Starting phenix.real_space_refine on Mon Dec 30 03:27:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rak_24363/12_2024/7rak_24363.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rak_24363/12_2024/7rak_24363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rak_24363/12_2024/7rak_24363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rak_24363/12_2024/7rak_24363.map" model { file = "/net/cci-nas-00/data/ceres_data/7rak_24363/12_2024/7rak_24363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rak_24363/12_2024/7rak_24363.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.009 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 48 5.49 5 S 384 5.16 5 C 37888 2.51 5 N 10592 2.21 5 O 12384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 61296 Number of models: 1 Model: "" Number of chains: 32 Chain: "U" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "A" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "B" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "C" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "D" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "E" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "F" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "G" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "H" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "I" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "J" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "K" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "L" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "M" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "N" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "O" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.12, per 1000 atoms: 0.41 Number of scatterers: 61296 At special positions: 0 Unit cell: (178.2, 178.2, 212.76, 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 384 16.00 P 48 15.00 O 12384 8.00 N 10592 7.00 C 37888 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: 12.20 Conformation dependent library (CDL) restraints added in 6.5 seconds 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15040 Finding SS restraints... Secondary structure from input PDB file: 335 helices and 64 sheets defined 46.4% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'U' and resid 12 through 27 removed outlier: 3.882A pdb=" N ARG U 16 " --> pdb=" O ARG U 12 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET U 17 " --> pdb=" O ASP U 13 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN U 18 " --> pdb=" O ALA U 14 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE U 24 " --> pdb=" O LEU U 20 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 61 removed outlier: 3.578A pdb=" N ARG U 60 " --> pdb=" O VAL U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 81 removed outlier: 4.241A pdb=" N MET U 71 " --> pdb=" O PRO U 67 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU U 72 " --> pdb=" O ALA U 68 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS U 81 " --> pdb=" O LYS U 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 105 removed outlier: 3.767A pdb=" N GLU U 103 " --> pdb=" O ARG U 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU U 104 " --> pdb=" O LYS U 100 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU U 105 " --> pdb=" O ALA U 101 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 108 No H-bonds generated for 'chain 'U' and resid 106 through 108' Processing helix chain 'U' and resid 112 through 130 removed outlier: 3.644A pdb=" N GLN U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS U 130 " --> pdb=" O GLN U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 151 Processing helix chain 'U' and resid 162 through 166 removed outlier: 3.804A pdb=" N GLU U 166 " --> pdb=" O LYS U 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 173 Processing helix chain 'U' and resid 248 through 274 removed outlier: 3.984A pdb=" N LEU U 252 " --> pdb=" O ASP U 248 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET U 253 " --> pdb=" O PRO U 249 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU U 254 " --> pdb=" O ALA U 250 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU U 263 " --> pdb=" O GLU U 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS U 264 " --> pdb=" O GLU U 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP U 265 " --> pdb=" O LYS U 261 " (cutoff:3.500A) Processing helix chain 'U' and resid 285 through 293 removed outlier: 4.330A pdb=" N HIS U 290 " --> pdb=" O LEU U 287 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR U 291 " --> pdb=" O ALA U 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 304 through 309 Processing helix chain 'U' and resid 368 through 390 removed outlier: 3.941A pdb=" N GLU U 372 " --> pdb=" O GLU U 368 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA U 377 " --> pdb=" O GLU U 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP U 379 " --> pdb=" O ALA U 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP U 380 " --> pdb=" O ARG U 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY U 383 " --> pdb=" O ASP U 379 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL U 384 " --> pdb=" O ASP U 380 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL U 385 " --> pdb=" O ALA U 381 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS U 387 " --> pdb=" O GLY U 383 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR U 388 " --> pdb=" O VAL U 384 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE U 389 " --> pdb=" O VAL U 385 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU U 390 " --> pdb=" O GLY U 386 " (cutoff:3.500A) Processing helix chain 'U' and resid 400 through 413 removed outlier: 3.555A pdb=" N LYS U 408 " --> pdb=" O GLU U 404 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU U 411 " --> pdb=" O MET U 407 " (cutoff:3.500A) Processing helix chain 'U' and resid 414 through 416 No H-bonds generated for 'chain 'U' and resid 414 through 416' Processing helix chain 'U' and resid 419 through 431 removed outlier: 4.191A pdb=" N ALA U 423 " --> pdb=" O ARG U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 441 removed outlier: 3.749A pdb=" N ARG U 436 " --> pdb=" O GLU U 432 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN U 441 " --> pdb=" O THR U 437 " (cutoff:3.500A) Processing helix chain 'U' and resid 447 through 456 removed outlier: 3.572A pdb=" N ALA U 455 " --> pdb=" O VAL U 451 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA U 456 " --> pdb=" O LYS U 452 " (cutoff:3.500A) Processing helix chain 'U' and resid 457 through 459 No H-bonds generated for 'chain 'U' and resid 457 through 459' Processing helix chain 'U' and resid 486 through 500 removed outlier: 3.557A pdb=" N ALA U 492 " --> pdb=" O VAL U 488 " (cutoff:3.500A) Processing helix chain 'U' and resid 500 through 505 removed outlier: 4.126A pdb=" N LEU U 504 " --> pdb=" O THR U 500 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG U 505 " --> pdb=" O GLU U 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 500 through 505' Processing helix chain 'A' and resid 12 through 27 removed outlier: 3.885A pdb=" N ARG A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.578A pdb=" N ARG A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 81 removed outlier: 4.241A pdb=" N MET A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.765A pdb=" N GLU A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 112 through 130 removed outlier: 3.644A pdb=" N GLN A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.802A pdb=" N GLU A 166 " --> pdb=" O LYS A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 248 through 274 removed outlier: 3.983A pdb=" N LEU A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 removed outlier: 4.330A pdb=" N HIS A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR A 291 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 368 through 390 removed outlier: 3.940A pdb=" N GLU A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 390 " --> pdb=" O GLY A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.554A pdb=" N LYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 419 through 431 removed outlier: 4.192A pdb=" N ALA A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.749A pdb=" N ARG A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A 441 " --> pdb=" O THR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 456 removed outlier: 3.562A pdb=" N ALA A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 486 through 500 removed outlier: 3.558A pdb=" N ALA A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 removed outlier: 4.128A pdb=" N LEU A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 500 through 505' Processing helix chain 'B' and resid 12 through 27 removed outlier: 3.883A pdb=" N ARG B 16 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.577A pdb=" N ARG B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 81 removed outlier: 4.241A pdb=" N MET B 71 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 105 removed outlier: 3.766A pdb=" N GLU B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 112 through 130 removed outlier: 3.644A pdb=" N GLN B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 130 " --> pdb=" O GLN B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.803A pdb=" N GLU B 166 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 248 through 274 removed outlier: 3.983A pdb=" N LEU B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 removed outlier: 4.330A pdb=" N HIS B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR B 291 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 368 through 390 removed outlier: 3.941A pdb=" N GLU B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP B 380 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 413 removed outlier: 3.553A pdb=" N LYS B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 419 through 431 removed outlier: 4.188A pdb=" N ALA B 423 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.750A pdb=" N ARG B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 456 removed outlier: 3.577A pdb=" N ALA B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 456 " --> pdb=" O LYS B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 459 No H-bonds generated for 'chain 'B' and resid 457 through 459' Processing helix chain 'B' and resid 486 through 500 removed outlier: 3.557A pdb=" N ALA B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 removed outlier: 4.127A pdb=" N LEU B 504 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 505 " --> pdb=" O GLU B 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 500 through 505' Processing helix chain 'C' and resid 12 through 27 removed outlier: 3.748A pdb=" N ARG C 16 " --> pdb=" O ARG C 12 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.577A pdb=" N ARG C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 81 removed outlier: 4.260A pdb=" N MET C 71 " --> pdb=" O PRO C 67 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 81 " --> pdb=" O LYS C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 104 removed outlier: 3.765A pdb=" N GLU C 103 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 removed outlier: 3.654A pdb=" N ASN C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 105 through 108' Processing helix chain 'C' and resid 112 through 130 removed outlier: 3.645A pdb=" N GLN C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'C' and resid 162 through 166 removed outlier: 3.802A pdb=" N GLU C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 248 through 274 removed outlier: 3.985A pdb=" N LEU C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 293 removed outlier: 4.333A pdb=" N HIS C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR C 291 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 Processing helix chain 'C' and resid 368 through 390 removed outlier: 3.939A pdb=" N GLU C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP C 380 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 383 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS C 387 " --> pdb=" O GLY C 383 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR C 388 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU C 390 " --> pdb=" O GLY C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 413 removed outlier: 3.555A pdb=" N LYS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 416 No H-bonds generated for 'chain 'C' and resid 414 through 416' Processing helix chain 'C' and resid 419 through 431 removed outlier: 4.195A pdb=" N ALA C 423 " --> pdb=" O ARG C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 441 removed outlier: 3.749A pdb=" N ARG C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN C 441 " --> pdb=" O THR C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 456 removed outlier: 3.571A pdb=" N ALA C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 456 " --> pdb=" O LYS C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.558A pdb=" N ALA C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 505 removed outlier: 4.104A pdb=" N LEU C 504 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 500 through 505' Processing helix chain 'D' and resid 12 through 27 removed outlier: 3.888A pdb=" N ARG D 16 " --> pdb=" O ARG D 12 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.568A pdb=" N ARG D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 4.245A pdb=" N MET D 71 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU D 72 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ILE D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 105 removed outlier: 3.766A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 112 through 130 removed outlier: 3.643A pdb=" N GLN D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 162 through 166 removed outlier: 3.802A pdb=" N GLU D 166 " --> pdb=" O LYS D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 248 through 274 removed outlier: 3.983A pdb=" N LEU D 252 " --> pdb=" O ASP D 248 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 293 removed outlier: 4.330A pdb=" N HIS D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR D 291 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 Processing helix chain 'D' and resid 368 through 390 removed outlier: 3.940A pdb=" N GLU D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR D 388 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 389 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU D 390 " --> pdb=" O GLY D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.555A pdb=" N LYS D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU D 411 " --> pdb=" O MET D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 419 through 431 removed outlier: 4.191A pdb=" N ALA D 423 " --> pdb=" O ARG D 419 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 431 " --> pdb=" O PHE D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 439 removed outlier: 3.762A pdb=" N ARG D 436 " --> pdb=" O GLU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 456 removed outlier: 3.579A pdb=" N ALA D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 456 " --> pdb=" O LYS D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 459 No H-bonds generated for 'chain 'D' and resid 457 through 459' Processing helix chain 'D' and resid 486 through 500 removed outlier: 3.558A pdb=" N ALA D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 505 removed outlier: 4.129A pdb=" N LEU D 504 " --> pdb=" O THR D 500 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 500 through 505' Processing helix chain 'E' and resid 12 through 27 removed outlier: 3.883A pdb=" N ARG E 16 " --> pdb=" O ARG E 12 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.578A pdb=" N ARG E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 81 removed outlier: 4.241A pdb=" N MET E 71 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU E 72 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE E 73 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS E 81 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 105 removed outlier: 3.767A pdb=" N GLU E 103 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 104 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 112 through 130 removed outlier: 3.643A pdb=" N GLN E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 162 through 166 removed outlier: 3.803A pdb=" N GLU E 166 " --> pdb=" O LYS E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 248 through 274 removed outlier: 3.984A pdb=" N LEU E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP E 265 " --> pdb=" O LYS E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 293 removed outlier: 4.329A pdb=" N HIS E 290 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR E 291 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 309 Processing helix chain 'E' and resid 368 through 390 removed outlier: 3.941A pdb=" N GLU