Starting phenix.real_space_refine on Tue Mar 12 03:29:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/03_2024/7rak_24363_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/03_2024/7rak_24363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/03_2024/7rak_24363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/03_2024/7rak_24363_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/03_2024/7rak_24363_updated.pdb" } 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 Residue "U TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 23.21, per 1000 atoms: 0.38 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 - 3.50 Amino acid : False - 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: 18.07 Conformation dependent library (CDL) restraints added in 8.4 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... running ksdssp... Secondary structure from input PDB file: 272 helices and 64 sheets defined 39.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.19 Creating SS restraints... Processing helix chain 'U' and resid 13 through 26 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 56 through 60 removed outlier: 3.578A pdb=" N ARG U 60 " --> pdb=" O VAL U 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 56 through 60' Processing helix chain 'U' and resid 67 through 80 removed outlier: 3.734A pdb=" N LYS U 70 " --> pdb=" O PRO U 67 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET U 71 " --> pdb=" O ALA U 68 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU U 72 " --> pdb=" O ALA U 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU U 80 " --> pdb=" O LYS U 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 88 through 107 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) removed outlier: 4.446A pdb=" N ASP U 106 " --> pdb=" O GLU U 102 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLN U 107 " --> pdb=" O GLU U 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 131 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) removed outlier: 3.821A pdb=" N THR U 131 " --> pdb=" O GLU U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 150 Processing helix chain 'U' and resid 169 through 172 No H-bonds generated for 'chain 'U' and resid 169 through 172' Processing helix chain 'U' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'U' and resid 286 through 288' Processing helix chain 'U' and resid 290 through 292 No H-bonds generated for 'chain 'U' and resid 290 through 292' Processing helix chain 'U' and resid 305 through 308 No H-bonds generated for 'chain 'U' and resid 305 through 308' Processing helix chain 'U' and resid 369 through 389 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) Processing helix chain 'U' and resid 401 through 415 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) removed outlier: 3.896A pdb=" N GLU U 414 " --> pdb=" O ARG U 410 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY U 415 " --> pdb=" O GLU U 411 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 440 removed outlier: 4.240A pdb=" N GLU U 432 " --> pdb=" O ALA U 428 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL U 433 " --> pdb=" O ASP U 429 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE U 434 " --> pdb=" O ALA U 430 " (cutoff:3.500A) Proline residue: U 435 - end of helix Processing helix chain 'U' and resid 448 through 458 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) removed outlier: 4.433A pdb=" N HIS U 457 " --> pdb=" O VAL U 453 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA U 492 " --> pdb=" O VAL U 488 " (cutoff:3.500A) Processing helix chain 'U' and resid 501 through 504 No H-bonds generated for 'chain 'U' and resid 501 through 504' Processing helix chain 'A' and resid 13 through 26 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 56 through 60 removed outlier: 3.578A pdb=" N ARG A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 60' Processing helix chain 'A' and resid 67 through 80 removed outlier: 3.733A pdb=" N LYS A 70 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET A 71 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 80 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 107 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) removed outlier: 4.447A pdb=" N ASP A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLN A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 131 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) removed outlier: 3.823A pdb=" N THR A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 305 through 308 No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 369 through 389 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) Processing helix chain 'A' and resid 401 through 415 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) removed outlier: 3.893A pdb=" N GLU A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 440 removed outlier: 4.246A pdb=" N GLU A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 448 through 458 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) removed outlier: 4.442A pdb=" N HIS A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 504 No H-bonds generated for 'chain 'A' and resid 501 through 504' Processing helix chain 'B' and resid 13 through 26 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 56 through 60 removed outlier: 3.577A pdb=" N ARG B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 67 through 80 removed outlier: 3.734A pdb=" N LYS B 70 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET B 71 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 80 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 107 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) removed outlier: 4.447A pdb=" N ASP B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 131 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) removed outlier: 3.822A pdb=" N THR B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 169 through 172 No H-bonds generated for 'chain 'B' and resid 169 through 172' Processing helix chain 'B' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 305 through 308 No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 369 through 389 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) Processing helix chain 'B' and resid 401 through 415 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) removed outlier: 3.894A pdb=" N GLU B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 440 removed outlier: 4.240A pdb=" N GLU B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 433 " --> pdb=" O ASP B 429 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Proline residue: B 435 - end of helix Processing helix chain 'B' and resid 448 through 458 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) removed outlier: 4.429A pdb=" N HIS B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 504 No H-bonds generated for 'chain 'B' and resid 501 through 504' Processing helix chain 'C' and resid 13 through 26 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 56 through 60 removed outlier: 3.577A pdb=" N ARG C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 68 through 80 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) Processing helix chain 'C' and resid 88 through 107 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) removed outlier: 3.537A pdb=" N LEU C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 131 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) removed outlier: 3.820A pdb=" N THR C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 169 through 172 No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 305 through 308 No H-bonds generated for 'chain 'C' and resid 305 through 308' Processing helix chain 'C' and resid 369 through 389 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) Processing helix chain 'C' and resid 401 through 415 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) removed outlier: 3.898A pdb=" N GLU C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 440 removed outlier: 4.243A pdb=" N GLU C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL C 433 " --> pdb=" O ASP C 429 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE C 434 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Proline residue: C 435 - end of helix Processing helix chain 'C' and resid 448 through 458 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) removed outlier: 4.431A pdb=" N HIS C 457 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 504 No H-bonds generated for 'chain 'C' and resid 501 through 504' Processing helix chain 'D' and resid 13 through 26 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 56 through 60 removed outlier: 3.568A pdb=" N ARG D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.735A pdb=" N LYS D 70 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET D 71 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 80 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 107 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) removed outlier: 4.449A pdb=" N ASP D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLN D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 131 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) removed outlier: 3.823A pdb=" N THR D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 169 through 172 No H-bonds generated for 'chain 'D' and resid 169 through 172' Processing helix chain 'D' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 305 through 308 No H-bonds generated for 'chain 'D' and resid 305 through 308' Processing helix chain 'D' and resid 369 through 389 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) Processing helix chain 'D' and resid 401 through 415 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) removed outlier: 3.902A pdb=" N GLU D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY D 415 " --> pdb=" O GLU D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 438 removed outlier: 3.500A pdb=" N LEU D 431 " --> pdb=" O PHE D 427 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL D 433 " --> pdb=" O ASP D 429 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Proline residue: D 435 - end of helix Processing helix chain 'D' and resid 448 through 458 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) removed outlier: 4.432A pdb=" N HIS D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA D 458 " --> pdb=" O ARG D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 504 No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'E' and resid 13 through 26 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 56 through 60 removed outlier: 3.578A pdb=" N ARG E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 60' Processing helix chain 'E' and resid 67 through 80 removed outlier: 3.733A pdb=" N LYS E 70 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET E 71 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU E 80 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 107 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) removed outlier: 4.446A pdb=" N ASP E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLN E 107 " --> pdb=" O GLU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 131 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) removed outlier: 3.822A pdb=" N THR E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 Processing helix chain 'E' and resid 169 through 172 No H-bonds generated for 'chain 'E' and resid 169 through 172' Processing helix chain 'E' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 290 through 292 No H-bonds generated for 'chain 'E' and resid 290 through 292' Processing helix chain 'E' and resid 305 through 308 No H-bonds generated for 'chain 'E' and resid 305 through 308' Processing helix chain 'E' and resid 369 through 389 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) Processing helix chain 'E' and resid 401 through 415 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) removed outlier: 3.896A pdb=" N GLU E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY E 415 " --> pdb=" O GLU E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 440 removed outlier: 4.240A pdb=" N GLU E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL E 433 " --> pdb=" O ASP E 429 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE E 434 " --> pdb=" O ALA E 430 " (cutoff:3.500A) Proline residue: E 435 - end of helix Processing helix chain 'E' and resid 448 through 458 