Starting phenix.real_space_refine on Sat Feb 7 16:18:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rl6_24518/02_2026/7rl6_24518.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rl6_24518/02_2026/7rl6_24518.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rl6_24518/02_2026/7rl6_24518.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rl6_24518/02_2026/7rl6_24518.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rl6_24518/02_2026/7rl6_24518.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rl6_24518/02_2026/7rl6_24518.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 21858 2.51 5 N 6144 2.21 5 O 6648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34854 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "B" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "C" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "D" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "E" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "F" Number of atoms: 5755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 5755 Classifications: {'peptide': 735} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 694} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.73, per 1000 atoms: 0.22 Number of scatterers: 34854 At special positions: 0 Unit cell: (178.2, 173.138, 99.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 24 15.00 O 6648 8.00 N 6144 7.00 C 21858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8220 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 36 sheets defined 46.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.770A pdb=" N MET A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 92 removed outlier: 3.718A pdb=" N ASN A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.535A pdb=" N PHE A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 140' Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.688A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.779A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.618A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.631A pdb=" N GLU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.391A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.501A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 4.127A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.852A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.847A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 removed outlier: 4.018A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 403 removed outlier: 4.390A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 431 removed outlier: 3.617A pdb=" N ALA A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.934A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 443' Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.959A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 453 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 494 removed outlier: 3.657A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 492 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 507 removed outlier: 4.026A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 535 removed outlier: 4.086A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 548 through 554 removed outlier: 4.178A pdb=" N PHE A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 548 through 554' Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.352A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 removed outlier: 3.529A pdb=" N LYS A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 removed outlier: 3.805A pdb=" N LEU A 605 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET A 608 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.859A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.504A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 removed outlier: 3.688A pdb=" N LEU A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 699 " --> pdb=" O CYS A 695 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 700 " --> pdb=" O LYS A 696 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 701 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 removed outlier: 4.236A pdb=" N GLU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 733 through 738' Processing helix chain 'A' and resid 739 through 743 Processing helix chain 'A' and resid 748 through 764 removed outlier: 3.899A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 removed outlier: 3.770A pdb=" N MET B 46 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 92 removed outlier: 3.718A pdb=" N ASN B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.536A pdb=" N PHE B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 135 through 140' Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.687A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.779A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.619A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.630A pdb=" N GLU B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 4.391A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 296 removed outlier: 3.502A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 4.127A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.852A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.846A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 4.018A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 384 " --> pdb=" O ILE B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 403 removed outlier: 4.389A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 431 removed outlier: 3.618A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU B 429 " --> pdb=" O LYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.934A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 438 through 443' Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.959A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 453 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 494 removed outlier: 3.657A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN B 494 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 507 removed outlier: 4.026A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 535 removed outlier: 4.086A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 548 Processing helix chain 'B' and resid 548 through 554 removed outlier: 4.179A pdb=" N PHE B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 553 " --> pdb=" O THR B 549 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 554 " --> pdb=" O MET B 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 548 through 554' Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.350A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE B 562 " --> pdb=" O ASN B 558 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE B 563 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 587 removed outlier: 3.530A pdb=" N LYS B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 610 removed outlier: 3.805A pdb=" N LEU B 605 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.859A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.504A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 removed outlier: 3.688A pdb=" N LEU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 699 " --> pdb=" O CYS B 695 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 701 " --> pdb=" O LEU B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 738 removed outlier: 4.236A pdb=" N GLU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 733 through 738' Processing helix chain 'B' and resid 739 through 743 Processing helix chain 'B' and resid 748 through 764 removed outlier: 3.899A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 49 removed outlier: 3.770A pdb=" N MET C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 removed outlier: 3.719A pdb=" N ASN C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 removed outlier: 3.535A pdb=" N PHE C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 140' Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.688A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 226 removed outlier: 3.778A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.618A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.630A pdb=" N GLU C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 removed outlier: 4.391A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 296 removed outlier: 