E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA E 377 " --> pdb=" O GLU E 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP E 380 " --> pdb=" O ARG E 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY E 383 " --> pdb=" O ASP E 379 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL E 385 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS E 387 " --> pdb=" O GLY E 383 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR E 388 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 389 " --> pdb=" O VAL E 385 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU E 390 " --> pdb=" O GLY E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 removed outlier: 3.555A pdb=" N LYS E 408 " --> pdb=" O GLU E 404 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU E 411 " --> pdb=" O MET E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 419 through 431 removed outlier: 4.182A pdb=" N ALA E 423 " --> pdb=" O ARG E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 441 removed outlier: 3.750A pdb=" N ARG E 436 " --> pdb=" O GLU E 432 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN E 441 " --> pdb=" O THR E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 456 removed outlier: 3.569A pdb=" N ALA E 455 " --> pdb=" O VAL E 451 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 456 " --> pdb=" O LYS E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 459 No H-bonds generated for 'chain 'E' and resid 457 through 459' Processing helix chain 'E' and resid 486 through 500 removed outlier: 3.559A pdb=" N ALA E 492 " --> pdb=" O VAL E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 505 removed outlier: 4.128A pdb=" N LEU E 504 " --> pdb=" O THR E 500 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG E 505 " --> pdb=" O GLU E 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 500 through 505' Processing helix chain 'F' and resid 12 through 27 removed outlier: 3.903A pdb=" N ARG F 16 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET F 17 " --> pdb=" O ASP F 13 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 removed outlier: 3.577A pdb=" N ARG F 60 " --> pdb=" O VAL F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 4.240A pdb=" N MET F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 104 removed outlier: 3.749A pdb=" N GLU F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 108 removed outlier: 3.724A pdb=" N ASN F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 108' Processing helix chain 'F' and resid 112 through 130 removed outlier: 3.508A pdb=" N LYS F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 130 " --> pdb=" O GLN F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'F' and resid 162 through 166 removed outlier: 3.802A pdb=" N GLU F 166 " --> pdb=" O LYS F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 248 through 274 removed outlier: 3.984A pdb=" N LEU F 252 " --> pdb=" O ASP F 248 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET F 253 " --> pdb=" O PRO F 249 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU F 263 " --> pdb=" O GLU F 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS F 264 " --> pdb=" O GLU F 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP F 265 " --> pdb=" O LYS F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 293 removed outlier: 4.329A pdb=" N HIS F 290 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR F 291 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 309 Processing helix chain 'F' and resid 368 through 390 removed outlier: 3.939A pdb=" N GLU F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA F 377 " --> pdb=" O GLU F 373 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP F 380 " --> pdb=" O ARG F 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY F 383 " --> pdb=" O ASP F 379 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL F 385 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS F 387 " --> pdb=" O GLY F 383 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR F 388 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE F 389 " --> pdb=" O VAL F 385 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU F 390 " --> pdb=" O GLY F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 413 removed outlier: 3.553A pdb=" N LYS F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU F 411 " --> pdb=" O MET F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 419 through 431 removed outlier: 4.204A pdb=" N ALA F 423 " --> pdb=" O ARG F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 441 removed outlier: 3.748A pdb=" N ARG F 436 " --> pdb=" O GLU F 432 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 456 removed outlier: 3.569A pdb=" N ALA F 455 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA F 456 " --> pdb=" O LYS F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 459 No H-bonds generated for 'chain 'F' and resid 457 through 459' Processing helix chain 'F' and resid 486 through 500 removed outlier: 3.556A pdb=" N ALA F 492 " --> pdb=" O VAL F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 505 removed outlier: 4.135A pdb=" N LEU F 504 " --> pdb=" O THR F 500 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG F 505 " --> pdb=" O GLU F 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 500 through 505' Processing helix chain 'G' and resid 12 through 27 removed outlier: 3.881A pdb=" N ARG G 16 " --> pdb=" O ARG G 12 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET G 17 " --> pdb=" O ASP G 13 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE G 24 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 removed outlier: 3.578A pdb=" N ARG G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 81 removed outlier: 4.237A pdb=" N MET G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 105 removed outlier: 3.768A pdb=" N GLU G 103 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU G 104 " --> pdb=" O LYS G 100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 105 " --> pdb=" O ALA G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 108 No H-bonds generated for 'chain 'G' and resid 106 through 108' Processing helix chain 'G' and resid 112 through 130 removed outlier: 3.643A pdb=" N GLN G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS G 130 " --> pdb=" O GLN G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'G' and resid 162 through 166 removed outlier: 3.803A pdb=" N GLU G 166 " --> pdb=" O LYS G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 173 Processing helix chain 'G' and resid 248 through 274 removed outlier: 3.983A pdb=" N LEU G 252 " --> pdb=" O ASP G 248 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET G 253 " --> pdb=" O PRO G 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU G 263 " --> pdb=" O GLU G 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP G 265 " --> pdb=" O LYS G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 293 removed outlier: 4.330A pdb=" N HIS G 290 " --> pdb=" O LEU G 287 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR G 291 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 309 Processing helix chain 'G' and resid 368 through 390 removed outlier: 3.939A pdb=" N GLU G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA G 377 " --> pdb=" O GLU G 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP G 379 " --> pdb=" O ALA G 375 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP G 380 " --> pdb=" O ARG G 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY G 383 " --> pdb=" O ASP G 379 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL G 384 " --> pdb=" O ASP G 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL G 385 " --> pdb=" O ALA G 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS G 387 " --> pdb=" O GLY G 383 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR G 388 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 389 " --> pdb=" O VAL G 385 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU G 390 " --> pdb=" O GLY G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 413 removed outlier: 3.554A pdb=" N LYS G 408 " --> pdb=" O GLU G 404 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU G 411 " --> pdb=" O MET G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 416 No H-bonds generated for 'chain 'G' and resid 414 through 416' Processing helix chain 'G' and resid 419 through 431 removed outlier: 4.189A pdb=" N ALA G 423 " --> pdb=" O ARG G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 441 removed outlier: 3.763A pdb=" N ARG G 436 " --> pdb=" O GLU G 432 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN G 441 " --> pdb=" O THR G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 456 removed outlier: 3.571A pdb=" N ALA G 455 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA G 456 " --> pdb=" O LYS G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 459 No H-bonds generated for 'chain 'G' and resid 457 through 459' Processing helix chain 'G' and resid 486 through 500 removed outlier: 3.557A pdb=" N ALA G 492 " --> pdb=" O VAL G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 500 through 505 removed outlier: 4.126A pdb=" N LEU G 504 " --> pdb=" O THR G 500 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG G 505 " --> pdb=" O GLU G 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 500 through 505' Processing helix chain 'H' and resid 12 through 27 removed outlier: 3.862A pdb=" N ARG H 16 " --> pdb=" O ARG H 12 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET H 17 " --> pdb=" O ASP H 13 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN H 18 " --> pdb=" O ALA H 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE H 24 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 61 removed outlier: 3.575A pdb=" N ARG H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 81 removed outlier: 4.242A pdb=" N MET H 71 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS H 81 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 104 removed outlier: 3.749A pdb=" N GLU H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU H 104 " --> pdb=" O LYS H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 108 removed outlier: 3.737A pdb=" N ASN H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 105 through 108' Processing helix chain 'H' and resid 112 through 130 removed outlier: 3.533A pdb=" N LYS H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS H 130 " --> pdb=" O GLN H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 151 Processing helix chain 'H' and resid 162 through 166 removed outlier: 3.803A pdb=" N GLU H 166 " --> pdb=" O LYS H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 173 Processing helix chain 'H' and resid 248 through 274 removed outlier: 3.983A pdb=" N LEU H 252 " --> pdb=" O ASP H 248 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET H 253 " --> pdb=" O PRO H 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU H 254 " --> pdb=" O ALA H 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU H 263 " --> pdb=" O GLU H 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS H 264 " --> pdb=" O GLU H 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP H 265 " --> pdb=" O LYS H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 293 removed outlier: 4.329A pdb=" N HIS H 290 " --> pdb=" O LEU H 287 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR H 291 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 309 Processing helix chain 'H' and resid 368 through 390 removed outlier: 3.940A pdb=" N GLU H 372 " --> pdb=" O GLU H 368 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA H 377 " --> pdb=" O GLU H 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP H 379 " --> pdb=" O ALA H 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP H 380 " --> pdb=" O ARG H 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY H 383 " --> pdb=" O ASP H 379 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL H 384 " --> pdb=" O ASP H 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS H 387 " --> pdb=" O GLY H 383 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR H 388 " --> pdb=" O VAL H 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE H 389 " --> pdb=" O VAL H 385 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU H 390 " --> pdb=" O GLY H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 400 through 413 removed outlier: 3.554A pdb=" N LYS H 408 " --> pdb=" O GLU H 404 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU H 411 " --> pdb=" O MET H 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 416 No H-bonds generated for 'chain 'H' and resid 414 through 416' Processing helix chain 'H' and resid 419 through 431 removed outlier: 4.177A pdb=" N ALA H 423 " --> pdb=" O ARG H 419 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 431 " --> pdb=" O PHE H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 439 removed outlier: 3.782A pdb=" N ARG H 436 " --> pdb=" O GLU H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 456 removed outlier: 3.576A pdb=" N ALA H 455 " --> pdb=" O VAL H 451 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA H 456 " --> pdb=" O LYS H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 459 No H-bonds generated for 'chain 'H' and resid 457 through 459' Processing helix chain 'H' and resid 486 through 500 removed outlier: 3.557A pdb=" N ALA H 492 " --> pdb=" O VAL H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 500 through 505 removed outlier: 4.131A pdb=" N LEU H 504 " --> pdb=" O THR H 500 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG H 505 " --> pdb=" O GLU H 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 500 through 505' Processing helix chain 'I' and resid 12 through 27 removed outlier: 3.884A pdb=" N ARG I 16 " --> pdb=" O ARG I 12 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET I 17 " --> pdb=" O ASP I 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN I 18 " --> pdb=" O ALA I 14 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE I 24 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 61 removed outlier: 3.577A pdb=" N ARG I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 81 removed outlier: 4.239A pdb=" N MET I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU I 72 " --> pdb=" O ALA I 68 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE I 73 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 105 removed outlier: 3.767A pdb=" N GLU I 103 " --> pdb=" O ARG I 99 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU I 105 " --> pdb=" O ALA I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 108 No H-bonds generated for 'chain 'I' and resid 106 through 108' Processing helix chain 'I' and resid 112 through 130 removed outlier: 3.642A pdb=" N GLN I 123 " --> pdb=" O GLN I 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS I 130 " --> pdb=" O GLN I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 151 Processing helix chain 'I' and resid 162 through 166 removed outlier: 3.803A pdb=" N GLU I 166 " --> pdb=" O LYS I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 173 Processing helix chain 'I' and resid 248 through 274 removed outlier: 3.984A pdb=" N LEU I 252 " --> pdb=" O ASP I 248 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET I 253 " --> pdb=" O PRO I 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU I 254 " --> pdb=" O ALA I 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU I 263 " --> pdb=" O GLU I 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS I 264 " --> pdb=" O GLU I 260 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP I 265 " --> pdb=" O LYS I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 293 removed outlier: 4.330A pdb=" N HIS I 290 " --> pdb=" O LEU I 287 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR I 291 " --> pdb=" O ALA I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 309 Processing helix chain 'I' and resid 368 through 390 removed outlier: 3.939A pdb=" N GLU I 372 " --> pdb=" O GLU I 368 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA I 377 " --> pdb=" O GLU I 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP I 379 " --> pdb=" O ALA I 375 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP I 380 " --> pdb=" O ARG I 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY I 383 " --> pdb=" O ASP I 379 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL I 384 " --> pdb=" O ASP I 380 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL I 385 " --> pdb=" O ALA I 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS I 387 " --> pdb=" O GLY I 383 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR I 388 " --> pdb=" O VAL I 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE I 389 " --> pdb=" O VAL I 385 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU I 390 " --> pdb=" O GLY I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 413 removed outlier: 3.554A pdb=" N LYS I 408 " --> pdb=" O GLU I 404 