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) removed outlier: 4.428A pdb=" N HIS E 457 " --> pdb=" O VAL E 453 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA E 458 " --> pdb=" O ARG E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 499 removed outlier: 3.559A pdb=" N ALA E 492 " --> pdb=" O VAL E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'F' and resid 13 through 26 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 56 through 60 removed outlier: 3.577A pdb=" N ARG F 60 " --> pdb=" O VAL F 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 60' Processing helix chain 'F' and resid 67 through 80 removed outlier: 3.734A pdb=" N LYS F 70 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET F 71 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU F 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 80 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 107 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) removed outlier: 3.553A pdb=" N LEU F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 131 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) removed outlier: 3.828A pdb=" N THR F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 169 through 172 No H-bonds generated for 'chain 'F' and resid 169 through 172' Processing helix chain 'F' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 290 through 292 No H-bonds generated for 'chain 'F' and resid 290 through 292' Processing helix chain 'F' and resid 305 through 308 No H-bonds generated for 'chain 'F' and resid 305 through 308' Processing helix chain 'F' and resid 369 through 389 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) Processing helix chain 'F' and resid 401 through 415 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) removed outlier: 3.892A pdb=" N GLU F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY F 415 " --> pdb=" O GLU F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 440 removed outlier: 4.230A pdb=" N GLU F 432 " --> pdb=" O ALA F 428 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL F 433 " --> pdb=" O ASP F 429 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) Proline residue: F 435 - end of helix Processing helix chain 'F' and resid 448 through 458 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) removed outlier: 4.433A pdb=" N HIS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA F 458 " --> pdb=" O ARG F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 499 removed outlier: 3.556A pdb=" N ALA F 492 " --> pdb=" O VAL F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 504 No H-bonds generated for 'chain 'F' and resid 501 through 504' Processing helix chain 'G' and resid 13 through 26 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 56 through 60 removed outlier: 3.578A pdb=" N ARG G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 60' Processing helix chain 'G' and resid 67 through 80 removed outlier: 3.732A pdb=" N LYS G 70 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET G 71 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU G 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU G 80 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 107 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) removed outlier: 4.447A pdb=" N ASP G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN G 107 " --> pdb=" O GLU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 131 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) removed outlier: 3.823A pdb=" N THR G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 150 Processing helix chain 'G' and resid 169 through 172 No H-bonds generated for 'chain 'G' and resid 169 through 172' Processing helix chain 'G' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 290 through 292 No H-bonds generated for 'chain 'G' and resid 290 through 292' Processing helix chain 'G' and resid 305 through 308 No H-bonds generated for 'chain 'G' and resid 305 through 308' Processing helix chain 'G' and resid 369 through 389 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) Processing helix chain 'G' and resid 401 through 415 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) removed outlier: 3.893A pdb=" N GLU G 414 " --> pdb=" O ARG G 410 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY G 415 " --> pdb=" O GLU G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 440 removed outlier: 4.240A pdb=" N GLU G 432 " --> pdb=" O ALA G 428 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL G 433 " --> pdb=" O ASP G 429 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE G 434 " --> pdb=" O ALA G 430 " (cutoff:3.500A) Proline residue: G 435 - end of helix Processing helix chain 'G' and resid 448 through 458 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) removed outlier: 4.444A pdb=" N HIS G 457 " --> pdb=" O VAL G 453 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA G 458 " --> pdb=" O ARG G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA G 492 " --> pdb=" O VAL G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 504 No H-bonds generated for 'chain 'G' and resid 501 through 504' Processing helix chain 'H' and resid 13 through 26 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 56 through 60 removed outlier: 3.575A pdb=" N ARG H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 56 through 60' Processing helix chain 'H' and resid 67 through 80 removed outlier: 3.735A pdb=" N LYS H 70 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET H 71 " --> pdb=" O ALA H 68 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU H 80 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 107 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) removed outlier: 3.555A pdb=" N LEU H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN H 107 " --> pdb=" O GLU H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 131 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) removed outlier: 3.827A pdb=" N THR H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 150 Processing helix chain 'H' and resid 169 through 172 No H-bonds generated for 'chain 'H' and resid 169 through 172' Processing helix chain 'H' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'H' and resid 286 through 288' Processing helix chain 'H' and resid 290 through 292 No H-bonds generated for 'chain 'H' and resid 290 through 292' Processing helix chain 'H' and resid 305 through 308 No H-bonds generated for 'chain 'H' and resid 305 through 308' Processing helix chain 'H' and resid 369 through 389 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) Processing helix chain 'H' and resid 401 through 415 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) removed outlier: 3.895A pdb=" N GLU H 414 " --> pdb=" O ARG H 410 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY H 415 " --> pdb=" O GLU H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 438 removed outlier: 3.503A pdb=" N LEU H 431 " --> pdb=" O PHE H 427 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU H 432 " --> pdb=" O ALA H 428 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL H 433 " --> pdb=" O ASP H 429 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE H 434 " --> pdb=" O ALA H 430 " (cutoff:3.500A) Proline residue: H 435 - end of helix Processing helix chain 'H' and resid 448 through 458 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) removed outlier: 4.395A pdb=" N HIS H 457 " --> pdb=" O VAL H 453 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA H 458 " --> pdb=" O ARG H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA H 492 " --> pdb=" O VAL H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 501 through 504 No H-bonds generated for 'chain 'H' and resid 501 through 504' Processing helix chain 'I' and resid 13 through 26 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 56 through 60 removed outlier: 3.577A pdb=" N ARG I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 56 through 60' Processing helix chain 'I' and resid 67 through 80 removed outlier: 3.733A pdb=" N LYS I 70 " --> pdb=" O PRO I 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET I 71 " --> pdb=" O ALA I 68 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU I 72 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU I 80 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 107 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) removed outlier: 4.447A pdb=" N ASP I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLN I 107 " --> pdb=" O GLU I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 131 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) removed outlier: 3.823A pdb=" N THR I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 150 Processing helix chain 'I' and resid 169 through 172 No H-bonds generated for 'chain 'I' and resid 169 through 172' Processing helix chain 'I' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 290 through 292 No H-bonds generated for 'chain 'I' and resid 290 through 292' Processing helix chain 'I' and resid 305 through 308 No H-bonds generated for 'chain 'I' and resid 305 through 308' Processing helix chain 'I' and resid 369 through 389 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) Processing helix chain 'I' and resid 401 through 415 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) removed outlier: 3.902A pdb=" N GLU I 414 " --> pdb=" O ARG I 410 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY I 415 " --> pdb=" O GLU I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 420 through 440 removed outlier: 4.245A pdb=" N GLU I 432 " --> pdb=" O ALA I 428 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL I 433 " --> pdb=" O ASP I 429 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE I 434 " --> pdb=" O ALA I 430 " (cutoff:3.500A) Proline residue: I 435 - end of helix Processing helix chain 'I' and resid 448 through 458 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) removed outlier: 4.441A pdb=" N HIS I 457 " --> pdb=" O VAL I 453 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA I 458 " --> pdb=" O ARG I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA I 492 " --> pdb=" O VAL I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 501 through 504 No H-bonds generated for 'chain 'I' and resid 501 through 504' Processing helix chain 'J' and resid 13 through 26 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 56 through 60 removed outlier: 3.578A pdb=" N ARG J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 60' Processing helix chain 'J' and resid 67 through 80 removed outlier: 3.734A pdb=" N LYS J 70 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET J 71 " --> pdb=" O ALA J 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU J 72 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU J 80 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 107 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) removed outlier: 3.553A pdb=" N LEU J 105 " --> pdb=" O ALA J 101 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN J 107 " --> pdb=" O GLU J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 131 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) removed outlier: 3.827A pdb=" N THR J 131 " --> pdb=" O GLU J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 150 Processing helix chain 'J' and resid 169 through 172 No H-bonds generated for 'chain 'J' and resid 169 through 172' Processing helix chain 'J' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'J' and resid 286 through 288' Processing helix chain 'J' and resid 290 through 292 No H-bonds generated for 'chain 'J' and resid 290 through 292' Processing helix chain 'J' and resid 305 through 308 No H-bonds generated for 'chain 'J' and resid 305 through 308' Processing helix chain 'J' and resid 369 through 389 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) Processing helix chain 'J' and resid 401 through 415 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) removed outlier: 3.893A pdb=" N GLU J 414 " --> pdb=" O ARG J 410 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY J 415 " --> pdb=" O GLU J 411 " (cutoff:3.500A) Processing helix chain 'J' and resid 420 through 440 removed outlier: 4.230A pdb=" N GLU J 432 " --> pdb=" O ALA J 428 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL J 433 " --> pdb=" O ASP J 429 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE J 434 " --> pdb=" O ALA J 430 " (cutoff:3.500A) Proline