3.501A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 4.127A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.852A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.847A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 removed outlier: 4.018A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 403 removed outlier: 4.390A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 431 removed outlier: 3.617A pdb=" N ALA C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.934A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.960A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 453 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 494 removed outlier: 3.657A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN C 494 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 507 removed outlier: 4.027A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 535 removed outlier: 4.087A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 548 Processing helix chain 'C' and resid 548 through 554 removed outlier: 4.179A pdb=" N PHE C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY C 553 " --> pdb=" O THR C 549 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU C 554 " --> pdb=" O MET C 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 548 through 554' Processing helix chain 'C' and resid 557 through 569 removed outlier: 4.351A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 562 " --> pdb=" O ASN C 558 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE C 563 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP C 564 " --> pdb=" O ARG C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 587 removed outlier: 3.529A pdb=" N LYS C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 610 removed outlier: 3.805A pdb=" N LEU C 605 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET C 608 " --> pdb=" O ILE C 604 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.860A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 678 removed outlier: 3.504A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 705 removed outlier: 3.688A pdb=" N LEU C 687 " --> pdb=" O SER C 683 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 699 " --> pdb=" O CYS C 695 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 700 " --> pdb=" O LYS C 696 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 701 " --> pdb=" O LEU C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 738 removed outlier: 4.236A pdb=" N GLU C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 733 through 738' Processing helix chain 'C' and resid 739 through 743 Processing helix chain 'C' and resid 748 through 764 removed outlier: 3.899A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.770A pdb=" N MET D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 removed outlier: 3.717A pdb=" N ASN D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.535A pdb=" N PHE D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 140 " --> pdb=" O LYS D 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 140' Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.688A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 226 removed outlier: 3.779A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.618A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.629A pdb=" N GLU D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 removed outlier: 4.391A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.502A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 4.127A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.852A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.846A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 386 removed outlier: 4.018A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 403 removed outlier: 4.389A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 431 removed outlier: 3.618A pdb=" N ALA D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 443 removed outlier: 3.933A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 438 through 443' Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.960A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D 453 " --> pdb=" O MET D 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 494 removed outlier: 3.657A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 493 " --> pdb=" O LEU D 489 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN D 494 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.027A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 535 removed outlier: 4.087A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 548 Processing helix chain 'D' and resid 548 through 554 removed outlier: 4.178A pdb=" N PHE D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY D 553 " --> pdb=" O THR D 549 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 554 " --> pdb=" O MET D 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 548 through 554' Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.351A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE D 562 " --> pdb=" O ASN D 558 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE D 563 " --> pdb=" O VAL D 559 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP D 564 " --> pdb=" O ARG D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 587 removed outlier: 3.529A pdb=" N LYS D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA D 585 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 610 removed outlier: 3.803A pdb=" N LEU D 605 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D 606 " --> pdb=" O ASN D 602 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET D 608 " --> pdb=" O ILE D 604 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.860A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 removed outlier: 3.504A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 removed outlier: 3.688A pdb=" N LEU D 687 " --> pdb=" O SER D 683 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 699 " --> pdb=" O CYS D 695 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG D 700 " --> pdb=" O LYS D 696 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 701 " --> pdb=" O LEU D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 738 removed outlier: 4.236A pdb=" N GLU D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU D 738 " --> pdb=" O ASP D 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 733 through 738' Processing helix chain 'D' and resid 739 through 743 Processing helix chain 'D' and resid 748 through 764 removed outlier: 3.899A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 removed outlier: 3.771A pdb=" N MET E 46 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 49 " --> pdb=" O LYS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 92 removed outlier: 3.718A pdb=" N ASN E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.535A pdb=" N PHE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 135 through 140' Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.687A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 226 removed outlier: 3.778A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU E 221 " --> pdb=" O LYS E 217 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.619A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.629A pdb=" N GLU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 removed outlier: 4.391A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.501A pdb=" N ALA E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 4.127A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.853A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.847A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 386 removed outlier: 4.018A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS E 384 " --> pdb=" O ILE E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 403 removed outlier: 4.390A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU E 402 " --> pdb=" O GLN E 398 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 431 removed outlier: 3.617A pdb=" N ALA E 412 " --> pdb=" O GLY E 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.934A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 438 through 443' Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.959A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG E 453 " --> pdb=" O MET E 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 494 removed outlier: 