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU I 411 " --> pdb=" O MET I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 416 No H-bonds generated for 'chain 'I' and resid 414 through 416' Processing helix chain 'I' and resid 419 through 431 removed outlier: 4.190A pdb=" N ALA I 423 " --> pdb=" O ARG I 419 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 441 removed outlier: 3.766A pdb=" N ARG I 436 " --> pdb=" O GLU I 432 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN I 441 " --> pdb=" O THR I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 447 through 456 removed outlier: 3.571A pdb=" N ALA I 455 " --> pdb=" O VAL I 451 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA I 456 " --> pdb=" O LYS I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 459 No H-bonds generated for 'chain 'I' and resid 457 through 459' Processing helix chain 'I' and resid 486 through 500 removed outlier: 3.557A pdb=" N ALA I 492 " --> pdb=" O VAL I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 500 through 505 removed outlier: 4.128A pdb=" N LEU I 504 " --> pdb=" O THR I 500 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG I 505 " --> pdb=" O GLU I 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 500 through 505' Processing helix chain 'J' and resid 12 through 27 removed outlier: 3.901A pdb=" N ARG J 16 " --> pdb=" O ARG J 12 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET J 17 " --> pdb=" O ASP J 13 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN J 18 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE J 24 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.578A pdb=" N ARG J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 81 removed outlier: 4.240A pdb=" N MET J 71 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU J 72 " --> pdb=" O ALA J 68 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE J 73 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS J 81 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 104 removed outlier: 3.748A pdb=" N GLU J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU J 104 " --> pdb=" O LYS J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 108 removed outlier: 3.724A pdb=" N ASN J 108 " --> pdb=" O LEU J 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 105 through 108' Processing helix chain 'J' and resid 112 through 130 removed outlier: 3.507A pdb=" N LYS J 116 " --> pdb=" O THR J 112 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN J 123 " --> pdb=" O GLN J 119 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS J 124 " --> pdb=" O ALA J 120 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS J 130 " --> pdb=" O GLN J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 151 Processing helix chain 'J' and resid 162 through 166 removed outlier: 3.803A pdb=" N GLU J 166 " --> pdb=" O LYS J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 173 Processing helix chain 'J' and resid 248 through 274 removed outlier: 3.983A pdb=" N LEU J 252 " --> pdb=" O ASP J 248 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET J 253 " --> pdb=" O PRO J 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU J 254 " --> pdb=" O ALA J 250 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU J 263 " --> pdb=" O GLU J 259 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS J 264 " --> pdb=" O GLU J 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP J 265 " --> pdb=" O LYS J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 293 removed outlier: 4.330A pdb=" N HIS J 290 " --> pdb=" O LEU J 287 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR J 291 " --> pdb=" O ALA J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 309 Processing helix chain 'J' and resid 368 through 390 removed outlier: 3.940A pdb=" N GLU J 372 " --> pdb=" O GLU J 368 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA J 377 " --> pdb=" O GLU J 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP J 379 " --> pdb=" O ALA J 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP J 380 " --> pdb=" O ARG J 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY J 383 " --> pdb=" O ASP J 379 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL J 384 " --> pdb=" O ASP J 380 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL J 385 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS J 387 " --> pdb=" O GLY J 383 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR J 388 " --> pdb=" O VAL J 384 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE J 389 " --> pdb=" O VAL J 385 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU J 390 " --> pdb=" O GLY J 386 " (cutoff:3.500A) Processing helix chain 'J' and resid 400 through 413 removed outlier: 3.554A pdb=" N LYS J 408 " --> pdb=" O GLU J 404 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU J 411 " --> pdb=" O MET J 407 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 416 No H-bonds generated for 'chain 'J' and resid 414 through 416' Processing helix chain 'J' and resid 419 through 431 removed outlier: 4.206A pdb=" N ALA J 423 " --> pdb=" O ARG J 419 " (cutoff:3.500A) Processing helix chain 'J' and resid 432 through 441 removed outlier: 3.747A pdb=" N ARG J 436 " --> pdb=" O GLU J 432 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN J 441 " --> pdb=" O THR J 437 " (cutoff:3.500A) Processing helix chain 'J' and resid 447 through 456 removed outlier: 3.571A pdb=" N ALA J 455 " --> pdb=" O VAL J 451 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA J 456 " --> pdb=" O LYS J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 459 No H-bonds generated for 'chain 'J' and resid 457 through 459' Processing helix chain 'J' and resid 486 through 500 removed outlier: 3.556A pdb=" N ALA J 492 " --> pdb=" O VAL J 488 " (cutoff:3.500A) Processing helix chain 'J' and resid 500 through 505 removed outlier: 4.133A pdb=" N LEU J 504 " --> pdb=" O THR J 500 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG J 505 " --> pdb=" O GLU J 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 500 through 505' Processing helix chain 'K' and resid 12 through 27 removed outlier: 3.894A pdb=" N ARG K 16 " --> pdb=" O ARG K 12 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN K 18 " --> pdb=" O ALA K 14 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE K 24 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 removed outlier: 3.579A pdb=" N ARG K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 81 removed outlier: 4.236A pdb=" N MET K 71 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU K 72 " --> pdb=" O ALA K 68 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE K 73 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS K 81 " --> pdb=" O LYS K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 104 removed outlier: 3.745A pdb=" N GLU K 103 " --> pdb=" O ARG K 99 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU K 104 " --> pdb=" O LYS K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 108 removed outlier: 3.720A pdb=" N ASN K 108 " --> pdb=" O LEU K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 105 through 108' Processing helix chain 'K' and resid 112 through 130 removed outlier: 3.636A pdb=" N GLN K 123 " --> pdb=" O GLN K 119 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 124 " --> pdb=" O ALA K 120 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 130 " --> pdb=" O GLN K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 151 Processing helix chain 'K' and resid 168 through 173 Processing helix chain 'K' and resid 248 through 274 removed outlier: 3.983A pdb=" N LEU K 252 " --> pdb=" O ASP K 248 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET K 253 " --> pdb=" O PRO K 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU K 254 " --> pdb=" O ALA K 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU K 263 " --> pdb=" O GLU K 259 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS K 264 " --> pdb=" O GLU K 260 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 293 removed outlier: 4.330A pdb=" N HIS K 290 " --> pdb=" O LEU K 287 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR K 291 " --> pdb=" O ALA K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 309 Processing helix chain 'K' and resid 368 through 390 removed outlier: 3.941A pdb=" N GLU K 372 " --> pdb=" O GLU K 368 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA K 377 " --> pdb=" O GLU K 373 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP K 379 " --> pdb=" O ALA K 375 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP K 380 " --> pdb=" O ARG K 376 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY K 383 " --> pdb=" O ASP K 379 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL K 384 " --> pdb=" O ASP K 380 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL K 385 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS K 387 " --> pdb=" O GLY K 383 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR K 388 " --> pdb=" O VAL K 384 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE K 389 " --> pdb=" O VAL K 385 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU K 390 " --> pdb=" O GLY K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 400 through 413 removed outlier: 3.544A pdb=" N LYS K 408 " --> pdb=" O GLU K 404 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU K 411 " --> pdb=" O MET K 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 416 No H-bonds generated for 'chain 'K' and resid 414 through 416' Processing helix chain 'K' and resid 419 through 431 removed outlier: 4.176A pdb=" N ALA K 423 " --> pdb=" O ARG K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 441 removed outlier: 3.761A pdb=" N ARG K 436 " --> pdb=" O GLU K 432 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN K 441 " --> pdb=" O THR K 437 " (cutoff:3.500A) Processing helix chain 'K' and resid 447 through 456 removed outlier: 3.570A pdb=" N ALA K 455 " --> pdb=" O VAL K 451 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA K 456 " --> pdb=" O LYS K 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 459 No H-bonds generated for 'chain 'K' and resid 457 through 459' Processing helix chain 'K' and resid 486 through 500 removed outlier: 3.556A pdb=" N ALA K 492 " --> pdb=" O VAL K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 500 through 505 removed outlier: 4.114A pdb=" N LEU K 504 " --> pdb=" O THR K 500 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG K 505 " --> pdb=" O GLU K 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 500 through 505' Processing helix chain 'L' and resid 12 through 27 removed outlier: 3.875A pdb=" N ARG L 16 " --> pdb=" O ARG L 12 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET L 17 " --> pdb=" O ASP L 13 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE L 24 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE L 25 " --> pdb=" O ALA L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 removed outlier: 3.577A pdb=" N ARG L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 81 removed outlier: 4.242A pdb=" N MET L 71 " --> pdb=" O PRO L 67 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE L 73 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS L 81 " --> pdb=" O LYS L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 105 removed outlier: 3.766A pdb=" N GLU L 103 " --> pdb=" O ARG L 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU L 104 " --> pdb=" O LYS L 100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU L 105 " --> pdb=" O ALA L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 108 No H-bonds generated for 'chain 'L' and resid 106 through 108' Processing helix chain 'L' and resid 112 through 130 removed outlier: 3.644A pdb=" N GLN L 123 " --> pdb=" O GLN L 119 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS L 130 " --> pdb=" O GLN L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 151 Processing helix chain 'L' and resid 162 through 166 removed outlier: 3.803A pdb=" N GLU L 166 " --> pdb=" O LYS L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 173 Processing helix chain 'L' and resid 248 through 274 removed outlier: 3.984A pdb=" N LEU L 252 " --> pdb=" O ASP L 248 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET L 253 " --> pdb=" O PRO L 249 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU L 254 " --> pdb=" O ALA L 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU L 263 " --> pdb=" O GLU L 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP L 265 " --> pdb=" O LYS L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 293 removed outlier: 4.330A pdb=" N HIS L 290 " --> pdb=" O LEU L 287 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR L 291 " --> pdb=" O ALA L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 309 Processing helix chain 'L' and resid 368 through 390 removed outlier: 3.939A pdb=" N GLU L 372 " --> pdb=" O GLU L 368 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA L 377 " --> pdb=" O GLU L 373 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP L 379 " --> pdb=" O ALA L 375 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP L 380 " --> pdb=" O ARG L 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY L 383 " --> pdb=" O ASP L 379 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL L 384 " --> pdb=" O ASP L 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL L 385 " --> pdb=" O ALA L 381 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS L 387 " --> pdb=" O GLY L 383 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR L 388 " --> pdb=" O VAL L 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE L 389 " --> pdb=" O VAL L 385 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU L 390 " --> pdb=" O GLY L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 413 removed outlier: 3.554A pdb=" N LYS L 408 " --> pdb=" O GLU L 404 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU L 411 " --> pdb=" O MET L 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 416 No H-bonds generated for 'chain 'L' and resid 414 through 416' Processing helix chain 'L' and resid 419 through 431 removed outlier: 4.194A pdb=" N ALA L 423 " --> pdb=" O ARG L 419 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 441 removed outlier: 3.761A pdb=" N ARG L 436 " --> pdb=" O GLU L 432 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN L 441 " --> pdb=" O THR L 437 " (cutoff:3.500A) Processing helix chain 'L' and resid 447 through 456 removed outlier: 3.568A pdb=" N ALA L 455 " --> pdb=" O VAL L 451 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA L 456 " --> pdb=" O LYS L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 459 No H-bonds generated for 'chain 'L' and resid 457 through 459' Processing helix chain 'L' and resid 486 through 500 removed outlier: 3.557A pdb=" N ALA L 492 " --> pdb=" O VAL L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 500 through 505 removed outlier: 4.126A pdb=" N LEU L 504 " --> pdb=" O THR L 500 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG L 505 " --> pdb=" O GLU L 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 500 through 505' Processing helix chain 'M' and resid 12 through 27 removed outlier: 3.750A pdb=" N ARG M 16 " --> pdb=" O ARG M 12 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET M 17 " --> pdb=" O ASP M 13 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE M 24 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE M 25 " --> pdb=" O ALA M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 61 removed outlier: 3.575A pdb=" N ARG M 60 " --> pdb=" O VAL M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 81 removed outlier: 4.259A pdb=" N MET M 71 " --> pdb=" O PRO M 67 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU M 72 " --> pdb=" O ALA M 68 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE M 73 " --> pdb=" O ALA M 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS M 81 " --> pdb=" O LYS M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 104 removed outlier: 3.765A pdb=" N GLU M 103 " --> pdb=" O ARG M 99 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU M 104 " --> pdb=" O LYS M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 108 removed outlier: 3.654A pdb=" N ASN M 108 " --> pdb=" O LEU M 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 105 through 108' Processing helix chain 'M' and resid 112 through 130 removed outlier: 3.643A pdb=" N GLN M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'M' and resid 162 through 166 removed outlier: 3.804A pdb=" N GLU M 166 " --> pdb=" O LYS M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 173 Processing helix chain 'M' and resid 248 through 274 removed outlier: 3.984A pdb=" N LEU M 252 " --> pdb=" O ASP M 248 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET M 253 " --> pdb=" O PRO M 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU M 254 " --> pdb=" O ALA M 