residue: J 435 - end of helix Processing helix chain 'J' and resid 448 through 458 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) removed outlier: 4.434A pdb=" N HIS J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA J 458 " --> pdb=" O ARG J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 499 removed outlier: 3.556A pdb=" N ALA J 492 " --> pdb=" O VAL J 488 " (cutoff:3.500A) Processing helix chain 'J' and resid 501 through 504 No H-bonds generated for 'chain 'J' and resid 501 through 504' Processing helix chain 'K' and resid 13 through 26 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 56 through 60 removed outlier: 3.579A pdb=" N ARG K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 60' Processing helix chain 'K' and resid 67 through 80 removed outlier: 3.733A pdb=" N LYS K 70 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N MET K 71 " --> pdb=" O ALA K 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU K 72 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU K 80 " --> pdb=" O LYS K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 107 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) removed outlier: 3.547A pdb=" N LEU K 105 " --> pdb=" O ALA K 101 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN K 107 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 131 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) removed outlier: 3.824A pdb=" N THR K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 169 through 172 No H-bonds generated for 'chain 'K' and resid 169 through 172' Processing helix chain 'K' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'K' and resid 286 through 288' Processing helix chain 'K' and resid 290 through 292 No H-bonds generated for 'chain 'K' and resid 290 through 292' Processing helix chain 'K' and resid 305 through 308 No H-bonds generated for 'chain 'K' and resid 305 through 308' Processing helix chain 'K' and resid 369 through 389 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) Processing helix chain 'K' and resid 401 through 415 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) removed outlier: 3.865A pdb=" N GLU K 414 " --> pdb=" O ARG K 410 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY K 415 " --> pdb=" O GLU K 411 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 440 removed outlier: 4.238A pdb=" N GLU K 432 " --> pdb=" O ALA K 428 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL K 433 " --> pdb=" O ASP K 429 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE K 434 " --> pdb=" O ALA K 430 " (cutoff:3.500A) Proline residue: K 435 - end of helix Processing helix chain 'K' and resid 448 through 458 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) removed outlier: 4.441A pdb=" N HIS K 457 " --> pdb=" O VAL K 453 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA K 458 " --> pdb=" O ARG K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 499 removed outlier: 3.556A pdb=" N ALA K 492 " --> pdb=" O VAL K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 504 No H-bonds generated for 'chain 'K' and resid 501 through 504' Processing helix chain 'L' and resid 13 through 26 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 56 through 60 removed outlier: 3.577A pdb=" N ARG L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 56 through 60' Processing helix chain 'L' and resid 67 through 80 removed outlier: 3.734A pdb=" N LYS L 70 " --> pdb=" O PRO L 67 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N MET L 71 " --> pdb=" O ALA L 68 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU L 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU L 80 " --> pdb=" O LYS L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 107 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) removed outlier: 4.439A pdb=" N ASP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN L 107 " --> pdb=" O GLU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 131 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) removed outlier: 3.822A pdb=" N THR L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 150 Processing helix chain 'L' and resid 169 through 172 No H-bonds generated for 'chain 'L' and resid 169 through 172' Processing helix chain 'L' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'L' and resid 286 through 288' Processing helix chain 'L' and resid 290 through 292 No H-bonds generated for 'chain 'L' and resid 290 through 292' Processing helix chain 'L' and resid 305 through 308 No H-bonds generated for 'chain 'L' and resid 305 through 308' Processing helix chain 'L' and resid 369 through 389 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) Processing helix chain 'L' and resid 401 through 415 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) removed outlier: 3.893A pdb=" N GLU L 414 " --> pdb=" O ARG L 410 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY L 415 " --> pdb=" O GLU L 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 440 removed outlier: 4.249A pdb=" N GLU L 432 " --> pdb=" O ALA L 428 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL L 433 " --> pdb=" O ASP L 429 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ILE L 434 " --> pdb=" O ALA L 430 " (cutoff:3.500A) Proline residue: L 435 - end of helix Processing helix chain 'L' and resid 448 through 458 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) removed outlier: 4.437A pdb=" N HIS L 457 " --> pdb=" O VAL L 453 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA L 458 " --> pdb=" O ARG L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA L 492 " --> pdb=" O VAL L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 501 through 504 No H-bonds generated for 'chain 'L' and resid 501 through 504' Processing helix chain 'M' and resid 13 through 26 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 56 through 60 removed outlier: 3.575A pdb=" N ARG M 60 " --> pdb=" O VAL M 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 56 through 60' Processing helix chain 'M' and resid 68 through 80 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) Processing helix chain 'M' and resid 88 through 107 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) removed outlier: 3.537A pdb=" N LEU M 105 " --> pdb=" O ALA M 101 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP M 106 " --> pdb=" O GLU M 102 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN M 107 " --> pdb=" O GLU M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 131 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) removed outlier: 3.820A pdb=" N THR M 131 " --> pdb=" O GLU M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 150 Processing helix chain 'M' and resid 169 through 172 No H-bonds generated for 'chain 'M' and resid 169 through 172' Processing helix chain 'M' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'M' and resid 286 through 288' Processing helix chain 'M' and resid 290 through 292 No H-bonds generated for 'chain 'M' and resid 290 through 292' Processing helix chain 'M' and resid 305 through 308 No H-bonds generated for 'chain 'M' and resid 305 through 308' Processing helix chain 'M' and resid 369 through 389 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) Processing helix chain 'M' and resid 401 through 415 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) removed outlier: 3.898A pdb=" N GLU M 414 " --> pdb=" O ARG M 410 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY M 415 " --> pdb=" O GLU M 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 440 removed outlier: 4.246A pdb=" N GLU M 432 " --> pdb=" O ALA M 428 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL M 433 " --> pdb=" O ASP M 429 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE M 434 " --> pdb=" O ALA M 430 " (cutoff:3.500A) Proline residue: M 435 - end of helix Processing helix chain 'M' and resid 448 through 458 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) removed outlier: 4.433A pdb=" N HIS M 457 " --> pdb=" O VAL M 453 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA M 458 " --> pdb=" O ARG M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA M 492 " --> pdb=" O VAL M 488 " (cutoff:3.500A) Processing helix chain 'M' and resid 501 through 504 No H-bonds generated for 'chain 'M' and resid 501 through 504' Processing helix chain 'N' and resid 13 through 26 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 56 through 60 removed outlier: 3.567A pdb=" N ARG N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 56 through 60' Processing helix chain 'N' and resid 67 through 80 removed outlier: 3.735A pdb=" N LYS N 70 " --> pdb=" O PRO N 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET N 71 " --> pdb=" O ALA N 68 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU N 72 " --> pdb=" O ALA N 69 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU N 80 " --> pdb=" O LYS N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 107 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) removed outlier: 4.449A pdb=" N ASP N 106 " --> pdb=" O GLU N 102 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN N 107 " --> pdb=" O GLU N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 131 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) removed outlier: 3.823A pdb=" N THR N 131 " --> pdb=" O GLU N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 150 Processing helix chain 'N' and resid 169 through 172 No H-bonds generated for 'chain 'N' and resid 169 through 172' Processing helix chain 'N' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'N' and resid 286 through 288' Processing helix chain 'N' and resid 290 through 292 No H-bonds generated for 'chain 'N' and resid 290 through 292' Processing helix chain 'N' and resid 305 through 308 No H-bonds generated for 'chain 'N' and resid 305 through 308' Processing helix chain 'N' and resid 369 through 389 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) Processing helix chain 'N' and resid 401 through 415 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) removed outlier: 3.894A pdb=" N GLU N 414 " --> pdb=" O ARG N 410 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY N 415 " --> pdb=" O GLU N 411 " (cutoff:3.500A) Processing helix chain 'N' and resid 420 through 438 removed outlier: 3.502A pdb=" N LEU N 431 " --> pdb=" O PHE N 427 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU N 432 " --> pdb=" O ALA N 428 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL N 433 " --> pdb=" O ASP N 429 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE N 434 " --> pdb=" O ALA N 430 " (cutoff:3.500A) Proline residue: N 435 - end of helix Processing helix chain 'N' and resid 448 through 458 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) removed outlier: 4.430A pdb=" N HIS N 457 " --> pdb=" O VAL N 453 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA N 458 " --> pdb=" O ARG N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA N 492 " --> pdb=" O VAL N 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 501 through 504 No H-bonds generated for 'chain 'N' and resid 501 through 504' Processing helix chain 'O' and resid 13 through 26 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 56 through 60 removed outlier: 3.578A pdb=" N ARG O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 56 through 60' Processing helix chain 'O' and resid 67 through 80 removed outlier: 3.736A pdb=" N LYS O 70 " --> pdb=" O PRO O 67 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET O 71 " --> pdb=" O ALA O 68 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU O 72 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU O 80 " --> pdb=" O LYS O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 107 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) removed outlier: 3.546A pdb=" N LEU O 105 " --> pdb=" O ALA O 101 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP O 106 " --> pdb=" O GLU O 102 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLN O 107 " --> pdb=" O GLU O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 131 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) removed outlier: 3.821A pdb=" N THR O 131 " --> pdb=" O GLU O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 150 Processing helix chain 'O' and resid 169 through 172 No H-bonds generated for 'chain 'O' and resid 169 through 172' Processing helix chain 'O' and resid 249 through 273 