Starting phenix.real_space_refine on Fri Mar 6 22:37:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rld_24526/03_2026/7rld_24526.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rld_24526/03_2026/7rld_24526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rld_24526/03_2026/7rld_24526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rld_24526/03_2026/7rld_24526.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rld_24526/03_2026/7rld_24526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rld_24526/03_2026/7rld_24526.map" } resolution = 3.4 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= 0.001 sd= 0.024 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 21852 2.51 5 N 6150 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 9.18, per 1000 atoms: 0.26 Number of scatterers: 34854 At special positions: 0 Unit cell: (173.262, 179.488, 101.675, 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 6150 7.00 C 21852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.6 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 24 sheets defined 45.2% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.575A pdb=" N ASP A 47 " --> pdb=" O GLN A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 47' Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.851A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.735A pdb=" N PHE A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 3.637A 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: 3.869A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.623A pdb=" N ALA A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 4.476A 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: 4.039A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.718A pdb=" N ILE A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.609A pdb=" N LEU A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 4.305A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.986A pdb=" N ILE A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 removed outlier: 4.511A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 395 through 403' Processing helix chain 'A' and resid 407 through 427 removed outlier: 3.740A pdb=" N ALA A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.632A pdb=" N TRP A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 491 removed outlier: 3.608A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.975A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 removed outlier: 3.755A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A 533 " --> pdb=" O LYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.753A pdb=" N LEU A 547 " --> pdb=" O LYS A 543 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.383A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 562 " --> pdb=" O ASN A 558 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 599 through 611 removed outlier: 3.565A pdb=" N GLY A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.889A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.501A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 677 " --> pdb=" O GLU A 673 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.671A pdb=" N ALA A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 707 " --> pdb=" O ILE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 removed outlier: 3.653A pdb=" N GLU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 743 No H-bonds generated for 'chain 'A' and resid 741 through 743' Processing helix chain 'A' and resid 749 through 764 removed outlier: 4.441A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 754 " --> pdb=" O ASN A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.574A pdb=" N ASP B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 47' Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.852A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.737A pdb=" N PHE B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.869A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.624A pdb=" N ALA B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 4.476A 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: 4.038A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 270 through 276 removed outlier: 3.717A pdb=" N ILE B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.607A pdb=" N LEU B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 4.304A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 323 " --> pdb=" O GLU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.986A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 removed outlier: 4.512A pdb=" N VAL B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 395 through 403' Processing helix chain 'B' and resid 407 through 427 removed outlier: 3.740A pdb=" N ALA B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.634A pdb=" N TRP B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 491 removed outlier: 3.608A pdb=" N ARG B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.976A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.755A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN B 533 " --> pdb=" O LYS B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 554 removed outlier: 3.753A pdb=" N LEU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.384A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 562 " --> pdb=" O ASN B 558 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 599 through 611 removed outlier: 3.566A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 661 removed outlier: 3.888A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.657A pdb=" N LYS B 677 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 686 No H-bonds generated for 'chain 'B' and resid 684 through 686' Processing helix chain 'B' and resid 687 through 707 removed outlier: 3.670A pdb=" N ALA B 698 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE B 707 " --> pdb=" O ILE B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 740 removed outlier: 3.653A pdb=" N GLU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 749 through 764 removed outlier: 4.442A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 47 removed outlier: 3.574A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 47' Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.852A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 removed