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU M 263 " --> pdb=" O GLU M 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS M 264 " --> pdb=" O GLU M 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 293 removed outlier: 4.330A pdb=" N HIS M 290 " --> pdb=" O LEU M 287 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR M 291 " --> pdb=" O ALA M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 304 through 309 Processing helix chain 'M' and resid 368 through 390 removed outlier: 3.940A pdb=" N GLU M 372 " --> pdb=" O GLU M 368 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA M 377 " --> pdb=" O GLU M 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP M 379 " --> pdb=" O ALA M 375 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP M 380 " --> pdb=" O ARG M 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY M 383 " --> pdb=" O ASP M 379 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL M 384 " --> pdb=" O ASP M 380 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL M 385 " --> pdb=" O ALA M 381 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS M 387 " --> pdb=" O GLY M 383 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR M 388 " --> pdb=" O VAL M 384 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE M 389 " --> pdb=" O VAL M 385 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU M 390 " --> pdb=" O GLY M 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 400 through 413 removed outlier: 3.554A pdb=" N LYS M 408 " --> pdb=" O GLU M 404 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU M 411 " --> pdb=" O MET M 407 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 416 No H-bonds generated for 'chain 'M' and resid 414 through 416' Processing helix chain 'M' and resid 419 through 431 removed outlier: 4.198A pdb=" N ALA M 423 " --> pdb=" O ARG M 419 " (cutoff:3.500A) Processing helix chain 'M' and resid 432 through 441 removed outlier: 3.752A pdb=" N ARG M 436 " --> pdb=" O GLU M 432 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN M 441 " --> pdb=" O THR M 437 " (cutoff:3.500A) Processing helix chain 'M' and resid 447 through 456 removed outlier: 3.569A pdb=" N ALA M 455 " --> pdb=" O VAL M 451 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA M 456 " --> pdb=" O LYS M 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 457 through 459 No H-bonds generated for 'chain 'M' and resid 457 through 459' Processing helix chain 'M' and resid 486 through 500 removed outlier: 3.558A pdb=" N ALA M 492 " --> pdb=" O VAL M 488 " (cutoff:3.500A) Processing helix chain 'M' and resid 500 through 505 removed outlier: 4.102A pdb=" N LEU M 504 " --> pdb=" O THR M 500 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG M 505 " --> pdb=" O GLU M 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 500 through 505' Processing helix chain 'N' and resid 12 through 27 removed outlier: 3.889A pdb=" N ARG N 16 " --> pdb=" O ARG N 12 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET N 17 " --> pdb=" O ASP N 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE N 24 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE N 25 " --> pdb=" O ALA N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 61 removed outlier: 3.567A pdb=" N ARG N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 81 removed outlier: 4.245A pdb=" N MET N 71 " --> pdb=" O PRO N 67 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU N 72 " --> pdb=" O ALA N 68 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE N 73 " --> pdb=" O ALA N 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS N 81 " --> pdb=" O LYS N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 105 removed outlier: 3.764A pdb=" N GLU N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU N 105 " --> pdb=" O ALA N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 108 No H-bonds generated for 'chain 'N' and resid 106 through 108' Processing helix chain 'N' and resid 112 through 130 removed outlier: 3.643A pdb=" N GLN N 123 " --> pdb=" O GLN N 119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS N 124 " --> pdb=" O ALA N 120 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS N 130 " --> pdb=" O GLN N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 Processing helix chain 'N' and resid 162 through 166 removed outlier: 3.804A pdb=" N GLU N 166 " --> pdb=" O LYS N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 173 Processing helix chain 'N' and resid 248 through 274 removed outlier: 3.983A pdb=" N LEU N 252 " --> pdb=" O ASP N 248 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET N 253 " --> pdb=" O PRO N 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU N 254 " --> pdb=" O ALA N 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU N 263 " --> pdb=" O GLU N 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS N 264 " --> pdb=" O GLU N 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP N 265 " --> pdb=" O LYS N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 285 through 293 removed outlier: 4.329A pdb=" N HIS N 290 " --> pdb=" O LEU N 287 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TYR N 291 " --> pdb=" O ALA N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 304 through 309 Processing helix chain 'N' and resid 368 through 390 removed outlier: 3.939A pdb=" N GLU N 372 " --> pdb=" O GLU N 368 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA N 377 " --> pdb=" O GLU N 373 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP N 379 " --> pdb=" O ALA N 375 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP N 380 " --> pdb=" O ARG N 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY N 383 " --> pdb=" O ASP N 379 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL N 384 " --> pdb=" O ASP N 380 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL N 385 " --> pdb=" O ALA N 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS N 387 " --> pdb=" O GLY N 383 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR N 388 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE N 389 " --> pdb=" O VAL N 385 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU N 390 " --> pdb=" O GLY N 386 " (cutoff:3.500A) Processing helix chain 'N' and resid 400 through 413 removed outlier: 3.555A pdb=" N LYS N 408 " --> pdb=" O GLU N 404 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU N 411 " --> pdb=" O MET N 407 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 416 No H-bonds generated for 'chain 'N' and resid 414 through 416' Processing helix chain 'N' and resid 419 through 431 removed outlier: 4.191A pdb=" N ALA N 423 " --> pdb=" O ARG N 419 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU N 431 " --> pdb=" O PHE N 427 " (cutoff:3.500A) Processing helix chain 'N' and resid 432 through 439 removed outlier: 3.763A pdb=" N ARG N 436 " --> pdb=" O GLU N 432 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 456 removed outlier: 3.579A pdb=" N ALA N 455 " --> pdb=" O VAL N 451 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA N 456 " --> pdb=" O LYS N 452 " (cutoff:3.500A) Processing helix chain 'N' and resid 457 through 459 No H-bonds generated for 'chain 'N' and resid 457 through 459' Processing helix chain 'N' and resid 486 through 500 removed outlier: 3.558A pdb=" N ALA N 492 " --> pdb=" O VAL N 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 500 through 505 removed outlier: 4.128A pdb=" N LEU N 504 " --> pdb=" O THR N 500 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG N 505 " --> pdb=" O GLU N 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 500 through 505' Processing helix chain 'O' and resid 12 through 27 removed outlier: 3.869A pdb=" N ARG O 16 " --> pdb=" O ARG O 12 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET O 17 " --> pdb=" O ASP O 13 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 61 removed outlier: 3.578A pdb=" N ARG O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 81 removed outlier: 4.244A pdb=" N MET O 71 " --> pdb=" O PRO O 67 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU O 72 " --> pdb=" O ALA O 68 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS O 81 " --> pdb=" O LYS O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 104 removed outlier: 3.752A pdb=" N GLU O 103 " --> pdb=" O ARG O 99 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 108 removed outlier: 3.674A pdb=" N ASN O 108 " --> pdb=" O LEU O 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 105 through 108' Processing helix chain 'O' and resid 112 through 130 removed outlier: 3.634A pdb=" N GLN O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS O 124 " --> pdb=" O ALA O 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS O 130 " --> pdb=" O GLN O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 151 Processing helix chain 'O' and resid 162 through 166 removed outlier: 3.803A pdb=" N GLU O 166 " --> pdb=" O LYS O 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 173 Processing helix chain 'O' and resid 248 through 274 removed outlier: 3.983A pdb=" N LEU O 252 " --> pdb=" O ASP O 248 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET O 253 " --> pdb=" O PRO O 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU O 254 " --> pdb=" O ALA O 250 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU O 263 " --> pdb=" O GLU O 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS O 264 " --> pdb=" O GLU O 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP O 265 " --> pdb=" O LYS O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 285 through 293 removed outlier: 4.330A pdb=" N HIS O 290 " --> pdb=" O LEU O 287 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR O 291 " --> pdb=" O ALA O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 304 through 309 Processing helix chain 'O' and resid 368 through 390 removed outlier: 3.940A pdb=" N GLU O 372 " --> pdb=" O GLU O 368 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA O 377 " --> pdb=" O GLU O 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP O 379 " --> pdb=" O ALA O 375 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP O 380 " --> pdb=" O ARG O 376 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY O 383 " --> pdb=" O ASP O 379 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL O 384 " --> pdb=" O ASP O 380 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL O 385 " --> pdb=" O ALA O 381 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS O 387 " --> pdb=" O GLY O 383 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR O 388 " --> pdb=" O VAL O 384 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE O 389 " --> pdb=" O VAL O 385 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU O 390 " --> pdb=" O GLY O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 400 through 413 removed outlier: 3.554A pdb=" N LYS O 408 " --> pdb=" O GLU O 404 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU O 411 " --> pdb=" O MET O 407 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 416 No H-bonds generated for 'chain 'O' and resid 414 through 416' Processing helix chain 'O' and resid 419 through 431 removed outlier: 4.223A pdb=" N ALA O 423 " --> pdb=" O ARG O 419 " (cutoff:3.500A) Processing helix chain 'O' and resid 432 through 441 removed outlier: 3.749A pdb=" N ARG O 436 " --> pdb=" O GLU O 432 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 447 through 456 removed outlier: 3.571A pdb=" N ALA O 455 " --> pdb=" O VAL O 451 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA O 456 " --> pdb=" O LYS O 452 " (cutoff:3.500A) Processing helix chain 'O' and resid 457 through 459 No H-bonds generated for 'chain 'O' and resid 457 through 459' Processing helix chain 'O' and resid 486 through 500 removed outlier: 3.558A pdb=" N ALA O 492 " --> pdb=" O VAL O 488 " (cutoff:3.500A) Processing helix chain 'O' and resid 500 through 505 removed outlier: 4.107A pdb=" N LEU O 504 " --> pdb=" O THR O 500 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG O 505 " --> pdb=" O GLU O 501 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 500 through 505' Processing sheet with id=AA1, first strand: chain 'U' and resid 50 through 52 removed outlier: 6.423A pdb=" N MET U 41 " --> pdb=" O ILE G 510 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 189 through 191 removed outlier: 4.359A pdb=" N GLU U 190 " --> pdb=" O MET U 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE U 363 " --> pdb=" O GLU U 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 205 through 208 removed outlier: 4.374A pdb=" N VAL U 337 " --> pdb=" O VAL U 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL U 221 " --> pdb=" O VAL U 337 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 226 through 228 removed outlier: 3.538A pdb=" N PHE U 279 " --> pdb=" O ALA U 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 509 through 511 removed outlier: 3.527A pdb=" N ILE U 510 " --> pdb=" O MET A 41 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 43 " --> pdb=" O ILE U 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 189 through 191 removed outlier: 4.358A pdb=" N GLU A 190 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE A 363 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 205 through 208 removed outlier: 4.376A pdb=" N VAL A 337 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A 221 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 226 through 228 removed outlier: 3.536A pdb=" N PHE A 279 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.527A pdb=" N ILE A 510 " --> pdb=" O MET B 41 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 43 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 189 through 191 removed outlier: 4.358A pdb=" N GLU B 190 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE B 363 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 205 through 208 removed outlier: 4.375A pdb=" N VAL B 337 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 221 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 226 through 228 removed outlier: 3.538A pdb=" N PHE B 279 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 509 through 511 removed outlier: 3.528A pdb=" N ILE B 510 " --> pdb=" O MET C 41 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 43 " --> pdb=" O ILE B 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 189 through 191 removed outlier: 4.360A pdb=" N GLU C 190 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE C 363 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 205 through 208 removed outlier: 4.374A pdb=" N VAL C 337 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL C 221 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 226 through 228 removed outlier: 3.539A pdb=" N PHE C 279 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 509 through 511 removed outlier: 3.510A pdb=" N ILE C 510 " --> pdb=" O MET D 41 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 43 " --> pdb=" O ILE C 510 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 189 through 191 removed outlier: 4.359A pdb=" N GLU D 190 " --> pdb=" O MET D 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE D 363 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 205 through 208 removed outlier: 4.375A pdb=" N VAL D 337 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL D 221 " --> pdb=" O VAL D 337 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 226 through 228 removed outlier: 3.536A pdb=" N PHE D 279 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 509 through 511 removed outlier: 3.527A pdb=" N ILE D 510 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL E 43 " --> pdb=" O ILE D 510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 189 through 191 removed outlier: 4.359A pdb=" N GLU E 190 " --> pdb=" O MET E 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE E 363 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 205 through 208 removed outlier: 4.374A pdb=" N VAL E 337 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL E 221 " --> pdb=" O VAL E 337 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 226 through 228 removed outlier: 3.536A pdb=" N PHE E 279 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 509 through 511 removed outlier: 3.528A pdb=" N ILE E 510 " --> pdb=" O MET F 41 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL F 43 " --> pdb=" O ILE E 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 189 through 191 removed outlier: 4.359A pdb=" N GLU F 190 " --> pdb=" O MET F 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE F 363 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 205 through 208 removed outlier: 4.374A pdb=" N VAL F 337 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL F 221 " --> pdb=" O VAL F 337 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 226 through 228 removed outlier: 3.537A pdb=" N PHE F 279 " --> pdb=" O ALA F 227 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 509 