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 286 through 288 No H-bonds generated for 'chain 'O' and resid 286 through 288' Processing helix chain 'O' and resid 290 through 292 No H-bonds generated for 'chain 'O' and resid 290 through 292' Processing helix chain 'O' and resid 305 through 308 No H-bonds generated for 'chain 'O' and resid 305 through 308' Processing helix chain 'O' and resid 369 through 389 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) Processing helix chain 'O' and resid 401 through 415 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) removed outlier: 3.897A pdb=" N GLU O 414 " --> pdb=" O ARG O 410 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY O 415 " --> pdb=" O GLU O 411 " (cutoff:3.500A) Processing helix chain 'O' and resid 420 through 440 removed outlier: 4.247A pdb=" N GLU O 432 " --> pdb=" O ALA O 428 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL O 433 " --> pdb=" O ASP O 429 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE O 434 " --> pdb=" O ALA O 430 " (cutoff:3.500A) Proline residue: O 435 - end of helix Processing helix chain 'O' and resid 448 through 458 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) removed outlier: 4.432A pdb=" N HIS O 457 " --> pdb=" O VAL O 453 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA O 458 " --> pdb=" O ARG O 454 " (cutoff:3.500A) Processing helix chain 'O' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA O 492 " --> pdb=" O VAL O 488 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 504 No H-bonds generated for 'chain 'O' and resid 501 through 504' Processing sheet with id= A, first strand: chain 'U' and resid 40 through 42 Processing sheet with id= B, first strand: chain 'U' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET U 361 " --> pdb=" O LYS U 188 " (cutoff:3.500A) 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= C, first strand: chain 'U' and resid 205 through 208 Processing sheet with id= D, first strand: chain 'U' and resid 226 through 229 removed outlier: 6.296A pdb=" N VAL U 277 " --> pdb=" O ALA U 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU U 229 " --> pdb=" O VAL U 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE U 279 " --> pdb=" O LEU U 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 40 through 42 Processing sheet with id= F, first strand: chain 'A' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET A 361 " --> pdb=" O LYS A 188 " (cutoff:3.500A) 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= G, first strand: chain 'A' and resid 205 through 208 Processing sheet with id= H, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL A 277 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU A 229 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE A 279 " --> pdb=" O LEU A 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 40 through 42 Processing sheet with id= J, first strand: chain 'B' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET B 361 " --> pdb=" O LYS B 188 " (cutoff:3.500A) 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= K, first strand: chain 'B' and resid 205 through 208 Processing sheet with id= L, first strand: chain 'B' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL B 277 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 229 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE B 279 " --> pdb=" O LEU B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 40 through 42 Processing sheet with id= N, first strand: chain 'C' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET C 361 " --> pdb=" O LYS C 188 " (cutoff:3.500A) 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= O, first strand: chain 'C' and resid 205 through 208 Processing sheet with id= P, first strand: chain 'C' and resid 226 through 229 removed outlier: 6.295A pdb=" N VAL C 277 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C 229 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N PHE C 279 " --> pdb=" O LEU C 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 40 through 42 Processing sheet with id= R, first strand: chain 'D' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET D 361 " --> pdb=" O LYS D 188 " (cutoff:3.500A) 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= S, first strand: chain 'D' and resid 205 through 208 Processing sheet with id= T, first strand: chain 'D' and resid 226 through 229 removed outlier: 6.296A pdb=" N VAL D 277 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU D 229 " --> pdb=" O VAL D 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE D 279 " --> pdb=" O LEU D 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 40 through 42 Processing sheet with id= V, first strand: chain 'E' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET E 361 " --> pdb=" O LYS E 188 " (cutoff:3.500A) 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= W, first strand: chain 'E' and resid 205 through 208 Processing sheet with id= X, first strand: chain 'E' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL E 277 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU E 229 " --> pdb=" O VAL E 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE E 279 " --> pdb=" O LEU E 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 40 through 42 Processing sheet with id= Z, first strand: chain 'F' and resid 188 through 191 removed outlier: 4.255A pdb=" N MET F 361 " --> pdb=" O LYS F 188 " (cutoff:3.500A) 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= AA, first strand: chain 'F' and resid 205 through 208 Processing sheet with id= AB, first strand: chain 'F' and resid 226 through 229 removed outlier: 6.296A pdb=" N VAL F 277 " --> pdb=" O ALA F 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU F 229 " --> pdb=" O VAL F 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE F 279 " --> pdb=" O LEU F 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'G' and resid 40 through 42 Processing sheet with id= AD, first strand: chain 'G' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET G 361 " --> pdb=" O LYS G 188 " (cutoff:3.500A) 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= AE, first strand: chain 'G' and resid 205 through 208 Processing sheet with id= AF, first strand: chain 'G' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL G 277 " --> pdb=" O ALA G 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU G 229 " --> pdb=" O VAL G 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE G 279 " --> pdb=" O LEU G 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'H' and resid 40 through 42 Processing sheet with id= AH, first strand: chain 'H' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET H 361 " --> pdb=" O LYS H 188 " (cutoff:3.500A) 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= AI, first strand: chain 'H' and resid 205 through 208 Processing sheet with id= AJ, first strand: chain 'H' and resid 226 through 229 removed outlier: 6.296A pdb=" N VAL H 277 " --> pdb=" O ALA H 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU H 229 " --> pdb=" O VAL H 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE H 279 " --> pdb=" O LEU H 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'I' and resid 40 through 42 Processing sheet with id= AL, first strand: chain 'I' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET I 361 " --> pdb=" O LYS I 188 " (cutoff:3.500A) 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= AM, first strand: chain 'I' and resid 205 through 208 Processing sheet with id= AN, first strand: chain 'I' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL I 277 " --> pdb=" O ALA I 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU I 229 " --> pdb=" O VAL I 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE I 279 " --> pdb=" O LEU I 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'J' and resid 40 through 42 Processing sheet with id= AP, first strand: chain 'J' and resid 188 through 191 removed outlier: 4.255A pdb=" N MET J 361 " --> pdb=" O LYS J 188 " (cutoff:3.500A) 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= AQ, first strand: chain 'J' and resid 205 through 208 Processing sheet with id= AR, first strand: chain 'J' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL J 277 " --> pdb=" O ALA J 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU J 229 " --> pdb=" O VAL J 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE J 279 " --> pdb=" O LEU J 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'K' and resid 40 through 42 Processing sheet with id= AT, first strand: chain 'K' and resid 188 through 191 removed outlier: 4.256A pdb=" N MET K 361 " --> pdb=" O LYS K 188 " (cutoff:3.500A) 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= AU, first strand: chain 'K' and resid 205 through 208 Processing sheet with id= AV, first strand: chain 'K' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL K 277 " --> pdb=" O ALA K 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU K 229 " --> pdb=" O VAL K 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE K 279 " --> pdb=" O LEU K 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'L' and resid 40 through 42 Processing sheet with id= AX, first strand: chain 'L' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET L 361 " --> pdb=" O LYS L 188 " (cutoff:3.500A) 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= AY, first strand: chain 'L' and resid 205 through 208 Processing sheet with id= AZ, first strand: chain 'L' and resid 226 through 229 removed outlier: 6.296A pdb=" N VAL L 277 " --> pdb=" O ALA L 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU L 229 " --> pdb=" O VAL L 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE L 279 " --> pdb=" O LEU L 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'M' and resid 40 through 42 Processing sheet with id= BB, first strand: chain 'M' and resid 188 through 191 removed outlier: 4.255A pdb=" N MET M 361 " --> pdb=" O LYS M 188 " (cutoff:3.500A) 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= BC, first strand: chain 'M' and resid 205 through 208 Processing sheet with id= BD, first strand: chain 'M' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL M 277 " --> pdb=" O ALA M 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU M 229 " --> pdb=" O VAL M 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE M 279 " --> pdb=" O LEU M 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'N' and resid 40 through 42 Processing sheet with id= BF, first strand: chain 'N' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET N 361 " --> pdb=" O LYS N 188 " (cutoff:3.500A) 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= BG, first strand: chain 'N' and resid 205 through 208 Processing sheet with id= BH, first strand: chain 'N' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL N 277 " --> pdb=" O ALA N 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU N 229 " --> pdb=" O VAL N 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE N 279 " --> pdb=" O LEU N 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'O' and resid 40 through 42 Processing sheet with id= BJ, first strand: chain 'O' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET O 361 " --> pdb=" O LYS O 188 " (cutoff:3.500A) 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= BK, first strand: chain 'O' and resid 205 through 208 Processing sheet with id= BL, first strand: chain 'O' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL O 277 " --> pdb=" O ALA O 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU O 229 " --> pdb=" O VAL O 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE O 279 " --> pdb=" O LEU O 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= BL 1735 hydrogen bonds defined for protein. 