outlier: 3.737A pdb=" N PHE C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.637A 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: 3.869A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 226 removed outlier: 3.622A pdb=" N ALA C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 216 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 4.477A 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: 4.038A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 276 removed outlier: 3.718A pdb=" N ILE C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.608A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 4.305A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.985A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 4.512A pdb=" N VAL C 399 " --> pdb=" O ASP C 395 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 400 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASN C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 395 through 403' Processing helix chain 'C' and resid 407 through 427 removed outlier: 3.741A pdb=" N ALA C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.633A pdb=" N TRP C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 491 removed outlier: 3.609A pdb=" N ARG C 487 " --> pdb=" O GLU C 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.975A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.755A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 554 removed outlier: 3.753A pdb=" N LEU C 547 " --> pdb=" O LYS C 543 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 569 removed outlier: 4.383A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 562 " --> pdb=" O ASN C 558 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN C 568 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 569 " --> pdb=" O LYS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 599 through 611 removed outlier: 3.564A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 649 through 661 removed outlier: 3.888A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 679 removed outlier: 3.659A pdb=" N LYS C 677 " --> pdb=" O GLU C 673 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 686 No H-bonds generated for 'chain 'C' and resid 684 through 686' Processing helix chain 'C' and resid 687 through 707 removed outlier: 3.670A pdb=" N ALA C 698 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE C 707 " --> pdb=" O ILE C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 740 removed outlier: 3.652A pdb=" N GLU C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 743 No H-bonds generated for 'chain 'C' and resid 741 through 743' Processing helix chain 'C' and resid 749 through 764 removed outlier: 4.442A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 47 removed outlier: 3.574A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 47' Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.852A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 removed outlier: 3.736A pdb=" N PHE D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.635A 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: 3.870A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 226 removed outlier: 3.624A pdb=" N ALA D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 216 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 4.476A 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: 4.039A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 276 removed outlier: 3.718A pdb=" N ILE D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 removed outlier: 3.609A pdb=" N LEU D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 4.305A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 323 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.986A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 removed outlier: 4.512A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU D 402 " --> pdb=" O GLN D 398 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 395 through 403' Processing helix chain 'D' and resid 407 through 427 removed outlier: 3.741A pdb=" N ALA D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.633A pdb=" N TRP D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 491 removed outlier: 3.608A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 507 removed outlier: 3.976A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.756A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN D 533 " --> pdb=" O LYS D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 554 removed outlier: 3.752A pdb=" N LEU D 547 " --> pdb=" O LYS D 543 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 569 removed outlier: 4.384A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 562 " --> pdb=" O ASN D 558 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN D 568 " --> pdb=" O ASP D 564 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 599 through 611 removed outlier: 3.565A pdb=" N GLY D 610 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 649 through 661 removed outlier: 3.888A pdb=" N VAL D 654 " --> pdb=" O GLU D 650 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 679 removed outlier: 3.501A pdb=" N LEU D 675 " --> pdb=" O ASP D 671 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 677 " --> pdb=" O GLU D 673 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET D 678 " --> pdb=" O PHE D 674 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 686 No H-bonds generated for 'chain 'D' and resid 684 through 686' Processing helix chain 'D' and resid 687 through 707 removed outlier: 3.671A pdb=" N ALA D 698 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE D 707 " --> pdb=" O ILE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 740 removed outlier: 3.653A pdb=" N GLU D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 749 through 764 removed outlier: 4.441A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 removed outlier: 3.575A pdb=" N ASP E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 43 through 47' Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 85 through 93 removed outlier: 3.852A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 removed outlier: 3.736A pdb=" N PHE E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.870A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 226 removed outlier: 3.623A pdb=" N ALA E 214 