3.657A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL E 493 " --> pdb=" O LEU E 489 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN E 494 " --> pdb=" O GLN E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 507 removed outlier: 4.027A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 535 removed outlier: 4.087A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E 534 " --> pdb=" O ALA E 530 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 548 Processing helix chain 'E' and resid 548 through 554 removed outlier: 4.178A pdb=" N PHE E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY E 553 " --> pdb=" O THR E 549 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU E 554 " --> pdb=" O MET E 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 548 through 554' Processing helix chain 'E' and resid 557 through 569 removed outlier: 4.350A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE E 562 " --> pdb=" O ASN E 558 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE E 563 " --> pdb=" O VAL E 559 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 587 removed outlier: 3.529A pdb=" N LYS E 584 " --> pdb=" O ASP E 580 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 585 " --> pdb=" O SER E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 610 removed outlier: 3.804A pdb=" N LEU E 605 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR E 606 " --> pdb=" O ASN E 602 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 607 " --> pdb=" O GLN E 603 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET E 608 " --> pdb=" O ILE E 604 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY E 610 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.859A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 removed outlier: 3.504A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 705 removed outlier: 3.688A pdb=" N LEU E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE E 699 " --> pdb=" O CYS E 695 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG E 700 " --> pdb=" O LYS E 696 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 701 " --> pdb=" O LEU E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 738 removed outlier: 4.236A pdb=" N GLU E 737 " --> pdb=" O ARG E 733 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU E 738 " --> pdb=" O ASP E 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 733 through 738' Processing helix chain 'E' and resid 739 through 743 Processing helix chain 'E' and resid 748 through 764 removed outlier: 3.899A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 3.770A pdb=" N MET F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU F 49 " --> pdb=" O LYS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 92 removed outlier: 3.718A pdb=" N ASN F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.535A pdb=" N PHE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU F 140 " --> pdb=" O LYS F 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 135 through 140' Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.688A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 226 removed outlier: 3.779A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.618A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.630A pdb=" N GLU F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 277 removed outlier: 4.391A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 296 removed outlier: 3.502A pdb=" N ALA F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 4.127A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.852A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.846A pdb=" N ARG F 359 " --> pdb=" O ALA F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 removed outlier: 4.017A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS F 384 " --> pdb=" O ILE F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 removed outlier: 4.390A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR F 403 " --> pdb=" O VAL F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 431 removed outlier: 3.617A pdb=" N ALA F 412 " --> pdb=" O GLY F 408 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.934A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 438 through 443' Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.959A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG F 453 " --> pdb=" O MET F 449 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 494 removed outlier: 3.657A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN F 494 " --> pdb=" O GLN F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 499 through 507 removed outlier: 4.027A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 535 removed outlier: 4.087A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN F 533 " --> pdb=" O LYS F 529 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU F 534 " --> pdb=" O ALA F 530 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS F 535 " --> pdb=" O ILE F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 548 Processing helix chain 'F' and resid 548 through 554 removed outlier: 4.177A pdb=" N PHE F 552 " --> pdb=" O LEU F 548 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU F 554 " --> pdb=" O MET F 550 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 548 through 554' Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.351A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE F 562 " --> pdb=" O ASN F 558 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE F 563 " --> pdb=" O VAL F 559 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP F 564 " --> pdb=" O ARG F 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 587 removed outlier: 3.529A pdb=" N LYS F 584 " --> pdb=" O ASP F 580 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA F 585 " --> pdb=" O SER F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 610 removed outlier: 3.805A pdb=" N LEU F 605 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR F 606 " --> pdb=" O ASN F 602 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU F 607 " --> pdb=" O GLN F 603 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET F 608 " --> pdb=" O ILE F 604 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.860A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.504A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 705 removed outlier: 3.687A pdb=" N LEU F 687 " --> pdb=" O SER F 683 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE F 699 " --> pdb=" O CYS F 695 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG F 700 " --> pdb=" O LYS F 696 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU F 701 " --> pdb=" O LEU F 697 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 738 removed outlier: 4.235A pdb=" N GLU F 737 " --> pdb=" O ARG F 733 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU F 738 " --> pdb=" O ASP F 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 733 through 738' Processing helix chain 'F' and resid 739 through 743 Processing helix chain 'F' and resid 748 through 764 removed outlier: 3.900A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS F 754 " --> pdb=" O ASN F 750 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 8.106A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET A 84 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP A 29 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 116 removed outlier: 3.547A pdb=" N ILE A 114 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS A 183 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 116 " --> pdb=" O HIS A 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 161 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.293A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 468 through 470 removed outlier: 4.694A pdb=" N VAL A 468 " --> pdb=" O SER A 541 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 572 through 576 removed outlier: 4.273A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 25 through 30 removed outlier: 8.106A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 113 through 116 removed outlier: 3.547A pdb=" N ILE B 114 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS B 183 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B 116 " --> pdb=" O HIS B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 161 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 265 through 269 removed