O ASN B 646 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE B 648 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU B 492 " --> pdb=" O ILE B 648 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 585 through 587 removed outlier: 3.597A pdb=" N LEU B 586 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 680 through 682 removed outlier: 3.775A pdb=" N GLU B 741 " --> pdb=" O ASP B 736 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 173 through 175 removed outlier: 6.319A pdb=" N THR C 244 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE C 283 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR C 246 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP C 285 " --> pdb=" O TYR C 246 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU C 248 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 280 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE C 319 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU C 282 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N SER C 321 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE C 284 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU C 211 " --> pdb=" O ILE C 344 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE C 346 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 213 " --> pdb=" O ILE C 346 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 372 through 373 removed outlier: 6.733A pdb=" N ARG C 372 " --> pdb=" O VAL C 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 490 through 494 removed outlier: 7.327A pdb=" N ALA C 559 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 602 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU C 561 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N THR C 604 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU C 563 " --> pdb=" O THR C 604 " (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 679 through 682 removed outlier: 6.163A pdb=" N SER C 679 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N VAL C 733 " --> pdb=" O SER C 679 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU C 681 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N LEU C 735 " --> pdb=" O GLU C 681 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 741 " --> pdb=" O ASP C 736 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 173 through 175 removed outlier: 6.206A pdb=" N THR D 244 " --> pdb=" O ILE D 281 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE D 283 " --> pdb=" O THR D 244 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR D 246 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASP D 285 " --> pdb=" O TYR D 246 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU D 248 " --> pdb=" O ASP D 285 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER D 280 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ILE D 319 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU D 282 " --> pdb=" O ILE D 319 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N SER D 321 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE D 284 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY D 214 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 372 through 373 removed outlier: 7.060A pdb=" N ARG D 372 " --> pdb=" O VAL D 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 489 through 494 removed outlier: 5.895A pdb=" N GLY D 489 " --> pdb=" O LEU D 601 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N MET D 603 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE D 491 " --> pdb=" O MET D 603 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N THR D 605 " --> pdb=" O PHE D 491 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE D 493 " --> pdb=" O THR D 605 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 680 through 682 removed outlier: 3.608A pdb=" N ASP D 736 " --> pdb=" O GLU D 741 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU D 741 " --> pdb=" O ASP D 736 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 173 through 175 removed outlier: 5.942A pdb=" N TYR E 246 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP E 285 " --> pdb=" O TYR E 246 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU E 248 " --> pdb=" O ASP E 285 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER E 321 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ASN E 209 " --> pdb=" O GLN E 342 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE E 344 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU E 211 " --> pdb=" O ILE E 344 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 372 through 373 removed outlier: 7.074A pdb=" N ARG E 372 " --> pdb=" O VAL E 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 515 through 520 removed outlier: 3.540A pdb=" N ASP E 564 " --> pdb=" O PHE E 519 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 600 " --> pdb=" O ALA E 559 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN E 646 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 492 " --> pdb=" O ASN E 646 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 585 through 587 removed outlier: 3.564A pdb=" N LEU E 586 " --> pdb=" O ALA E 594 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 680 through 681 Processing sheet with id=AC6, first strand: chain 'E' and resid 734 through 735 Processing sheet with id=AC7, first strand: chain 'F' and resid 174 through 175 removed outlier: 3.640A pdb=" N THR F 174 " --> pdb=" O SER F 247 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR F 244 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE F 283 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR F 246 " --> pdb=" O PHE F 283 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG F 317 " --> pdb=" O SER F 280 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 210 through 213 Processing sheet with id=AC9, first strand: chain 'F' and resid 515 through 520 removed outlier: 3.840A pdb=" N ASP F 564 " --> pdb=" O PHE F 519 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL F 602 " --> pdb=" O ALA F 559 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU F 561 " --> pdb=" O VAL F 602 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR F 604 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 563 " --> pdb=" O THR F 604 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE F 491 " --> pdb=" O LEU F 601 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU F 492 " --> pdb=" O ILE F 648 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 585 through 587 removed outlier: 3.553A pdb=" N ALA F 594 " --> pdb=" O LEU F 586 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 732 through 736 removed outlier: 3.506A pdb=" N THR F 732 " --> pdb=" O GLY F 745 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU F 741 " --> pdb=" O ASP F 736 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 5 through 8 removed outlier: 3.573A pdb=" N ARG H 15 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 28 through 32 removed outlier: 6.557A pdb=" N ILE H 59 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE H 90 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU H 61 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N PHE H 112 " --> pdb=" O VAL H 87 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N THR H 89 " --> pdb=" O PHE H 112 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS H 113 " --> pdb=" O SER H 187 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 94 through 95 removed outlier: 6.102A pdb=" N ALA H 95 " --> pdb=" O MET H 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 5 through 9 Processing sheet with id=AD7, first strand: chain 'I' and resid 28 through 32 removed outlier: 6.504A pdb=" N ILE I 59 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE I 90 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU I 61 " --> pdb=" O ILE I 90 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N PHE I 112 " --> pdb=" O VAL I 87 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N THR I 89 " --> pdb=" O PHE I 112 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG I 111 " --> pdb=" O SER I 187 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 94 through 95 removed outlier: 6.349A pdb=" N ALA I 95 " --> pdb=" O MET I 120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 5 through 9 Processing sheet with id=AE1, first strand: chain 'J' and resid 28 through 32 removed outlier: 6.899A pdb=" N ILE J 29 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ASN J 64 " --> pdb=" O ILE J 29 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU J 31 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE J 59 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ILE J 90 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU J 61 " --> pdb=" O ILE J 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 94 through 95 removed outlier: 5.846A pdb=" N ALA J 95 " --> pdb=" O MET J 120 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 112 through 113 Processing sheet with id=AE4, first strand: chain 'K' and resid 5 through 9 Processing sheet with id=AE5, first strand: chain 'K' and resid 28 through 32 removed outlier: 6.031A pdb=" N ILE K 59 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE K 90 " --> pdb=" O ILE K 59 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU K 61 " --> pdb=" O ILE K 90 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N PHE K 112 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR K 89 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG K 111 " --> pdb=" O SER K 187 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 94 through 95 removed outlier: 6.086A pdb=" N ALA K 95 " --> pdb=" O MET K 120 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE K 121 " --> pdb=" O ARG K 172 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 5 through 9 Processing sheet with id=AE8, first strand: chain 'L' and resid 28 through 31 removed outlier: 6.845A pdb=" N ILE L 29 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE L 59 " --> pdb=" O SER L 88 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE L 90 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU L 61 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N PHE L 112 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR L 89 " --> pdb=" O PHE L 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'L' and resid 94 through 95 removed outlier: 6.080A pdb=" N ALA L 95 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 5 through 9 Processing sheet with id=AF2, first strand: chain 'M' and resid 28 through 32 removed outlier: 6.902A pdb=" N ILE M 59 " --> pdb=" O SER M 88 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ILE M 90 " --> pdb=" O ILE M 59 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU M 61 " --> pdb=" O ILE M 90 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE M 112 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N THR M 89 " --> pdb=" O PHE M 112 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 118 through 121 Processing sheet with id=AF4, first strand: chain 'N' and resid 5 through 9 removed outlier: 3.524A pdb=" N ARG N 15 " --> pdb=" O GLU N 8 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 28 through 29 removed outlier: 6.855A pdb=" N ILE N 29 " --> pdb=" O TYR N 62 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE N 59 " --> pdb=" O SER N 88 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE N 90 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU N 61 " --> pdb=" O ILE N 90 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N PHE N 112 " --> pdb=" O VAL N 87 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THR N 89 " --> pdb=" O PHE N 112 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N CYS N 113 " --> pdb=" O SER N 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'N' and resid 118 through 121 1748 hydrogen bonds defined for protein. 