through 511 removed outlier: 3.553A pdb=" N ILE F 510 " --> pdb=" O MET G 41 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL G 43 " --> pdb=" O ILE F 510 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 189 through 191 removed outlier: 4.358A pdb=" N GLU G 190 " --> pdb=" O MET G 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE G 363 " --> pdb=" O GLU G 190 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 205 through 208 removed outlier: 4.374A pdb=" N VAL G 337 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL G 221 " --> pdb=" O VAL G 337 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 226 through 228 removed outlier: 3.537A pdb=" N PHE G 279 " --> pdb=" O ALA G 227 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 50 through 52 removed outlier: 6.421A pdb=" N MET H 41 " --> pdb=" O ILE O 510 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 189 through 191 removed outlier: 4.359A pdb=" N GLU H 190 " --> pdb=" O MET H 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE H 363 " --> pdb=" O GLU H 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 205 through 208 removed outlier: 4.375A pdb=" N VAL H 337 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL H 221 " --> pdb=" O VAL H 337 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 226 through 228 removed outlier: 3.537A pdb=" N PHE H 279 " --> pdb=" O ALA H 227 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 509 through 511 removed outlier: 3.535A pdb=" N ILE H 510 " --> pdb=" O MET I 41 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL I 43 " --> pdb=" O ILE H 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 189 through 191 removed outlier: 4.359A pdb=" N GLU I 190 " --> pdb=" O MET I 361 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE I 363 " --> pdb=" O GLU I 190 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 205 through 208 removed outlier: 4.375A pdb=" N VAL I 337 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL I 221 " --> pdb=" O VAL I 337 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 226 through 228 removed outlier: 3.536A pdb=" N PHE I 279 " --> pdb=" O ALA I 227 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 509 through 511 removed outlier: 3.527A pdb=" N ILE I 510 " --> pdb=" O MET J 41 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL J 43 " --> pdb=" O ILE I 510 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 189 through 191 removed outlier: 4.359A pdb=" N GLU J 190 " --> pdb=" O MET J 361 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE J 363 " --> pdb=" O GLU J 190 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 205 through 208 removed outlier: 4.374A pdb=" N VAL J 337 " --> pdb=" O VAL J 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL J 221 " --> pdb=" O VAL J 337 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 226 through 228 removed outlier: 3.537A pdb=" N PHE J 279 " --> pdb=" O ALA J 227 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 509 through 511 removed outlier: 3.553A pdb=" N ILE J 510 " --> pdb=" O MET K 41 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL K 43 " --> pdb=" O ILE J 510 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 189 through 191 removed outlier: 4.359A pdb=" N GLU K 190 " --> pdb=" O MET K 361 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE K 363 " --> pdb=" O GLU K 190 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 205 through 208 removed outlier: 4.375A pdb=" N VAL K 337 " --> pdb=" O VAL K 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL K 221 " --> pdb=" O VAL K 337 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 226 through 228 removed outlier: 3.537A pdb=" N PHE K 279 " --> pdb=" O ALA K 227 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 509 through 511 removed outlier: 3.534A pdb=" N ILE K 510 " --> pdb=" O MET L 41 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL L 43 " --> pdb=" O ILE K 510 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 189 through 191 removed outlier: 4.358A pdb=" N GLU L 190 " --> pdb=" O MET L 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE L 363 " --> pdb=" O GLU L 190 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 205 through 208 removed outlier: 4.375A pdb=" N VAL L 337 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL L 221 " --> pdb=" O VAL L 337 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 226 through 228 removed outlier: 3.537A pdb=" N PHE L 279 " --> pdb=" O ALA L 227 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 509 through 511 removed outlier: 3.538A pdb=" N ILE L 510 " --> pdb=" O MET M 41 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL M 43 " --> pdb=" O ILE L 510 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 189 through 191 removed outlier: 4.359A pdb=" N GLU M 190 " --> pdb=" O MET M 361 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE M 363 " --> pdb=" O GLU M 190 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 205 through 208 removed outlier: 4.375A pdb=" N VAL M 337 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL M 221 " --> pdb=" O VAL M 337 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 226 through 228 removed outlier: 3.537A pdb=" N PHE M 279 " --> pdb=" O ALA M 227 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 509 through 511 removed outlier: 3.510A pdb=" N ILE M 510 " --> pdb=" O MET N 41 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL N 43 " --> pdb=" O ILE M 510 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 189 through 191 removed outlier: 4.359A pdb=" N GLU N 190 " --> pdb=" O MET N 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE N 363 " --> pdb=" O GLU N 190 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 205 through 208 removed outlier: 4.375A pdb=" N VAL N 337 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL N 221 " --> pdb=" O VAL N 337 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 226 through 228 removed outlier: 3.536A pdb=" N PHE N 279 " --> pdb=" O ALA N 227 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 509 through 511 removed outlier: 3.527A pdb=" N ILE N 510 " --> pdb=" O MET O 41 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL O 43 " --> pdb=" O ILE N 510 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 189 through 191 removed outlier: 4.359A pdb=" N GLU O 190 " --> pdb=" O MET O 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE O 363 " --> pdb=" O GLU O 190 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'O' and resid 205 through 208 removed outlier: 4.375A pdb=" N VAL O 337 " --> pdb=" O VAL O 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL O 221 " --> pdb=" O VAL O 337 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 226 through 228 removed outlier: 3.537A pdb=" N PHE O 279 " --> pdb=" O ALA O 227 " (cutoff:3.500A) 2118 hydrogen bonds defined for protein. 5877 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: 22.43 Time building geometry restraints manager: 14.48 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: 21152 1.34 - 1.46: 9431 1.46 - 1.58: 30345 1.58 - 1.69: 80 1.69 - 1.81: 656 Bond restraints: 61664 Sorted by residual: bond pdb=" C4 ATP I 601 " pdb=" C5 ATP I 601 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.01e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.00e+01 bond pdb=" C4 ATP N 601 " pdb=" C5 ATP N 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C4 ATP M 601 " pdb=" C5 ATP M 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP K 601 " pdb=" C5 ATP K 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.92e+01 ... (remaining 61659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.80: 82788 3.80 - 7.59: 220 7.59 - 11.39: 48 11.39 - 15.18: 16 15.18 - 18.98: 16 Bond angle restraints: 83088 Sorted by residual: angle pdb=" PB ATP N 601 " pdb=" O3B ATP N 601 " pdb=" PG ATP N 601 " ideal model delta sigma weight residual 139.87 120.89 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP I 601 " pdb=" O3B ATP I 601 " pdb=" PG ATP I 601 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP L 601 " pdb=" O3B ATP L 601 " pdb=" PG ATP L 601 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 ... (remaining 83083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 38127 17.94 - 35.88: 868 35.88 - 53.83: 45 53.83 - 71.77: 16 71.77 - 89.71: 16 Dihedral angle restraints: 39072 sinusoidal: 15888 harmonic: 23184 Sorted by residual: dihedral pdb=" CB MET H 502 " pdb=" CG MET H 502 " pdb=" SD MET H 502 " pdb=" CE MET H 502 " ideal model delta sinusoidal sigma weight residual 60.00 101.48 -41.48 3 1.50e+01 4.44e-03 7.42e+00 dihedral pdb=" CB MET M 502 " pdb=" CG MET M 502 " pdb=" SD MET M 502 " pdb=" CE MET M 502 " ideal model delta sinusoidal sigma weight residual 60.00 101.46 -41.46 3 1.50e+01 4.44e-03 7.42e+00 dihedral pdb=" CB MET C 502 " pdb=" CG MET C 502 " pdb=" SD MET C 502 " pdb=" CE MET C 502 " ideal model delta sinusoidal sigma weight residual 60.00 101.44 -41.44 3 1.50e+01 4.44e-03 7.41e+00 ... (remaining 39069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 5371 0.023 - 0.046: 2952 0.046 - 0.070: 988 0.070 - 0.093: 428 0.093 - 0.116: 421 Chirality restraints: 10160 Sorted by residual: chirality pdb=" CA ILE E 363 " pdb=" N ILE E 363 " pdb=" C ILE E 363 " pdb=" CB ILE E 363 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE K 363 " pdb=" N ILE K 363 " pdb=" C ILE K 363 " pdb=" CB ILE K 363 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA ILE C 363 " pdb=" N ILE C 363 " pdb=" C ILE C 363 " pdb=" CB ILE C 363 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 10157 not shown) Planarity restraints: 10656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 66 " -0.014 5.00e-02 4.00e+02 2.05e-02 6.71e-01 pdb=" N PRO B 67 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO B 67 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 67 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS K 66 " 0.013 5.00e-02 4.00e+02 2.04e-02 6.65e-01 pdb=" N PRO K 67 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO K 67 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO K 67 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 66 " 0.013 5.00e-02 4.00e+02 2.03e-02 6.62e-01 pdb=" N PRO I 67 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO I 67 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO I 67 " 0.011 5.00e-02 4.00e+02 ... (remaining 10653 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 16046 2.81 - 3.33: 54600 3.33 - 3.85: 88982 3.85 - 4.38: 101193 4.38 - 4.90: 176125 Nonbonded interactions: 436946 Sorted by model distance: nonbonded pdb=" O VAL L 109 " pdb=" ND1 HIS L 110 " model vdw 2.283 3.120 nonbonded pdb=" O VAL M 109 " pdb=" ND1 HIS M 110 " model vdw 2.285 3.120 nonbonded pdb=" O VAL C 109 " pdb=" ND1 HIS C 110 " model vdw 2.286 3.120 nonbonded pdb=" O VAL U 109 " pdb=" ND1 HIS U 110 " model vdw 2.289 3.120 nonbonded pdb=" O VAL E 109 " pdb=" ND1 HIS E 110 " model vdw 2.290 3.120 ... (remaining 436941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 0.100 Extract box with map and model: 1.980 Check model and map are aligned: 0.360 Set scattering table: 0.470 Process input model: 104.080 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5860 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 : 0.003 0.084 61664 Z= 0.190 Angle : 0.606 18.976 83088 Z= 0.476 Chirality : 0.038 0.116 10160 Planarity : 0.002 0.020 10656 Dihedral : 7.023 89.711 24032 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.99 % Allowed : 13.96 % Favored : 85.05 % Rotamer: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.08), residues: 8080 helix: -2.12 (0.08), residues: 3216 sheet: -0.11 (0.19), residues: 832 loop : -3.60 (0.07), residues: 4032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 110 PHE 0.003 0.001 PHE O 349 TYR 0.002 0.000 TYR K 412 ARG 0.001 0.000 ARG U 505 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 772 time to evaluate : 5.119 Fit side-chains REVERT: U 253 MET cc_start: 0.3322 (mmt) cc_final: 0.1680 (ttp) REVERT: A 17 MET cc_start: 0.7019 (tmm) cc_final: 0.6771 (tmm) REVERT: A 253 MET cc_start: 0.3713 (mmt) cc_final: 0.2235 (ttp) REVERT: B 253 MET cc_start: 0.2404 (mmt) cc_final: 0.1701 (ttp) REVERT: C 17 MET cc_start: 0.7067 (tmm) cc_final: 0.6800 (tmm) REVERT: C 253 MET cc_start: 0.3666 (mmt) cc_final: 0.2230 (ttp) REVERT: D 17 MET cc_start: 0.7455 (tmm) cc_final: 0.7245 (tmm) REVERT: D 253 MET cc_start: 0.2674 (mmt) cc_final: 0.1747 (ttp) REVERT: F 17 MET cc_start: 0.7317 (tmm) cc_final: 0.7116 (tmm) REVERT: F 506 ILE cc_start: 0.7724 (mm) cc_final: 0.7448 (mm) REVERT: G 17 MET cc_start: 0.7156 (tmm) cc_final: 0.6910 (tmm) REVERT: H 17 MET cc_start: 0.7391 (tmm) cc_final: 0.7164 (tmm) REVERT: H 253 MET cc_start: 0.4311 (mmt) cc_final: 0.2058 (ttp) REVERT: I 17 MET cc_start: 0.7251 (tmm) cc_final: 0.7028 (tmm) REVERT: J 506 ILE cc_start: 0.7654 (mm) cc_final: 0.7349 (mm) REVERT: K 17 MET cc_start: 0.7218 (tmm) cc_final: 0.6953 (tmm) REVERT: L 39 ASP cc_start: 0.7582 (m-30) cc_final: 0.7371 (m-30) REVERT: L 253 MET cc_start: 0.3322 (mmt) cc_final: 0.1993 (ttm) REVERT: M 17 MET cc_start: 0.7069 (tmm) cc_final: 0.6850 (tmm) REVERT: M 253 MET cc_start: 0.3364 (mmt) cc_final: 0.2091 (ttp) REVERT: N 17 MET cc_start: 0.7305 (tmm) cc_final: 0.7068 (tmm) REVERT: N 217 MET cc_start: 0.1088 (mmm) cc_final: 0.0761 (ttt) REVERT: N 253 MET cc_start: 0.2269 (mmt) cc_final: 0.1569 (ttp) REVERT: O 253 MET cc_start: 0.3179 (mmt) cc_final: 0.1894 (ttp) outliers start: 0 outliers final: 0 residues processed: 772 average time/residue: 0.5469 time to fit residues: 719.4982 Evaluate side-chains 478 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 478 time to evaluate : 5.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 675 optimal weight: 6.9990 chunk 606 optimal weight: 9.9990 chunk 336 optimal weight: 40.0000 chunk 207 optimal weight: 5.9990 chunk 409 optimal weight: 4.9990 chunk 323 optimal weight: 20.0000 chunk 627 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 381 optimal weight: 5.9990 chunk 466 optimal weight: 40.0000 chunk 726 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 457 HIS A 457 HIS B 355 HIS B 457 HIS C 15 GLN C 355 HIS C 457 HIS D 15 GLN D 457 HIS E 369 HIS E 457 HIS F 457 HIS G 457 HIS H 369 HIS H 457 HIS I 369 HIS I 457 HIS J 457 HIS K 457 HIS L 457 HIS M 457 HIS N 457 HIS O 369 HIS O 457 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 61664 Z= 0.448 Angle : 0.789 8.758 83088 Z= 0.407 Chirality : 0.050 0.210 10160 Planarity : 0.005 0.044 10656 Dihedral : 6.366 78.837 9040 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.57 % Favored : 90.04 % Rotamer: Outliers : 2.21 % Allowed : 5.84 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.08), residues: 8080 helix: -1.62 (0.08), residues: 3408 sheet: -0.12 (0.18), residues: 896 loop : -3.40 (0.08), residues: 3776 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS C 110 PHE 0.015 0.002 PHE M 427 TYR 0.012 0.002 TYR N 412 ARG 0.007 0.001 ARG D 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 591 time to evaluate : 5.241 Fit side-chains revert: symmetry clash REVERT: U 167 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6509 (pp) REVERT: U 217 MET cc_start: 0.2877 (mmt) cc_final: 0.0625 (ttt) REVERT: U 477 MET cc_start: 0.8478 (mmm) cc_final: 0.7842 (mmm) REVERT: A 110 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7992 (p-80) REVERT: A 167 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6486 (pp) REVERT: A 217 MET cc_start: 0.1492 (mmt) cc_final: -0.0048 (ttt) REVERT: B 477 MET cc_start: 0.8514 (mmm) cc_final: 0.7855 (mmm) REVERT: C 71 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7427 (mtm) REVERT: C 167 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6507 (pp) REVERT: C 217 MET cc_start: 0.2455 (mmt) cc_final: -0.0062 (ttt) REVERT: D 167 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6678 (pp) REVERT: D 477 MET cc_start: 0.8603 (mmm) cc_final: 0.7987 (mmm) REVERT: E 110 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.7956 (p-80) REVERT: E 167 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6664 (pp) REVERT: F 167 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6545 (pp) REVERT: F 477 MET cc_start: 0.8548 (mmm) cc_final: 0.7895 (mmm) REVERT: G 110 HIS cc_start: 0.8394 (OUTLIER) cc_final: 0.8021 (p-80) REVERT: G 167 ILE cc_start: 0.6753 (OUTLIER) cc_final: 0.6425 (pp) REVERT: H 167 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6665 (pp) REVERT: H 217 MET cc_start: 0.1989 (mmt) cc_final: 0.0099 (ttt) REVERT: H 477 MET cc_start: 0.8422 (mmm) cc_final: 0.7703 (mmm) REVERT: I 110 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.8003 (p-80) REVERT: I 167 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6584 (pp) REVERT: J 10 MET cc_start: 0.2208 (OUTLIER) cc_final: 0.1707 (ptp) REVERT: J 167 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6403 (pp) REVERT: J 477 MET cc_start: 0.8537 (mmm) cc_final: 0.7915 (mmm) REVERT: K 110 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.8182 (p-80) REVERT: K 167 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6631 (pp) REVERT: K 217 MET cc_start: 0.1625 (mmt) cc_final: -0.0360 (ttt) REVERT: L 167 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6504 (pp) REVERT: L 217 MET cc_start: 0.2369 (mmt) cc_final: 0.0538 (ttt) REVERT: L 477 MET cc_start: 0.8488 (mmm) cc_final: 0.7845 (mmm) REVERT: M 167 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6250 (pp) REVERT: M 217 MET cc_start: 0.2028 (mmt) cc_final: 0.0035 (ttt) REVERT: N 167 ILE cc_start: 0.6981 (OUTLIER) cc_final: 0.6749 (pp) REVERT: N 217 MET cc_start: 0.1296 (mmm) cc_final: 0.0630 (ttt) REVERT: N 477 MET cc_start: 0.8399 (mmm) cc_final: 0.7818 (mmm) REVERT: O 167 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6644 (pp) REVERT: O 477 MET cc_start: 0.8438 (mmm) cc_final: 0.7877 (mmm) outliers start: 144 outliers final: 53 residues processed: 713 average time/residue: 0.5739 time to fit residues: 717.8856 Evaluate side-chains 513 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 438 time to evaluate : 5.