outlier: 6.294A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 468 through 470 removed outlier: 4.694A pdb=" N VAL B 468 " --> pdb=" O SER B 541 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 572 through 576 removed outlier: 4.273A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 30 removed outlier: 8.106A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.548A pdb=" N ILE C 114 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS C 183 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL C 116 " --> pdb=" O HIS C 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE C 152 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 265 through 269 removed outlier: 6.293A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 468 through 470 removed outlier: 4.693A pdb=" N VAL C 468 " --> pdb=" O SER C 541 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 572 through 576 removed outlier: 4.272A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 25 through 30 removed outlier: 8.107A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 113 through 116 removed outlier: 3.548A pdb=" N ILE D 114 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS D 183 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL D 116 " --> pdb=" O HIS D 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 161 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 265 through 269 removed outlier: 6.294A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 468 through 470 removed outlier: 4.693A pdb=" N VAL D 468 " --> pdb=" O SER D 541 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 572 through 576 removed outlier: 4.272A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 25 through 30 removed outlier: 8.107A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 113 through 116 removed outlier: 3.548A pdb=" N ILE E 114 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS E 183 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 116 " --> pdb=" O HIS E 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE E 152 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 161 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 265 through 269 removed outlier: 6.294A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 468 through 470 removed outlier: 4.693A pdb=" N VAL E 468 " --> pdb=" O SER E 541 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 572 through 576 removed outlier: 4.272A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 25 through 30 removed outlier: 8.106A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 113 through 116 removed outlier: 3.548A pdb=" N ILE F 114 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS F 183 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL F 116 " --> pdb=" O HIS F 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 152 through 155 removed outlier: 3.921A pdb=" N PHE F 152 " --> pdb=" O PHE F 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F 161 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 265 through 269 removed outlier: 6.294A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 468 through 470 removed outlier: 4.694A pdb=" N VAL F 468 " --> pdb=" O SER F 541 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 572 through 576 removed outlier: 4.273A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) 1026 hydrogen bonds defined for protein. 2898 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: 7.97 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11897 1.34 - 1.46: 5904 1.46 - 1.58: 17335 1.58 - 1.69: 36 1.69 - 1.81: 288 Bond restraints: 35460 Sorted by residual: bond pdb=" C4 ADP D1001 " pdb=" C5 ADP D1001 " ideal model delta sigma weight residual 1.490 1.453 0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C4 ADP A1001 " pdb=" C5 ADP A1001 " ideal model delta sigma weight residual 1.490 1.454 0.036 2.00e-02 2.50e+03 3.21e+00 bond pdb=" C4 ADP F1001 " pdb=" C5 ADP F1001 " ideal model delta sigma weight residual 1.490 1.454 0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" C4 ADP C1001 " pdb=" C5 ADP C1001 " ideal model delta sigma weight residual 1.490 1.455 0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C4 ADP B1001 " pdb=" C5 ADP B1001 " ideal model delta sigma weight residual 1.490 1.456 0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 35455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 46104 1.57 - 3.14: 1429 3.14 - 4.71: 268 4.71 - 6.28: 111 6.28 - 7.84: 40 Bond angle restraints: 47952 Sorted by residual: angle pdb=" C SER B 171 " pdb=" N PRO B 172 " pdb=" CD PRO B 172 " ideal model delta sigma weight residual 120.60 112.76 7.84 2.20e+00 2.07e-01 1.27e+01 angle pdb=" C SER F 171 " pdb=" N PRO F 172 " pdb=" CD PRO F 172 " ideal model delta sigma weight residual 120.60 112.79 7.81 2.20e+00 2.07e-01 1.26e+01 angle pdb=" C SER E 171 " pdb=" N PRO E 172 " pdb=" CD PRO E 172 " ideal model delta sigma weight residual 120.60 112.82 7.78 2.20e+00 2.07e-01 1.25e+01 angle pdb=" C SER C 171 " pdb=" N PRO C 172 " pdb=" CD PRO C 172 " ideal model delta sigma weight residual 120.60 112.82 7.78 2.20e+00 2.07e-01 1.25e+01 angle pdb=" C SER D 171 " pdb=" N PRO D 172 " pdb=" CD PRO D 172 " ideal model delta sigma weight residual 120.60 112.83 7.77 2.20e+00 2.07e-01 1.25e+01 ... (remaining 47947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.54: 21148 32.54 - 65.09: 687 65.09 - 97.63: 55 97.63 - 130.17: 10 130.17 - 162.72: 6 Dihedral angle restraints: 21906 sinusoidal: 9222 harmonic: 12684 Sorted by residual: dihedral pdb=" O1B ADP C1002 " pdb=" O3A ADP C1002 " pdb=" PB ADP C1002 " pdb=" PA ADP C1002 " ideal model delta sinusoidal sigma weight residual 300.00 137.28 162.72 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O1B ADP E1002 " pdb=" O3A ADP E1002 " pdb=" PB ADP E1002 " pdb=" PA ADP E1002 " ideal model delta sinusoidal sigma weight residual 300.00 141.55 158.45 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" O2A ADP D1002 " pdb=" O3A ADP D1002 " pdb=" PA ADP D1002 " pdb=" PB ADP D1002 " ideal model delta sinusoidal sigma weight residual -60.00 96.86 -156.86 1 2.00e+01 2.50e-03 4.61e+01 ... (remaining 21903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2724 0.027 - 0.054: 1698 0.054 - 0.082: 460 0.082 - 0.109: 356 0.109 - 0.136: 138 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CA MET F 332 " pdb=" N MET F 332 " pdb=" C MET F 332 " pdb=" CB MET F 332 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA MET D 332 " pdb=" N MET D 332 " pdb=" C MET D 332 " pdb=" CB MET D 332 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA MET A 332 " pdb=" N MET A 332 " pdb=" C MET A 332 " pdb=" CB MET A 332 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 5373 not shown) Planarity restraints: 6300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 271 " -0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 272 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 271 " -0.060 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO A 272 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 271 " -0.060 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO E 272 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO E 272 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 272 " -0.050 5.00e-02 4.00e+02 ... (remaining 6297 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 284 2.53 - 3.12: 25360 3.12 - 3.72: 54449 3.72 - 4.31: 71731 4.31 - 4.90: 117213 Nonbonded interactions: 269037 Sorted by model distance: nonbonded pdb=" N LYS A 524 " pdb=" O2B ADP A1002 " model vdw 1.941 2.496 nonbonded pdb=" N LYS E 524 " pdb=" O2B ADP E1002 " model vdw 1.967 2.496 nonbonded pdb=" N LYS B 524 " pdb=" O2B ADP B1002 " model vdw 1.969 2.496 nonbonded pdb=" CB LYS C 524 " pdb=" O2B ADP C1002 " model vdw 2.010 2.752 nonbonded pdb=" CG LYS C 524 " pdb=" O2B ADP C1002 " model vdw 2.064 3.440 ... (remaining 269032 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.090 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 : 0.012 0.753 35473 Z= 1.215 Angle : 0.724 7.844 47952 Z= 0.385 Chirality : 0.044 0.136 5376 Planarity : 0.004 0.091 6300 Dihedral : 15.387 162.719 13686 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.88 % Favored : 94.85 % Rotamer: Outliers : 0.32 % Allowed : 0.64 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.13), residues: 4386 helix: -1.44 (0.13), residues: 1416 sheet: 0.01 (0.23), residues: 546 loop : -1.32 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 465 TYR 0.021 0.001 TYR A 173 PHE 0.017 0.001 PHE E 452 TRP 0.007 0.001 TRP F 454 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00274 (35460) covalent geometry : angle 0.72360 (47952) hydrogen bonds : bond 0.26370 ( 1026) hydrogen bonds : angle 7.03055 ( 2898) Misc. bond : bond 0.63028 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 1.297 Fit side-chains REVERT: A 46 MET cc_start: 0.7150 (tpp) cc_final: 0.6947 (tpp) REVERT: B 46 MET cc_start: 0.7245 (tpp) cc_final: 0.7023 (tpp) REVERT: B 275 MET cc_start: 0.8423 (mpp) cc_final: 0.8105 (mpp) REVERT: B 601 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6899 (mm) REVERT: C 46 MET cc_start: 0.6990 (tpp) cc_final: 0.6772 (tpp) REVERT: C 275 MET cc_start: 0.8365 (mpp) cc_final: 0.8120 (mpp) REVERT: D 46 MET cc_start: 0.6908 (tpp) cc_final: 0.6693 (tpp) REVERT: D 198 LEU cc_start: 0.9335 (tt) cc_final: 0.8821 (tt) REVERT: E 46 MET cc_start: 0.7308 (tpp) cc_final: 0.7088 (tpp) REVERT: E 601 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6763 (mm) REVERT: E 757 MET cc_start: 0.9084 (ptt) cc_final: 0.8827 (ppp) REVERT: F 46 MET cc_start: 0.7089 (tpp) cc_final: 0.6884 (tpp) REVERT: F 601 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6762 (mm) REVERT: F 678 MET cc_start: 0.8645 (ppp) cc_final: 0.8418 (ppp) outliers start: 12 outliers final: 2 residues processed: 200 average time/residue: 0.1946 time to fit residues: 67.2543 Evaluate side-chains 157 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain E residue 601 ILE Chi-restraints excluded: chain F residue 601 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.0060 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 9.9990 overall best weight: 1.1838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 351 ASN A 533 ASN B 36 ASN B 351 ASN B 533 ASN C 36 ASN C 351 ASN C 533 ASN D 36 ASN D 351 ASN D 533 ASN E 36 ASN E 351 ASN E 533 ASN F 36 ASN F 351 ASN F 533 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.096711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.070696 restraints weight = 147112.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.072264 restraints weight = 87855.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.073056 restraints weight = 66183.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.073476 restraints weight = 57459.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.073816 restraints weight = 53621.865| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35473 Z= 0.124 Angle : 0.640 7.213 47952 Z= 0.301 Chirality : 0.045 0.184 5376 Planarity : 0.004 0.088 6300 Dihedral : 8.916 150.046 4924 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.13 % Favored : 95.60 % Rotamer: Outliers : 0.29 % Allowed : 6.05 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.13), residues: 4386 helix: -1.01 (0.13), residues: 1500 sheet: -0.31 (0.22), residues: 600 loop : -1.09 (0.14), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 86 TYR 0.018 0.001 TYR A 173 PHE 0.008 0.001 PHE E 452 TRP 0.006 0.001 TRP C 476 HIS 0.003 0.001 HIS B 340 Details of bonding type rmsd covalent geometry : bond 0.00272 (35460) covalent geometry : angle 0.63972 (47952) hydrogen bonds : bond 0.04632 ( 1026) hydrogen bonds : angle 5.30116 ( 2898) Misc. bond : bond 0.00273 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 1.395 Fit side-chains REVERT: A 275 MET cc_start: 0.8203 (mpp) cc_final: 0.7916 (mpp) REVERT: A 427 MET cc_start: 0.7295 (tpt) cc_final: 0.7067 (tpt) REVERT: B 427 MET cc_start: 0.7260 (tpt) cc_final: 0.7021 (tpt) REVERT: B 508 MET cc_start: -0.1079 (mtt) cc_final: -0.1295 (mtt) REVERT: C 442 MET cc_start: 0.9074 (mmm) cc_final: 0.8861 (mmm) outliers start: 11 outliers final: 6 residues processed: 157 average time/residue: 0.1941 time to fit residues: 53.8319 Evaluate side-chains 150 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 332 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 385 optimal weight: 7.9990 chunk 269 optimal weight: 9.9990 chunk 330 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 236 optimal weight: 40.0000 chunk 175 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 358 optimal weight: 20.0000 chunk 229 optimal weight: 40.0000 chunk 378 optimal weight: 50.0000 chunk 312 optimal weight: 6.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 215 GLN C 215 GLN D 215 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 215 GLN ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN F 215 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.086212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056734 restraints weight = 134480.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.057836 restraints weight = 85583.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058569 restraints weight = 65660.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.058862 restraints weight = 56187.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.058871 restraints weight = 53065.648| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.103 35473 Z= 0.380 Angle : 0.921 14.843 47952 Z= 0.449 Chirality : 0.052 0.314 5376 Planarity : 0.006 0.100 6300 Dihedral : 9.216 151.930 4914 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.42 % Favored : 95.03 % Rotamer: Outliers : 1.87 % Allowed : 8.85 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.12), residues: 4386 helix: -1.24 (0.12), residues: 1620 sheet: -0.44 (0.20), residues: 648 loop : -1.28 (0.14), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 465 TYR 0.021 0.002 TYR A 203 PHE 0.037 0.004 PHE B 516 TRP 0.012 0.002 TRP B 551 HIS 0.007 0.002 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00856 (35460) covalent geometry : angle 0.92063 (47952) hydrogen bonds : bond 0.04499 ( 1026) hydrogen bonds : angle 5.28190 ( 2898) Misc. bond : bond 0.00334 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 149 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7652 (tpp) cc_final: 0.7411 (tpt) REVERT: A 163 PHE cc_start: 0.6816 (t80) cc_final: 0.6435 (t80) REVERT: A 611 MET cc_start: 0.7583 (ppp) cc_final: 0.7074 (ppp) REVERT: A 678 MET cc_start: 0.8926 (ppp) cc_final: 0.8669 (ppp) REVERT: B 46 MET cc_start: 0.7807 (tpp) cc_final: 0.7560 (tpt) REVERT: B 608 MET cc_start: 0.9360 (ptt) cc_final: 0.8986 (ptp) REVERT: B 678 MET cc_start: 0.8943 (ppp) cc_final: 0.8724 (ppp) REVERT: C 46 MET cc_start: 0.7576 (tpp) cc_final: 0.7349 (tpt) REVERT: C 163 PHE cc_start: 0.7014 (t80) cc_final: 0.6582 (t80) REVERT: C 403 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.8066 (t) REVERT: C 442 MET cc_start: 0.9173 (mmm) cc_final: 0.8969 (mmm) REVERT: D 46 MET cc_start: 0.7719 (tpp) cc_final: 0.7423 (tpt) REVERT: D 84 MET cc_start: 0.7791 (tmm) cc_final: 0.7511 (tmm) REVERT: D 163 PHE cc_start: 0.6950 (t80) cc_final: 0.6569 (t80) REVERT: D 427 MET cc_start: 0.8055 (tpt) cc_final: 0.7797 (tpt) REVERT: D 678 MET cc_start: 0.8814 (ppp) cc_final: 0.8613 (ppp) REVERT: E 46 MET cc_start: 0.7934 (tpp) cc_final: 0.7690 (tpt) REVERT: E 608 MET cc_start: 0.9393 (ptp) cc_final: 0.8965 (ptp) REVERT: F 403 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7567 (t) outliers start: 70 outliers final: 43 residues processed: 202 average time/residue: 0.1793 time to fit residues: 64.7312 Evaluate side-chains 181 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 136 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 173 TYR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 573 VAL Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 617 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 388 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 228 optimal weight: 30.0000 chunk 62 optimal weight: 5.9990 chunk 420 optimal weight: 5.9990 chunk 219 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 263 optimal weight: 0.8980 chunk 121 optimal weight: 0.0970 chunk 88 optimal weight: 0.0970 chunk 304 optimal weight: 0.1980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 382 GLN F 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.089119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.060628 restraints weight = 137296.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.061918 restraints weight = 82700.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.062669 restraints weight = 62306.