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE E 216 " --> pdb=" O GLN E 212 " (cutoff:3.500A) removed outlier: 4.477A 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: 4.040A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 270 through 276 removed outlier: 3.718A pdb=" N ILE E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 removed outlier: 3.608A pdb=" N LEU E 286 " --> pdb=" O SER E 282 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 291 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 4.304A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.987A pdb=" N ILE E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 removed outlier: 4.511A pdb=" N VAL E 399 " --> pdb=" O ASP E 395 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU E 402 " --> pdb=" O GLN E 398 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 395 through 403' Processing helix chain 'E' and resid 407 through 427 removed outlier: 3.740A pdb=" N ALA E 412 " --> pdb=" O GLY E 408 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.631A pdb=" N TRP E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 455 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 491 removed outlier: 3.608A pdb=" N ARG E 487 " --> pdb=" O GLU E 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.975A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.755A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 554 removed outlier: 3.753A pdb=" N LEU E 547 " --> pdb=" O LYS E 543 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET E 550 " --> pdb=" O GLU E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 569 removed outlier: 4.383A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE E 562 " --> pdb=" O ASN E 558 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN E 568 " --> pdb=" O ASP E 564 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E 569 " --> pdb=" O LYS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 599 through 611 removed outlier: 3.564A pdb=" N GLY E 610 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 649 through 661 removed outlier: 3.889A pdb=" N VAL E 654 " --> pdb=" O GLU E 650 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.657A pdb=" N LYS E 677 " --> pdb=" O GLU E 673 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET E 678 " --> pdb=" O PHE E 674 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 686 No H-bonds generated for 'chain 'E' and resid 684 through 686' Processing helix chain 'E' and resid 687 through 707 removed outlier: 3.672A pdb=" N ALA E 698 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE E 707 " --> pdb=" O ILE E 703 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 740 removed outlier: 3.653A pdb=" N GLU E 737 " --> pdb=" O ARG E 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 743 No H-bonds generated for 'chain 'E' and resid 741 through 743' Processing helix chain 'E' and resid 749 through 764 removed outlier: 4.442A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 47 removed outlier: 3.574A pdb=" N ASP F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 43 through 47' Processing helix chain 'F' and resid 48 through 50 No H-bonds generated for 'chain 'F' and resid 48 through 50' Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.850A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU F 92 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 removed outlier: 3.735A pdb=" N PHE F 139 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.870A pdb=" N ILE F 206 " --> pdb=" O TYR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 226 removed outlier: 3.624A pdb=" N ALA F 214 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE F 216 " --> pdb=" O GLN F 212 " (cutoff:3.500A) removed outlier: 4.476A 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: 4.040A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 270 through 276 removed outlier: 3.718A pdb=" N ILE F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 296 removed outlier: 3.608A pdb=" N LEU F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 4.304A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.985A pdb=" N ILE F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 385 Processing helix chain 'F' and resid 395 through 403 removed outlier: 4.512A pdb=" N VAL F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA F 400 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR F 403 " --> pdb=" O VAL F 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 395 through 403' Processing helix chain 'F' and resid 407 through 427 removed outlier: 3.740A pdb=" N ALA F 412 " --> pdb=" O GLY F 408 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.632A pdb=" N TRP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 491 removed outlier: 3.609A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 488 " --> pdb=" O ASP F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.974A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.754A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN F 533 " --> pdb=" O LYS F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 554 removed outlier: 3.754A pdb=" N LEU F 547 " --> pdb=" O LYS F 543 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 569 removed outlier: 4.383A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE F 562 " --> pdb=" O ASN F 558 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN F 568 " --> pdb=" O ASP F 564 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 569 " --> pdb=" O LYS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 599 through 611 removed outlier: 3.565A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 634 Processing helix chain 'F' and resid 649 through 661 removed outlier: 3.888A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.658A pdb=" N LYS F 677 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET F 678 " --> pdb=" O PHE F 674 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 686 No H-bonds generated for 'chain 'F' and resid 684 through 686' Processing helix chain 'F' and resid 687 through 707 removed outlier: 3.672A pdb=" N ALA F 698 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE F 707 " --> pdb=" O ILE F 703 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 740 removed outlier: 3.654A pdb=" N GLU F 737 " --> pdb=" O ARG F 733 