5145 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: 30.48 Time building geometry restraints manager: 19.42 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: 38364 1.06 - 1.28: 6563 1.28 - 1.50: 15559 1.50 - 1.73: 16310 1.73 - 1.95: 307 Bond restraints: 77103 Sorted by residual: bond pdb=" C4 ADP F 802 " pdb=" C5 ADP F 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 E 802 " pdb=" C5 ADP E 802 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4 ADP E 801 " pdb=" C5 ADP E 801 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C5 ADP E 802 " pdb=" C6 ADP E 802 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C5 ADP E 801 " pdb=" C6 ADP E 801 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.70e+01 ... (remaining 77098 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.12: 139623 6.12 - 12.23: 93 12.23 - 18.35: 7 18.35 - 24.46: 7 24.46 - 30.58: 8 Bond angle restraints: 139738 Sorted by residual: angle pdb="HG22 THR D 626 " pdb=" CG2 THR D 626 " pdb="HG23 THR D 626 " ideal model delta sigma weight residual 109.00 78.42 30.58 3.00e+00 1.11e-01 1.04e+02 angle pdb="HG21 THR D 626 " pdb=" CG2 THR D 626 " pdb="HG22 THR D 626 " ideal model delta sigma weight residual 109.00 78.80 30.20 3.00e+00 1.11e-01 1.01e+02 angle pdb="HD11 ILE A 620 " pdb=" CD1 ILE A 620 " pdb="HD13 ILE A 620 " ideal model delta sigma weight residual 110.00 79.99 30.01 3.00e+00 1.11e-01 1.00e+02 angle pdb="HD11 ILE A 620 " pdb=" CD1 ILE A 620 " pdb="HD12 ILE A 620 " ideal model delta sigma weight residual 110.00 80.30 29.70 3.00e+00 1.11e-01 9.80e+01 angle pdb=" CG1 ILE A 620 " pdb=" CD1 ILE A 620 " pdb="HD13 ILE A 620 " ideal model delta sigma weight residual 109.00 80.45 28.55 3.00e+00 1.11e-01 9.06e+01 ... (remaining 139733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.51: 34489 30.51 - 61.03: 1152 61.03 - 91.54: 60 91.54 - 122.05: 13 122.05 - 152.57: 7 Dihedral angle restraints: 35721 sinusoidal: 20151 harmonic: 15570 Sorted by residual: dihedral pdb=" O2A ADP F 802 " pdb=" O3A ADP F 802 " pdb=" PA ADP F 802 " pdb=" PB ADP F 802 " ideal model delta sinusoidal sigma weight residual 300.00 171.56 128.45 1 2.00e+01 2.50e-03 3.89e+01 dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 61.48 -121.48 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" O1B ADP F 802 " pdb=" O3A ADP F 802 " pdb=" PB ADP F 802 " pdb=" PA ADP F 802 " ideal model delta sinusoidal sigma weight residual -60.00 54.81 -114.82 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 35718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.342: 6000 0.342 - 0.684: 0 0.684 - 1.026: 0 1.026 - 1.367: 0 1.367 - 1.709: 1 Chirality restraints: 6001 Sorted by residual: chirality pdb=" CG LEU E 725 " pdb=" CB LEU E 725 " pdb=" CD1 LEU E 725 " pdb=" CD2 LEU E 725 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.30e+01 chirality pdb=" C3' ADP E 802 " pdb=" C2' ADP E 802 " pdb=" C4' ADP E 802 " pdb=" O3' ADP E 802 " both_signs ideal model delta sigma weight residual False -2.51 -2.71 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ILE F 436 " pdb=" N ILE F 436 " pdb=" C ILE F 436 " pdb=" CB ILE F 436 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 5998 not shown) Planarity restraints: 11404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 702 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 703 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 703 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 703 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 84 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO J 85 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO J 85 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 85 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 412 " 0.034 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO E 413 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 413 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 413 " 0.028 5.00e-02 4.00e+02 ... (remaining 11401 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 9043 2.26 - 2.84: 177142 2.84 - 3.43: 198680 3.43 - 4.01: 276001 4.01 - 4.60: 426427 Nonbonded interactions: 1087293 Sorted by model distance: nonbonded pdb=" HG1 THR D 502 " pdb="MG MG D 804 " model vdw 1.674 1.700 nonbonded pdb=" HG1 THR B 221 " pdb="MG MG B 803 " model vdw 1.684 1.700 nonbonded pdb=" OE1 GLU E 484 " pdb=" H GLU E 484 " model vdw 1.690 2.450 nonbonded pdb=" O TYR E 246 " pdb=" H PHE E 283 " model vdw 1.700 2.450 nonbonded pdb=" HG1 THR C 502 " pdb="MG MG C 804 " model vdw 1.702 1.700 ... (remaining 1087288 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 347 or (resid 348 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name \ HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 349 through 352 or \ (resid 353 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 OE2 or name HA or name HB2 or name HB3 or name HG2 o \ r name HG3)) or resid 354 through 462 or (resid 463 and (name N or name CA or na \ me 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 name HB2 or name HB3 or name HG2 or name HG3 or name HE21)) or r \ esid 464 through 474 or (resid 475 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name CE or name NZ or name H or name HA or nam \ e HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or \ name HE3)) or resid 476 through 496 or (resid 497 and (name N or name CA or nam \ e 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 498 through 597 or (resid 598 \ and (name N or name CA or name C or name O or name CB or name CG or name OD1 or \ name ND2 or name H or name HA or name HB2 or name HB3)) or resid 599 through 60 \ 0 or (resid 601 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG or name H \ D11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) or resid \ 602 through 622 or (resid 623 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) or r \ esid 624 through 696 or (resid 697 and (name N or name CA or name C or name O or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or \ name HD3 or name HE or name HH21)) or resid 698 through 729 or (resid 730 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name O \ E1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or name \ HG3)) or resid 731 through 748 or resid 803)) selection = (chain 'B' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 347 or (resid 348 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 OE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3)) or resid 349 through 352 or (res \ id 353 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 OE2 or name HA or name HB2 or name HB3 or name HG2 or nam \ e HG3)) or resid 354 through 431 or (resid 432 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 433 throug \ h 454 or (resid 455 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE or name HH11 or name HH12 or name HH22)) or resid 456 through 462 or (resi \ d 463 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HE21)) or resid 464 through 474 or (resid 475 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 476 through 496 or (resid \ 497 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or r \ esid 498 through 597 or (resid 598 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or \ name HB3)) or resid 599 through 600 or (resid 601 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB \ 2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 602 through 622 or (resid 623 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name OD2 or name \ HA or name HB2 or name HB3)) or resid 624 through 696 or (resid 697 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE or n \ ame CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or n \ ame HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH21)) or resid 6 \ 98 through 729 or (resid 730 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 name HB \ 2 or name HB3 or name HG2 or name HG3)) or resid 731 through 748 or resid 803)) selection = (chain 'C' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 347 or (resid 348 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 OE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3)) or resid 349 through 352 or (res \ id 353 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 OE2 or name HA or name HB2 or name HB3 or name HG2 or nam \ e HG3)) or resid 354 through 431 or (resid 432 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 433 throug \ h 454 or (resid 455 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE or name HH11 or name HH12 or name HH22)) or resid 456 through 462 or (resi \ d 463 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HE21)) or resid 464 through 474 or (resid 475 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 476 through 496 or (resid \ 497 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or r \ esid 498 through 597 or (resid 598 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or \ name HB3)) or resid 599 through 600 or (resid 601 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB \ 2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 602 through 622 or (resid 623 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name OD2 or name \ HA or name HB2 or name HB3)) or resid 624 through 696 