4671 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: 17.00 Time building geometry restraints manager: 19.89 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: 100.79 - 107.86: 1363 107.86 - 114.93: 40096 114.93 - 122.01: 28658 122.01 - 129.08: 12827 129.08 - 136.15: 144 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: 16062 2.81 - 3.33: 54875 3.33 - 3.85: 89384 3.85 - 4.38: 101911 4.38 - 4.90: 176246 Nonbonded interactions: 438478 Sorted by model distance: nonbonded pdb=" O VAL L 109 " pdb=" ND1 HIS L 110 " model vdw 2.283 2.520 nonbonded pdb=" O VAL M 109 " pdb=" ND1 HIS M 110 " model vdw 2.285 2.520 nonbonded pdb=" O VAL C 109 " pdb=" ND1 HIS C 110 " model vdw 2.286 2.520 nonbonded pdb=" O VAL U 109 " pdb=" ND1 HIS U 110 " model vdw 2.289 2.520 nonbonded pdb=" O VAL E 109 " pdb=" ND1 HIS E 110 " model vdw 2.290 2.520 ... (remaining 438473 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.530 Check model and map are aligned: 0.820 Set scattering table: 0.400 Process input model: 116.620 Find NCS groups from input model: 3.540 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.990 ------------------------------------------------------------------------------- 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= 0.193 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 fitting. rotamer outliers: 0 poor density : 772 time to evaluate : 5.347 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: 0.5452 time to fit residues: 718.0216 Evaluate side-chains 478 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 4.969 ------------------------------------------------------------------------------- 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: 2.9990 chunk 606 optimal weight: 0.7980 chunk 336 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 409 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 chunk 627 optimal weight: 0.3980 chunk 242 optimal weight: 0.6980 chunk 381 optimal weight: 5.9990 chunk 466 optimal weight: 20.0000 chunk 726 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 457 HIS C 457 HIS D 457 HIS E 457 HIS F 15 GLN F 457 HIS G 457 HIS H 15 GLN H 457 HIS I 457 HIS J 457 HIS K 457 HIS L 457 HIS M 457 HIS N 421 GLN N 457 HIS O 457 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 61664 Z= 0.225 Angle : 0.547 7.207 83088 Z= 0.285 Chirality : 0.043 0.209 10160 Planarity : 0.003 0.027 10656 Dihedral : 4.743 68.675 9040 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.43 % Favored : 91.18 % Rotamer: Outliers : 1.56 % Allowed : 6.00 % Favored : 92.43 % 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: -3.08 (0.08), residues: 8080 helix: -1.32 (0.09), residues: 3264 sheet: -0.09 (0.18), residues: 896 loop : -3.26 (0.08), residues: 3920 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS O 369 PHE 0.009 0.001 PHE F 427 TYR 0.006 0.001 TYR L 291 ARG 0.004 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 649 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 547 time to evaluate : 5.011 Fit side-chains REVERT: U 167 ILE cc_start: 0.6784 (OUTLIER) cc_final: 0.6523 (pp) REVERT: U 217 MET cc_start: 0.2888 (mmt) cc_final: 0.0847 (ttt) REVERT: U 477 MET cc_start: 0.8403 (mmm) cc_final: 0.7706 (mmm) REVERT: U 506 ILE cc_start: 0.8685 (mm) cc_final: 0.8204 (mt) REVERT: A 167 ILE cc_start: 0.6671 (OUTLIER) cc_final: 0.6343 (pp) REVERT: A 217 MET cc_start: 0.1509 (mmt) cc_final: -0.0291 (ttt) REVERT: B 167 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6601 (pp) REVERT: B 477 MET cc_start: 0.8435 (mmm) cc_final: 0.7677 (mmm) REVERT: B 506 ILE cc_start: 0.8611 (mm) cc_final: 0.8153 (mt) REVERT: C 167 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6192 (pp) REVERT: C 217 MET cc_start: 0.2243 (mmt) cc_final: -0.0076 (ttt) REVERT: D 167 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6584 (pp) REVERT: D 477 MET cc_start: 0.8530 (mmm) cc_final: 0.7805 (mmm) REVERT: D 506 ILE cc_start: 0.8575 (mm) cc_final: 0.8102 (mt) REVERT: E 167 ILE cc_start: 0.6832 (OUTLIER) cc_final: 0.6493 (pp) REVERT: E 506 ILE cc_start: 0.8452 (mm) cc_final: 0.8248 (mm) REVERT: F 167 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6356 (pp) REVERT: F 506 ILE cc_start: 0.8608 (mm) cc_final: 0.8121 (mt) REVERT: G 167 ILE cc_start: 0.6623 (OUTLIER) cc_final: 0.6321 (pp) REVERT: H 167 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6546 (pp) REVERT: H 217 MET cc_start: 0.1590 (mmt) cc_final: -0.0211 (ttt) REVERT: H 253 MET cc_start: 0.4291 (mmt) cc_final: 0.2055 (ttt) REVERT: H 477 MET cc_start: 0.8350 (mmm) cc_final: 0.7583 (mmm) REVERT: I 167 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6262 (pp) REVERT: I 217 MET cc_start: 0.2354 (mmt) cc_final: 0.0242 (ttt) REVERT: J 167 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6292 (pp) REVERT: J 506 ILE cc_start: 0.8589 (mm) cc_final: 0.8090 (mt) REVERT: K 167 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6517 (pp) REVERT: K 217 MET cc_start: 0.1478 (mmt) cc_final: -0.0256 (ttt) REVERT: K 477 MET cc_start: 0.8420 (mmm) cc_final: 0.8172 (mmm) REVERT: L 167 ILE cc_start: 0.6631 (OUTLIER) cc_final: 0.6407 (pp) REVERT: L 217 MET cc_start: 0.1792 (mmt) cc_final: -0.0217 (ttt) REVERT: L 477 MET cc_start: 0.8382 (mmm) cc_final: 0.7695 (mmm) REVERT: M 167 ILE cc_start: 0.6588 (OUTLIER) cc_final: 0.6175 (pp) REVERT: M 217 MET cc_start: 0.1865 (mmt) cc_final: -0.0258 (ttt) REVERT: N 167 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6536 (pp) REVERT: N 217 MET cc_start: 0.0982 (mmm) cc_final: 0.0508 (ttt) REVERT: N 477 MET cc_start: 0.8469 (mmm) cc_final: 0.7838 (mmm) REVERT: N 506 ILE cc_start: 0.8561 (mm) cc_final: 0.8120 (mt) REVERT: O 167 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6447 (pp) outliers start: 102 outliers final: 31 residues processed: 626 average time/residue: 0.5214 time to fit residues: 568.6414 Evaluate side-chains 492 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 445 time to evaluate : 4.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 THR 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 167 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain D residue 32 THR 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 167 ILE Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 308 MET Chi-restraints excluded: chain H residue 469 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain J residue 131 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 469 VAL Chi-restraints excluded: chain L residue 32 THR 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 167 ILE Chi-restraints excluded: chain M residue 469 VAL Chi-restraints excluded: chain N residue 32 THR 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 167 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 403 optimal weight: 0.9990 chunk 225 optimal weight: 20.0000 chunk 604 optimal weight: 5.9990 chunk 494 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 727 optimal weight: 8.9990 chunk 786 optimal weight: 10.0000 chunk 648 optimal weight: 0.9990 chunk 721 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 583 optimal weight: 50.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 GLN H 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 61664 Z= 0.182 Angle : 0.483 10.133 83088 Z= 0.249 Chirality : 0.042 0.198 10160 Planarity : 0.003 0.095 10656 Dihedral : 4.597 59.082 9040 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.63 % Favored : 90.98 % Rotamer: Outliers : 1.53 % Allowed : 7.52 % Favored : 90.95 % 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: -2.53 (0.09), residues: 8080 helix: -0.71 (0.09), residues: 3216 sheet: 0.33 (0.19), residues: 896 loop : -3.11 (0.08), residues: 3968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 110 PHE 0.006 0.001 PHE G 427 TYR 0.006 0.001 TYR J 412 ARG 0.003 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 612 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 512 time to evaluate : 5.078 Fit side-chains revert: symmetry clash REVERT: U 167 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6575 (pp) REVERT: U 217 MET cc_start: 0.2868 (mmp) cc_final: 0.0753 (ttt) REVERT: U 477 MET cc_start: 0.8392 (mmm) cc_final: 0.7679 (mmm) REVERT: A 167 ILE cc_start: 0.6990 (OUTLIER) cc_final: 0.6662 (pp) REVERT: A 217 MET cc_start: 0.1280 (mmt) cc_final: -0.0376 (ttt) REVERT: B 167 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6481 (pp) REVERT: B 477 MET cc_start: 0.8459 (mmm) cc_final: 0.7696 (mmm) REVERT: C 62 MET cc_start: 0.7592 (mtp) cc_final: 0.7356 (mtp) REVERT: C 167 ILE cc_start: 0.6572 (OUTLIER) cc_final: 0.6241 (pp) REVERT: C 217 MET cc_start: 0.2261 (mmt) cc_final: -0.0248 (ttt) REVERT: D 167 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6678 (pp) REVERT: D 477 MET cc_start: 0.8488 (mmm) cc_final: 0.7865 (mmm) REVERT: D 506 ILE cc_start: 0.8844 (mm) cc_final: 0.8477 (mt) REVERT: E 54 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: E 71 MET cc_start: 0.7111 (mtp) cc_final: 0.6795 (mtm) REVERT: E 167 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6524 (pp) REVERT: F 167 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6389 (pp) REVERT: G 62 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7528 (mtp) REVERT: G 217 MET cc_start: 0.1781 (mmt) cc_final: -0.0400 (ttt) REVERT: H 167 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6690 (pp) REVERT: H 217 MET cc_start: 0.1712 (mmt) cc_final: -0.0006 (ttt) REVERT: H 477 MET cc_start: 0.8337 (mmm) cc_final: 0.7613 (mmm) REVERT: I 167 ILE cc_start: 0.6798 (OUTLIER) cc_final: 0.6504 (pp) REVERT: J 167 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6467 (pp) REVERT: K 217 MET cc_start: 0.1484 (mmt) cc_final: -0.0222 (ttt) REVERT: L 167 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6524 (pp) REVERT: L 217 MET cc_start: 0.2029 (mmt) cc_final: 0.0082 (ttt) REVERT: L 477 MET cc_start: 0.8393 (mmm) cc_final: 0.7715 (mmm) REVERT: M 167 ILE cc_start: 0.6594 (OUTLIER) cc_final: 0.6233 (pp) REVERT: M 217 MET cc_start: 0.1998 (mmt) cc_final: -0.0220 (ttt) REVERT: N 167 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6551 (pp) REVERT: N 217 MET cc_start: 0.1247 (mmm) cc_final: 0.0599 (ttt) REVERT: N 477 MET cc_start: 0.8413 (mmm) cc_final: 0.7789 (mmm) REVERT: N 506 ILE cc_start: 0.8850 (mm) cc_final: 0.8469 (mt) REVERT: O 54 ASP cc_start: 0.7309 (m-30) cc_final: 0.7092 (m-30) REVERT: O 167 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6534 (pp) REVERT: O 217 MET cc_start: 0.2559 (tpp) cc_final: 0.0246 (ttt) outliers start: 100 outliers final: 46 residues processed: 585 average time/residue: 0.5082 time to fit residues: 523.7378 Evaluate side-chains 506 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 444 time to evaluate : 5.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 32 THR 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 32 THR Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain D residue 32 THR 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 451 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 110 HIS Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 469 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain H residue 32 THR 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 52 THR Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain I residue 167 ILE 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 32 THR Chi-restraints excluded: chain K residue 509 VAL Chi-restraints excluded: chain L residue 32 THR 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 167 ILE Chi-restraints excluded: chain N residue 32 THR 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 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: 0.6980 chunk 377 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 347 optimal weight: 0.5980 chunk 488 optimal weight: 9.9990 chunk 730 optimal weight: 0.0170 chunk 773 optimal weight: 0.1980 chunk 381 optimal weight: 20.0000 chunk 692 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.035 61664 Z= 0.097 Angle : 0.418 8.147 83088 Z= 0.215 Chirality : 0.039 0.120 10160 Planarity : 0.002 0.026 10656 Dihedral : 4.311 51.870 9040 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.64 % Favored : 94.96 % Rotamer: Outliers : 1.56 % Allowed : 8.62 % Favored : 89.81 % 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: -2.09 (0.09), residues: 8080 helix: -0.31 (0.10), residues: 3184 sheet: 0.61 (0.19), residues: 896 loop : -2.90 (0.08), residues: 4000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS I 355 PHE 0.003 0.000 PHE F 427 TYR 0.005 0.000 TYR E 291 ARG 0.006 0.000 ARG N 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 578 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 476 time to evaluate : 5.093 Fit side-chains revert: symmetry clash REVERT: U 167 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6384 (pp) REVERT: U 217 MET cc_start: 0.2811 (mmp) cc_final: 0.0768 (ttt) REVERT: U 477 MET cc_start: 0.8395 (mmm) cc_final: 0.7689 (mmm) REVERT: A 167 ILE cc_start: 0.6872 (OUTLIER) cc_final: 0.6538 (pp) REVERT: A 217 MET cc_start: 0.1198 (mmt) cc_final: -0.0401 (ttt) REVERT: B 167 