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 743 No H-bonds generated for 'chain 'F' and resid 741 through 743' Processing helix chain 'F' and resid 749 through 764 removed outlier: 4.442A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 4.071A 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 27 removed outlier: 6.522A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP A 74 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU A 41 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 156 removed outlier: 3.681A pdb=" N PHE A 152 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 156 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 166 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.171A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 540 through 542 removed outlier: 6.910A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 27 removed outlier: 6.522A pdb=" N VAL B 39 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 74 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU B 41 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.682A pdb=" N PHE B 152 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 156 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL B 166 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 265 through 269 removed outlier: 6.170A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 540 through 542 removed outlier: 6.840A pdb=" N GLY B 513 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE B 643 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU B 515 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 27 removed outlier: 6.520A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP C 74 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU C 41 " --> pdb=" O ASP C 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.681A pdb=" N PHE C 152 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY C 156 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL C 166 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE C 114 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 265 through 269 removed outlier: 6.171A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 540 through 542 removed outlier: 6.909A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 25 through 27 removed outlier: 6.523A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP D 74 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU D 41 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 151 through 156 removed outlier: 3.681A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY D 156 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL D 166 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 265 through 269 removed outlier: 6.171A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 540 through 542 removed outlier: 6.909A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 25 through 27 removed outlier: 6.522A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP E 74 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU E 41 " --> pdb=" O ASP E 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 151 through 156 removed outlier: 3.681A pdb=" N PHE E 152 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY E 156 " --> pdb=" O ARG E 159 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 265 through 269 removed outlier: 6.171A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 540 through 542 removed outlier: 6.910A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 25 through 27 removed outlier: 6.520A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP F 74 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU F 41 " --> pdb=" O ASP F 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 151 through 156 removed outlier: 3.681A pdb=" N PHE F 152 " --> pdb=" O PHE F 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY F 156 " --> pdb=" O ARG F 159 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL F 166 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE F 114 " --> pdb=" O HIS F 183 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 265 through 269 removed outlier: 6.171A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLY F 240 " --> pdb=" O ARG F 365 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL F 367 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 540 through 542 removed outlier: 6.910A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 3033 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: 7.11 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11877 1.34 - 1.46: 6598 1.46 - 1.58: 16655 1.58 - 1.70: 36 1.70 - 1.81: 288 Bond restraints: 35454 Sorted by residual: bond pdb=" C ARG C 635 " pdb=" N PRO C 636 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 2.75e+00 bond pdb=" C ARG F 635 " pdb=" N PRO F 636 " ideal model delta sigma weight residual 1.332 1.351 -0.019 1.12e-02 7.97e+03 2.75e+00 bond pdb=" C ARG D 635 " pdb=" N PRO D 636 " ideal model delta sigma weight residual 1.332 1.350 -0.018 1.12e-02 7.97e+03 2.59e+00 bond pdb=" C ARG E 635 " pdb=" N PRO E 636 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.12e-02 7.97e+03 2.33e+00 bond pdb=" C ARG B 635 " pdb=" N PRO B 636 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.12e-02 7.97e+03 2.29e+00 ... (remaining 35449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 47038 2.07 - 4.15: 712 4.15 - 6.22: 184 6.22 - 8.29: 0 8.29 - 10.37: 6 Bond angle restraints: 47940 Sorted by residual: angle pdb=" C MET E 508 " pdb=" N THR E 509 " pdb=" CA THR E 509 " ideal model delta sigma weight residual 120.68 126.30 -5.62 1.52e+00 4.33e-01 1.37e+01 angle pdb=" C MET C 508 " pdb=" N THR C 509 " pdb=" CA THR C 509 " ideal model delta sigma weight residual 120.68 126.28 -5.60 1.52e+00 4.33e-01 1.36e+01 angle pdb=" C MET F 508 " pdb=" N THR F 509 " pdb=" CA THR F 509 " ideal model delta sigma weight residual 120.68 126.28 -5.60 1.52e+00 4.33e-01 1.36e+01 angle pdb=" C MET D 508 " pdb=" N THR D 509 " pdb=" CA THR D 509 " ideal model delta sigma weight residual 120.68 126.27 -5.59 1.52e+00 4.33e-01 1.35e+01 angle pdb=" C MET B 508 " pdb=" N THR B 509 " pdb=" CA THR B 509 " ideal model delta sigma weight residual 120.68 126.25 -5.57 1.52e+00 4.33e-01 1.34e+01 ... (remaining 47935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.34: 21065 27.34 - 54.69: 769 54.69 - 