or (resid 697 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE or n \ ame CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or n \ ame HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH21)) or resid 6 \ 98 through 748 or resid 803)) selection = (chain 'D' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 347 or (resid 348 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 OE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3)) or resid 349 through 352 or (res \ id 353 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 OE2 or name HA or name HB2 or name HB3 or name HG2 or nam \ e HG3)) or resid 354 through 431 or (resid 432 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 433 throug \ h 454 or (resid 455 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE or name HH11 or name HH12 or name HH22)) or resid 456 through 462 or (resi \ d 463 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HE21)) or resid 464 through 474 or (resid 475 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 476 through 496 or (resid \ 497 and (name N or name CA or name C or name O or name CB or name OG1 or name C \ G2 or name H or name HA or name HB or name HG21 or name HG22 or name HG23)) or r \ esid 498 through 597 or (resid 598 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or \ name HB3)) or resid 599 through 600 or (resid 601 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name HB \ 2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 602 through 622 or (resid 623 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name OD2 or name \ HA or name HB2 or name HB3)) or resid 624 through 696 or (resid 697 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name NE or n \ ame CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB3 or n \ ame HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH21)) or resid 6 \ 98 through 729 or (resid 730 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 name HB \ 2 or name HB3 or name HG2 or name HG3)) or resid 731 through 748 or resid 803)) selection = (chain 'E' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 431 or (resid 432 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 433 throug \ h 454 or (resid 455 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE or name HH11 or name HH12 or name HH22)) or resid 456 through 462 or (resi \ d 463 and (name N or name CA or name C or name O or name CB or name CG or name C \ D or name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ G2 or name HG3 or name HE21)) or resid 464 through 474 or (resid 475 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE or n \ ame NZ or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3)) or resid 476 through 597 or (resid \ 598 and (name N or name CA or name C or name O or name CB or name CG or name OD \ 1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 599 throug \ h 600 or (resid 601 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG or na \ me HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) or re \ sid 602 through 622 or (resid 623 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2 or name HA or name HB2 or name HB3)) \ or resid 624 through 729 or (resid 730 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 name HB2 or name HB3 or name HG2 or name HG3)) or resid 731 through 748 or re \ sid 803)) selection = (chain 'F' and ((resid 172 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 173 through 347 or (resid 348 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 OE2 or name HA or \ name HB2 or name HB3 or name HG2 or name HG3)) or resid 349 through 352 or (res \ id 353 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 OE2 or name HA or name HB2 or name HB3 or name HG2 or nam \ e HG3)) or resid 354 through 431 or (resid 432 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2 or name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or \ name HD2 or name HD3 or name HE or name HH11 or name HH21)) or resid 433 throug \ h 454 or (resid 455 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name NE or name CZ or name NH1 or name NH2 or name H or name \ HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or na \ me HE or name HH11 or name HH12 or name HH22)) or resid 456 through 496 or (resi \ d 497 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 498 through 696 or (resid 697 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 or \ name H or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 o \ r name HD3 or name HE or name HH21)) or resid 698 through 729 or (resid 730 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 name HB2 or name HB3 or name HG2 or name \ HG3)) or resid 731 through 748 or resid 803)) } 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' and resid 2 through 191) selection = chain 'M' 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.060 Extract box with map and model: 2.560 Check model and map are aligned: 0.450 Set scattering table: 0.570 Process input model: 131.460 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.220 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 38713 Z= 0.265 Angle : 0.749 13.518 52313 Z= 0.367 Chirality : 0.047 1.709 6001 Planarity : 0.004 0.051 6750 Dihedral : 13.793 152.566 14761 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -1.03 (0.11), residues: 4809 helix: -0.43 (0.09), residues: 2332 sheet: -0.72 (0.19), residues: 696 loop : -0.75 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 229 HIS 0.008 0.001 HIS D 393 PHE 0.029 0.001 PHE M 82 TYR 0.021 0.001 TYR F 540 ARG 0.004 0.000 ARG F 532 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1556 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1556 time to evaluate : 4.504 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: A 266 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7925 (tpt-90) REVERT: A 288 HIS cc_start: 0.8262 (p90) cc_final: 0.7839 (p90) REVERT: A 570 HIS cc_start: 0.7880 (t-90) cc_final: 0.7619 (t-90) REVERT: A 572 ASP cc_start: 0.7991 (m-30) cc_final: 0.7745 (m-30) REVERT: A 684 GLN cc_start: 0.7853 (tp40) cc_final: 0.7617 (tp-100) REVERT: A 693 LYS cc_start: 0.7864 (tttp) cc_final: 0.7516 (tttm) REVERT: A 731 VAL cc_start: 0.7974 (m) cc_final: 0.7510 (p) REVERT: B 194 GLU cc_start: 0.8177 (mp0) cc_final: 0.7775 (mp0) REVERT: B 258 LYS cc_start: 0.7870 (tttt) cc_final: 0.7640 (tttm) REVERT: B 343 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8773 (ttmt) REVERT: B 450 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8529 (tttp) REVERT: C 637 THR cc_start: 0.8882 (t) cc_final: 0.8591 (p) REVERT: D 317 ARG cc_start: 0.8152 (mtm180) cc_final: 0.7710 (mtm180) REVERT: D 366 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8125 (mt-10) REVERT: D 372 ARG cc_start: 0.7503 (ttp80) cc_final: 0.7216 (ttt90) REVERT: D 526 GLU cc_start: 0.7111 (mp0) cc_final: 0.6789 (mp0) REVERT: E 194 GLU cc_start: 0.8370 (mp0) cc_final: 0.7907 (mp0) REVERT: E 530 VAL cc_start: 0.9363 (p) cc_final: 0.9155 (p) REVERT: E 611 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7353 (mm-30) REVERT: F 317 ARG cc_start: 0.6907 (ptp-170) cc_final: 0.5787 (ptt180) REVERT: F 357 ILE cc_start: 0.8586 (mt) cc_final: 0.8382 (mt) REVERT: F 362 LYS cc_start: 0.8597 (tttt) cc_final: 0.8211 (ttpt) REVERT: F 464 ASP cc_start: 0.8435 (m-30) cc_final: 0.8127 (m-30) REVERT: F 468 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7956 (mt-10) REVERT: F 633 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7499 (mttp) REVERT: F 636 PHE cc_start: 0.8112 (m-80) cc_final: 0.7790 (m-80) REVERT: F 639 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8693 (pt0) REVERT: F 659 HIS cc_start: 0.8816 (m-70) cc_final: 0.8521 (m-70) REVERT: F 699 MET cc_start: 0.7534 (mmm) cc_final: 0.7326 (mmm) REVERT: F 711 ASN cc_start: 0.7930 (m110) cc_final: 0.7514 (m110) REVERT: F 713 LYS cc_start: 0.7649 (mtpt) cc_final: 0.7321 (mtpp) REVERT: F 740 ASN cc_start: 0.8183 (m-40) cc_final: 0.7902 (p0) REVERT: H 58 ASP cc_start: 0.7755 (m-30) cc_final: 0.7478 (m-30) REVERT: H 71 THR cc_start: 0.8967 (p) cc_final: 0.8759 (p) REVERT: H 78 ASP cc_start: 0.8468 (m-30) cc_final: 0.8038 (m-30) REVERT: H 110 LYS cc_start: 0.8265 (mttt) cc_final: 0.8028 (mttt) REVERT: H 136 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7527 (tm-30) REVERT: H 141 GLU cc_start: 0.8096 (tp30) cc_final: 0.7868 (tp30) REVERT: I 141 GLU cc_start: 0.7303 (tt0) cc_final: 0.7030 (tt0) REVERT: I 161 LEU cc_start: 0.7188 (pp) cc_final: 0.6987 (tp) REVERT: I 185 VAL cc_start: 0.8813 (t) cc_final: 0.8575 (m) REVERT: J 25 LYS cc_start: 0.8869 (tttm) cc_final: 0.8414 (ttmm) REVERT: J 110 LYS cc_start: 0.7848 (mttp) cc_final: 0.7253 (mttp) REVERT: J 125 LEU cc_start: 0.7147 (tp) cc_final: 0.6888 (tp) REVERT: K 18 ASP cc_start: 0.7512 (p0) cc_final: 0.7248 (p0) REVERT: K 35 VAL cc_start: 0.8893 (t) cc_final: 0.8657 (t) REVERT: K 78 ASP cc_start: 0.8499 (m-30) cc_final: 0.8082 (m-30) REVERT: K 138 HIS cc_start: 0.8589 (m-70) cc_final: 0.8365 (m-70) REVERT: K 155 LEU cc_start: 0.8370 (tp) cc_final: 0.8131 (tt) REVERT: M 144 LYS cc_start: 0.8064 (ttmm) cc_final: 0.7737 (mtpp) REVERT: M 146 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7972 (ttmt) REVERT: N 8 GLU cc_start: 0.6842 (tt0) cc_final: 0.6636 (tt0) REVERT: N 110 LYS cc_start: 0.7739 (mttt) cc_final: 0.7477 (mttp) REVERT: N 136 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7758 (tm-30) REVERT: N 141 GLU cc_start: 0.8250 (tp30) cc_final: 0.8048 (tp30) outliers start: 0 outliers final: 0 residues processed: 1556 average time/residue: 1.1750 time to fit residues: 2862.7023 Evaluate side-chains 1254 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1254 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 406 optimal weight: 7.9990 chunk 364 optimal weight: 6.9990 chunk 202 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 377 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 436 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN A 622 GLN B 209 ASN B 579 GLN B 606 ASN C 233 GLN C 305 ASN C 606 ASN D 684 GLN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 GLN ** E 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN F 279 ASN F 356 GLN F 451 ASN F 672 GLN I 41 ASN I 156 HIS K 116 ASN L 41 ASN L 116 ASN M 116 ASN N 116 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38713 Z= 0.274 Angle : 0.608 9.816 52313 Z= 0.325 Chirality : 0.047 1.723 6001 Planarity : 0.005 0.061 6750 Dihedral : 10.030 167.887 5443 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.01 % Allowed : 10.49 % Favored : 88.50 % 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 (0.11), residues: 4809 helix: 0.50 (0.10), residues: 2497 sheet: -0.75 (0.20), residues: 640 loop : -0.59 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 229 HIS 0.009 0.001 HIS F 570 PHE 0.015 0.001 PHE C 543 TYR 0.015 0.001 TYR I 128 ARG 0.007 0.001 ARG D 706 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1370 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1329 time to evaluate : 4.486 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 266 ARG cc_start: 0.8257 (mtt180) cc_final: 0.8017 (mmm-85) REVERT: A 359 ASN cc_start: 0.8755 (m-40) cc_final: 0.8528 (m110) REVERT: A 554 ILE cc_start: 0.8358 (mt) cc_final: 0.8132 (mt) REVERT: A 564 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.7662 (t0) REVERT: A 570 HIS cc_start: 0.8037 (t-90) cc_final: 0.7454 (t-90) REVERT: A 592 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7501 (ttp80) REVERT: A 668 GLU cc_start: 0.7280 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 681 GLU cc_start: 0.6799 (mp0) cc_final: 0.6417 (mp0) REVERT: A 731 VAL cc_start: 0.7925 (m) cc_final: 0.7429 (p) REVERT: A 736 ASP cc_start: 0.6521 (m-30) cc_final: 0.6008 (t0) REVERT: A 741 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 194 GLU cc_start: 0.8422 (mp0) cc_final: 0.7779 (mp0) REVERT: B 258 LYS cc_start: 0.7964 (tttt) cc_final: 0.7720 (tttm) REVERT: B 425 ASP cc_start: 0.8294 (m-30) cc_final: 0.8073 (m-30) REVERT: B 450 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8577 (tttp) REVERT: B 451 ASN cc_start: 0.7603 (m-40) cc_final: 0.7121 (m110) REVERT: D 317 ARG cc_start: 0.8235 (mtm180) cc_final: 0.7833 (mtm180) REVERT: D 372 ARG cc_start: 0.7480 (ttp80) cc_final: 0.7212 (ttt90) REVERT: D 410 ARG cc_start: 0.7917 (tmm-80) cc_final: 0.7659 (ttp80) REVERT: D 605 THR cc_start: 0.8692 (t) cc_final: 0.8283 (t) REVERT: D 606 ASN cc_start: 0.7772 (p0) cc_final: 0.7480 (p0) REVERT: D 693 LYS cc_start: 0.8581 (tptp) cc_final: 0.8329 (tptt) REVERT: E 194 GLU cc_start: 0.8411 (mp0) cc_final: 0.8111 (mp0) REVERT: E 264 GLU cc_start: 0.8776 (mp0) cc_final: 0.7810 (mp0) REVERT: E 272 LYS cc_start: 0.8160 (tttt) cc_final: 0.7866 (tppt) REVERT: E 425 ASP cc_start: 0.8028 (m-30) cc_final: 0.7731 (m-30) REVERT: E 515 GLU cc_start: 0.7220 (tp30) cc_final: 0.6911 (tp30) REVERT: E 525 MET cc_start: 0.8348 (mmm) cc_final: 0.8026 (mmm) REVERT: E 582 ASP cc_start: 0.8479 (t0) cc_final: 0.8180 (t0) REVERT: F 229 TRP cc_start: 0.8019 (t60) cc_final: 0.7347 (t60) REVERT: F 230 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7760 (mtp180) REVERT: F 464 ASP cc_start: 0.8413 (m-30) cc_final: 0.8103 (m-30) REVERT: F 465 LYS cc_start: 0.9146 (tppt) cc_final: 0.8724 (mmmm) REVERT: F 639 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8634 (pm20) REVERT: F 668 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8076 (tm-30) REVERT: F 687 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7796 (mpt180) REVERT: F 709 GLN cc_start: 0.8040 (tt0) cc_final: 0.7762 (tt0) REVERT: F 711 ASN cc_start: 0.8046 (m110) cc_final: 0.7552 (m110) REVERT: F 719 GLU cc_start: 0.7838 (tp30) cc_final: 0.7538 (tp30) REVERT: H 17 PHE cc_start: 0.7675 (m-80) cc_final: 0.7444 (m-80) REVERT: H 64 ASN cc_start: 0.8630 (t0) cc_final: 0.8425 (t0) REVERT: H 78 ASP cc_start: 0.8481 (m-30) cc_final: 0.8125 (m-30) REVERT: H 84 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7843 (mtmm) REVERT: H 137 ILE cc_start: 0.8902 (mm) cc_final: 0.8657 (mm) REVERT: I 171 ASP cc_start: 0.7490 (p0) cc_final: 0.7259 (p0) REVERT: J 125 LEU cc_start: 0.7166 (tp) cc_final: 0.6889 (tp) REVERT: K 78 ASP cc_start: 0.8670 (m-30) cc_final: 0.8150 (m-30) REVERT: K 138 HIS cc_start: 0.8687 (m-70) cc_final: 0.8342 (m-70) REVERT: K 140 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7858 (ttm110) REVERT: K 141 GLU cc_start: 0.7967 (tp30) cc_final: 0.7741 (tp30) REVERT: K 155 LEU cc_start: 0.8535 (tp) cc_final: 0.8254 (tt) REVERT: K 160 SER cc_start: 0.7708 (t) cc_final: 0.6746 (p) REVERT: K 167 ASP cc_start: 0.7414 (m-30) cc_final: 0.7012 (m-30) REVERT: L 116 ASN cc_start: 0.8631 (m-40) cc_final: 0.8253 (m-40) REVERT: L 161 LEU cc_start: 0.8344 (mt) cc_final: 0.7932 (tp) REVERT: M 26 GLU cc_start: 0.7281 (mp0) cc_final: 0.6458 (mp0) REVERT: M 144 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7670 (mtpp) REVERT: M 146 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8028 (ttmt) REVERT: N 8 GLU cc_start: 0.6986 (tt0) cc_final: 0.6711 (tt0) REVERT: N 136 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7999 (tm-30) REVERT: N 170 ARG cc_start: 0.8221 (tpp-160) cc_final: 0.7879 (tpp80) outliers start: 41 outliers final: 29 residues processed: 1344 average time/residue: 1.1647 time to fit residues: 2443.8533 Evaluate side-chains 1271 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1241 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 679 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 74 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 242 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 363 optimal weight: 20.0000 chunk 297 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 437 optimal weight: 5.9990 chunk 472 optimal weight: 10.0000 chunk 389 optimal weight: 9.9990 chunk 433 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 351 optimal weight: 6.9990 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 622 GLN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 HIS C 305 ASN D 305 ASN D 675 GLN D 684 GLN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 672 GLN F 443 GLN F 659 HIS ** H 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 116 ASN ** K 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 38713 Z= 0.376 Angle : 0.607 10.122 52313 Z= 0.320 Chirality : 0.048 1.700 6001 Planarity : 0.004 0.083 6750 Dihedral : 10.061 176.324 5443 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.62 % Allowed : 12.28 % Favored : 86.10 % 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 (0.11), residues: 4809 helix: 0.54 (0.10), residues: 2509 sheet: -0.92 (0.20), residues: 636 loop : -0.72 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 229 HIS 0.010 0.001 HIS A 570 PHE 0.032 0.002 PHE E 596 TYR 0.021 0.002 TYR I 128 ARG 0.009 0.001 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1417 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1351 time to evaluate : 4.513 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: A 264 GLU cc_start: 0.8299 (mp0) cc_final: 0.8005 (mp0) REVERT: A 266 ARG cc_start: 0.8301 (mtt180) cc_final: 0.8073 (mmm160) REVERT: A 359 ASN cc_start: 0.8698 (m-40) cc_final: 0.8437 (m110) REVERT: A 362 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8690 (ttpt) REVERT: A 510 LYS cc_start: 0.8465 (mmtp) cc_final: 0.8155 (mmtp) REVERT: A 558 HIS cc_start: 0.7978 (m-70) cc_final: 0.7429 (m-70) REVERT: A 566 ILE cc_start: 0.9032 (pt) cc_final: 0.8797 (tp) REVERT: A 570 HIS cc_start: 0.8526 (t-90) cc_final: 0.8245 (t-90) REVERT: A 663 ASP cc_start: 0.8022 (m-30) cc_final: 0.7810 (m-30) REVERT: A 681 GLU cc_start: 0.7015 (mp0) cc_final: 0.6490 (mp0) REVERT: A 731 VAL cc_start: 0.8109 (m) cc_final: 0.7184 (p) REVERT: A 741 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 207 LYS cc_start: 0.8328 (mmtm) cc_final: 0.8019 (mmtm) REVERT: B 258 LYS cc_start: 0.8121 (tttt) cc_final: 0.7870 (tttm) REVERT: B 275 GLU cc_start: 0.7138 (pt0) cc_final: 0.6908 (pt0) REVERT: B 450 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8632 (tttp) REVERT: B 451 ASN cc_start: 0.7694 (m-40) cc_final: 0.7201 (m110) REVERT: D 286 GLU cc_start: 0.7913 (mp0) cc_final: 0.7689 (mp0) REVERT: D 302 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6847 (m-30) REVERT: D 372 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7244 (ttt90) REVERT: D 605 THR cc_start: 0.8859 (t) cc_final: 0.8549 (t) REVERT: D 693 LYS cc_start: 0.8780 (tptp) cc_final: 0.8497 (tppt) REVERT: E 425 ASP cc_start: 0.8129 (m-30) cc_final: 0.7910 (m-30) REVERT: E 651 ASP cc_start: 0.7228 (p0) cc_final: 0.6895 (p0) REVERT: F 286 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7787 (mm-30) REVERT: F 326 GLU cc_start: 0.7664 (mp0) cc_final: 0.7351 (mp0) REVERT: F 340 ARG cc_start: 0.7508 (mmt180) cc_final: 0.6973 (mmm160) REVERT: F 365 TYR cc_start: 0.8094 (m-80) cc_final: 0.7838 (m-80) REVERT: F 465 LYS cc_start: 0.9139 (tppt) cc_final: 0.8753 (mmmm) REVERT: F 631 GLU cc_start: 0.8073 (mp0) cc_final: 0.7840 (mp0) REVERT: F 639 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8675 (pm20) REVERT: F 659 HIS cc_start: 0.8752 (m-70) cc_final: 0.8022 (m90) REVERT: F 687 ARG cc_start: 0.8020 (mtt90) cc_final: 0.7812 (mtt-85) REVERT: F 711 ASN cc_start: 0.8098 (m110) cc_final: 0.7875 (m110) REVERT: F 719 GLU cc_start: 0.7828 (tp30) cc_final: 0.7201 (tp30) REVERT: H 36 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: H 78 ASP cc_start: 0.8505 (m-30) cc_final: 0.7940 (m-30) REVERT: H 84 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7884 (mtmm) REVERT: H 137 ILE cc_start: 0.8930 (mm) cc_final: 0.8692 (mm) REVERT: H 159 GLN cc_start: 0.8159 (mp10) cc_final: 0.7905 (mp10) REVERT: I 51 GLU cc_start: 0.7750 (tt0) cc_final: 0.7353 (tt0) REVERT: J 125 LEU cc_start: 0.7157 (tp) cc_final: 0.6853 (tp) REVERT: J 169 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6542 (mm-30) REVERT: J 173 PHE cc_start: 0.8645 (m-80) cc_final: 0.8203 (m-80) REVERT: K 8 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6994 (tp30) REVERT: K 18 ASP cc_start: 0.8422 (p0) cc_final: 0.8183 (p0) REVERT: K 78 ASP cc_start: 0.8733 (m-30) cc_final: 0.8393 (m-30) REVERT: K 138 HIS cc_start: 0.8686 (m-70) cc_final: 0.8219 (m-70) REVERT: K 140 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7753 (ttm110) REVERT: K 141 GLU cc_start: 0.8023 (tp30) cc_final: 0.7615 (tp30) REVERT: K 155 LEU cc_start: 0.8691 (tp) cc_final: 0.8439 (tt) REVERT: L 12 ARG cc_start: 0.6909 (ttm110) cc_final: 0.6707 (ptp-110) REVERT: L 161 LEU cc_start: 0.8365 (mt) cc_final: 0.7937 (tp) REVERT: M 146 LYS cc_start: 0.8393 (ttpt) cc_final: 0.8091 (ttmt) REVERT: M 163 GLN cc_start: 0.7646 (tp40) cc_final: 0.7443 (tp-100) REVERT: M 172 ARG cc_start: 0.7343 (tpt-90) cc_final: 0.7092 (tpt-90) REVERT: M 178 GLU cc_start: 0.7970 (mp0) cc_final: 0.7719 (mp0) REVERT: N 8 GLU cc_start: 0.6941 (tt0) cc_final: 0.6652 (tt0) REVERT: N 32 THR cc_start: 0.9149 (t) cc_final: 0.8796 (m) REVERT: N 136 GLU cc_start: 0.8581 (tm-30) cc_final: 0.7893 (tm-30) REVERT: N 146 LYS cc_start: 0.8704 (tttt) cc_final: 0.8334 (tttt) REVERT: N 170 ARG cc_start: 0.8212 (tpp-160) cc_final: 0.7891 (tpp80) outliers start: 66 outliers final: 52 residues processed: 1370 average time/residue: 1.1433 time to fit residues: 2445.3305 Evaluate side-chains 1331 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1276 time to evaluate : 4.