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 110 HIS Chi-restraints excluded: chain U residue 167 ILE Chi-restraints excluded: chain U residue 451 VAL Chi-restraints excluded: chain U residue 469 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 131 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 110 HIS Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 110 HIS Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 451 VAL Chi-restraints excluded: chain L residue 469 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 52 THR Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 110 HIS Chi-restraints excluded: chain N residue 167 ILE Chi-restraints excluded: chain N residue 451 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 403 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 chunk 604 optimal weight: 3.9990 chunk 494 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 727 optimal weight: 9.9990 chunk 786 optimal weight: 20.0000 chunk 648 optimal weight: 1.9990 chunk 721 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 583 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 15 GLN D 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 61664 Z= 0.191 Angle : 0.509 8.169 83088 Z= 0.262 Chirality : 0.042 0.196 10160 Planarity : 0.003 0.035 10656 Dihedral : 5.531 72.190 9040 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.56 % Favored : 92.04 % Rotamer: Outliers : 1.42 % Allowed : 9.05 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.09), residues: 8080 helix: -0.87 (0.09), residues: 3376 sheet: 0.07 (0.18), residues: 896 loop : -3.27 (0.08), residues: 3808 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 110 PHE 0.005 0.001 PHE F 427 TYR 0.004 0.001 TYR E 291 ARG 0.004 0.000 ARG D 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 476 time to evaluate : 5.136 Fit side-chains revert: symmetry clash REVERT: U 167 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6335 (pp) REVERT: U 217 MET cc_start: 0.2678 (mmp) cc_final: 0.0469 (ttt) REVERT: U 477 MET cc_start: 0.8427 (mmm) cc_final: 0.7759 (mmm) REVERT: A 167 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6585 (pp) REVERT: A 217 MET cc_start: 0.1963 (mmt) cc_final: 0.0524 (ttt) REVERT: B 167 ILE cc_start: 0.7059 (pp) cc_final: 0.6824 (pp) REVERT: B 477 MET cc_start: 0.8458 (mmm) cc_final: 0.7931 (mmm) REVERT: C 71 MET cc_start: 0.7493 (mtm) cc_final: 0.7221 (mtm) REVERT: C 167 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6634 (pp) REVERT: C 217 MET cc_start: 0.2594 (mmt) cc_final: 0.0145 (ttt) REVERT: D 167 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6473 (pp) REVERT: D 477 MET cc_start: 0.8434 (mmm) cc_final: 0.7899 (mmm) REVERT: E 167 ILE cc_start: 0.6968 (OUTLIER) cc_final: 0.6558 (pp) REVERT: E 217 MET cc_start: 0.1694 (mmt) cc_final: 0.0540 (ttt) REVERT: F 167 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6518 (pp) REVERT: F 477 MET cc_start: 0.8441 (mmm) cc_final: 0.7928 (mmm) REVERT: G 167 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6513 (pp) REVERT: G 217 MET cc_start: 0.1690 (mmt) cc_final: -0.0465 (ttt) REVERT: G 513 GLU cc_start: 0.6935 (pm20) cc_final: 0.6712 (pm20) REVERT: H 167 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6484 (pp) REVERT: H 217 MET cc_start: 0.1767 (mmt) cc_final: 0.0003 (ttt) REVERT: H 253 MET cc_start: 0.4448 (mmp) cc_final: 0.1205 (ttt) REVERT: H 477 MET cc_start: 0.8374 (mmm) cc_final: 0.7738 (mmm) REVERT: I 167 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6524 (pp) REVERT: I 217 MET cc_start: 0.1365 (mmt) cc_final: 0.0280 (ttt) REVERT: J 10 MET cc_start: 0.2242 (OUTLIER) cc_final: 0.1800 (ptp) REVERT: J 167 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6516 (pp) REVERT: J 477 MET cc_start: 0.8469 (mmm) cc_final: 0.7977 (mmm) REVERT: K 217 MET cc_start: 0.1281 (mmt) cc_final: -0.0350 (ttt) REVERT: L 167 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6300 (pp) REVERT: L 217 MET cc_start: 0.2263 (mmt) cc_final: 0.0481 (ttt) REVERT: L 477 MET cc_start: 0.8364 (mmm) cc_final: 0.7707 (mmm) REVERT: M 167 ILE cc_start: 0.6530 (OUTLIER) cc_final: 0.6220 (pp) REVERT: M 217 MET cc_start: 0.2109 (mmt) cc_final: 0.0670 (ttt) REVERT: N 167 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6581 (pp) REVERT: N 217 MET cc_start: 0.1195 (mmm) cc_final: 0.0563 (ttt) REVERT: N 477 MET cc_start: 0.8398 (mmm) cc_final: 0.7936 (mmm) REVERT: O 167 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6575 (pp) REVERT: O 217 MET cc_start: 0.2844 (mmt) cc_final: 0.0269 (ttt) REVERT: O 477 MET cc_start: 0.8369 (mmm) cc_final: 0.7817 (mmm) outliers start: 93 outliers final: 46 residues processed: 551 average time/residue: 0.5050 time to fit residues: 499.3529 Evaluate side-chains 501 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 440 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 110 HIS Chi-restraints excluded: chain U residue 167 ILE Chi-restraints excluded: chain U residue 469 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 131 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 110 HIS Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 469 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 110 HIS Chi-restraints excluded: chain N residue 167 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 110 HIS Chi-restraints excluded: chain O residue 167 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 719 optimal weight: 40.0000 chunk 547 optimal weight: 6.9990 chunk 377 optimal weight: 40.0000 chunk 80 optimal weight: 0.0970 chunk 347 optimal weight: 6.9990 chunk 488 optimal weight: 9.9990 chunk 730 optimal weight: 50.0000 chunk 773 optimal weight: 6.9990 chunk 381 optimal weight: 40.0000 chunk 692 optimal weight: 1.9990 chunk 208 optimal weight: 0.6980 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 355 HIS U 369 HIS A 355 HIS A 369 HIS B 369 HIS C 369 HIS D 355 HIS D 369 HIS E 289 GLN E 355 HIS F 355 HIS F 369 HIS G 355 HIS G 369 HIS H 355 HIS I 289 GLN J 369 HIS K 355 HIS K 369 HIS L 355 HIS L 369 HIS M 355 HIS M 369 HIS N 355 HIS N 369 HIS O 355 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 61664 Z= 0.290 Angle : 0.593 8.970 83088 Z= 0.300 Chirality : 0.044 0.140 10160 Planarity : 0.004 0.038 10656 Dihedral : 5.839 59.197 9040 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.56 % Favored : 91.06 % Rotamer: Outliers : 2.54 % Allowed : 9.87 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.09), residues: 8080 helix: -0.75 (0.09), residues: 3360 sheet: 0.23 (0.19), residues: 896 loop : -3.19 (0.08), residues: 3824 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS G 110 PHE 0.007 0.001 PHE J 427 TYR 0.008 0.002 TYR A 412 ARG 0.007 0.001 ARG G 516 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 481 time to evaluate : 5.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 71 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.6782 (mtt) REVERT: U 167 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6379 (pp) REVERT: U 217 MET cc_start: 0.2894 (mmp) cc_final: 0.0552 (ttt) REVERT: U 477 MET cc_start: 0.8450 (mmm) cc_final: 0.7944 (mmm) REVERT: A 110 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7989 (p-80) REVERT: A 167 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6537 (pp) REVERT: A 217 MET cc_start: 0.1346 (mmt) cc_final: 0.0084 (ttt) REVERT: B 71 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.6873 (mtt) REVERT: B 167 ILE cc_start: 0.7113 (pp) cc_final: 0.6824 (pp) REVERT: B 477 MET cc_start: 0.8502 (mmm) cc_final: 0.8027 (mmm) REVERT: C 71 MET cc_start: 0.7793 (mtm) cc_final: 0.7497 (mtm) REVERT: C 110 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7981 (p-80) REVERT: C 167 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6618 (pp) REVERT: C 217 MET cc_start: 0.2067 (mmt) cc_final: 0.0368 (ttt) REVERT: D 71 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6866 (mtt) REVERT: D 167 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6638 (pp) REVERT: D 477 MET cc_start: 0.8468 (mmm) cc_final: 0.8016 (mmm) REVERT: E 110 HIS cc_start: 0.8403 (OUTLIER) cc_final: 0.7980 (p-80) REVERT: E 167 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6517 (pp) REVERT: E 217 MET cc_start: 0.2049 (mmt) cc_final: 0.0499 (ttt) REVERT: E 513 GLU cc_start: 0.7166 (pm20) cc_final: 0.6605 (pm20) REVERT: F 71 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.6754 (mtt) REVERT: F 167 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6632 (pp) REVERT: F 477 MET cc_start: 0.8473 (mmm) cc_final: 0.7998 (mmm) REVERT: G 110 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.8037 (p-80) REVERT: G 167 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6527 (pp) REVERT: G 217 MET cc_start: 0.1022 (mmt) cc_final: -0.0248 (ttt) REVERT: G 262 MET cc_start: 0.3875 (tpp) cc_final: 0.3653 (tpp) REVERT: G 477 MET cc_start: 0.8467 (mmm) cc_final: 0.8191 (mmm) REVERT: H 71 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6845 (mtt) REVERT: H 167 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6502 (pp) REVERT: H 217 MET cc_start: 0.1452 (mmt) cc_final: 0.0210 (ttt) REVERT: H 477 MET cc_start: 0.8396 (mmm) cc_final: 0.7789 (mmm) REVERT: I 71 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7416 (mtm) REVERT: I 110 HIS cc_start: 0.8474 (OUTLIER) cc_final: 0.8043 (p-80) REVERT: I 167 ILE cc_start: 0.7000 (OUTLIER) cc_final: 0.6644 (pp) REVERT: I 217 MET cc_start: 0.1638 (mmt) cc_final: 0.0414 (ttt) REVERT: I 513 GLU cc_start: 0.7116 (pm20) cc_final: 0.6621 (pm20) REVERT: J 10 MET cc_start: 0.2804 (OUTLIER) cc_final: 0.1870 (ptp) REVERT: J 71 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6721 (mtt) REVERT: J 167 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6513 (pp) REVERT: J 477 MET cc_start: 0.8481 (mmm) cc_final: 0.8016 (mmm) REVERT: K 110 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8136 (p-80) REVERT: K 167 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6664 (pp) REVERT: K 217 MET cc_start: 0.1273 (mmt) cc_final: 0.0074 (ttt) REVERT: L 71 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6868 (mtt) REVERT: L 167 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6393 (pp) REVERT: L 217 MET cc_start: 0.2497 (mmt) cc_final: 0.0598 (ttt) REVERT: L 477 MET cc_start: 0.8400 (mmm) cc_final: 0.7825 (mmm) REVERT: M 62 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7513 (mtp) REVERT: M 110 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.7902 (p-80) REVERT: M 167 ILE cc_start: 0.6682 (OUTLIER) cc_final: 0.6229 (pp) REVERT: M 217 MET cc_start: 0.2068 (mmt) cc_final: 0.0625 (ttt) REVERT: M 513 GLU cc_start: 0.6985 (pm20) cc_final: 0.6735 (pm20) REVERT: N 71 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.6855 (mtt) REVERT: N 167 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6617 (pp) REVERT: N 217 MET cc_start: 0.1215 (mmm) cc_final: 0.0356 (ttt) REVERT: N 477 MET cc_start: 0.8421 (mmm) cc_final: 0.7968 (mmm) REVERT: O 71 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7393 (mtm) REVERT: O 110 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7973 (p-80) REVERT: O 167 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6590 (pp) REVERT: O 217 MET cc_start: 0.1898 (mmt) cc_final: 0.0353 (ttt) outliers start: 166 outliers final: 98 residues processed: 606 average time/residue: 0.4898 time to fit residues: 529.8122 Evaluate side-chains 556 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 423 time to evaluate : 5.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 71 MET Chi-restraints excluded: chain U residue 110 HIS Chi-restraints excluded: chain U residue 167 ILE Chi-restraints excluded: chain U residue 433 VAL Chi-restraints excluded: chain U residue 451 VAL Chi-restraints excluded: chain U residue 469 VAL Chi-restraints excluded: chain U residue 488 VAL Chi-restraints excluded: chain U residue 493 ILE Chi-restraints excluded: chain U residue 509 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain I residue 128 LEU Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 71 MET Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 131 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 110 HIS Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 71 MET Chi-restraints excluded: chain L residue 110 HIS Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain L residue 451 VAL Chi-restraints excluded: chain L residue 469 VAL Chi-restraints excluded: chain L residue 488 VAL Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 62 MET Chi-restraints excluded: chain M residue 110 HIS Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 449 ILE Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 71 MET Chi-restraints excluded: chain N residue 110 HIS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 167 ILE Chi-restraints excluded: chain N residue 433 VAL Chi-restraints excluded: chain N residue 451 VAL Chi-restraints excluded: chain N residue 493 ILE Chi-restraints excluded: chain N residue 509 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 71 MET Chi-restraints excluded: chain O residue 110 HIS Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 167 ILE Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 508 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 644 optimal weight: 3.9990 chunk 438 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 575 optimal weight: 5.9990 chunk 319 optimal weight: 20.0000 chunk 659 optimal weight: 4.9990 chunk 534 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 394 optimal weight: 2.9990 chunk 694 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 289 GLN ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 289 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 61664 Z= 0.205 Angle : 0.501 9.039 83088 Z= 0.256 Chirality : 0.041 0.139 10160 Planarity : 0.003 0.038 10656 Dihedral : 5.515 50.201 9040 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.83 % Favored : 93.97 % Rotamer: Outliers : 2.22 % Allowed : 11.75 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.09), residues: 8080 helix: -0.43 (0.09), residues: 3360 sheet: 0.43 (0.19), residues: 896 loop : -3.09 (0.08), residues: 3824 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS J 355 PHE 0.006 0.001 PHE J 427 TYR 0.005 0.001 TYR A 412 ARG 0.003 0.000 ARG M 516 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 453 time to evaluate : 5.