82.03: 48 82.03 - 109.37: 0 109.37 - 136.71: 36 Dihedral angle restraints: 21918 sinusoidal: 9234 harmonic: 12684 Sorted by residual: dihedral pdb=" C5' ADP B1001 " pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " pdb=" O2A ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 76.72 -136.71 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" C5' ADP C1001 " pdb=" O5' ADP C1001 " pdb=" PA ADP C1001 " pdb=" O2A ADP C1001 " ideal model delta sinusoidal sigma weight residual -60.00 76.71 -136.71 1 2.00e+01 2.50e-03 4.15e+01 dihedral pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " pdb=" O2A ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 76.69 -136.68 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 21915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3391 0.035 - 0.070: 1414 0.070 - 0.105: 388 0.105 - 0.140: 177 0.140 - 0.175: 6 Chirality restraints: 5376 Sorted by residual: chirality pdb=" CG LEU E 135 " pdb=" CB LEU E 135 " pdb=" CD1 LEU E 135 " pdb=" CD2 LEU E 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CG LEU B 135 " pdb=" CB LEU B 135 " pdb=" CD1 LEU B 135 " pdb=" CD2 LEU B 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CG LEU F 135 " pdb=" CB LEU F 135 " pdb=" CD1 LEU F 135 " pdb=" CD2 LEU F 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 5373 not shown) Planarity restraints: 6300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 187 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO F 188 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 188 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 188 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 187 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO E 188 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 188 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 188 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 187 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO C 188 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 188 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 188 " -0.031 5.00e-02 4.00e+02 ... (remaining 6297 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 32 2.33 - 2.98: 16478 2.98 - 3.62: 49982 3.62 - 4.26: 77749 4.26 - 4.90: 123971 Nonbonded interactions: 268212 Sorted by model distance: nonbonded pdb=" OD2 ASP F 368 " pdb=" NE2 GLN F 568 " model vdw 1.692 3.120 nonbonded pdb=" OD2 ASP A 368 " pdb=" NE2 GLN A 568 " model vdw 1.693 3.120 nonbonded pdb=" OD2 ASP E 368 " pdb=" NE2 GLN E 568 " model vdw 1.693 3.120 nonbonded pdb=" OD2 ASP D 368 " pdb=" NE2 GLN D 568 " model vdw 1.694 3.120 nonbonded pdb=" OD2 ASP C 368 " pdb=" NE2 GLN C 568 " model vdw 1.694 3.120 ... (remaining 268207 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.980 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 0.002 0.044 35454 Z= 0.132 Angle : 0.664 10.366 47940 Z= 0.361 Chirality : 0.043 0.175 5376 Planarity : 0.003 0.056 6300 Dihedral : 14.568 136.715 13698 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.83 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -1.35 (0.12), residues: 4386 helix: -0.68 (0.13), residues: 1428 sheet: 0.79 (0.22), residues: 648 loop : -1.56 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 635 TYR 0.016 0.001 TYR D 495 PHE 0.010 0.001 PHE B 360 TRP 0.003 0.001 TRP B 551 HIS 0.003 0.001 HIS C 499 Details of bonding type rmsd covalent geometry : bond 0.00249 (35454) covalent geometry : angle 0.66441 (47940) hydrogen bonds : bond 0.29994 ( 1065) hydrogen bonds : angle 7.62211 ( 3033) *********************** 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 190 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.205 Fit side-chains REVERT: A 146 ILE cc_start: 0.9049 (mm) cc_final: 0.8758 (mp) REVERT: A 206 ILE cc_start: 0.7095 (mm) cc_final: 0.6804 (mm) REVERT: A 332 MET cc_start: 0.8387 (mmm) cc_final: 0.8126 (mmt) REVERT: C 146 ILE cc_start: 0.9158 (mm) cc_final: 0.8871 (mp) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.2066 time to fit residues: 65.7918 Evaluate side-chains 142 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 4.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 499 HIS B 90 ASN C 90 ASN D 90 ASN E 90 ASN F 90 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.088970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.064764 restraints weight = 109657.971| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.67 r_work: 0.3000 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 35454 Z= 0.244 Angle : 0.732 8.499 47940 Z= 0.354 Chirality : 0.049 0.208 5376 Planarity : 0.005 0.048 6300 Dihedral : 11.173 139.686 4920 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.15 % Favored : 95.71 % Rotamer: Outliers : 0.56 % Allowed : 4.77 % Favored : 94.67 % 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: -1.13 (0.13), residues: 4386 helix: -0.57 (0.12), residues: 1608 sheet: 0.75 (0.23), residues: 666 loop : -1.35 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 159 TYR 0.041 0.002 TYR B 244 PHE 0.024 0.002 PHE A 563 TRP 0.009 0.002 TRP A 476 HIS 0.006 0.001 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00557 (35454) covalent geometry : angle 0.73168 (47940) hydrogen bonds : bond 0.04136 ( 1065) hydrogen bonds : angle 5.07872 ( 3033) *********************** 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 172 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.515 Fit side-chains REVERT: A 146 ILE cc_start: 0.9331 (mm) cc_final: 0.9120 (mp) REVERT: B 84 MET cc_start: 0.8892 (ptm) cc_final: 0.8600 (ptm) REVERT: C 146 ILE cc_start: 0.9369 (mm) cc_final: 0.9167 (mp) REVERT: D 244 TYR cc_start: 0.8020 (m-80) cc_final: 0.7691 (m-80) outliers start: 21 outliers final: 11 residues processed: 167 average time/residue: 0.1885 time to fit residues: 54.8196 Evaluate side-chains 143 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 404 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 385 optimal weight: 0.9990 chunk 269 optimal weight: 0.8980 chunk 330 optimal weight: 2.9990 chunk 350 optimal weight: 0.6980 chunk 236 optimal weight: 0.9990 chunk 175 optimal weight: 0.4980 chunk 16 optimal weight: 7.9990 chunk 358 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 378 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 90 ASN C 90 ASN D 90 ASN F 90 