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 302 ASP Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 39 MET Chi-restraints excluded: chain N residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 8.9990 chunk 328 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 293 optimal weight: 0.8980 chunk 439 optimal weight: 20.0000 chunk 464 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 416 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN D 200 GLN D 684 GLN D 730 GLN E 579 GLN E 672 GLN F 558 HIS ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 41 ASN K 41 ASN ** K 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 ASN N 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 38713 Z= 0.365 Angle : 0.583 9.810 52313 Z= 0.306 Chirality : 0.047 1.703 6001 Planarity : 0.004 0.062 6750 Dihedral : 9.865 177.510 5443 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.97 % Allowed : 14.39 % Favored : 83.64 % 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: -0.24 (0.12), residues: 4809 helix: 0.56 (0.10), residues: 2507 sheet: -1.13 (0.19), residues: 643 loop : -0.68 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 229 HIS 0.007 0.001 HIS I 122 PHE 0.031 0.002 PHE E 596 TYR 0.017 0.002 TYR I 128 ARG 0.010 0.001 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1403 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1323 time to evaluate : 4.533 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: A 264 GLU cc_start: 0.8376 (mp0) cc_final: 0.8172 (mp0) REVERT: A 266 ARG cc_start: 0.8329 (mtt180) cc_final: 0.8121 (mmm160) REVERT: A 359 ASN cc_start: 0.8634 (m-40) cc_final: 0.8336 (m110) REVERT: A 663 ASP cc_start: 0.8079 (m-30) cc_final: 0.7872 (m-30) REVERT: A 681 GLU cc_start: 0.7118 (mp0) cc_final: 0.6599 (mp0) REVERT: A 731 VAL cc_start: 0.8295 (m) cc_final: 0.7322 (p) REVERT: A 741 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7614 (mm-30) REVERT: B 207 LYS cc_start: 0.8343 (mmtm) cc_final: 0.8057 (mmtm) REVERT: B 258 LYS cc_start: 0.8100 (tttt) cc_final: 0.7822 (tttm) REVERT: B 275 GLU cc_start: 0.7268 (pt0) cc_final: 0.6994 (pt0) REVERT: B 343 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8857 (ttmt) REVERT: B 379 ARG cc_start: 0.8530 (tpp-160) cc_final: 0.7959 (ttm-80) REVERT: B 447 ASP cc_start: 0.7420 (m-30) cc_final: 0.6828 (m-30) REVERT: B 450 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8638 (tttp) REVERT: B 451 ASN cc_start: 0.7744 (m-40) cc_final: 0.7226 (m-40) REVERT: B 674 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7962 (t0) REVERT: C 527 ARG cc_start: 0.8504 (mtp-110) cc_final: 0.8273 (mtp-110) REVERT: D 286 GLU cc_start: 0.7905 (mp0) cc_final: 0.7556 (mp0) REVERT: D 372 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7236 (ttt90) REVERT: D 719 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6948 (mm-30) REVERT: E 273 GLN cc_start: 0.7785 (mt0) cc_final: 0.7579 (mt0) REVERT: E 651 ASP cc_start: 0.7425 (p0) cc_final: 0.7109 (p0) REVERT: F 229 TRP cc_start: 0.8062 (t60) cc_final: 0.7391 (t60) REVERT: F 272 LYS cc_start: 0.8607 (mttt) cc_final: 0.8378 (mtpp) REVERT: F 326 GLU cc_start: 0.7703 (mp0) cc_final: 0.7382 (mp0) REVERT: F 365 TYR cc_start: 0.8121 (m-80) cc_final: 0.7918 (m-80) REVERT: F 465 LYS cc_start: 0.9120 (tppt) cc_final: 0.8767 (mmmm) REVERT: F 631 GLU cc_start: 0.8048 (mp0) cc_final: 0.7794 (mp0) REVERT: F 639 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8610 (pm20) REVERT: F 659 HIS cc_start: 0.8791 (m-70) cc_final: 0.8025 (m90) REVERT: F 711 ASN cc_start: 0.8072 (m110) cc_final: 0.7491 (m110) REVERT: F 719 GLU cc_start: 0.7859 (tp30) cc_final: 0.7264 (tp30) REVERT: H 34 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7748 (mm-40) REVERT: H 36 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: H 64 ASN cc_start: 0.9141 (t0) cc_final: 0.8927 (t0) REVERT: H 78 ASP cc_start: 0.8386 (m-30) cc_final: 0.8061 (m-30) REVERT: H 136 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7718 (tm-30) REVERT: H 159 GLN cc_start: 0.8269 (mp10) cc_final: 0.7946 (mp10) REVERT: I 64 ASN cc_start: 0.9232 (t0) cc_final: 0.9004 (t0) REVERT: J 125 LEU cc_start: 0.7186 (tp) cc_final: 0.6862 (tp) REVERT: J 173 PHE cc_start: 0.8524 (m-80) cc_final: 0.8162 (m-80) REVERT: K 18 ASP cc_start: 0.8316 (p0) cc_final: 0.7978 (p0) REVERT: K 78 ASP cc_start: 0.8761 (m-30) cc_final: 0.8453 (m-30) REVERT: K 141 GLU cc_start: 0.7977 (tp30) cc_final: 0.7514 (tp30) REVERT: K 145 VAL cc_start: 0.9361 (t) cc_final: 0.8880 (m) REVERT: K 155 LEU cc_start: 0.8684 (tp) cc_final: 0.8447 (tt) REVERT: L 12 ARG cc_start: 0.6944 (ttm110) cc_final: 0.6673 (ptp-110) REVERT: L 140 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.8038 (tpp80) REVERT: L 161 LEU cc_start: 0.8330 (mt) cc_final: 0.7917 (tp) REVERT: M 26 GLU cc_start: 0.7592 (mp0) cc_final: 0.6759 (mp0) REVERT: M 146 LYS cc_start: 0.8393 (ttpt) cc_final: 0.8111 (ttmt) REVERT: M 178 GLU cc_start: 0.7987 (mp0) cc_final: 0.7627 (mp0) REVERT: N 8 GLU cc_start: 0.7028 (tt0) cc_final: 0.6744 (tt0) REVERT: N 22 ARG cc_start: 0.8358 (tpt90) cc_final: 0.7779 (tpt170) REVERT: N 32 THR cc_start: 0.9194 (t) cc_final: 0.8844 (m) REVERT: N 136 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8261 (tm-30) REVERT: N 170 ARG cc_start: 0.8333 (tpp-160) cc_final: 0.8121 (tpp80) REVERT: N 178 GLU cc_start: 0.8058 (mp0) cc_final: 0.7759 (mp0) outliers start: 80 outliers final: 60 residues processed: 1345 average time/residue: 1.1504 time to fit residues: 2419.6739 Evaluate side-chains 1333 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1271 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 612 THR Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 345 ASP Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 556 HIS Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 174 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 387 optimal weight: 10.0000 chunk 263 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 346 optimal weight: 20.0000 chunk 191 optimal weight: 3.9990 chunk 396 optimal weight: 10.0000 chunk 321 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 237 optimal weight: 5.9990 chunk 417 optimal weight: 30.0000 chunk 117 optimal weight: 2.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 GLN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 730 GLN D 675 GLN D 684 GLN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 81 GLN ** K 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 38713 Z= 0.346 Angle : 0.566 9.945 52313 Z= 0.298 Chirality : 0.047 1.693 6001 Planarity : 0.004 0.070 6750 Dihedral : 9.859 175.118 5443 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.01 % Allowed : 15.48 % Favored : 82.51 % 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: -0.20 (0.12), residues: 4809 helix: 0.64 (0.10), residues: 2504 sheet: -1.22 (0.19), residues: 623 loop : -0.69 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 649 HIS 0.008 0.001 HIS I 122 PHE 0.030 0.001 PHE E 596 TYR 0.016 0.001 TYR I 128 ARG 0.010 0.000 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1398 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1316 time to evaluate : 4.624 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: A 279 ASN cc_start: 0.8405 (p0) cc_final: 0.8075 (p0) REVERT: A 359 ASN cc_start: 0.8614 (m-40) cc_final: 0.8396 (m110) REVERT: A 451 ASN cc_start: 0.7719 (p0) cc_final: 0.7057 (p0) REVERT: A 663 ASP cc_start: 0.8101 (m-30) cc_final: 0.7880 (m-30) REVERT: A 741 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 207 LYS cc_start: 0.8361 (mmtm) cc_final: 0.8089 (mmtm) REVERT: B 258 LYS cc_start: 0.8094 (tttt) cc_final: 0.7842 (tttm) REVERT: B 275 GLU cc_start: 0.7285 (pt0) cc_final: 0.7021 (pt0) REVERT: B 343 LYS cc_start: 0.9074 (ttpp) cc_final: 0.8821 (ttmt) REVERT: B 447 ASP cc_start: 0.7498 (m-30) cc_final: 0.6896 (t0) REVERT: B 450 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8654 (tttp) REVERT: B 451 ASN cc_start: 0.7809 (m-40) cc_final: 0.7314 (m-40) REVERT: B 674 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7952 (t0) REVERT: B 722 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8894 (p90) REVERT: C 527 ARG cc_start: 0.8516 (mtp-110) cc_final: 0.8292 (mtp-110) REVERT: D 286 GLU cc_start: 0.7880 (mp0) cc_final: 0.7446 (mp0) REVERT: D 372 ARG cc_start: 0.7516 (ttp80) cc_final: 0.7243 (ttt90) REVERT: D 719 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6954 (mm-30) REVERT: E 370 ASP cc_start: 0.7995 (t0) cc_final: 0.7722 (t0) REVERT: E 651 ASP cc_start: 0.7629 (p0) cc_final: 0.7322 (p0) REVERT: F 229 TRP cc_start: 0.8019 (t60) cc_final: 0.7362 (t60) REVERT: F 286 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7850 (mm-30) REVERT: F 326 GLU cc_start: 0.7713 (mp0) cc_final: 0.7382 (mp0) REVERT: F 340 ARG cc_start: 0.7438 (mmt180) cc_final: 0.6962 (mmm160) REVERT: F 465 LYS cc_start: 0.9107 (tppt) cc_final: 0.8795 (mmmm) REVERT: F 631 GLU cc_start: 0.8051 (mp0) cc_final: 0.7815 (mp0) REVERT: F 639 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8609 (pm20) REVERT: F 659 HIS cc_start: 0.8799 (m-70) cc_final: 0.8023 (m90) REVERT: F 719 GLU cc_start: 0.7834 (tp30) cc_final: 0.7336 (tp30) REVERT: H 36 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: H 78 ASP cc_start: 0.8378 (m-30) cc_final: 0.8063 (m-30) REVERT: H 136 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7751 (tm-30) REVERT: I 64 ASN cc_start: 0.9253 (t0) cc_final: 0.9031 (t0) REVERT: J 125 LEU cc_start: 0.7201 (tp) cc_final: 0.6863 (tp) REVERT: J 150 ASN cc_start: 0.8490 (m110) cc_final: 0.8240 (m110) REVERT: J 165 GLU cc_start: 0.6537 (tm-30) cc_final: 0.5945 (tm-30) REVERT: J 173 PHE cc_start: 0.8473 (m-80) cc_final: 0.8168 (m-80) REVERT: K 18 ASP cc_start: 0.8317 (p0) cc_final: 0.7955 (p0) REVERT: K 78 ASP cc_start: 0.8755 (m-30) cc_final: 0.8473 (m-30) REVERT: K 140 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7776 (ttm-80) REVERT: K 141 GLU cc_start: 0.7951 (tp30) cc_final: 0.7354 (tp30) REVERT: K 145 VAL cc_start: 0.9350 (t) cc_final: 0.8776 (m) REVERT: K 151 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7513 (mt-10) REVERT: K 155 LEU cc_start: 0.8772 (tp) cc_final: 0.8527 (tt) REVERT: L 12 ARG cc_start: 0.6895 (ttm110) cc_final: 0.6669 (ptp-110) REVERT: L 161 LEU cc_start: 0.8299 (mt) cc_final: 0.7885 (tp) REVERT: M 146 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8105 (ttmt) REVERT: M 178 GLU cc_start: 0.7995 (mp0) cc_final: 0.7539 (mp0) REVERT: N 8 GLU cc_start: 0.7049 (tt0) cc_final: 0.6778 (tt0) REVERT: N 22 ARG cc_start: 0.8415 (tpt90) cc_final: 0.7749 (tpt170) REVERT: N 32 THR cc_start: 0.9237 (t) cc_final: 0.8867 (m) REVERT: N 136 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8273 (tm-30) REVERT: N 178 GLU cc_start: 0.8029 (mp0) cc_final: 0.7745 (mp0) outliers start: 82 outliers final: 67 residues processed: 1339 average time/residue: 1.1611 time to fit residues: 2436.7452 Evaluate side-chains 1354 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1284 time to evaluate : 4.