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.062904 restraints weight = 54337.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.063157 restraints weight = 51401.577| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 35473 Z= 0.112 Angle : 0.634 8.059 47952 Z= 0.296 Chirality : 0.045 0.161 5376 Planarity : 0.004 0.090 6300 Dihedral : 8.561 142.691 4914 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.22 % Favored : 95.44 % Rotamer: Outliers : 1.12 % Allowed : 12.40 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 4386 helix: -0.67 (0.13), residues: 1614 sheet: -0.53 (0.20), residues: 642 loop : -1.02 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 358 TYR 0.012 0.001 TYR A 173 PHE 0.021 0.001 PHE B 516 TRP 0.009 0.001 TRP B 551 HIS 0.002 0.001 HIS F 155 Details of bonding type rmsd covalent geometry : bond 0.00247 (35460) covalent geometry : angle 0.63399 (47952) hydrogen bonds : bond 0.03033 ( 1026) hydrogen bonds : angle 4.68115 ( 2898) Misc. bond : bond 0.00198 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 1.202 Fit side-chains REVERT: A 46 MET cc_start: 0.7426 (tpp) cc_final: 0.7129 (tpp) REVERT: B 46 MET cc_start: 0.7655 (tpp) cc_final: 0.7382 (tpp) REVERT: B 605 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9003 (pp) REVERT: B 608 MET cc_start: 0.9313 (ptt) cc_final: 0.8877 (ptp) REVERT: C 46 MET cc_start: 0.7460 (tpp) cc_final: 0.7198 (tpp) REVERT: C 117 LEU cc_start: 0.8578 (tp) cc_final: 0.8372 (tt) REVERT: C 163 PHE cc_start: 0.7038 (t80) cc_final: 0.6587 (t80) REVERT: C 442 MET cc_start: 0.9114 (mmm) cc_final: 0.8906 (mmm) REVERT: C 605 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9056 (pp) REVERT: D 46 MET cc_start: 0.7359 (tpp) cc_final: 0.7032 (tpp) REVERT: D 84 MET cc_start: 0.7932 (tmm) cc_final: 0.7504 (tmm) REVERT: E 84 MET cc_start: 0.7511 (ttt) cc_final: 0.6848 (tmm) REVERT: E 605 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9018 (pp) REVERT: E 608 MET cc_start: 0.9327 (ptp) cc_final: 0.8893 (ptp) REVERT: F 46 MET cc_start: 0.7735 (tpt) cc_final: 0.7535 (tpp) REVERT: F 84 MET cc_start: 0.7657 (ttt) cc_final: 0.7194 (tmm) REVERT: F 382 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8723 (pm20) outliers start: 42 outliers final: 16 residues processed: 169 average time/residue: 0.1743 time to fit residues: 51.8805 Evaluate side-chains 151 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 382 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 70 optimal weight: 8.9990 chunk 83 optimal weight: 30.0000 chunk 86 optimal weight: 4.9990 chunk 117 optimal weight: 0.3980 chunk 414 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 419 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 296 optimal weight: 50.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 270 ASN F 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.087773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.060002 restraints weight = 138604.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.060786 restraints weight = 84581.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.061269 restraints weight = 63441.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.061315 restraints weight = 57748.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.061335 restraints weight = 56023.011| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35473 Z= 0.154 Angle : 0.637 9.355 47952 Z= 0.295 Chirality : 0.045 0.166 5376 Planarity : 0.004 0.093 6300 Dihedral : 8.200 139.913 4914 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.20 % Favored : 95.53 % Rotamer: Outliers : 1.81 % Allowed : 13.73 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4386 helix: -0.35 (0.13), residues: 1620 sheet: -0.51 (0.20), residues: 660 loop : -0.85 (0.15), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 377 TYR 0.008 0.001 TYR A 173 PHE 0.021 0.002 PHE B 516 TRP 0.006 0.001 TRP F 551 HIS 0.003 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00360 (35460) covalent geometry : angle 0.63727 (47952) hydrogen bonds : bond 0.02929 ( 1026) hydrogen bonds : angle 4.36637 ( 2898) Misc. bond : bond 0.00133 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 140 time to evaluate : 1.368 Fit side-chains REVERT: A 46 MET cc_start: 0.7211 (tpp) cc_final: 0.6999 (tpt) REVERT: A 382 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8828 (mp10) REVERT: A 608 MET cc_start: 0.9186 (ptp) cc_final: 0.8825 (ptp) REVERT: B 605 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8696 (pp) REVERT: B 608 MET cc_start: 0.9352 (ptp) cc_final: 0.8986 (ptp) REVERT: C 117 LEU cc_start: 0.8555 (tp) cc_final: 0.8342 (tt) REVERT: C 163 PHE cc_start: 0.7201 (t80) cc_final: 0.6745 (t80) REVERT: C 403 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7973 (t) REVERT: C 442 MET cc_start: 0.9256 (mmm) cc_final: 0.9010 (mmm) REVERT: C 605 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9123 (pp) REVERT: D 46 MET cc_start: 0.7354 (tpp) cc_final: 0.7108 (tpt) REVERT: D 84 MET cc_start: 0.7924 (tmm) cc_final: 0.7405 (tmm) REVERT: D 608 MET cc_start: 0.9218 (ptp) cc_final: 0.8936 (ptp) REVERT: E 46 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7324 (tpt) REVERT: E 605 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8675 (pp) REVERT: E 608 MET cc_start: 0.9370 (ptp) cc_final: 0.8977 (ptp) REVERT: F 46 MET cc_start: 0.7547 (tpt) cc_final: 0.7323 (tpp) REVERT: F 403 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7449 (t) outliers start: 68 outliers final: 29 residues processed: 186 average time/residue: 0.1764 time to fit residues: 58.3246 Evaluate side-chains 167 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 403 THR Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 611 MET Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 403 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 358 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 398 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 307 optimal weight: 50.0000 chunk 192 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 276 optimal weight: 40.0000 chunk 368 optimal weight: 50.0000 chunk 214 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS B 36 ASN B 382 GLN C 340 HIS D 340 HIS E 36 ASN F 36 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.085753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055997 restraints weight = 126328.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.057037 restraints weight = 81710.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.057510 restraints weight = 63646.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.058112 restraints weight = 57432.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057973 restraints weight = 51756.417| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 35473 Z= 0.284 Angle : 0.759 12.039 47952 Z= 0.362 Chirality : 0.048 0.208 5376 Planarity : 0.005 0.094 6300 Dihedral : 8.287 140.003 4914 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.49 % Favored : 95.10 % Rotamer: Outliers : 2.56 % Allowed : 14.08 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 4386 helix: -0.39 (0.13), residues: 1656 sheet: -0.33 (0.20), residues: 636 loop : -0.87 (0.15), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 560 TYR 0.013 0.002 TYR D 495 PHE 0.030 0.003 PHE E 516 TRP 0.009 0.002 TRP B 551 HIS 0.006 0.001 HIS E 406 Details of bonding type rmsd covalent geometry : bond 0.00640 (35460) covalent geometry : angle 0.75925 (47952) hydrogen bonds : bond 0.03521 ( 1026) hydrogen bonds : angle 4.59702 ( 2898) Misc. bond : bond 0.00129 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 141 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.6923 (t80) cc_final: 0.6661 (m-80) REVERT: A 508 MET cc_start: 0.0663 (mtt) cc_final: 0.0453 (mtt) REVERT: B 605 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9274 (pp) REVERT: B 608 MET cc_start: 0.9380 (ptp) cc_final: 0.9075 (ptp) REVERT: C 84 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6700 (tmm) REVERT: C 117 LEU cc_start: 0.8532 (tp) cc_final: 0.8281 (tt) REVERT: C 163 PHE cc_start: 0.6990 (t80) cc_final: 0.6533 (t80) REVERT: C 442 MET cc_start: 0.9220 (mmm) cc_final: 0.8975 (mmm) REVERT: C 605 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9215 (pp) REVERT: C 678 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8111 (mtm) REVERT: D 