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6509 (pp) REVERT: B 477 MET cc_start: 0.8385 (mmm) cc_final: 0.7630 (mmm) REVERT: B 506 ILE cc_start: 0.8775 (mm) cc_final: 0.8437 (mt) REVERT: C 167 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6314 (pp) REVERT: C 217 MET cc_start: 0.2263 (mmt) cc_final: -0.0240 (ttt) REVERT: D 167 ILE cc_start: 0.6831 (OUTLIER) cc_final: 0.6447 (pp) REVERT: D 477 MET cc_start: 0.8429 (mmm) cc_final: 0.7825 (mmm) REVERT: D 506 ILE cc_start: 0.8816 (mm) cc_final: 0.8376 (mt) REVERT: E 54 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: E 71 MET cc_start: 0.6802 (mtp) cc_final: 0.6574 (mtm) REVERT: E 167 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6472 (pp) REVERT: E 217 MET cc_start: 0.2662 (mmt) cc_final: 0.0023 (ttt) REVERT: F 167 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6265 (pp) REVERT: F 217 MET cc_start: 0.1877 (mmt) cc_final: 0.0824 (ttt) REVERT: F 347 MET cc_start: 0.3951 (mpp) cc_final: 0.3553 (mpp) REVERT: F 477 MET cc_start: 0.8193 (mmm) cc_final: 0.7756 (mmm) REVERT: F 506 ILE cc_start: 0.8882 (mm) cc_final: 0.8434 (mt) REVERT: G 217 MET cc_start: 0.1499 (mmt) cc_final: -0.0521 (ttt) REVERT: H 167 ILE cc_start: 0.7047 (OUTLIER) cc_final: 0.6803 (pp) REVERT: H 217 MET cc_start: 0.1238 (mmt) cc_final: 0.0294 (ttt) REVERT: H 253 MET cc_start: 0.4510 (mmp) cc_final: 0.1251 (ttt) REVERT: H 477 MET cc_start: 0.8404 (mmm) cc_final: 0.7637 (mmm) REVERT: I 167 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6428 (pp) REVERT: I 217 MET cc_start: 0.2069 (mmt) cc_final: -0.0082 (ttt) REVERT: J 167 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6435 (pp) REVERT: J 347 MET cc_start: 0.3867 (mpp) cc_final: 0.3551 (mpp) REVERT: J 477 MET cc_start: 0.8227 (mmm) cc_final: 0.7805 (mmm) REVERT: K 62 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7340 (mtp) REVERT: K 167 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6530 (pp) REVERT: K 217 MET cc_start: 0.1308 (mmt) cc_final: -0.0271 (ttt) REVERT: K 404 GLU cc_start: 0.7828 (tp30) cc_final: 0.7544 (tp30) REVERT: L 167 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6471 (pp) REVERT: L 217 MET cc_start: 0.2035 (mmt) cc_final: 0.0052 (ttt) REVERT: L 477 MET cc_start: 0.8384 (mmm) cc_final: 0.7624 (mmm) REVERT: M 167 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6138 (pp) REVERT: M 217 MET cc_start: 0.2182 (mmt) cc_final: 0.0034 (ttt) REVERT: M 404 GLU cc_start: 0.7799 (tp30) cc_final: 0.7502 (tp30) REVERT: N 167 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6528 (pp) REVERT: N 217 MET cc_start: 0.1282 (mmm) cc_final: 0.0702 (ttt) REVERT: N 477 MET cc_start: 0.8302 (mmm) cc_final: 0.7457 (mmm) REVERT: N 506 ILE cc_start: 0.8828 (mm) cc_final: 0.8402 (mt) REVERT: O 167 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6576 (pp) outliers start: 102 outliers final: 39 residues processed: 550 average time/residue: 0.5219 time to fit residues: 508.0764 Evaluate side-chains 481 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 425 time to evaluate : 5.977 ------------------------------------------------------------------------------- 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 167 ILE Chi-restraints excluded: chain U residue 235 ILE Chi-restraints excluded: chain A residue 10 MET Chi-restraints excluded: chain A residue 20 LEU 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 167 ILE Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 32 THR 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 110 HIS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 10 MET Chi-restraints excluded: chain I residue 32 THR 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 167 ILE Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain L residue 10 MET Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain M residue 32 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 110 HIS Chi-restraints excluded: chain N residue 167 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 167 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 644 optimal weight: 4.9990 chunk 438 optimal weight: 0.0970 chunk 11 optimal weight: 5.9990 chunk 575 optimal weight: 10.0000 chunk 319 optimal weight: 10.0000 chunk 659 optimal weight: 0.6980 chunk 534 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 394 optimal weight: 0.6980 chunk 694 optimal weight: 2.9990 chunk 195 optimal weight: 9.9990 overall best weight: 1.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 355 HIS ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 61664 Z= 0.178 Angle : 0.473 10.194 83088 Z= 0.239 Chirality : 0.041 0.123 10160 Planarity : 0.002 0.029 10656 Dihedral : 4.573 46.577 9040 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.56 % Favored : 93.04 % Rotamer: Outliers : 1.64 % Allowed : 9.96 % Favored : 88.40 % 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: -2.07 (0.09), residues: 8080 helix: -0.35 (0.09), residues: 3216 sheet: 0.81 (0.20), residues: 896 loop : -2.91 (0.08), residues: 3968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS H 355 PHE 0.003 0.001 PHE J 427 TYR 0.009 0.001 TYR O 291 ARG 0.005 0.000 ARG N 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 562 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 455 time to evaluate : 5.060 Fit side-chains REVERT: U 167 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6479 (pp) REVERT: U 217 MET cc_start: 0.2731 (mmp) cc_final: 0.0772 (ttt) REVERT: U 477 MET cc_start: 0.8502 (mmm) cc_final: 0.7799 (mmm) REVERT: A 167 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6632 (pp) REVERT: A 217 MET cc_start: 0.1592 (mmt) cc_final: -0.0165 (ttt) REVERT: B 167 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6391 (pp) REVERT: B 477 MET cc_start: 0.8460 (mmm) cc_final: 0.7765 (mmm) REVERT: C 71 MET cc_start: 0.7358 (mtm) cc_final: 0.7049 (mtm) REVERT: C 167 ILE cc_start: 0.6610 (OUTLIER) cc_final: 0.6274 (pp) REVERT: C 217 MET cc_start: 0.1938 (mmt) cc_final: 0.0266 (ttt) REVERT: D 167 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6607 (pp) REVERT: D 477 MET cc_start: 0.8474 (mmm) cc_final: 0.7854 (mmm) REVERT: E 54 ASP cc_start: 0.7880 (m-30) cc_final: 0.7535 (m-30) REVERT: E 167 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6568 (pp) REVERT: E 217 MET cc_start: 0.2049 (mmt) cc_final: 0.0101 (ttt) REVERT: F 167 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6422 (pp) REVERT: F 217 MET cc_start: 0.2017 (mmt) cc_final: 0.0865 (ttt) REVERT: F 477 MET cc_start: 0.8286 (mmm) cc_final: 0.7809 (mmm) REVERT: G 217 MET cc_start: 0.1283 (mmt) cc_final: -0.0178 (ttt) REVERT: G 404 GLU cc_start: 0.7888 (tp30) cc_final: 0.7619 (tp30) REVERT: H 167 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6660 (pp) REVERT: H 217 MET cc_start: 0.1241 (mmp) cc_final: 0.0347 (ttt) REVERT: H 262 MET cc_start: 0.3815 (tpp) cc_final: 0.1146 (ttt) REVERT: H 477 MET cc_start: 0.8459 (mmm) cc_final: 0.7717 (mmm) REVERT: I 167 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6418 (pp) REVERT: I 217 MET cc_start: 0.1860 (mmt) cc_final: -0.0263 (ttt) REVERT: J 167 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6556 (pp) REVERT: J 477 MET cc_start: 0.8300 (mmm) cc_final: 0.7880 (mmm) REVERT: K 167 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6409 (pp) REVERT: K 217 MET cc_start: 0.1317 (mmt) cc_final: -0.0302 (ttt) REVERT: L 167 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6447 (pp) REVERT: L 217 MET cc_start: 0.2115 (mmt) cc_final: 0.0066 (ttt) REVERT: L 477 MET cc_start: 0.8490 (mmm) cc_final: 0.7782 (mmm) REVERT: M 167 ILE cc_start: 0.6538 (OUTLIER) cc_final: 0.6234 (pp) REVERT: M 217 MET cc_start: 0.1695 (mmt) cc_final: 0.0170 (ttt) REVERT: N 167 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6578 (pp) REVERT: N 217 MET cc_start: 0.1337 (mmm) cc_final: 0.0622 (ttt) REVERT: N 477 MET cc_start: 0.8467 (mmm) cc_final: 0.7526 (mmm) REVERT: O 167 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6677 (pp) REVERT: O 217 MET cc_start: 0.1902 (mmt) cc_final: 0.0176 (ttt) outliers start: 107 outliers final: 60 residues processed: 535 average time/residue: 0.4899 time to fit residues: 470.5613 Evaluate side-chains 487 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 412 time to evaluate : 5.034 ------------------------------------------------------------------------------- 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 110 HIS Chi-restraints excluded: chain U residue 167 ILE Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 89 THR 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 110 HIS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 110 HIS Chi-restraints excluded: chain E residue 131 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 32 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 110 HIS Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 110 HIS Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 110 HIS Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 10 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 32 THR 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 L residue 20 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 110 HIS Chi-restraints excluded: chain L residue 167 ILE Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain M residue 10 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 89 THR 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 20 LEU Chi-restraints excluded: chain N residue 32 THR 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 32 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 167 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 260 optimal weight: 0.5980 chunk 696 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 454 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 774 optimal weight: 40.0000 chunk 642 optimal weight: 0.5980 chunk 358 optimal weight: 0.9980 chunk 64 optimal weight: 0.0170 chunk 256 optimal weight: 0.8980 chunk 406 optimal weight: 0.0970 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 355 HIS A 355 HIS B 355 HIS C 355 HIS D 355 HIS E 355 HIS F 355 HIS G 355 HIS I 355 HIS J 355 HIS ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 355 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.031 61664 Z= 0.094 Angle : 0.422 9.298 83088 Z= 0.213 Chirality : 0.039 0.117 10160 Planarity : 0.002 0.031 10656 Dihedral : 4.281 43.783 9040 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.41 % Favored : 95.21 % Rotamer: Outliers : 1.21 % Allowed : 10.88 % Favored : 87.91 % 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: -1.73 (0.09), residues: 8080 helix: -0.03 (0.10), residues: 3216 sheet: 1.01 (0.20), residues: 896 loop : -2.75 (0.08), residues: 3968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS E 355 PHE 0.003 0.000 PHE H 255 TYR 0.003 0.000 TYR B 412 ARG 0.004 0.000 ARG N 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 557 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 478 time to evaluate : 5.065 Fit side-chains REVERT: U 167 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6705 (pp) REVERT: U 217 MET cc_start: 0.2706 (mmp) cc_final: 0.0801 (ttt) REVERT: U 477 MET cc_start: 0.8350 (mmm) cc_final: 0.7664 (mmm) REVERT: A 167 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6602 (pp) REVERT: A 217 MET cc_start: 0.1394 (mmt) cc_final: -0.0342 (ttt) REVERT: B 167 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6343 (pp) REVERT: B 477 MET cc_start: 0.8394 (mmm) cc_final: 0.7774 (mmm) REVERT: C 167 ILE cc_start: 0.6629 (OUTLIER) cc_final: 0.6237 (pp) REVERT: C 217 MET cc_start: 0.1920 (mmt) cc_final: 0.0374 (ttt) REVERT: D 167 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6542 (pp) REVERT: D 477 MET cc_start: 0.8419 (mmm) cc_final: 0.7653 (mmm) REVERT: E 54 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: E 167 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6452 (pp) REVERT: E 217 MET cc_start: 0.1634 (mmt) cc_final: 0.0232 (ttt) REVERT: E 513 GLU cc_start: 0.7049 (pm20) cc_final: 0.6809 (pm20) REVERT: F 167 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6483 (pp) REVERT: F 217 MET cc_start: 0.1857 (mmt) cc_final: 0.0807 (ttt) REVERT: F 477 MET cc_start: 0.8298 (mmm) cc_final: 0.7763 (mmm) REVERT: G 217 MET cc_start: 0.1275 (mmt) cc_final: -0.0189 (ttt) REVERT: G 404 GLU cc_start: 0.7811 (tp30) cc_final: 0.7543 (tp30) REVERT: H 144 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7583 (tt) REVERT: H 167 