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 436 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 617 ILE Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 612 THR Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 556 HIS Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 134 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 174 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 156 optimal weight: 6.9990 chunk 418 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 465 optimal weight: 3.9990 chunk 386 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 244 optimal weight: 8.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 684 GLN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 38713 Z= 0.273 Angle : 0.542 9.968 52313 Z= 0.283 Chirality : 0.046 1.699 6001 Planarity : 0.004 0.067 6750 Dihedral : 9.751 173.690 5443 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.16 % Allowed : 16.26 % Favored : 81.58 % 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: -0.08 (0.12), residues: 4809 helix: 0.77 (0.10), residues: 2503 sheet: -1.28 (0.19), residues: 634 loop : -0.64 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 229 HIS 0.010 0.001 HIS A 288 PHE 0.026 0.001 PHE E 596 TYR 0.017 0.001 TYR I 128 ARG 0.008 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1400 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1312 time to evaluate : 4.627 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: A 264 GLU cc_start: 0.8367 (mp0) cc_final: 0.8156 (pm20) REVERT: A 279 ASN cc_start: 0.8387 (p0) cc_final: 0.8103 (p0) REVERT: A 359 ASN cc_start: 0.8582 (m-40) cc_final: 0.8351 (m110) REVERT: A 564 ASP cc_start: 0.9213 (OUTLIER) cc_final: 0.8314 (t0) REVERT: A 629 MET cc_start: 0.7451 (ttt) cc_final: 0.7126 (ttm) REVERT: A 663 ASP cc_start: 0.8080 (m-30) cc_final: 0.7861 (m-30) REVERT: A 741 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 258 LYS cc_start: 0.8069 (tttt) cc_final: 0.7807 (tttm) REVERT: B 275 GLU cc_start: 0.7281 (pt0) cc_final: 0.7022 (pt0) REVERT: B 343 LYS cc_start: 0.9085 (ttpp) cc_final: 0.8819 (ttmt) REVERT: B 447 ASP cc_start: 0.7513 (m-30) cc_final: 0.6897 (t0) REVERT: B 450 LYS cc_start: 0.8874 (ttpt) cc_final: 0.8646 (tttp) REVERT: B 451 ASN cc_start: 0.7799 (m-40) cc_final: 0.7298 (m-40) REVERT: B 455 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7448 (mtp85) REVERT: B 674 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7940 (t0) REVERT: B 722 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8867 (p90) REVERT: C 527 ARG cc_start: 0.8518 (mtp-110) cc_final: 0.8313 (mtp-110) REVERT: D 286 GLU cc_start: 0.7894 (mp0) cc_final: 0.7487 (mp0) REVERT: D 372 ARG cc_start: 0.7517 (ttp80) cc_final: 0.7244 (ttt90) REVERT: D 719 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6960 (mm-30) REVERT: E 370 ASP cc_start: 0.7994 (t0) cc_final: 0.7694 (t0) REVERT: E 651 ASP cc_start: 0.7686 (p0) cc_final: 0.7374 (p0) REVERT: F 259 TYR cc_start: 0.7524 (OUTLIER) cc_final: 0.7011 (t80) REVERT: F 286 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7839 (mm-30) REVERT: F 326 GLU cc_start: 0.7645 (mp0) cc_final: 0.7335 (mp0) REVERT: F 340 ARG cc_start: 0.7455 (mmt180) cc_final: 0.7007 (mmm160) REVERT: F 465 LYS cc_start: 0.9100 (tppt) cc_final: 0.8827 (mmmm) REVERT: F 631 GLU cc_start: 0.8042 (mp0) cc_final: 0.7819 (mp0) REVERT: F 639 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8601 (pm20) REVERT: F 659 HIS cc_start: 0.8809 (m-70) cc_final: 0.8054 (m90) REVERT: F 718 ASN cc_start: 0.8202 (t0) cc_final: 0.7983 (t0) REVERT: F 719 GLU cc_start: 0.7815 (tp30) cc_final: 0.7351 (tp30) REVERT: H 36 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: H 78 ASP cc_start: 0.8373 (m-30) cc_final: 0.8060 (m-30) REVERT: H 136 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7743 (tm-30) REVERT: H 181 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7960 (pt0) REVERT: I 26 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8133 (mm-30) REVERT: I 64 ASN cc_start: 0.9251 (t0) cc_final: 0.9042 (t0) REVERT: J 125 LEU cc_start: 0.7203 (tp) cc_final: 0.6865 (tp) REVERT: J 150 ASN cc_start: 0.8569 (m110) cc_final: 0.8359 (m110) REVERT: J 165 GLU cc_start: 0.6471 (tm-30) cc_final: 0.6259 (tm-30) REVERT: J 169 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6640 (mm-30) REVERT: J 173 PHE cc_start: 0.8388 (m-80) cc_final: 0.8095 (m-80) REVERT: K 78 ASP cc_start: 0.8769 (m-30) cc_final: 0.8492 (m-30) REVERT: K 140 ARG cc_start: 0.8070 (ttm-80) cc_final: 0.7735 (ttm-80) REVERT: K 141 GLU cc_start: 0.7910 (tp30) cc_final: 0.7289 (tp30) REVERT: K 145 VAL cc_start: 0.9327 (t) cc_final: 0.8711 (m) REVERT: K 155 LEU cc_start: 0.8794 (tp) cc_final: 0.8553 (tt) REVERT: L 161 LEU cc_start: 0.8265 (mt) cc_final: 0.7861 (tp) REVERT: M 146 LYS cc_start: 0.8392 (ttpt) cc_final: 0.8091 (ttmt) REVERT: M 149 MET cc_start: 0.7899 (mmt) cc_final: 0.7676 (mmt) REVERT: M 178 GLU cc_start: 0.8029 (mp0) cc_final: 0.7539 (mp0) REVERT: N 8 GLU cc_start: 0.7017 (tt0) cc_final: 0.6751 (tt0) REVERT: N 22 ARG cc_start: 0.8413 (tpt90) cc_final: 0.7730 (tpt170) REVERT: N 32 THR cc_start: 0.9239 (t) cc_final: 0.8861 (m) REVERT: N 136 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8263 (tm-30) REVERT: N 178 GLU cc_start: 0.8017 (mp0) cc_final: 0.7748 (mp0) outliers start: 88 outliers final: 73 residues processed: 1338 average time/residue: 1.1535 time to fit residues: 2436.1071 Evaluate side-chains 1361 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1282 time to evaluate : 4.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 556 HIS Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 84 LYS Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 174 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 448 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 265 optimal weight: 8.9990 chunk 339 optimal weight: 20.0000 chunk 263 optimal weight: 9.9990 chunk 391 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 463 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 chunk 282 optimal weight: 30.0000 chunk 214 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN D 675 GLN D 684 GLN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS F 711 ASN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 38713 Z= 0.253 Angle : 0.543 10.016 52313 Z= 0.282 Chirality : 0.045 1.698 6001 Planarity : 0.004 0.075 6750 Dihedral : 9.711 179.320 5443 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.31 % Allowed : 16.46 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4809 helix: 0.84 (0.10), residues: 2514 sheet: -1.31 (0.19), residues: 632 loop : -0.54 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 649 HIS 0.008 0.001 HIS I 122 PHE 0.033 0.001 PHE L 173 TYR 0.017 0.001 TYR I 128 ARG 0.010 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1399 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1305 time to evaluate : 4.540 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: A 264 GLU cc_start: 0.8316 (mp0) cc_final: 0.8074 (pm20) REVERT: A 359 ASN cc_start: 0.8583 (m-40) cc_final: 0.8369 (m110) REVERT: A 564 ASP cc_start: 0.9201 (OUTLIER) cc_final: 0.8306 (t0) REVERT: A 633 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7966 (mmtt) REVERT: A 663 ASP cc_start: 0.8076 (m-30) cc_final: 0.7852 (m-30) REVERT: A 741 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 207 LYS cc_start: 0.8363 (mmtm) cc_final: 0.7797 (mtmt) REVERT: B 258 LYS cc_start: 0.8066 (tttt) cc_final: 0.7788 (tttm) REVERT: B 275 GLU cc_start: 0.7261 (pt0) cc_final: 0.7013 (pt0) REVERT: B 343 LYS cc_start: 0.9074 (ttpp) cc_final: 0.8817 (ttmt) REVERT: B 447 ASP cc_start: 0.7503 (m-30) cc_final: 0.6866 (t0) REVERT: B 450 LYS cc_start: 0.8867 (ttpt) cc_final: 0.8649 (tttp) REVERT: B 451 ASN cc_start: 0.7781 (m-40) cc_final: 0.7320 (m110) REVERT: B 455 ARG cc_start: 0.7747 (mtp85) cc_final: 0.7462 (mtp85) REVERT: B 674 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7932 (t0) REVERT: D 286 GLU cc_start: 0.7887 (mp0) cc_final: 0.7446 (mp0) REVERT: D 372 ARG cc_start: 0.7515 (ttp80) cc_final: 0.7227 (ttt90) REVERT: D 719 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6959 (mm-30) REVERT: E 370 ASP cc_start: 0.7991 (t0) cc_final: 0.7663 (t0) REVERT: E 651 ASP cc_start: 0.7748 (p0) cc_final: 0.7407 (p0) REVERT: F 229 TRP cc_start: 0.8016 (t60) cc_final: 0.7328 (t60) REVERT: F 259 TYR cc_start: 0.7513 (OUTLIER) cc_final: 0.6987 (t80) REVERT: F 286 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7838 (mm-30) REVERT: F 326 GLU cc_start: 0.7653 (mp0) cc_final: 0.7334 (mp0) REVERT: F 340 ARG cc_start: 0.7415 (mmt180) cc_final: 0.6970 (mmm160) REVERT: F 631 GLU cc_start: 0.8055 (mp0) cc_final: 0.7817 (mp0) REVERT: F 639 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8573 (pm20) REVERT: F 659 HIS cc_start: 0.8826 (m-70) cc_final: 0.8049 (m90) REVERT: F 718 ASN cc_start: 0.8184 (t0) cc_final: 0.7953 (t0) REVERT: F 719 GLU cc_start: 0.7825 (tp30) cc_final: 0.7406 (tp30) REVERT: H 36 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: H 78 ASP cc_start: 0.8369 (m-30) cc_final: 0.8061 (m-30) REVERT: H 136 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7789 (tm-30) REVERT: H 181 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7960 (pt0) REVERT: I 26 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8162 (mm-30) REVERT: I 64 ASN cc_start: 0.9254 (t0) cc_final: 0.9054 (t0) REVERT: J 125 LEU cc_start: 0.7217 (tp) cc_final: 0.6866 (tp) REVERT: J 165 GLU cc_start: 0.6365 (tm-30) cc_final: 0.6082 (tm-30) REVERT: J 169 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6612 (mm-30) REVERT: J 173 PHE cc_start: 0.8322 (m-80) cc_final: 0.8063 (m-80) REVERT: K 18 ASP cc_start: 0.8286 (p0) cc_final: 0.7918 (p0) REVERT: K 78 ASP cc_start: 0.8770 (m-30) cc_final: 0.8491 (m-30) REVERT: K 140 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7733 (ttm-80) REVERT: K 141 GLU cc_start: 0.7892 (tp30) cc_final: 0.7440 (tp30) REVERT: K 145 VAL cc_start: 0.9293 (t) cc_final: 0.8702 (m) REVERT: K 155 LEU cc_start: 0.8799 (tp) cc_final: 0.8564 (tt) REVERT: L 161 LEU cc_start: 0.8245 (mt) cc_final: 0.7869 (tp) REVERT: M 26 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8022 (mm-30) REVERT: M 146 LYS cc_start: 0.8397 (ttpt) cc_final: 0.8087 (ttmt) REVERT: M 149 MET cc_start: 0.7811 (mmt) cc_final: 0.7533 (mmt) REVERT: M 178 GLU cc_start: 0.8080 (mp0) cc_final: 0.7778 (mp0) REVERT: N 8 GLU cc_start: 0.7018 (tt0) cc_final: 0.6758 (tt0) REVERT: N 22 ARG cc_start: 0.8405 (tpt90) cc_final: 0.7721 (tpt170) REVERT: N 56 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7327 (mm-30) REVERT: N 136 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8284 (tm-30) REVERT: N 178 GLU cc_start: 0.8028 (mp0) cc_final: 0.7765 (mp0) outliers start: 94 outliers final: 80 residues processed: 1335 average time/residue: 1.1274 time to fit residues: 2364.5567 Evaluate side-chains 1360 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1275 time to evaluate : 4.