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.089387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.065174 restraints weight = 108587.298| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.64 r_work: 0.3014 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 35454 Z= 0.111 Angle : 0.567 7.210 47940 Z= 0.262 Chirality : 0.043 0.149 5376 Planarity : 0.004 0.051 6300 Dihedral : 10.747 133.213 4920 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.85 % Favored : 96.01 % Rotamer: Outliers : 0.56 % Allowed : 7.17 % Favored : 92.27 % 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: -0.79 (0.13), residues: 4386 helix: 0.01 (0.13), residues: 1644 sheet: 0.55 (0.22), residues: 636 loop : -1.27 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 159 TYR 0.013 0.001 TYR C 244 PHE 0.012 0.001 PHE F 563 TRP 0.002 0.001 TRP B 454 HIS 0.002 0.001 HIS F 499 Details of bonding type rmsd covalent geometry : bond 0.00258 (35454) covalent geometry : angle 0.56731 (47940) hydrogen bonds : bond 0.03386 ( 1065) hydrogen bonds : angle 4.47607 ( 3033) *********************** 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 161 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.436 Fit side-chains revert: symmetry clash REVERT: B 46 MET cc_start: 0.7222 (tpt) cc_final: 0.7019 (tpt) REVERT: C 46 MET cc_start: 0.7395 (tpt) cc_final: 0.7163 (tpt) REVERT: C 427 MET cc_start: 0.7482 (tpt) cc_final: 0.7100 (tpt) REVERT: D 449 MET cc_start: 0.8453 (mmm) cc_final: 0.8216 (tpp) REVERT: F 46 MET cc_start: 0.7458 (tpt) cc_final: 0.7249 (tpt) outliers start: 21 outliers final: 8 residues processed: 157 average time/residue: 0.1875 time to fit residues: 51.3417 Evaluate side-chains 136 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain F residue 404 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 388 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 420 optimal weight: 0.4980 chunk 219 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.085323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.059946 restraints weight = 107520.158| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.44 r_work: 0.2895 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35454 Z= 0.200 Angle : 0.623 8.803 47940 Z= 0.289 Chirality : 0.046 0.153 5376 Planarity : 0.004 0.044 6300 Dihedral : 10.887 143.329 4920 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.72 % Allowed : 8.51 % Favored : 90.77 % 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: -0.63 (0.13), residues: 4386 helix: 0.14 (0.13), residues: 1656 sheet: 0.46 (0.21), residues: 654 loop : -1.13 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 93 TYR 0.019 0.002 TYR A 244 PHE 0.017 0.001 PHE C 563 TRP 0.005 0.001 TRP B 551 HIS 0.004 0.001 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00472 (35454) covalent geometry : angle 0.62297 (47940) hydrogen bonds : bond 0.03101 ( 1065) hydrogen bonds : angle 4.33637 ( 3033) *********************** 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 172 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.7100 (tpt) cc_final: 0.6771 (tpt) REVERT: B 46 MET cc_start: 0.7287 (tpt) cc_final: 0.7024 (tpt) REVERT: B 404 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7844 (p-80) REVERT: C 46 MET cc_start: 0.7478 (tpt) cc_final: 0.6969 (tpt) REVERT: D 46 MET cc_start: 0.7002 (tpt) cc_final: 0.6676 (tpt) REVERT: D 244 TYR cc_start: 0.8016 (m-80) cc_final: 0.7694 (m-80) REVERT: F 46 MET cc_start: 0.7417 (tpt) cc_final: 0.6914 (tpt) REVERT: F 206 ILE cc_start: 0.8978 (mm) cc_final: 0.8702 (mm) REVERT: F 427 MET cc_start: 0.7391 (tpt) cc_final: 0.7133 (tpt) outliers start: 27 outliers final: 16 residues processed: 164 average time/residue: 0.2076 time to fit residues: 57.6944 Evaluate side-chains 152 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 70 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 chunk 414 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 419 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 296 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.085288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060096 restraints weight = 108741.328| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.42 r_work: 0.2896 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35454 Z= 0.123 Angle : 0.572 10.423 47940 Z= 0.264 Chirality : 0.044 0.136 5376 Planarity : 0.003 0.044 6300 Dihedral : 10.576 141.199 4920 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.07 % Allowed : 8.99 % Favored : 89.95 % 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: -0.43 (0.13), residues: 4386 helix: 0.37 (0.13), residues: 1668 sheet: 0.41 (0.21), residues: 654 loop : -1.02 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 159 TYR 0.013 0.001 TYR E 244 PHE 0.013 0.001 PHE C 563 TRP 0.002 0.001 TRP E 476 HIS 0.002 0.001 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00291 (35454) covalent geometry : angle 0.57216 (47940) hydrogen bonds : bond 0.02663 ( 1065) hydrogen bonds : angle 4.16061 ( 3033) *********************** 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 183 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: B 46 MET cc_start: 0.7383 (tpt) cc_final: 0.7145 (tpt) REVERT: B 404 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7830 (p-80) REVERT: C 46 MET cc_start: 0.7150 (tpt) cc_final: 0.6669 (tpt) REVERT: C 206 ILE cc_start: 0.8926 (mm) cc_final: 0.8667 (mm) REVERT: E 46 MET cc_start: 0.7676 (tpt) cc_final: 0.7413 (tpt) REVERT: E 404 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7913 (p-80) REVERT: F 46 MET cc_start: 0.7148 (tpt) cc_final: 0.6683 (tpt) REVERT: F 206 ILE cc_start: 0.8969 (mm) cc_final: 0.8710 (mm) REVERT: F 427 MET cc_start: 0.7566 (tpt) cc_final: 0.7360 (tpt) outliers start: 40 outliers final: 25 residues processed: 177 average time/residue: 0.1859 time to fit residues: 57.4718 Evaluate side-chains 163 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 358 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 398 optimal weight: 0.2980 chunk 212 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 chunk 368 optimal weight: 20.0000 chunk 214 optimal weight: 0.0770 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.085296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.061020 restraints weight = 107274.691| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.57 