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 71 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.6677 (mtt) REVERT: U 167 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6446 (pp) REVERT: U 217 MET cc_start: 0.2887 (mmp) cc_final: 0.0555 (ttt) REVERT: U 477 MET cc_start: 0.8394 (mmm) cc_final: 0.8007 (mmm) REVERT: A 110 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.7971 (p-80) REVERT: A 167 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6567 (pp) REVERT: A 217 MET cc_start: 0.1349 (mmt) cc_final: 0.0058 (ttt) REVERT: A 513 GLU cc_start: 0.7094 (pm20) cc_final: 0.6673 (pm20) REVERT: B 71 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6789 (mtt) REVERT: B 167 ILE cc_start: 0.7020 (pp) cc_final: 0.6713 (pp) REVERT: B 477 MET cc_start: 0.8434 (mmm) cc_final: 0.8028 (mmm) REVERT: C 110 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.7920 (p-80) REVERT: C 167 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6604 (pp) REVERT: C 217 MET cc_start: 0.1914 (mmt) cc_final: 0.0609 (ttt) REVERT: C 513 GLU cc_start: 0.7146 (pm20) cc_final: 0.6939 (pm20) REVERT: D 71 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6742 (mtt) REVERT: D 167 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6487 (pp) REVERT: D 477 MET cc_start: 0.8374 (mmm) cc_final: 0.8067 (mmm) REVERT: E 167 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6584 (pp) REVERT: E 217 MET cc_start: 0.1731 (mmt) cc_final: 0.0378 (ttt) REVERT: F 71 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6617 (mtt) REVERT: F 167 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6517 (pp) REVERT: F 477 MET cc_start: 0.8412 (mmm) cc_final: 0.8039 (mmm) REVERT: G 110 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.8010 (p-80) REVERT: G 167 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6605 (pp) REVERT: G 217 MET cc_start: 0.0999 (mmp) cc_final: -0.0274 (ttt) REVERT: G 477 MET cc_start: 0.8478 (mmm) cc_final: 0.8248 (mmm) REVERT: H 71 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.6763 (mtt) REVERT: H 167 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6630 (pp) REVERT: H 262 MET cc_start: 0.3863 (tpp) cc_final: 0.1247 (ttt) REVERT: H 477 MET cc_start: 0.8385 (mmm) cc_final: 0.7949 (mmm) REVERT: I 167 ILE cc_start: 0.6948 (OUTLIER) cc_final: 0.6668 (pp) REVERT: I 217 MET cc_start: 0.1517 (mmp) cc_final: 0.0472 (ttt) REVERT: I 513 GLU cc_start: 0.7083 (pm20) cc_final: 0.6578 (pm20) REVERT: J 10 MET cc_start: 0.2861 (OUTLIER) cc_final: 0.1970 (ptp) REVERT: J 71 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6634 (mtt) REVERT: J 167 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6420 (pp) REVERT: J 477 MET cc_start: 0.8417 (mmm) cc_final: 0.8059 (mmm) REVERT: K 167 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6710 (pp) REVERT: K 217 MET cc_start: 0.1328 (mmt) cc_final: -0.0237 (ttt) REVERT: K 513 GLU cc_start: 0.7198 (pm20) cc_final: 0.6922 (pm20) REVERT: L 71 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6769 (mtt) REVERT: L 167 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.6314 (pp) REVERT: L 217 MET cc_start: 0.2541 (mmt) cc_final: 0.0406 (ttt) REVERT: L 477 MET cc_start: 0.8393 (mmm) cc_final: 0.7975 (mmm) REVERT: M 62 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7501 (mtp) REVERT: M 167 ILE cc_start: 0.6497 (OUTLIER) cc_final: 0.6154 (pp) REVERT: M 217 MET cc_start: 0.1647 (mmt) cc_final: 0.0236 (ttt) REVERT: M 513 GLU cc_start: 0.6970 (pm20) cc_final: 0.6615 (pm20) REVERT: N 71 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.6774 (mtt) REVERT: N 167 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6504 (pp) REVERT: N 217 MET cc_start: 0.1238 (mmm) cc_final: 0.0361 (ttt) REVERT: N 477 MET cc_start: 0.8334 (mmm) cc_final: 0.7886 (mmm) REVERT: N 513 GLU cc_start: 0.7121 (pm20) cc_final: 0.6819 (pm20) REVERT: O 110 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.7984 (p-80) REVERT: O 167 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6721 (pp) REVERT: O 217 MET cc_start: 0.1900 (mmt) cc_final: 0.0549 (ttt) outliers start: 145 outliers final: 84 residues processed: 563 average time/residue: 0.4964 time to fit residues: 504.1316 Evaluate side-chains 551 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 438 time to evaluate : 5.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 71 MET Chi-restraints excluded: chain U residue 110 HIS Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 167 ILE Chi-restraints excluded: chain U residue 433 VAL Chi-restraints excluded: chain U residue 469 VAL Chi-restraints excluded: chain U residue 509 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 308 MET Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 508 ASP Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 43 VAL Chi-restraints excluded: chain J residue 71 MET Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 131 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 308 MET Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain K residue 508 ASP Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 71 MET Chi-restraints excluded: chain L residue 110 HIS Chi-restraints excluded: chain L residue 143 ILE Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 62 MET Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 449 ILE Chi-restraints excluded: chain M residue 509 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 71 MET Chi-restraints excluded: chain N residue 110 HIS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 167 ILE Chi-restraints excluded: chain N residue 433 VAL Chi-restraints excluded: chain N residue 509 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 110 HIS Chi-restraints excluded: chain O residue 167 ILE Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain O residue 509 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 260 optimal weight: 0.6980 chunk 696 optimal weight: 0.0000 chunk 152 optimal weight: 2.9990 chunk 454 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 774 optimal weight: 6.9990 chunk 642 optimal weight: 0.8980 chunk 358 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 256 optimal weight: 0.8980 chunk 406 optimal weight: 4.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 GLN C 289 GLN G 289 GLN I 355 HIS K 289 GLN L 289 GLN M 289 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 61664 Z= 0.110 Angle : 0.445 8.906 83088 Z= 0.226 Chirality : 0.039 0.151 10160 Planarity : 0.002 0.031 10656 Dihedral : 4.961 44.594 9040 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.09 % Favored : 94.72 % Rotamer: Outliers : 1.84 % Allowed : 12.10 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.09), residues: 8080 helix: -0.06 (0.10), residues: 3376 sheet: 0.68 (0.19), residues: 896 loop : -2.93 (0.08), residues: 3808 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS J 355 PHE 0.003 0.000 PHE J 427 TYR 0.003 0.000 TYR I 291 ARG 0.004 0.000 ARG M 516 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 494 time to evaluate : 5.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 217 MET cc_start: 0.2637 (mmp) cc_final: 0.0370 (ttt) REVERT: U 477 MET cc_start: 0.8321 (mmm) cc_final: 0.7874 (mmm) REVERT: U 513 GLU cc_start: 0.6995 (pm20) cc_final: 0.6671 (pm20) REVERT: A 167 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6629 (pp) REVERT: A 217 MET cc_start: 0.1176 (mmt) cc_final: 0.0015 (ttt) REVERT: A 513 GLU cc_start: 0.6937 (pm20) cc_final: 0.6528 (pm20) REVERT: B 71 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6630 (mtt) REVERT: B 167 ILE cc_start: 0.7085 (pp) cc_final: 0.6574 (pp) REVERT: B 477 MET cc_start: 0.8359 (mmm) cc_final: 0.7944 (mmm) REVERT: C 217 MET cc_start: 0.1824 (mmt) cc_final: 0.0469 (ttt) REVERT: D 71 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6604 (mtt) REVERT: D 167 ILE cc_start: 0.6800 (OUTLIER) cc_final: 0.6446 (pp) REVERT: D 477 MET cc_start: 0.8319 (mmm) cc_final: 0.7966 (mmm) REVERT: E 167 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6598 (pp) REVERT: E 217 MET cc_start: 0.1736 (mmt) cc_final: 0.0339 (ttt) REVERT: E 513 GLU cc_start: 0.6934 (pm20) cc_final: 0.6519 (pm20) REVERT: F 71 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.6482 (mtt) REVERT: F 167 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6441 (pp) REVERT: F 477 MET cc_start: 0.8333 (mmm) cc_final: 0.7951 (mmm) REVERT: G 217 MET cc_start: 0.1074 (mmp) cc_final: -0.0171 (ttt) REVERT: H 71 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6616 (mtt) REVERT: H 262 MET cc_start: 0.3911 (tpp) cc_final: 0.1331 (ttt) REVERT: H 477 MET cc_start: 0.8323 (mmm) cc_final: 0.7831 (mmm) REVERT: I 167 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6705 (pp) REVERT: I 217 MET cc_start: 0.1427 (mmp) cc_final: 0.0425 (ttt) REVERT: J 10 MET cc_start: 0.2803 (OUTLIER) cc_final: 0.1977 (ptp) REVERT: J 71 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6484 (mtt) REVERT: J 167 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6350 (pp) REVERT: J 477 MET cc_start: 0.8337 (mmm) cc_final: 0.7967 (mmm) REVERT: K 167 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6557 (pp) REVERT: K 217 MET cc_start: 0.1313 (mmt) cc_final: -0.0245 (ttt) REVERT: K 513 GLU cc_start: 0.7146 (pm20) cc_final: 0.6847 (pm20) REVERT: L 71 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6573 (mtt) REVERT: L 217 MET cc_start: 0.2252 (mmt) cc_final: 0.0696 (ttt) REVERT: L 477 MET cc_start: 0.8303 (mmm) cc_final: 0.7854 (mmm) REVERT: M 62 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7440 (mtp) REVERT: M 167 ILE cc_start: 0.6260 (OUTLIER) cc_final: 0.5988 (pp) REVERT: M 217 MET cc_start: 0.1529 (mmt) cc_final: -0.0060 (ttt) REVERT: N 71 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6613 (mtt) REVERT: N 167 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6492 (pp) REVERT: N 217 MET cc_start: 0.1191 (mmm) cc_final: 0.0335 (ttt) REVERT: N 477 MET cc_start: 0.8299 (mmm) cc_final: 0.7855 (mmm) REVERT: N 513 GLU cc_start: 0.7013 (pm20) cc_final: 0.6736 (pm20) REVERT: O 167 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6783 (pp) REVERT: O 217 MET cc_start: 0.1794 (mmt) cc_final: 0.0239 (ttt) outliers start: 120 outliers final: 53 residues processed: 570 average time/residue: 0.4910 time to fit residues: 505.9067 Evaluate side-chains 527 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 455 time to evaluate : 5.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 110 HIS Chi-restraints excluded: chain U residue 235 ILE Chi-restraints excluded: chain U residue 509 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 62 MET Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 71 MET Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 110 HIS Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 71 MET Chi-restraints excluded: chain L residue 110 HIS Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 469 VAL Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain M residue 62 MET Chi-restraints excluded: chain M residue 110 HIS Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 71 MET Chi-restraints excluded: chain N residue 110 HIS Chi-restraints excluded: chain N residue 167 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 110 HIS Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 167 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 746 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 441 optimal weight: 4.9990 chunk 565 optimal weight: 0.3980 chunk 437 optimal weight: 20.0000 chunk 651 optimal weight: 0.6980 chunk 432 optimal weight: 50.0000 chunk 771 optimal weight: 0.1980 chunk 482 optimal weight: 40.0000 chunk 470 optimal weight: 0.2980 chunk 355 optimal weight: 0.4980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 GLN D 289 GLN H 289 GLN J 289 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 61664 Z= 0.100 Angle : 0.439 9.554 83088 Z= 0.224 Chirality : 0.039 0.152 10160 Planarity : 0.002 0.030 10656 Dihedral : 4.642 42.846 9040 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.22 % Favored : 94.58 % Rotamer: Outliers : 1.52 % Allowed : 12.81 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.09), residues: 8080 helix: 0.19 (0.10), residues: 3376 sheet: 0.84 (0.19), residues: 896 loop : -2.77 (0.08), residues: 3808 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 355 PHE 0.004 0.000 PHE U 349 TYR 0.004 0.000 TYR B 412 ARG 0.002 0.000 ARG M 516 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 479 time to evaluate : 5.292 Fit side-chains revert: symmetry clash REVERT: U 71 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6464 (mtt) REVERT: U 217 MET cc_start: 0.2883 (mmp) cc_final: 0.0804 (ttt) REVERT: U 477 MET cc_start: 0.8313 (mmm) cc_final: 0.7820 (mmm) REVERT: U 513 GLU cc_start: 0.6937 (pm20) cc_final: 0.6411 (pm20) REVERT: A 217 MET cc_start: 0.1128 (mmt) cc_final: -0.0059 (ttt) REVERT: A 513 GLU cc_start: 0.6839 (pm20) cc_final: 0.6453 (pm20) REVERT: B 477 MET cc_start: 0.8333 (mmm) cc_final: 0.7881 (mmm) REVERT: B 513 GLU cc_start: 0.7064 (pm20) cc_final: 0.6843 (pm20) REVERT: C 39 ASP cc_start: 0.8242 (m-30) cc_final: 0.8029 (m-30) REVERT: C 217 MET cc_start: 0.1643 (mmt) cc_final: 0.0388 (ttt) REVERT: D 62 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7438 (ttp) REVERT: D 167 ILE cc_start: 0.6800 (OUTLIER) cc_final: 0.6556 (pp) REVERT: D 477 MET cc_start: 0.8279 (mmm) cc_final: 0.7898 (mmm) REVERT: E 167 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6742 (pp) REVERT: E 217 MET cc_start: 0.1727 (mmt) cc_final: 0.0329 (ttt) REVERT: E 513 GLU cc_start: 0.6830 (pm20) cc_final: 0.6406 (pm20) REVERT: F 71 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6429 (mtt) REVERT: F 144 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7208 (tt) REVERT: F 167 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.6335 (pp) REVERT: F 477 MET cc_start: 0.8319 (mmm) cc_final: 0.7904 (mmm) REVERT: G 217 MET cc_start: 0.1018 (mmp) cc_final: -0.0229 (ttt) REVERT: H 71 MET cc_start: 0.7343 (OUTLIER) cc_final: 0.6557 (mtt) REVERT: H 217 MET cc_start: 0.1020 (mmp) cc_final: -0.0031 (ttt) REVERT: H 262 MET cc_start: 0.3953 (tpp) cc_final: 0.1387 (ttt) REVERT: H 477 MET cc_start: 0.8301 (mmm) cc_final: 0.7755 (mmm) REVERT: I 217 MET cc_start: 0.1139 (mmp) cc_final: 0.0197 (ttt) REVERT: I 513 GLU cc_start: 0.6887 (pm20) cc_final: 0.6527 (pm20) REVERT: J 10 MET cc_start: 0.2803 (OUTLIER) cc_final: 0.1950 (ptp) REVERT: J 167 ILE cc_start: 0.6584 (OUTLIER) cc_final: 0.6284 (pp) REVERT: J 477 MET cc_start: 0.8323 (mmm) cc_final: 0.7925 (mmm) REVERT: K 18 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8396 (m-40) REVERT: K 167 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6624 (pp) REVERT: K 217 MET cc_start: 0.1329 (mmt) cc_final: -0.0280 (ttt) REVERT: K 513 GLU cc_start: 0.7094 (pm20) cc_final: 0.6788 (pm20) REVERT: L 71 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6532 (mtt) REVERT: L 217 MET cc_start: 0.1930 (mmt) cc_final: 0.0789 (ttt) REVERT: L 477 MET cc_start: 0.8304 (mmm) cc_final: 0.7800 (mmm) REVERT: M 18 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8451 (m-40) REVERT: M 167 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6238 (pp) REVERT: M 217 MET cc_start: 0.1352 (mmt) cc_final: 0.0067 (ttt) REVERT: N 62 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7425 (ttp) REVERT: N 167 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6716 (pp) REVERT: N 217 MET cc_start: 0.1187 (mmm) cc_final: 0.0313 (ttt) REVERT: N 477 MET cc_start: 0.8299 (mmm) cc_final: 0.7782 (mmm) REVERT: N 513 GLU cc_start: 0.6999 (pm20) cc_final: 0.6520 (pm20) REVERT: O 217 MET cc_start: 0.1804 (mmt) cc_final: 0.0343 (ttt) outliers start: 99 outliers final: 53 residues processed: 532 average time/residue: 0.4936 time to fit residues: 473.9876 Evaluate side-chains 521 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 451 time to evaluate : 5.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 71 MET Chi-restraints excluded: chain U residue 110 HIS Chi-restraints excluded: chain U residue 235 ILE Chi-restraints excluded: chain U residue 509 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 25 ILE Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 110 HIS Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 308 MET Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 71 MET Chi-restraints excluded: chain L residue 110 HIS Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 469 VAL Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 110 HIS Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 110 HIS Chi-restraints excluded: chain N residue 167 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain O residue 110 HIS Chi-restraints excluded: chain O residue 143 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 477 optimal weight: 5.9990 chunk 307 optimal weight: 9.9990 chunk 460 optimal weight: 0.9980 chunk 232 optimal weight: 40.0000 chunk 151 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 490 optimal weight: 0.4980 chunk 525 optimal weight: 7.9990 chunk 381 optimal weight: 30.0000 chunk 71 optimal weight: 8.9990 chunk 606 optimal weight: 1.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 289 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 61664 Z= 0.244 Angle : 0.533 10.298 83088 Z= 0.268 Chirality : 0.042 0.148 10160 Planarity : 0.003 0.030 10656 Dihedral : 5.210 42.779 9040 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.24 % Favored : 92.56 % Rotamer: Outliers : 1.93 % Allowed : 12.64 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.09), residues: 8080 helix: 0.04 (0.10), residues: 3344 sheet: 0.80 (0.19), residues: 896 loop : -2.81 (0.08), residues: 3840 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 110 PHE 0.006 0.001 PHE J 427 TYR 0.007 0.001 TYR K 412 ARG 0.002 0.000 ARG G 516 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 421 time to evaluate : 5.