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 36 GLU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 174 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 286 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 276 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 294 optimal weight: 9.9990 chunk 315 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 364 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 ASN ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 684 GLN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS F 711 ASN ** H 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN ** K 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 159 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 38713 Z= 0.251 Angle : 0.541 10.042 52313 Z= 0.281 Chirality : 0.045 1.699 6001 Planarity : 0.004 0.079 6750 Dihedral : 9.610 172.429 5443 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.21 % Allowed : 16.51 % Favored : 81.28 % 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: 0.09 (0.12), residues: 4809 helix: 0.89 (0.10), residues: 2517 sheet: -1.30 (0.19), residues: 633 loop : -0.50 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 689 HIS 0.007 0.001 HIS I 122 PHE 0.024 0.001 PHE E 596 TYR 0.018 0.001 TYR I 128 ARG 0.009 0.000 ARG I 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1375 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1285 time to evaluate : 4.618 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: A 264 GLU cc_start: 0.8341 (mp0) cc_final: 0.8120 (pm20) REVERT: A 279 ASN cc_start: 0.8396 (p0) cc_final: 0.8120 (p0) REVERT: A 359 ASN cc_start: 0.8570 (m-40) cc_final: 0.8329 (m110) REVERT: A 468 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7207 (mt-10) REVERT: A 472 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 564 ASP cc_start: 0.9201 (OUTLIER) cc_final: 0.8302 (t0) REVERT: A 633 LYS cc_start: 0.8310 (mmtt) cc_final: 0.7931 (mmtt) REVERT: A 663 ASP cc_start: 0.8073 (m-30) cc_final: 0.7854 (m-30) REVERT: A 681 GLU cc_start: 0.7182 (mp0) cc_final: 0.6727 (mp0) REVERT: B 207 LYS cc_start: 0.8367 (mmtm) cc_final: 0.7807 (mtmt) REVERT: B 258 LYS cc_start: 0.8055 (tttt) cc_final: 0.7760 (tttm) REVERT: B 275 GLU cc_start: 0.7234 (pt0) cc_final: 0.6996 (pt0) REVERT: B 343 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8821 (ttmt) REVERT: B 447 ASP cc_start: 0.7545 (m-30) cc_final: 0.6986 (t0) REVERT: B 450 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8661 (tttp) REVERT: B 451 ASN cc_start: 0.7762 (m-40) cc_final: 0.7320 (m110) REVERT: B 455 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7460 (mtp85) REVERT: B 674 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7940 (t0) REVERT: D 286 GLU cc_start: 0.7880 (mp0) cc_final: 0.7495 (mp0) REVERT: D 372 ARG cc_start: 0.7522 (ttp80) cc_final: 0.7248 (ttt90) REVERT: D 633 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8041 (mptt) REVERT: D 719 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7036 (mm-30) REVERT: E 272 LYS cc_start: 0.8412 (tttt) cc_final: 0.7967 (ttmt) REVERT: E 370 ASP cc_start: 0.7989 (t0) cc_final: 0.7670 (t0) REVERT: E 651 ASP cc_start: 0.7771 (p0) cc_final: 0.7459 (p0) REVERT: F 229 TRP cc_start: 0.8005 (t60) cc_final: 0.7322 (t60) REVERT: F 259 TYR cc_start: 0.7583 (OUTLIER) cc_final: 0.7022 (t80) REVERT: F 286 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7818 (mm-30) REVERT: F 326 GLU cc_start: 0.7657 (mp0) cc_final: 0.7333 (mp0) REVERT: F 340 ARG cc_start: 0.7392 (mmt180) cc_final: 0.6994 (mmm160) REVERT: F 631 GLU cc_start: 0.8048 (mp0) cc_final: 0.7809 (mp0) REVERT: F 639 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8574 (pm20) REVERT: F 659 HIS cc_start: 0.8842 (m-70) cc_final: 0.8051 (m90) REVERT: F 718 ASN cc_start: 0.8182 (t0) cc_final: 0.7978 (t0) REVERT: F 719 GLU cc_start: 0.7792 (tp30) cc_final: 0.7415 (tp30) REVERT: H 36 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: H 78 ASP cc_start: 0.8366 (m-30) cc_final: 0.8066 (m-30) REVERT: H 136 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7789 (tm-30) REVERT: H 181 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: I 26 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8120 (mm-30) REVERT: J 125 LEU cc_start: 0.7226 (tp) cc_final: 0.6885 (tp) REVERT: J 173 PHE cc_start: 0.8299 (m-80) cc_final: 0.8029 (m-80) REVERT: K 18 ASP cc_start: 0.8276 (p0) cc_final: 0.7900 (p0) REVERT: K 78 ASP cc_start: 0.8804 (m-30) cc_final: 0.8418 (m-30) REVERT: K 120 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6430 (tmm) REVERT: K 121 ILE cc_start: 0.7913 (tp) cc_final: 0.7644 (tp) REVERT: K 140 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7730 (ttm-80) REVERT: K 141 GLU cc_start: 0.7867 (tp30) cc_final: 0.7362 (tp30) REVERT: K 155 LEU cc_start: 0.8802 (tp) cc_final: 0.8574 (tt) REVERT: L 161 LEU cc_start: 0.8248 (mt) cc_final: 0.7867 (tp) REVERT: M 146 LYS cc_start: 0.8399 (ttpt) cc_final: 0.8079 (ttmt) REVERT: N 8 GLU cc_start: 0.7000 (tt0) cc_final: 0.6769 (tt0) REVERT: N 22 ARG cc_start: 0.8426 (tpt90) cc_final: 0.7751 (tpt170) REVERT: N 56 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7393 (mm-30) REVERT: N 136 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8260 (tm-30) REVERT: N 178 GLU cc_start: 0.8045 (mp0) cc_final: 0.7809 (mp0) outliers start: 90 outliers final: 79 residues processed: 1315 average time/residue: 1.0949 time to fit residues: 2245.8997 Evaluate side-chains 1357 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1272 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 556 HIS Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 41 ASN Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 57 LYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 174 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 421 optimal weight: 9.9990 chunk 444 optimal weight: 5.9990 chunk 405 optimal weight: 0.5980 chunk 432 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 339 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 390 optimal weight: 0.8980 chunk 408 optimal weight: 7.9990 chunk 430 optimal weight: 6.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 684 GLN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 HIS F 485 HIS F 558 HIS H 116 ASN I 81 GLN ** K 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN N 159 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 38713 Z= 0.242 Angle : 0.540 10.058 52313 Z= 0.280 Chirality : 0.045 1.699 6001 Planarity : 0.004 0.081 6750 Dihedral : 9.545 172.076 5443 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.26 % Allowed : 16.65 % Favored : 81.09 % 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: 0.14 (0.12), residues: 4809 helix: 0.92 (0.10), residues: 2524 sheet: -1.25 (0.19), residues: 645 loop : -0.45 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 689 HIS 0.007 0.001 HIS F 485 PHE 0.023 0.001 PHE E 596 TYR 0.017 0.001 TYR I 128 ARG 0.013 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1380 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1288 time to evaluate : 4.525 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: A 264 GLU cc_start: 0.8348 (mp0) cc_final: 0.8119 (pm20) REVERT: A 266 ARG cc_start: 0.8506 (mmm160) cc_final: 0.8286 (mmm-85) REVERT: A 279 ASN cc_start: 0.8377 (p0) cc_final: 0.8110 (p0) REVERT: A 359 ASN cc_start: 0.8567 (m-40) cc_final: 0.8327 (m110) REVERT: A 468 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7206 (mt-10) REVERT: A 472 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7689 (mt-10) REVERT: A 564 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8288 (t0) REVERT: A 663 ASP cc_start: 0.8060 (m-30) cc_final: 0.7852 (m-30) REVERT: A 681 GLU cc_start: 0.7182 (mp0) cc_final: 0.6732 (mp0) REVERT: B 207 LYS cc_start: 0.8361 (mmtm) cc_final: 0.7815 (mtmt) REVERT: B 275 GLU cc_start: 0.7228 (pt0) cc_final: 0.6996 (pt0) REVERT: B 343 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8820 (ttmt) REVERT: B 447 ASP cc_start: 0.7538 (m-30) cc_final: 0.6986 (t0) REVERT: B 450 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8662 (tttp) REVERT: B 451 ASN cc_start: 0.7783 (m-40) cc_final: 0.7342 (m110) REVERT: B 455 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7473 (mtp85) REVERT: B 674 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7936 (t0) REVERT: C 432 ARG cc_start: 0.8456 (ttt90) cc_final: 0.8245 (ttt90) REVERT: D 286 GLU cc_start: 0.7886 (mp0) cc_final: 0.7534 (mp0) REVERT: D 372 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7241 (ttt90) REVERT: D 633 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8040 (mptt) REVERT: D 719 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7025 (mm-30) REVERT: E 272 LYS cc_start: 0.8429 (tttt) cc_final: 0.7981 (ttmt) REVERT: E 370 ASP cc_start: 0.8001 (t0) cc_final: 0.7651 (t0) REVERT: E 651 ASP cc_start: 0.7786 (p0) cc_final: 0.7476 (p0) REVERT: F 229 TRP cc_start: 0.7987 (t60) cc_final: 0.7293 (t60) REVERT: F 259 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.7022 (t80) REVERT: F 286 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7835 (mm-30) REVERT: F 326 GLU cc_start: 0.7658 (mp0) cc_final: 0.7338 (mp0) REVERT: F 340 ARG cc_start: 0.7368 (mmt180) cc_final: 0.6956 (mmm160) REVERT: F 631 GLU cc_start: 0.8039 (mp0) cc_final: 0.7810 (mp0) REVERT: F 639 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8573 (pm20) REVERT: F 659 HIS cc_start: 0.8849 (m-70) cc_final: 0.8050 (m90) REVERT: F 699 MET cc_start: 0.7451 (mmm) cc_final: 0.7213 (mmm) REVERT: F 711 ASN cc_start: 0.8188 (m-40) cc_final: 0.7929 (m110) REVERT: F 719 GLU cc_start: 0.7779 (tp30) cc_final: 0.7438 (tp30) REVERT: H 36 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: H 78 ASP cc_start: 0.8359 (m-30) cc_final: 0.8098 (m-30) REVERT: H 136 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7790 (tm-30) REVERT: H 181 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: I 26 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8108 (mm-30) REVERT: J 125 LEU cc_start: 0.7225 (tp) cc_final: 0.6879 (tp) REVERT: J 173 PHE cc_start: 0.8276 (m-80) cc_final: 0.8000 (m-80) REVERT: K 18 ASP cc_start: 0.8283 (p0) cc_final: 0.7907 (p0) REVERT: K 78 ASP cc_start: 0.8784 (m-30) cc_final: 0.8392 (m-30) REVERT: K 120 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6347 (tmm) REVERT: K 121 ILE cc_start: 0.7886 (tp) cc_final: 0.7627 (tp) REVERT: K 140 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7729 (ttm-80) REVERT: K 141 GLU cc_start: 0.7881 (tp30) cc_final: 0.7378 (tp30) REVERT: K 155 LEU cc_start: 0.8798 (tp) cc_final: 0.8578 (tt) REVERT: L 161 LEU cc_start: 0.8236 (mt) cc_final: 0.7867 (tp) REVERT: M 146 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8066 (ttmt) REVERT: N 8 GLU cc_start: 0.6995 (tt0) cc_final: 0.6766 (tt0) REVERT: N 22 ARG cc_start: 0.8421 (tpt90) cc_final: 0.7742 (tpt170) REVERT: N 136 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8235 (tm-30) REVERT: N 178 GLU cc_start: 0.8050 (mp0) cc_final: 0.7811 (mp0) outliers start: 92 outliers final: 83 residues processed: 1319 average time/residue: 1.1314 time to fit residues: 2332.5410 Evaluate side-chains 1357 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1268 time to evaluate : 4.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 666 ILE Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 485 HIS Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 556 HIS Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 174 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 283 optimal weight: 20.0000 chunk 456 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 216 optimal weight: 7.9990 chunk 317 optimal weight: 30.0000 chunk 479 optimal weight: 7.9990 chunk 441 optimal weight: 9.9990 chunk 381 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 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 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 579 GLN D 684 GLN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS I 81 GLN ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 38713 Z= 0.283 Angle : 0.656 59.194 52313 Z= 0.377 Chirality : 0.047 1.700 6001 Planarity : 0.005 0.180 6750 Dihedral : 9.544 171.949 5443 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.21 % Allowed : 16.75 % Favored : 81.04 % Cbeta Deviations : 0.02 % 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: 0.14 (0.12), residues: 4809 helix: 0.92 (0.10), residues: 2524 sheet: -1.25 (0.19), residues: 645 loop : -0.46 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 689 HIS 0.305 0.002 HIS F 485 PHE 0.024 0.001 PHE E 596 TYR 0.015 0.001 TYR I 128 ARG 0.011 0.000 ARG C 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9618 Ramachandran restraints generated. 4809 Oldfield, 0 Emsley, 4809 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 497 is missing expected H atoms. Skipping. Residue LYS 475 is missing expected H atoms. Skipping. Evaluate side-chains 1359 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1269 time to evaluate : 4.490 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: A 264 GLU cc_start: 0.8351 (mp0) cc_final: 0.8120 (pm20) REVERT: A 266 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8287 (mmm-85) REVERT: A 279 ASN cc_start: 0.8381 (p0) cc_final: 0.8109 (p0) REVERT: A 359 ASN cc_start: 0.8568 (m-40) cc_final: 0.8328 (m110) REVERT: A 468 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 472 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7691 (mt-10) REVERT: A 564 ASP cc_start: 0.9201 (OUTLIER) cc_final: 0.8294 (t0) REVERT: A 663 ASP cc_start: 0.8066 (m-30) cc_final: 0.7856 (m-30) REVERT: A 681 GLU cc_start: 0.7185 (mp0) cc_final: 0.6735 (mp0) REVERT: A 741 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7559 (mm-30) REVERT: B 207 LYS cc_start: 0.8364 (mmtm) cc_final: 0.7816 (mtmt) REVERT: B 343 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8822 (ttmt) REVERT: B 447 ASP cc_start: 0.7544 (m-30) cc_final: 0.6993 (t0) REVERT: B 450 LYS cc_start: 0.8874 (ttpt) cc_final: 0.8661 (tttp) REVERT: B 451 ASN cc_start: 0.7789 (m-40) cc_final: 0.7348 (m110) REVERT: B 455 ARG cc_start: 0.7769 (mtp85) cc_final: 0.7479 (mtp85) REVERT: B 674 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7939 (t0) REVERT: C 432 ARG cc_start: 0.8461 (ttt90) cc_final: 0.8246 (ttt90) REVERT: D 286 GLU cc_start: 0.7888 (mp0) cc_final: 0.7538 (mp0) REVERT: D 372 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7245 (ttt90) REVERT: D 633 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8045 (mptt) REVERT: D 719 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7028 (mm-30) REVERT: E 272 LYS cc_start: 0.8429 (tttt) cc_final: 0.7984 (ttmt) REVERT: E 370 ASP cc_start: 0.8005 (t0) cc_final: 0.7655 (t0) REVERT: E 651 ASP cc_start: 0.7794 (p0) cc_final: 0.7480 (p0) REVERT: F 229 TRP cc_start: 0.7991 (t60) cc_final: 0.7296 (t60) REVERT: F 259 TYR cc_start: 0.7594 (OUTLIER) cc_final: 0.7023 (t80) REVERT: F 286 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7861 (mm-30) REVERT: F 326 GLU cc_start: 0.7663 (mp0) cc_final: 0.7341 (mp0) REVERT: F 340 ARG cc_start: 0.7372 (mmt180) cc_final: 0.6962 (mmm160) REVERT: F 631 GLU cc_start: 0.8040 (mp0) cc_final: 0.7810 (mp0) REVERT: F 639 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8575 (pm20) REVERT: F 659 HIS cc_start: 0.8851 (m-70) cc_final: 0.8052 (m90) REVERT: F 699 MET cc_start: 0.7453 (mmm) cc_final: 0.7213 (mmm) REVERT: F 711 ASN cc_start: 0.8190 (m-40) cc_final: 0.7925 (m110) REVERT: F 719 GLU cc_start: 0.7835 (tp30) cc_final: 0.7440 (tp30) REVERT: H 36 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6892 (mp0) REVERT: H 78 ASP cc_start: 0.8352 (m-30) cc_final: 0.8104 (m-30) REVERT: H 136 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7793 (tm-30) REVERT: H 181 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7969 (pt0) REVERT: I 26 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8112 (mm-30) REVERT: J 125 LEU cc_start: 0.7226 (tp) cc_final: 0.6881 (tp) REVERT: J 173 PHE cc_start: 0.8264 (m-80) cc_final: 0.8002 (m-80) REVERT: K 18 ASP cc_start: 0.8288 (p0) cc_final: 0.7913 (p0) REVERT: K 78 ASP cc_start: 0.8788 (m-30) cc_final: 0.8392 (m-30) REVERT: K 120 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6353 (tmm) REVERT: K 121 ILE cc_start: 0.7892 (tp) cc_final: 0.7630 (tp) REVERT: K 140 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7729 (ttm-80) REVERT: K 141 GLU cc_start: 0.7885 (tp30) cc_final: 0.7381 (tp30) REVERT: K 155 LEU cc_start: 0.8799 (tp) cc_final: 0.8580 (tt) REVERT: L 161 LEU cc_start: 0.8237 (mt) cc_final: 0.7868 (tp) REVERT: M 146 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8068 (ttmt) REVERT: N 8 GLU cc_start: 0.7000 (tt0) cc_final: 0.6765 (tt0) REVERT: N 22 ARG cc_start: 0.8425 (tpt90) cc_final: 0.7744 (tpt170) REVERT: N 56 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7274 (mm-30) REVERT: N 136 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8238 (tm-30) REVERT: N 178 GLU cc_start: 0.8050 (mp0) cc_final: 0.7814 (mp0) outliers start: 90 outliers final: 83 residues processed: 1301 average time/residue: 1.1020 time to fit residues: 2234.4371 Evaluate side-chains 1356 residues out of total 4071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1267 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 622 GLN Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 710 ASP Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 605 THR Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 743 THR Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 332 GLU Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain F residue 194 GLU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 259 TYR Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 447 ASP Chi-restraints excluded: chain F residue 456 LEU Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 556 HIS Chi-restraints excluded: chain F residue 583 ASN Chi-restraints excluded: chain F residue 604 THR Chi-restraints excluded: chain F residue 621 HIS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 181 GLU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 123 GLN Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain L residue 18 ASP Chi-restraints excluded: chain L residue 41 ASN Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 79 THR Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 174 LEU Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 174 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 303 optimal weight: 7.9990 chunk 406 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 351 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 382 optimal weight: 8.9990 chunk 159 optimal weight: 8.9990 chunk 392 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 684 GLN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 558 HIS I 81 GLN ** L 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN ** N 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116876 restraints weight = 145806.217| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.47 r_work: 0.2896 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 38713 Z= 0.283 Angle : 0.656 59.194 52313 Z= 0.377 Chirality : 0.047 1.700 6001 Planarity : 0.005 0.180 6750 Dihedral : 9.544 171.949 5443 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.19 % Allowed : 16.78 % Favored : 81.04 % Cbeta Deviations : 0.02 % 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: 0.14 (0.12), residues: 4809 helix: 0.92 (0.10), residues: 2524 sheet: -1.25 (0.19), residues: 645 loop : -0.46 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 689 HIS 0.305 0.002 HIS F 485 PHE 0.024 0.001 PHE E 596 TYR 0.015 0.001 TYR I 128 ARG 0.011 0.000 ARG C 340 =============================================================================== Job complete usr+sys time: 31593.05 seconds wall clock time: 533 minutes 18.62 seconds (31998.62 seconds total)