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6776 (pp) REVERT: H 217 MET cc_start: 0.1134 (mmp) cc_final: 0.0313 (ttt) REVERT: H 253 MET cc_start: 0.4565 (mmp) cc_final: 0.1034 (ttm) REVERT: H 262 MET cc_start: 0.3884 (tpp) cc_final: 0.1179 (ttt) REVERT: H 477 MET cc_start: 0.8325 (mmm) cc_final: 0.7597 (mmm) REVERT: I 167 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6375 (pp) REVERT: I 217 MET cc_start: 0.1927 (mmt) cc_final: -0.0173 (ttt) REVERT: J 167 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6623 (pp) REVERT: J 477 MET cc_start: 0.8317 (mmm) cc_final: 0.7783 (mmm) REVERT: K 167 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6347 (pp) REVERT: K 217 MET cc_start: 0.1301 (mmt) cc_final: -0.0247 (ttt) REVERT: L 217 MET cc_start: 0.2176 (mmt) cc_final: -0.0123 (ttt) REVERT: L 477 MET cc_start: 0.8341 (mmm) cc_final: 0.7365 (mmm) REVERT: M 167 ILE cc_start: 0.6505 (OUTLIER) cc_final: 0.6173 (pp) REVERT: M 217 MET cc_start: 0.1681 (mmt) cc_final: 0.0041 (ttt) REVERT: N 167 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6489 (pp) REVERT: N 217 MET cc_start: 0.1316 (mmm) cc_final: 0.0696 (ttt) REVERT: N 477 MET cc_start: 0.8327 (mmm) cc_final: 0.7471 (mmm) REVERT: O 217 MET cc_start: 0.2408 (mmt) cc_final: -0.0215 (ttt) outliers start: 79 outliers final: 49 residues processed: 521 average time/residue: 0.4916 time to fit residues: 458.4730 Evaluate side-chains 492 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 428 time to evaluate : 4.945 ------------------------------------------------------------------------------- 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 110 HIS Chi-restraints excluded: chain U residue 167 ILE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 89 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 110 HIS Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 89 THR 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 167 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 54 ASP 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 20 LEU Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 32 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 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 89 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 32 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 167 ILE Chi-restraints excluded: chain K residue 32 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 167 ILE Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain M residue 10 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 110 HIS 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 167 ILE Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 110 HIS Chi-restraints excluded: chain O residue 143 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 746 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 441 optimal weight: 2.9990 chunk 565 optimal weight: 0.0040 chunk 437 optimal weight: 5.9990 chunk 651 optimal weight: 2.9990 chunk 432 optimal weight: 30.0000 chunk 771 optimal weight: 40.0000 chunk 482 optimal weight: 40.0000 chunk 470 optimal weight: 10.0000 chunk 355 optimal weight: 0.9980 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 355 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 61664 Z= 0.160 Angle : 0.459 10.602 83088 Z= 0.231 Chirality : 0.040 0.122 10160 Planarity : 0.002 0.032 10656 Dihedral : 4.484 41.399 9040 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.52 % Favored : 94.18 % Rotamer: Outliers : 1.56 % Allowed : 11.04 % Favored : 87.39 % 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: -0.03 (0.10), residues: 3216 sheet: 1.06 (0.20), residues: 896 loop : -2.75 (0.08), residues: 3968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS M 355 PHE 0.003 0.001 PHE J 427 TYR 0.005 0.001 TYR I 412 ARG 0.005 0.000 ARG E 393 *********************** 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 534 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 432 time to evaluate : 5.218 Fit side-chains REVERT: U 167 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6483 (pp) REVERT: U 217 MET cc_start: 0.2764 (mmp) cc_final: 0.0812 (ttt) REVERT: U 477 MET cc_start: 0.8431 (mmm) cc_final: 0.7608 (mmm) REVERT: A 167 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6529 (pp) REVERT: A 217 MET cc_start: 0.1150 (mmt) cc_final: 0.0104 (ttt) REVERT: B 167 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6599 (pp) REVERT: B 477 MET cc_start: 0.8453 (mmm) cc_final: 0.7621 (mmm) REVERT: C 167 ILE cc_start: 0.6667 (OUTLIER) cc_final: 0.6387 (pp) REVERT: C 217 MET cc_start: 0.1828 (mmt) cc_final: 0.0217 (ttt) REVERT: D 167 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6601 (pp) REVERT: D 217 MET cc_start: 0.3409 (mtp) cc_final: -0.0120 (ttt) REVERT: D 477 MET cc_start: 0.8435 (mmm) cc_final: 0.7673 (mmm) REVERT: E 54 ASP cc_start: 0.7826 (m-30) cc_final: 0.7531 (m-30) REVERT: E 167 ILE cc_start: 0.6832 (OUTLIER) cc_final: 0.6451 (pp) REVERT: E 217 MET cc_start: 0.1604 (mmt) cc_final: 0.0513 (ttt) REVERT: F 167 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6438 (pp) REVERT: F 217 MET cc_start: 0.1923 (mmt) cc_final: 0.0820 (ttt) REVERT: F 477 MET cc_start: 0.8326 (mmm) cc_final: 0.7802 (mmm) REVERT: G 217 MET cc_start: 0.1356 (mmt) cc_final: -0.0205 (ttt) REVERT: G 404 GLU cc_start: 0.7907 (tp30) cc_final: 0.7680 (tp30) REVERT: H 167 ILE cc_start: 0.6951 (OUTLIER) cc_final: 0.6666 (pp) REVERT: H 217 MET cc_start: 0.1007 (mmp) cc_final: 0.0007 (ttt) REVERT: H 253 MET cc_start: 0.4505 (mmp) cc_final: 0.1105 (ttm) REVERT: H 262 MET cc_start: 0.4017 (tpp) cc_final: 0.1232 (ttt) REVERT: H 477 MET cc_start: 0.8399 (mmm) cc_final: 0.7785 (mmm) REVERT: I 217 MET cc_start: 0.1299 (mmt) cc_final: -0.0006 (ttt) REVERT: J 167 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6623 (pp) REVERT: J 477 MET cc_start: 0.8346 (mmm) cc_final: 0.7782 (mmm) REVERT: K 167 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6464 (pp) REVERT: K 217 MET cc_start: 0.1094 (mmt) cc_final: 0.0085 (ttt) REVERT: L 217 MET cc_start: 0.2388 (mmt) cc_final: 0.0176 (ttt) REVERT: L 477 MET cc_start: 0.8434 (mmm) cc_final: 0.7583 (mmm) REVERT: M 167 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6109 (pp) REVERT: M 217 MET cc_start: 0.1737 (mmt) cc_final: 0.0406 (ttt) REVERT: N 167 ILE cc_start: 0.6869 (OUTLIER) cc_final: 0.6472 (pp) REVERT: N 217 MET cc_start: 0.1393 (mmm) cc_final: 0.0602 (ttt) REVERT: N 477 MET cc_start: 0.8443 (mmm) cc_final: 0.7666 (mmm) REVERT: O 217 MET cc_start: 0.1896 (mmt) cc_final: 0.0190 (ttt) outliers start: 102 outliers final: 79 residues processed: 511 average time/residue: 0.5614 time to fit residues: 522.3262 Evaluate side-chains 507 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 416 time to evaluate : 5.059 ------------------------------------------------------------------------------- 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 110 HIS Chi-restraints excluded: chain U residue 167 ILE Chi-restraints excluded: chain U residue 433 VAL Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 110 HIS Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 433 VAL 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 167 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 394 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 E residue 20 LEU Chi-restraints excluded: chain E residue 32 THR 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 394 ILE Chi-restraints excluded: chain E residue 433 VAL 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 F residue 433 VAL Chi-restraints excluded: chain F residue 513 GLU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 THR 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 20 LEU Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 394 ILE 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 110 HIS Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 433 VAL Chi-restraints excluded: chain K residue 32 THR 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 235 ILE Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 110 HIS Chi-restraints excluded: chain L residue 235 ILE Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 89 THR 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 M residue 433 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR 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 O residue 20 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 477 optimal weight: 50.0000 chunk 307 optimal weight: 10.0000 chunk 460 optimal weight: 0.7980 chunk 232 optimal weight: 7.9990 chunk 151 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 490 optimal weight: 0.7980 chunk 525 optimal weight: 6.9990 chunk 381 optimal weight: 50.0000 chunk 71 optimal weight: 0.6980 chunk 606 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 355 HIS M 355 HIS N 355 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 61664 Z= 0.099 Angle : 0.427 9.948 83088 Z= 0.214 Chirality : 0.039 0.115 10160 Planarity : 0.002 0.031 10656 Dihedral : 4.277 40.220 9040 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 1.19 % Allowed : 11.44 % Favored : 87.36 % 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: -1.46 (0.09), residues: 8080 helix: 0.22 (0.10), residues: 3200 sheet: 1.18 (0.20), residues: 896 loop : -2.63 (0.08), residues: 3984 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS L 355 PHE 0.003 0.000 PHE U 349 TYR 0.003 0.000 TYR B 412 ARG 0.003 0.000 ARG E 393 *********************** 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 519 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 441 time to evaluate : 6.222 Fit side-chains REVERT: U 167 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6591 (pp) REVERT: U 217 MET cc_start: 0.2572 (mmp) cc_final: 0.0768 (ttt) REVERT: U 477 MET cc_start: 0.8397 (mmm) cc_final: 0.7587 (mmm) REVERT: A 167 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.6296 (pp) REVERT: A 217 MET cc_start: 0.1231 (mmt) cc_final: 0.0159 (ttt) REVERT: A 513 GLU cc_start: 0.7117 (pm20) cc_final: 0.6818 (pm20) REVERT: B 167 ILE cc_start: 0.6909 (OUTLIER) cc_final: 0.6616 (pp) REVERT: B 477 MET cc_start: 0.8420 (mmm) cc_final: 0.7616 (mmm) REVERT: C 167 ILE cc_start: 0.6620 (OUTLIER) cc_final: 0.6311 (pp) REVERT: C 217 MET cc_start: 0.1930 (mmt) cc_final: 0.0288 (ttt) REVERT: D 167 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6583 (pp) REVERT: D 477 MET cc_start: 0.8391 (mmm) cc_final: 0.7644 (mmm) REVERT: E 54 ASP cc_start: 0.7655 (m-30) cc_final: 0.7365 (m-30) REVERT: E 167 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6382 (pp) REVERT: E 217 MET cc_start: 0.1621 (mmt) cc_final: 0.0499 (ttt) REVERT: E 513 GLU cc_start: 0.7106 (pm20) cc_final: 0.6573 (pm20) REVERT: F 167 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6329 (pp) REVERT: F 217 MET cc_start: 0.1915 (mmt) cc_final: 0.0882 (ttt) REVERT: F 477 MET cc_start: 0.8289 (mmm) cc_final: 0.7785 (mmm) REVERT: G 217 MET cc_start: 0.1461 (mmt) cc_final: -0.0173 (ttt) REVERT: G 513 GLU cc_start: 0.7068 (pm20) cc_final: 0.6752 (pm20) REVERT: H 167 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6838 (pp) REVERT: H 217 MET cc_start: 0.0997 (mmp) cc_final: 0.0011 (ttt) REVERT: H 253 MET cc_start: 0.4607 (mmp) cc_final: 0.1388 (ttm) REVERT: H 262 MET cc_start: 0.3998 (tpp) cc_final: 0.1216 (ttt) REVERT: H 477 MET cc_start: 0.8363 (mmm) cc_final: 0.7741 (mmm) REVERT: I 167 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6617 (pp) REVERT: I 217 MET cc_start: 0.1244 (mmt) cc_final: -0.0011 (ttt) REVERT: J 167 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6605 (pp) REVERT: J 477 MET cc_start: 0.8285 (mmm) cc_final: 0.7786 (mmm) REVERT: K 167 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6462 (pp) REVERT: K 217 MET cc_start: 0.1584 (mmt) cc_final: 0.0472 (ttt) REVERT: L 217 MET cc_start: 0.2314 (mmt) cc_final: 0.0217 (ttt) REVERT: L 477 MET cc_start: 0.8387 (mmm) cc_final: 0.7544 (mmm) REVERT: M 167 ILE cc_start: 0.6543 (OUTLIER) cc_final: 0.6233 (pp) REVERT: M 217 MET cc_start: 0.1460 (mmt) cc_final: 0.0176 (ttt) REVERT: N 167 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6422 (pp) REVERT: N 217 MET cc_start: 0.1356 (mmm) cc_final: 0.0588 (ttt) REVERT: N 477 MET cc_start: 0.8372 (mmm) cc_final: 0.7587 (mmm) REVERT: O 217 MET cc_start: 0.1919 (mmt) cc_final: 0.0174 (ttt) outliers start: 78 outliers final: 61 residues processed: 493 average time/residue: 0.4983 time to fit residues: 