r_work: 0.2900 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 35454 Z= 0.107 Angle : 0.568 10.657 47940 Z= 0.261 Chirality : 0.043 0.138 5376 Planarity : 0.003 0.044 6300 Dihedral : 10.183 138.015 4920 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.96 % Allowed : 9.79 % Favored : 89.25 % 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: -0.28 (0.13), residues: 4386 helix: 0.54 (0.13), residues: 1668 sheet: 0.53 (0.21), residues: 642 loop : -0.99 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 64 TYR 0.009 0.001 TYR B 495 PHE 0.010 0.001 PHE C 563 TRP 0.002 0.000 TRP D 454 HIS 0.001 0.000 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00258 (35454) covalent geometry : angle 0.56762 (47940) hydrogen bonds : bond 0.02434 ( 1065) hydrogen bonds : angle 4.02944 ( 3033) *********************** 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 179 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 MET cc_start: 0.7265 (tpt) cc_final: 0.7045 (tpt) REVERT: B 404 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7792 (p-80) REVERT: C 46 MET cc_start: 0.7167 (tpt) cc_final: 0.6897 (tpt) REVERT: C 206 ILE cc_start: 0.8863 (mm) cc_final: 0.8610 (mm) REVERT: C 427 MET cc_start: 0.7507 (tpt) cc_final: 0.7233 (tpt) REVERT: E 46 MET cc_start: 0.7662 (tpt) cc_final: 0.7353 (tpt) REVERT: F 46 MET cc_start: 0.7119 (tpt) cc_final: 0.6857 (tpt) REVERT: F 206 ILE cc_start: 0.8893 (mm) cc_final: 0.8661 (mm) outliers start: 36 outliers final: 23 residues processed: 172 average time/residue: 0.1902 time to fit residues: 57.2094 Evaluate side-chains 161 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 611 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 160 optimal weight: 5.9990 chunk 286 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 380 optimal weight: 0.0020 chunk 217 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 304 optimal weight: 20.0000 chunk 246 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 265 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 overall best weight: 3.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 HIS C 384 HIS D 384 HIS F 384 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.081522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.055511 restraints weight = 107506.554| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.41 r_work: 0.2749 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 35454 Z= 0.244 Angle : 0.717 10.103 47940 Z= 0.336 Chirality : 0.047 0.150 5376 Planarity : 0.004 0.047 6300 Dihedral : 11.152 164.093 4920 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.25 % Allowed : 10.69 % Favored : 88.05 % 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: -0.41 (0.13), residues: 4386 helix: 0.34 (0.13), residues: 1722 sheet: 0.36 (0.20), residues: 672 loop : -0.99 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 144 TYR 0.023 0.002 TYR F 244 PHE 0.019 0.002 PHE C 563 TRP 0.008 0.002 TRP B 551 HIS 0.006 0.001 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00577 (35454) covalent geometry : angle 0.71690 (47940) hydrogen bonds : bond 0.03362 ( 1065) hydrogen bonds : angle 4.34372 ( 3033) *********************** 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 196 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 TYR cc_start: 0.8010 (m-80) cc_final: 0.7676 (m-80) REVERT: A 427 MET cc_start: 0.7685 (tpt) cc_final: 0.7282 (tpt) REVERT: B 404 HIS cc_start: 0.8221 (OUTLIER) cc_final: 0.7941 (p-80) REVERT: C 46 MET cc_start: 0.7384 (tpt) cc_final: 0.6955 (tpt) REVERT: C 244 TYR cc_start: 0.8154 (m-80) cc_final: 0.7849 (m-80) REVERT: D 244 TYR cc_start: 0.8028 (m-80) cc_final: 0.7676 (m-80) REVERT: D 492 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9299 (tt) REVERT: E 46 MET cc_start: 0.7729 (tpt) cc_final: 0.7434 (tpt) REVERT: E 404 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7863 (p-80) REVERT: F 46 MET cc_start: 0.7231 (tpt) cc_final: 0.6837 (tpt) REVERT: F 244 TYR cc_start: 0.8149 (m-80) cc_final: 0.7828 (m-80) outliers start: 47 outliers final: 22 residues processed: 185 average time/residue: 0.1995 time to fit residues: 62.4506 Evaluate side-chains 165 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 474 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 226 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 267 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.0060 chunk 273 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.083459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.057681 restraints weight = 106042.843| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.44 r_work: 0.2803 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35454 Z= 0.110 Angle : 0.611 16.483 47940 Z= 0.281 Chirality : 0.044 0.152 5376 Planarity : 0.004 0.045 6300 Dihedral : 10.865 162.726 4920 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.04 % Allowed : 11.31 % Favored : 87.65 % 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: -0.19 (0.13), residues: 4386 helix: 0.59 (0.13), residues: 1722 sheet: 0.40 (0.20), residues: 642 loop : -0.88 (0.15), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 64 TYR 0.009 0.001 TYR E 143 PHE 0.012 0.001 PHE A 563 TRP 0.003 0.001 TRP D 454 HIS 0.002 0.000 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00263 (35454) covalent geometry : angle 0.61074 (47940) hydrogen bonds : bond 0.02465 ( 1065) hydrogen bonds : angle 4.10346 ( 3033) *********************** 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 184 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7802 (tpt) cc_final: 0.7466 (tpt) REVERT: B 404 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7918 (p-80) REVERT: C 46 MET cc_start: 0.7395 (tpt) cc_final: 0.7082 (tpt) REVERT: D 492 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9304 (tt) REVERT: E 46 MET cc_start: 0.7748 (tpt) cc_final: 0.7460 (tpt) REVERT: E 404 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7940 (p-80) REVERT: E 442 MET cc_start: 0.9217 (tpp) cc_final: 0.8832 (mmt) REVERT: F 46 MET cc_start: 0.7263 (tpt) cc_final: 0.6996 (tpt) outliers start: 39 outliers final: 25 residues processed: 177 average time/residue: 0.1836 time to fit residues: 56.5264 Evaluate side-chains 172 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 474 VAL 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: 10.0000 chunk 118 optimal weight: 0.0170 chunk 357 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 362 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 overall best weight: 2.