117 LEU cc_start: 0.8575 (tp) cc_final: 0.8231 (tt) REVERT: D 163 PHE cc_start: 0.6941 (t80) cc_final: 0.6306 (t80) REVERT: D 678 MET cc_start: 0.8757 (ptp) cc_final: 0.8159 (mtm) REVERT: E 608 MET cc_start: 0.9412 (ptp) cc_final: 0.9048 (ptp) REVERT: F 46 MET cc_start: 0.7777 (tpt) cc_final: 0.7568 (tpp) REVERT: F 403 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8292 (t) outliers start: 96 outliers final: 61 residues processed: 210 average time/residue: 0.1761 time to fit residues: 65.0951 Evaluate side-chains 200 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 134 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 678 MET Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 617 VAL Chi-restraints excluded: chain F residue 628 ILE Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 160 optimal weight: 40.0000 chunk 286 optimal weight: 20.0000 chunk 77 optimal weight: 40.0000 chunk 380 optimal weight: 50.0000 chunk 217 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 304 optimal weight: 20.0000 chunk 246 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN E 340 HIS F 340 HIS F 384 HIS ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.085075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.057146 restraints weight = 128002.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.057323 restraints weight = 81831.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.057383 restraints weight = 65786.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057509 restraints weight = 63912.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.057530 restraints weight = 61054.040| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 35473 Z= 0.296 Angle : 0.755 13.949 47952 Z= 0.359 Chirality : 0.048 0.178 5376 Planarity : 0.005 0.092 6300 Dihedral : 8.223 136.896 4914 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.58 % Favored : 95.03 % Rotamer: Outliers : 2.69 % Allowed : 15.09 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 4386 helix: -0.37 (0.13), residues: 1662 sheet: -0.54 (0.20), residues: 666 loop : -0.81 (0.15), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 625 TYR 0.013 0.002 TYR D 495 PHE 0.030 0.002 PHE A 516 TRP 0.011 0.002 TRP F 551 HIS 0.007 0.001 HIS C 406 Details of bonding type rmsd covalent geometry : bond 0.00670 (35460) covalent geometry : angle 0.75470 (47952) hydrogen bonds : bond 0.03501 ( 1026) hydrogen bonds : angle 4.64963 ( 2898) Misc. bond : bond 0.00146 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 141 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 163 PHE cc_start: 0.6934 (t80) cc_final: 0.6661 (t80) REVERT: A 382 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8886 (mp10) REVERT: A 508 MET cc_start: 0.0653 (mtt) cc_final: 0.0388 (mtt) REVERT: B 608 MET cc_start: 0.9394 (ptp) cc_final: 0.9134 (ptp) REVERT: C 84 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6974 (tmm) REVERT: C 117 LEU cc_start: 0.8593 (tp) cc_final: 0.8314 (tt) REVERT: C 163 PHE cc_start: 0.7109 (t80) cc_final: 0.6651 (t80) REVERT: C 219 MET cc_start: 0.8909 (ttm) cc_final: 0.8669 (ttm) REVERT: C 442 MET cc_start: 0.9225 (mmm) cc_final: 0.8983 (mmm) REVERT: C 605 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9251 (pp) REVERT: D 46 MET cc_start: 0.7470 (tpp) cc_final: 0.7194 (tpt) REVERT: D 117 LEU cc_start: 0.8619 (tp) cc_final: 0.8224 (tt) REVERT: D 163 PHE cc_start: 0.6944 (t80) cc_final: 0.6196 (t80) REVERT: D 678 MET cc_start: 0.8828 (ptp) cc_final: 0.8103 (mtm) REVERT: E 449 MET cc_start: 0.8546 (tpp) cc_final: 0.8291 (tpp) REVERT: E 492 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8987 (tt) REVERT: E 608 MET cc_start: 0.9409 (ptp) cc_final: 0.9114 (ptp) REVERT: F 403 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8509 (t) REVERT: F 678 MET cc_start: 0.8751 (ptp) cc_final: 0.8499 (ptp) outliers start: 101 outliers final: 69 residues processed: 217 average time/residue: 0.1862 time to fit residues: 70.2148 Evaluate side-chains 208 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 134 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 277 LYS Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 679 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 173 TYR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain F residue 403 THR Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 617 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 226 optimal weight: 7.9990 chunk 294 optimal weight: 0.0570 chunk 45 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 30.0000 chunk 273 optimal weight: 0.9980 chunk 12 optimal weight: 30.0000 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.087182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.057800 restraints weight = 125066.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.058871 restraints weight = 78728.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.059658 restraints weight = 61554.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.059788 restraints weight = 52974.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.060079 restraints weight = 51536.881| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35473 Z= 0.112 Angle : 0.663 13.404 47952 Z= 0.308 Chirality : 0.046 0.282 5376 Planarity : 0.004 0.089 6300 Dihedral : 7.806 129.285 4914 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.17 % Favored : 95.55 % Rotamer: Outliers : 1.76 % Allowed : 16.83 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4386 helix: -0.13 (0.13), residues: 1650 sheet: -0.35 (0.20), residues: 636 loop : -0.70 (0.15), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 745 TYR 0.012 0.001 TYR D 203 PHE 0.020 0.001 PHE E 742 TRP 0.008 0.001 TRP C 551 HIS 0.002 0.001 HIS E 735 Details of bonding type rmsd covalent geometry : bond 0.00258 (35460) covalent geometry : angle 0.66309 (47952) hydrogen bonds : bond 0.02757 ( 1026) hydrogen bonds : angle 4.45228 ( 2898) Misc. bond : bond 0.00184 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 134 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7973 (tpt) cc_final: 0.7684 (tpp) REVERT: A 163 PHE cc_start: 0.7173 (t80) cc_final: 0.6947 (t80) REVERT: B 608 MET cc_start: 0.9375 (ptp) cc_final: 0.9141 (ptp) REVERT: B 678 MET cc_start: 0.8679 (ptp) cc_final: 0.8365 (mtm) REVERT: C 84 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6928 (tmm) REVERT: C 117 LEU cc_start: 0.8547 (tp) cc_final: 0.8230 (tt) REVERT: C 163 PHE cc_start: 0.7146 (t80) cc_final: 0.6522 (t80) REVERT: C 605 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9157 (pp) REVERT: D 46 MET cc_start: 0.7452 (tpp) cc_final: 0.7187 (tpt) REVERT: D 117 LEU cc_start: 0.8509 (tp) cc_final: 0.8182 (tt) REVERT: D 163 PHE cc_start: 0.6849 (t80) cc_final: 0.6184 (t80) REVERT: D 382 GLN cc_start: 0.9254 (OUTLIER) cc_final: 0.8789 (mp10) REVERT: D 678 MET cc_start: 0.8818 (ptp) cc_final: 0.8196 (mtm) REVERT: E 449 MET cc_start: 0.8586 (tpp) cc_final: 0.8346 (tpp) REVERT: E 492 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8921 (tt) REVERT: E 605 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8887 (pp) REVERT: E 608 MET cc_start: 0.9359 (ptp) cc_final: 0.9104 (ptp) REVERT: E 678 MET cc_start: 0.9018 (ptp) cc_final: 0.8544 (mtm) REVERT: F 84 MET cc_start: 0.7683 (ttt) cc_final: 0.7144 (tmm) outliers start: 66 outliers final: 43 residues processed: 176 average time/residue: 0.1793 time to fit residues: 56.0875 Evaluate side-chains 176 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 382 GLN Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 492 LEU Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 493 VAL Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 150 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 357 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 30.0000 chunk 3 optimal weight: 30.0000 chunk 294 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 362 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.085131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.055511 restraints weight = 130259.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056498 restraints weight = 83293.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057168 restraints weight = 65326.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.057605 restraints weight = 57204.