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 71 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.6673 (mtt) REVERT: U 217 MET cc_start: 0.2546 (mmp) cc_final: 0.0299 (ttt) REVERT: U 477 MET cc_start: 0.8381 (mmm) cc_final: 0.7975 (mmm) REVERT: A 217 MET cc_start: 0.1087 (mmt) cc_final: -0.0085 (ttt) REVERT: A 513 GLU cc_start: 0.7022 (pm20) cc_final: 0.6699 (pm20) REVERT: B 71 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6778 (mtt) REVERT: B 477 MET cc_start: 0.8410 (mmm) cc_final: 0.7983 (mmm) REVERT: B 513 GLU cc_start: 0.7217 (pm20) cc_final: 0.6778 (pm20) REVERT: C 110 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7981 (p-80) REVERT: C 217 MET cc_start: 0.1644 (mmt) cc_final: 0.0273 (ttt) REVERT: D 167 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6676 (pp) REVERT: D 477 MET cc_start: 0.8409 (mmm) cc_final: 0.8024 (mmm) REVERT: E 167 ILE cc_start: 0.6933 (OUTLIER) cc_final: 0.6596 (pp) REVERT: E 217 MET cc_start: 0.1757 (mmt) cc_final: 0.0320 (ttt) REVERT: E 513 GLU cc_start: 0.7004 (pm20) cc_final: 0.6491 (pm20) REVERT: F 71 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6607 (mtt) REVERT: F 167 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6489 (pp) REVERT: F 477 MET cc_start: 0.8395 (mmm) cc_final: 0.7982 (mmm) REVERT: G 217 MET cc_start: 0.1011 (mmp) cc_final: 0.0030 (ttt) REVERT: H 71 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.6759 (mtt) REVERT: H 477 MET cc_start: 0.8358 (mmm) cc_final: 0.7910 (mmm) REVERT: I 71 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7226 (mtm) REVERT: I 217 MET cc_start: 0.1527 (mmp) cc_final: 0.0415 (ttt) REVERT: I 513 GLU cc_start: 0.7053 (pm20) cc_final: 0.6564 (pm20) REVERT: J 10 MET cc_start: 0.2711 (OUTLIER) cc_final: 0.1635 (ptp) REVERT: J 167 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6447 (pp) REVERT: J 477 MET cc_start: 0.8426 (mmm) cc_final: 0.8059 (mmm) REVERT: K 18 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8451 (m-40) REVERT: K 167 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6358 (pp) REVERT: K 217 MET cc_start: 0.1418 (mmt) cc_final: -0.0237 (ttt) REVERT: K 513 GLU cc_start: 0.7127 (pm20) cc_final: 0.6790 (pm20) REVERT: L 71 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6727 (mtt) REVERT: L 217 MET cc_start: 0.1961 (mmt) cc_final: 0.0757 (ttt) REVERT: L 477 MET cc_start: 0.8390 (mmm) cc_final: 0.7913 (mmm) REVERT: M 18 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8561 (m-40) REVERT: M 167 ILE cc_start: 0.6463 (OUTLIER) cc_final: 0.6132 (pp) REVERT: M 217 MET cc_start: 0.1353 (mmt) cc_final: 0.0175 (ttt) REVERT: N 167 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6444 (pp) REVERT: N 217 MET cc_start: 0.1322 (mmm) cc_final: 0.0289 (ttt) REVERT: N 477 MET cc_start: 0.8332 (mmm) cc_final: 0.7842 (mmm) REVERT: N 513 GLU cc_start: 0.7108 (pm20) cc_final: 0.6753 (pm20) REVERT: O 71 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7191 (mtm) REVERT: O 110 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.7961 (p-80) REVERT: O 217 MET cc_start: 0.1757 (mmt) cc_final: 0.0315 (ttt) outliers start: 126 outliers final: 87 residues processed: 513 average time/residue: 0.4922 time to fit residues: 457.0678 Evaluate side-chains 519 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 413 time to evaluate : 5.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 71 MET Chi-restraints excluded: chain U residue 110 HIS Chi-restraints excluded: chain U residue 131 THR Chi-restraints excluded: chain U residue 235 ILE Chi-restraints excluded: chain U residue 433 VAL Chi-restraints excluded: chain U residue 493 ILE Chi-restraints excluded: chain U residue 509 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 131 THR Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 235 ILE Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 308 MET Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 71 MET Chi-restraints excluded: chain L residue 110 HIS Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain L residue 469 VAL Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 509 VAL Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 110 HIS Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 167 ILE Chi-restraints excluded: chain N residue 509 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 71 MET Chi-restraints excluded: chain O residue 110 HIS Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain O residue 509 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 701 optimal weight: 0.4980 chunk 738 optimal weight: 0.9980 chunk 673 optimal weight: 20.0000 chunk 718 optimal weight: 10.0000 chunk 432 optimal weight: 50.0000 chunk 313 optimal weight: 8.9990 chunk 564 optimal weight: 5.9990 chunk 220 optimal weight: 50.0000 chunk 649 optimal weight: 0.8980 chunk 679 optimal weight: 50.0000 chunk 716 optimal weight: 40.0000 overall best weight: 3.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 61664 Z= 0.284 Angle : 0.584 11.172 83088 Z= 0.290 Chirality : 0.043 0.151 10160 Planarity : 0.003 0.033 10656 Dihedral : 5.765 41.722 9040 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.07 % Favored : 92.74 % Rotamer: Outliers : 2.05 % Allowed : 12.84 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.09), residues: 8080 helix: -0.20 (0.09), residues: 3392 sheet: 0.72 (0.19), residues: 896 loop : -2.74 (0.08), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 110 PHE 0.008 0.001 PHE J 427 TYR 0.006 0.001 TYR C 118 ARG 0.003 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 409 time to evaluate : 5.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 71 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.6667 (mtt) REVERT: U 217 MET cc_start: 0.2335 (mmp) cc_final: 0.0610 (ttt) REVERT: U 477 MET cc_start: 0.8401 (mmm) cc_final: 0.8070 (mmm) REVERT: A 217 MET cc_start: 0.1315 (mmt) cc_final: 0.0323 (ttt) REVERT: A 513 GLU cc_start: 0.7040 (pm20) cc_final: 0.6722 (pm20) REVERT: B 71 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6828 (mtt) REVERT: B 477 MET cc_start: 0.8469 (mmm) cc_final: 0.8109 (mmm) REVERT: B 513 GLU cc_start: 0.7288 (pm20) cc_final: 0.6803 (pm20) REVERT: C 110 HIS cc_start: 0.8440 (OUTLIER) cc_final: 0.8051 (p-80) REVERT: C 217 MET cc_start: 0.1638 (mmt) cc_final: 0.0540 (ttt) REVERT: D 167 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6595 (pp) REVERT: D 477 MET cc_start: 0.8414 (mmm) cc_final: 0.8054 (mmm) REVERT: E 167 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.6212 (pp) REVERT: E 217 MET cc_start: 0.1770 (mmt) cc_final: 0.0554 (ttt) REVERT: F 71 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.6652 (mtt) REVERT: F 167 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6449 (pp) REVERT: F 477 MET cc_start: 0.8446 (mmm) cc_final: 0.8117 (mmm) REVERT: G 217 MET cc_start: 0.1009 (mmp) cc_final: -0.0336 (ttt) REVERT: G 361 MET cc_start: 0.4499 (mmt) cc_final: 0.4129 (mmt) REVERT: H 71 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6813 (mtt) REVERT: H 217 MET cc_start: 0.1084 (mmp) cc_final: 0.0119 (ttt) REVERT: H 262 MET cc_start: 0.4025 (tpp) cc_final: 0.1314 (ttt) REVERT: H 477 MET cc_start: 0.8380 (mmm) cc_final: 0.8021 (mmm) REVERT: I 71 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7331 (mtm) REVERT: I 217 MET cc_start: 0.1533 (mmp) cc_final: 0.0177 (ttt) REVERT: J 10 MET cc_start: 0.2946 (OUTLIER) cc_final: 0.2207 (mtp) REVERT: J 167 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6411 (pp) REVERT: J 262 MET cc_start: 0.4166 (tpp) cc_final: 0.1015 (ttt) REVERT: J 477 MET cc_start: 0.8438 (mmm) cc_final: 0.8131 (mmm) REVERT: K 18 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8525 (m-40) REVERT: K 217 MET cc_start: 0.1537 (mmt) cc_final: -0.0277 (ttt) REVERT: K 513 GLU cc_start: 0.7186 (pm20) cc_final: 0.6747 (pm20) REVERT: L 71 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.6836 (mtt) REVERT: L 217 MET cc_start: 0.2045 (mmt) cc_final: 0.0743 (ttt) REVERT: L 477 MET cc_start: 0.8412 (mmm) cc_final: 0.8070 (mmm) REVERT: M 18 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8622 (m-40) REVERT: M 167 ILE cc_start: 0.6512 (OUTLIER) cc_final: 0.6138 (pp) REVERT: M 217 MET cc_start: 0.1302 (mmt) cc_final: 0.0324 (ttt) REVERT: N 167 ILE cc_start: 0.6760 (OUTLIER) cc_final: 0.6426 (pp) REVERT: N 217 MET cc_start: 0.1400 (mmm) cc_final: 0.0175 (ttt) REVERT: N 477 MET cc_start: 0.8334 (mmm) cc_final: 0.7877 (mmm) REVERT: N 513 GLU cc_start: 0.7211 (pm20) cc_final: 0.6706 (pm20) REVERT: O 71 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7286 (mtm) REVERT: O 110 HIS cc_start: 0.8510 (OUTLIER) cc_final: 0.8045 (p-80) REVERT: O 217 MET cc_start: 0.1812 (mmt) cc_final: 0.0479 (ttt) REVERT: O 262 MET cc_start: 0.3184 (tpp) cc_final: 0.2348 (tpp) outliers start: 134 outliers final: 105 residues processed: 519 average time/residue: 0.5064 time to fit residues: 472.9936 Evaluate side-chains 522 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 399 time to evaluate : 5.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 71 MET Chi-restraints excluded: chain U residue 110 HIS Chi-restraints excluded: chain U residue 131 THR Chi-restraints excluded: chain U residue 235 ILE Chi-restraints excluded: chain U residue 433 VAL Chi-restraints excluded: chain U residue 493 ILE Chi-restraints excluded: chain U residue 509 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 508 ASP Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 308 MET Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain H residue 493 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 131 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 308 MET Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 71 MET Chi-restraints excluded: chain L residue 110 HIS Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain L residue 469 VAL Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 433 VAL Chi-restraints excluded: chain M residue 509 VAL Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 110 HIS Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 167 ILE Chi-restraints excluded: chain N residue 433 VAL Chi-restraints excluded: chain N residue 509 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 71 MET Chi-restraints excluded: chain O residue 110 HIS Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain O residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 471 optimal weight: 30.0000 chunk 759 optimal weight: 1.9990 chunk 463 optimal weight: 6.9990 chunk 360 optimal weight: 0.5980 chunk 528 optimal weight: 40.0000 chunk 797 optimal weight: 3.9990 chunk 733 optimal weight: 8.9990 chunk 634 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 490 optimal weight: 0.9990 chunk 389 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 61664 Z= 0.167 Angle : 0.505 10.575 83088 Z= 0.252 Chirality : 0.040 0.138 10160 Planarity : 0.002 0.031 10656 Dihedral : 5.318 44.190 9040 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.06 % Favored : 93.74 % Rotamer: Outliers : 1.55 % Allowed : 13.31 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.09), residues: 8080 helix: 0.09 (0.10), residues: 3392 sheet: 0.83 (0.20), residues: 896 loop : -2.65 (0.09), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 110 PHE 0.006 0.001 PHE J 427 TYR 0.004 0.001 TYR E 412 ARG 0.003 0.000 ARG D 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 425 time to evaluate : 5.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 71 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6566 (mtt) REVERT: U 217 MET cc_start: 0.2289 (mmp) cc_final: 0.0581 (ttt) REVERT: U 477 MET cc_start: 0.8360 (mmm) cc_final: 0.8062 (mmm) REVERT: A 217 MET cc_start: 0.1270 (mmt) cc_final: 0.0296 (ttt) REVERT: A 513 GLU cc_start: 0.6985 (pm20) cc_final: 0.6715 (pm20) REVERT: B 71 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6702 (mtt) REVERT: B 477 MET cc_start: 0.8413 (mmm) cc_final: 0.8043 (mmm) REVERT: B 513 GLU cc_start: 0.7237 (pm20) cc_final: 0.6782 (pm20) REVERT: C 217 MET cc_start: 0.1577 (mmt) cc_final: 0.0613 (ttt) REVERT: D 167 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6510 (pp) REVERT: D 477 MET cc_start: 0.8347 (mmm) cc_final: 0.8050 (mmm) REVERT: E 167 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6319 (pp) REVERT: E 217 MET cc_start: 0.1742 (mmt) cc_final: 0.0522 (ttt) REVERT: F 71 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6546 (mtt) REVERT: F 167 ILE cc_start: 0.6602 (OUTLIER) cc_final: 0.6327 (pp) REVERT: F 477 MET cc_start: 0.8378 (mmm) cc_final: 0.8078 (mmm) REVERT: G 217 MET cc_start: 0.1123 (mmp) cc_final: -0.0229 (ttt) REVERT: G 361 MET cc_start: 0.4363 (mmt) cc_final: 0.4135 (mmt) REVERT: H 71 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.6681 (mtt) REVERT: H 217 MET cc_start: 0.1048 (mmp) cc_final: 0.0121 (ttt) REVERT: H 262 MET cc_start: 0.4005 (tpp) cc_final: 0.1325 (ttt) REVERT: H 477 MET cc_start: 0.8354 (mmm) cc_final: 0.8018 (mmm) REVERT: I 71 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7283 (mtm) REVERT: I 217 MET cc_start: 0.1220 (mmp) cc_final: -0.0066 (ttt) REVERT: J 10 MET cc_start: 0.3134 (OUTLIER) cc_final: 0.2385 (mtp) REVERT: J 167 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6346 (pp) REVERT: J 477 MET cc_start: 0.8372 (mmm) cc_final: 0.8099 (mmm) REVERT: K 217 MET cc_start: 0.1575 (mmt) cc_final: 0.0016 (ttt) REVERT: K 513 GLU cc_start: 0.7131 (pm20) cc_final: 0.6779 (pm20) REVERT: L 10 MET cc_start: 0.3095 (ptp) cc_final: 0.2674 (mtp) REVERT: L 71 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.6694 (mtt) REVERT: L 477 MET cc_start: 0.8394 (mmm) cc_final: 0.8026 (mmm) REVERT: M 18 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8515 (m-40) REVERT: M 167 ILE cc_start: 0.6412 (OUTLIER) cc_final: 0.6107 (pp) REVERT: M 217 MET cc_start: 0.1386 (mmt) cc_final: 0.0401 (ttt) REVERT: N 217 MET cc_start: 0.1386 (mmm) cc_final: 0.0166 (ttt) REVERT: N 477 MET cc_start: 0.8277 (mmm) cc_final: 0.7848 (mmm) REVERT: N 513 GLU cc_start: 0.7185 (pm20) cc_final: 0.6805 (pm20) REVERT: O 71 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7223 (mtm) REVERT: O 110 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.8030 (p-80) REVERT: O 217 MET cc_start: 0.1662 (mmt) cc_final: 0.0528 (ttt) REVERT: O 262 MET cc_start: 0.3097 (tpp) cc_final: 0.2290 (tpp) outliers start: 101 outliers final: 72 residues processed: 493 average time/residue: 0.4956 time to fit residues: 439.1849 Evaluate side-chains 504 residues out of total 6528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 417 time to evaluate : 5.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 43 VAL Chi-restraints excluded: chain U residue 71 MET Chi-restraints excluded: chain U residue 110 HIS Chi-restraints excluded: chain U residue 509 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 110 HIS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 71 MET Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 71 MET Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 71 MET Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain I residue 308 MET Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 10 MET Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 110 HIS Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 71 MET Chi-restraints excluded: chain L residue 110 HIS Chi-restraints excluded: chain L residue 469 VAL Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 509 VAL Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 110 HIS Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 509 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain N residue 110 HIS Chi-restraints excluded: chain N residue 509 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 71 MET Chi-restraints excluded: chain O residue 110 HIS Chi-restraints excluded: chain O residue 143 ILE Chi-restraints excluded: chain O residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 504 optimal weight: 5.9990 chunk 676 optimal weight: 50.0000 chunk 194 optimal weight: 0.8980 chunk 585 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 176 optimal weight: 50.0000 chunk 635 optimal weight: 50.0000 chunk 266 optimal weight: 20.0000 chunk 652 optimal weight: 0.8980 chunk 80 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 = 0.4986 r_free = 0.4986 target = 0.265706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.220350 restraints weight = 72392.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.219035 restraints weight = 179836.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.217074 restraints weight = 118807.556| |-----------------------------------------------------------------------------| r_work (final): 0.4590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 61664 Z= 0.128 Angle : 0.485 13.029 83088 Z= 0.241 Chirality : 0.040 0.128 10160 Planarity : 0.002 0.030 10656 Dihedral : 4.943 45.967 9040 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.42 % Favored : 94.38 % Rotamer: Outliers : 1.30 % Allowed : 13.69 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.09), residues: 8080 helix: 0.32 (0.10), residues: 3392 sheet: 0.94 (0.20), residues: 896 loop : -2.57 (0.09), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS J 355 PHE 0.004 0.001 PHE J 427 TYR 0.004 0.001 TYR E 412 ARG 0.002 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9605.94 seconds wall clock time: 171 minutes 30.16 seconds (10290.16 seconds total)