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** E 616 ASN ** 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 = 0.3648 r_free = 0.3648 target = 0.081649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.055869 restraints weight = 106817.658| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.39 r_work: 0.2770 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35454 Z= 0.191 Angle : 0.640 11.649 47940 Z= 0.296 Chirality : 0.045 0.153 5376 Planarity : 0.004 0.047 6300 Dihedral : 10.963 164.571 4920 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.07 % Allowed : 11.15 % Favored : 87.79 % 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: -0.20 (0.13), residues: 4386 helix: 0.57 (0.13), residues: 1734 sheet: 0.35 (0.20), residues: 672 loop : -0.88 (0.15), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 159 TYR 0.020 0.002 TYR E 244 PHE 0.013 0.001 PHE A 139 TRP 0.003 0.001 TRP B 551 HIS 0.004 0.001 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00461 (35454) covalent geometry : angle 0.64012 (47940) hydrogen bonds : bond 0.02727 ( 1065) hydrogen bonds : angle 4.11522 ( 3033) *********************** 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 185 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7776 (tpt) cc_final: 0.7481 (tpt) REVERT: B 404 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7912 (p-80) REVERT: C 46 MET cc_start: 0.7308 (tpt) cc_final: 0.7080 (tpt) REVERT: D 492 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9342 (tt) REVERT: E 46 MET cc_start: 0.7841 (tpt) cc_final: 0.7587 (tpt) REVERT: E 388 MET cc_start: 0.8630 (ptp) cc_final: 0.8315 (ptp) REVERT: E 404 HIS cc_start: 0.8145 (OUTLIER) cc_final: 0.7886 (p-80) outliers start: 40 outliers final: 30 residues processed: 175 average time/residue: 0.1909 time to fit residues: 57.6955 Evaluate side-chains 177 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 611 MET Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 474 VAL 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 37 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 431 optimal weight: 3.9990 chunk 312 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 337 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 328 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** 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 = 0.3671 r_free = 0.3671 target = 0.082650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.057012 restraints weight = 107050.553| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.41 r_work: 0.2800 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 35454 Z= 0.121 Angle : 0.608 13.656 47940 Z= 0.279 Chirality : 0.044 0.133 5376 Planarity : 0.004 0.046 6300 Dihedral : 10.739 167.866 4920 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.96 % Allowed : 11.31 % Favored : 87.73 % 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: -0.12 (0.13), residues: 4386 helix: 0.67 (0.13), residues: 1728 sheet: 0.41 (0.20), residues: 660 loop : -0.86 (0.15), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 159 TYR 0.009 0.001 TYR A 110 PHE 0.012 0.001 PHE D 363 TRP 0.003 0.001 TRP D 454 HIS 0.003 0.000 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00295 (35454) covalent geometry : angle 0.60820 (47940) hydrogen bonds : bond 0.02402 ( 1065) hydrogen bonds : angle 4.00210 ( 3033) ********************** 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 186 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 MET cc_start: 0.7787 (tpt) cc_final: 0.7441 (tpt) REVERT: B 404 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7969 (p-80) REVERT: D 427 MET cc_start: 0.7710 (tpt) cc_final: 0.7397 (tpt) REVERT: D 492 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9313 (tt) REVERT: E 46 MET cc_start: 0.7769 (tpt) cc_final: 0.7509 (tpt) REVERT: E 404 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7976 (p-80) outliers start: 36 outliers final: 32 residues processed: 177 average time/residue: 0.1982 time to fit residues: 60.3127 Evaluate side-chains 179 residues out of total 3750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 110 TYR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 404 HIS Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 611 MET Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 404 HIS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 611 MET Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 110 TYR Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 474 VAL 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: 5.9990 chunk 273 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 328 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 179 optimal weight: 0.0770 chunk 42 optimal weight: 0.0020 chunk 231 optimal weight: 3.9990 overall best weight: 1.1750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** 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 = 0.3664 r_free = 0.3664 target = 0.082362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.056953 restraints weight = 106779.649| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.36 r_work: 0.2800 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.5434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35454 Z= 0.127 Angle : 0.613 13.391 47940 Z= 0.282 Chirality : 0.044 0.134 5376 Planarity : 0.004 0.046 6300 Dihedral : 10.513 171.311 4920 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.01 % Allowed : 11.55 % Favored : 87.44 % 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: -0.09 (0.13), residues: 4386 helix: 0.68 (0.13), residues: 1734 sheet: 0.43 (0.20), residues: 660 loop : -0.84 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 159 TYR 0.010 0.001 TYR A 495 PHE 0.016 0.001 PHE C 363 TRP 0.002 0.001 TRP A 476 HIS 0.003 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00311 (35454) covalent geometry : angle 0.61347 (47940) hydrogen bonds : bond 0.02393 ( 1065) hydrogen bonds : angle 3.96244 ( 3033) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6742.98 seconds wall clock time: 116 minutes 30.91 seconds (6990.91 seconds total)