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.057696 restraints weight = 54104.898| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35473 Z= 0.213 Angle : 0.710 15.477 47952 Z= 0.330 Chirality : 0.046 0.152 5376 Planarity : 0.005 0.094 6300 Dihedral : 7.787 132.664 4914 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.70 % Favored : 95.03 % Rotamer: Outliers : 2.05 % Allowed : 16.77 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 4386 helix: -0.21 (0.13), residues: 1674 sheet: -0.37 (0.20), residues: 642 loop : -0.67 (0.15), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 53 TYR 0.011 0.001 TYR D 495 PHE 0.023 0.002 PHE D 516 TRP 0.007 0.001 TRP C 551 HIS 0.005 0.001 HIS F 406 Details of bonding type rmsd covalent geometry : bond 0.00490 (35460) covalent geometry : angle 0.71039 (47952) hydrogen bonds : bond 0.03027 ( 1026) hydrogen bonds : angle 4.41482 ( 2898) Misc. bond : bond 0.00171 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 128 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 PHE cc_start: 0.7174 (t80) cc_final: 0.6926 (m-80) REVERT: A 678 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8128 (mtm) REVERT: B 46 MET cc_start: 0.7899 (mpp) cc_final: 0.6168 (tpt) REVERT: B 608 MET cc_start: 0.9363 (ptp) cc_final: 0.9145 (ptp) REVERT: B 678 MET cc_start: 0.8749 (ptp) cc_final: 0.8368 (mtm) REVERT: C 84 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6706 (tmm) REVERT: C 117 LEU cc_start: 0.8557 (tp) cc_final: 0.8259 (tt) REVERT: C 163 PHE cc_start: 0.6998 (t80) cc_final: 0.6398 (t80) REVERT: C 442 MET cc_start: 0.9237 (mmm) cc_final: 0.8782 (mpp) REVERT: C 605 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9214 (pp) REVERT: D 46 MET cc_start: 0.7473 (tpp) cc_final: 0.7232 (tpt) REVERT: D 117 LEU cc_start: 0.8466 (tp) cc_final: 0.8093 (tt) REVERT: D 163 PHE cc_start: 0.6850 (t80) cc_final: 0.6158 (t80) REVERT: D 678 MET cc_start: 0.8772 (ptp) cc_final: 0.8180 (mtm) REVERT: E 605 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9023 (pp) REVERT: E 608 MET cc_start: 0.9355 (ptp) cc_final: 0.9117 (ptp) outliers start: 77 outliers final: 56 residues processed: 180 average time/residue: 0.1927 time to fit residues: 61.2082 Evaluate side-chains 188 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 128 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 611 MET Chi-restraints excluded: chain F residue 617 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 37 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 431 optimal weight: 20.0000 chunk 312 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 337 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 328 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.085504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055926 restraints weight = 127925.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.056913 restraints weight = 82453.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057479 restraints weight = 63640.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.057894 restraints weight = 56019.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.057894 restraints weight = 52878.314| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35473 Z= 0.180 Angle : 0.701 16.343 47952 Z= 0.323 Chirality : 0.046 0.176 5376 Planarity : 0.004 0.090 6300 Dihedral : 7.689 131.480 4914 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.47 % Favored : 95.26 % Rotamer: Outliers : 1.73 % Allowed : 17.25 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.13), residues: 4386 helix: -0.20 (0.13), residues: 1674 sheet: -0.36 (0.20), residues: 642 loop : -0.66 (0.15), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 53 TYR 0.011 0.001 TYR E 495 PHE 0.023 0.002 PHE E 516 TRP 0.008 0.001 TRP C 551 HIS 0.005 0.001 HIS F 406 Details of bonding type rmsd covalent geometry : bond 0.00416 (35460) covalent geometry : angle 0.70130 (47952) hydrogen bonds : bond 0.02911 ( 1026) hydrogen bonds : angle 4.43309 ( 2898) Misc. bond : bond 0.00164 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8772 Ramachandran restraints generated. 4386 Oldfield, 0 Emsley, 4386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 131 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.7990 (tmm) cc_final: 0.7776 (tmm) REVERT: A 163 PHE cc_start: 0.7190 (t80) cc_final: 0.6942 (m-80) REVERT: A 449 MET cc_start: 0.8430 (tpp) cc_final: 0.7899 (tpp) REVERT: A 678 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8166 (mtm) REVERT: B 449 MET cc_start: 0.8380 (tpp) cc_final: 0.7959 (tpp) REVERT: B 608 MET cc_start: 0.9365 (ptp) cc_final: 0.9157 (ptp) REVERT: B 678 MET cc_start: 0.8752 (ptp) cc_final: 0.8388 (mtm) REVERT: C 84 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6782 (tmm) REVERT: C 117 LEU cc_start: 0.8575 (tp) cc_final: 0.8277 (tt) REVERT: C 163 PHE cc_start: 0.6728 (t80) cc_final: 0.6152 (t80) REVERT: C 442 MET cc_start: 0.9163 (mmm) cc_final: 0.8661 (mpp) REVERT: C 605 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9225 (pp) REVERT: C 678 MET cc_start: 0.8635 (ptp) cc_final: 0.8051 (mtm) REVERT: D 46 MET cc_start: 0.7486 (tpp) cc_final: 0.7234 (tpt) REVERT: D 117 LEU cc_start: 0.8484 (tp) cc_final: 0.8112 (tt) REVERT: D 163 PHE cc_start: 0.6858 (t80) cc_final: 0.6195 (t80) REVERT: D 449 MET cc_start: 0.8297 (tpp) cc_final: 0.7776 (tpp) REVERT: D 678 MET cc_start: 0.8826 (ptp) cc_final: 0.8150 (mtm) REVERT: E 605 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9020 (pp) REVERT: E 608 MET cc_start: 0.9360 (ptp) cc_final: 0.9126 (ptp) REVERT: F 46 MET cc_start: 0.8136 (mtt) cc_final: 0.6412 (tpt) outliers start: 65 outliers final: 55 residues processed: 170 average time/residue: 0.1945 time to fit residues: 57.7885 Evaluate side-chains 188 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 129 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 678 MET Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 573 VAL Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 550 MET Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 542 ILE Chi-restraints excluded: chain D residue 550 MET Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 277 LYS Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 493 VAL Chi-restraints excluded: chain E residue 550 MET Chi-restraints excluded: chain E residue 573 VAL Chi-restraints excluded: chain E residue 605 LEU Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain E residue 617 VAL Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 269 ILE Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 550 MET Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 375 optimal weight: 0.0030 chunk 273 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 198 optimal weight: 7.9990 chunk 328 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 291 optimal weight: 50.0000 chunk 179 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 231 optimal weight: 40.0000 overall best weight: 3.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.085088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.055884 restraints weight = 129726.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.056860 restraints weight = 81798.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.057394 restraints weight = 62979.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.057904 restraints weight = 55484.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.057914 restraints weight = 52374.225| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35473 Z= 0.176 Angle : 0.698 15.842 47952 Z= 0.321 Chirality : 0.046 0.167 5376 Planarity : 0.005 0.092 6300 Dihedral : 7.552 130.502 4914 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.58 % Favored : 95.14 % Rotamer: Outliers : 1.95 % Allowed : 17.15 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.13), residues: 4386 helix: -0.17 (0.13), residues: 1668 sheet: -0.19 (0.20), residues: 630 loop : -0.61 (0.15), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 89 TYR 0.018 0.001 TYR F 495 PHE 0.021 0.002 PHE B 516 TRP 0.008 0.001 TRP C 551 HIS 0.005 0.001 HIS F 406 Details of bonding type rmsd covalent geometry : bond 0.00408 (35460) covalent geometry : angle 0.69764 (47952) hydrogen bonds : bond 0.02845 ( 1026) hydrogen bonds : angle 4.37267 ( 2898) Misc. bond : bond 0.00140 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5233.76 seconds wall clock time: 92 minutes 1.46 seconds (5521.46 seconds total)