442.8752 Evaluate side-chains 502 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 428 time to evaluate : 5.090 ------------------------------------------------------------------------------- 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 A residue 32 THR Chi-restraints excluded: chain A residue 89 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 167 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 89 THR 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 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 E residue 20 LEU Chi-restraints excluded: chain E residue 32 THR 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 20 LEU 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 89 THR Chi-restraints excluded: chain G residue 110 HIS 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 20 LEU 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 20 LEU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 32 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 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 M residue 20 LEU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 110 HIS 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 O residue 20 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 110 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 701 optimal weight: 1.9990 chunk 738 optimal weight: 9.9990 chunk 673 optimal weight: 6.9990 chunk 718 optimal weight: 9.9990 chunk 432 optimal weight: 40.0000 chunk 313 optimal weight: 8.9990 chunk 564 optimal weight: 0.0670 chunk 220 optimal weight: 6.9990 chunk 649 optimal weight: 3.9990 chunk 679 optimal weight: 50.0000 chunk 716 optimal weight: 20.0000 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 369 HIS B 369 HIS C 369 HIS D 369 HIS F 369 HIS H 369 HIS J 369 HIS L 369 HIS N 369 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 61664 Z= 0.337 Angle : 0.613 11.341 83088 Z= 0.306 Chirality : 0.044 0.160 10160 Planarity : 0.003 0.028 10656 Dihedral : 5.457 43.561 9040 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.97 % Favored : 91.82 % Rotamer: Outliers : 1.72 % Allowed : 11.08 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.09), residues: 8080 helix: -0.63 (0.09), residues: 3312 sheet: 0.93 (0.20), residues: 896 loop : -2.77 (0.08), residues: 3872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS L 110 PHE 0.008 0.001 PHE N 427 TYR 0.014 0.002 TYR E 412 ARG 0.005 0.000 ARG E 393 *********************** 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 514 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 402 time to evaluate : 6.828 Fit side-chains REVERT: U 167 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6518 (pp) REVERT: U 217 MET cc_start: 0.2748 (mmp) cc_final: 0.0762 (ttt) REVERT: U 477 MET cc_start: 0.8420 (mmm) cc_final: 0.7885 (mmm) REVERT: A 167 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6488 (pp) REVERT: A 217 MET cc_start: 0.1314 (mmt) cc_final: 0.0173 (ttt) REVERT: B 167 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6428 (pp) REVERT: B 477 MET cc_start: 0.8509 (mmm) cc_final: 0.8003 (mmm) REVERT: C 167 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6547 (pp) REVERT: C 217 MET cc_start: 0.1856 (mmt) cc_final: 0.0721 (ttt) REVERT: D 167 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6806 (pp) REVERT: D 477 MET cc_start: 0.8480 (mmm) cc_final: 0.7908 (mmm) REVERT: E 110 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.8032 (p-80) REVERT: E 167 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6526 (pp) REVERT: E 217 MET cc_start: 0.1635 (mmt) cc_final: 0.0507 (ttt) REVERT: F 167 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6437 (pp) REVERT: F 217 MET cc_start: 0.1695 (mmt) cc_final: 0.1153 (ttt) REVERT: F 477 MET cc_start: 0.8304 (mmm) cc_final: 0.7782 (mmm) REVERT: G 217 MET cc_start: 0.1165 (mmt) cc_final: -0.0084 (ttt) REVERT: G 513 GLU cc_start: 0.7234 (pm20) cc_final: 0.6820 (pm20) REVERT: H 167 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6664 (pp) REVERT: H 217 MET cc_start: 0.1058 (mmp) cc_final: 0.0013 (ttt) REVERT: H 477 MET cc_start: 0.8449 (mmm) cc_final: 0.7968 (mmm) REVERT: I 167 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6729 (pp) REVERT: I 217 MET cc_start: 0.0968 (mmt) cc_final: -0.0045 (ttt) REVERT: J 127 GLU cc_start: 0.8201 (tp30) cc_final: 0.7913 (tp30) REVERT: J 167 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6694 (pp) REVERT: J 477 MET cc_start: 0.8284 (mmm) cc_final: 0.7772 (mmm) REVERT: K 217 MET cc_start: 0.1043 (mmt) cc_final: -0.0185 (ttt) REVERT: L 217 MET cc_start: 0.2718 (mmt) cc_final: 0.0455 (ttt) REVERT: L 477 MET cc_start: 0.8422 (mmm) cc_final: 0.7866 (mmm) REVERT: M 167 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6427 (pp) REVERT: M 217 MET cc_start: 0.1606 (mmt) cc_final: 0.0163 (ttt) REVERT: N 167 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6669 (pp) REVERT: N 477 MET cc_start: 0.8396 (mmm) cc_final: 0.7874 (mmm) REVERT: O 217 MET cc_start: 0.1678 (mmt) cc_final: 0.0378 (ttt) outliers start: 112 outliers final: 78 residues processed: 502 average time/residue: 0.4878 time to fit residues: 444.2914 Evaluate side-chains 483 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 392 time to evaluate : 5.031 ------------------------------------------------------------------------------- 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 433 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 25 ILE 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 167 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 25 ILE 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 131 THR 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 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 E residue 433 VAL 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 F residue 433 VAL Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 433 VAL 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 433 VAL Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 167 ILE Chi-restraints excluded: chain I residue 433 VAL 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 J residue 433 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 433 VAL 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 235 ILE Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 32 THR 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 N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR 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 433 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 131 THR Chi-restraints excluded: chain O residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 471 optimal weight: 6.9990 chunk 759 optimal weight: 0.9990 chunk 463 optimal weight: 5.9990 chunk 360 optimal weight: 0.5980 chunk 528 optimal weight: 8.9990 chunk 797 optimal weight: 2.9990 chunk 733 optimal weight: 5.9990 chunk 634 optimal weight: 50.0000 chunk 65 optimal weight: 3.9990 chunk 490 optimal weight: 2.9990 chunk 389 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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: 0.6736 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 61664 Z= 0.176 Angle : 0.508 11.565 83088 Z= 0.249 Chirality : 0.040 0.130 10160 Planarity : 0.002 0.029 10656 Dihedral : 5.181 47.074 9040 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.79 % Favored : 95.01 % Rotamer: Outliers : 1.24 % Allowed : 11.95 % Favored : 86.81 % 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: -1.83 (0.09), residues: 8080 helix: -0.24 (0.09), residues: 3232 sheet: 0.99 (0.20), residues: 896 loop : -2.71 (0.08), residues: 3952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS L 110 PHE 0.005 0.001 PHE J 427 TYR 0.003 0.001 TYR N 291 ARG 0.004 0.000 ARG E 393 ********************** 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 490 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 409 time to evaluate : 5.157 Fit side-chains REVERT: U 39 ASP cc_start: 0.8283 (m-30) cc_final: 0.8003 (m-30) REVERT: U 167 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6560 (pp) REVERT: U 217 MET cc_start: 0.2694 (mmp) cc_final: 0.0772 (ttt) REVERT: U 477 MET cc_start: 0.8374 (mmm) cc_final: 0.7788 (mmm) REVERT: A 167 ILE cc_start: 0.6741 (OUTLIER) cc_final: 0.6381 (pp) REVERT: A 217 MET cc_start: 0.1176 (mmt) cc_final: -0.0126 (ttt) REVERT: B 167 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6390 (pp) REVERT: B 477 MET cc_start: 0.8447 (mmm) cc_final: 0.7843 (mmm) REVERT: C 167 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6398 (pp) REVERT: C 217 MET cc_start: 0.1847 (mmt) cc_final: 0.0496 (ttt) REVERT: D 39 ASP cc_start: 0.8324 (m-30) cc_final: 0.8051 (m-30) REVERT: D 167 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6822 (pp) REVERT: D 477 MET cc_start: 0.8416 (mmm) cc_final: 0.7816 (mmm) REVERT: E 167 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6400 (pp) REVERT: E 217 MET cc_start: 0.1516 (mmt) cc_final: 0.0368 (ttt) REVERT: F 167 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6403 (pp) REVERT: F 217 MET cc_start: 0.1722 (mmt) cc_final: 0.0908 (ttt) REVERT: F 477 MET cc_start: 0.8297 (mmm) cc_final: 0.7832 (mmm) REVERT: G 217 MET cc_start: 0.1191 (mmt) cc_final: -0.0031 (ttt) REVERT: G 513 GLU cc_start: 0.7174 (pm20) cc_final: 0.6761 (pm20) REVERT: H 39 ASP cc_start: 0.8284 (m-30) cc_final: 0.8014 (m-30) REVERT: H 167 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6692 (pp) REVERT: H 217 MET cc_start: 0.1054 (mmp) cc_final: 0.0084 (ttt) REVERT: H 253 MET cc_start: 0.4500 (mmp) cc_final: 0.0929 (ttp) REVERT: H 262 MET cc_start: 0.3656 (tpp) cc_final: 0.1184 (ttt) REVERT: H 477 MET cc_start: 0.8388 (mmm) cc_final: 0.7763 (mmm) REVERT: I 217 MET cc_start: 0.1053 (mmt) cc_final: 0.0181 (ttt) REVERT: J 39 ASP cc_start: 0.8294 (m-30) cc_final: 0.8002 (m-30) REVERT: J 167 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6600 (pp) REVERT: J 262 MET cc_start: 0.4129 (tpp) cc_final: 0.1246 (ttt) REVERT: J 477 MET cc_start: 0.8268 (mmm) cc_final: 0.7813 (mmm) REVERT: K 217 MET cc_start: 0.1154 (mmt) cc_final: 0.0115 (ttt) REVERT: L 217 MET cc_start: 0.2471 (mmt) cc_final: 0.0742 (ttt) REVERT: L 477 MET cc_start: 0.8362 (mmm) cc_final: 0.7753 (mmm) REVERT: M 167 ILE cc_start: 0.6705 (OUTLIER) cc_final: 0.6358 (pp) REVERT: M 217 MET cc_start: 0.1195 (mmt) cc_final: -0.0056 (ttt) REVERT: N 167 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6409 (pp) REVERT: N 347 MET cc_start: 0.2688 (mmm) cc_final: 0.2372 (mmp) REVERT: N 477 MET cc_start: 0.8363 (mmm) cc_final: 0.7761 (mmm) REVERT: O 217 MET cc_start: 0.1647 (mmt) cc_final: 0.0339 (ttt) outliers start: 81 outliers final: 64 residues processed: 476 average time/residue: 0.4989 time to fit residues: 426.6684 Evaluate side-chains 474 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 399 time to evaluate : 5.054 ------------------------------------------------------------------------------- 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 A residue 32 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 235 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 167 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 501 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 433 VAL 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 E residue 20 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 43 VAL 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 F residue 433 VAL 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 433 VAL 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 I residue 20 LEU 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 308 MET Chi-restraints excluded: chain J residue 20 LEU 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 32 THR Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 235 ILE Chi-restraints excluded: chain K residue 433 VAL 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 M residue 20 LEU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 167 ILE Chi-restraints excluded: chain M residue 235 ILE Chi-restraints excluded: chain M residue 308 MET Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR 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 O residue 20 LEU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 391 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 504 optimal weight: 2.9990 chunk 676 optimal weight: 0.0670 chunk 194 optimal weight: 0.0770 chunk 585 optimal weight: 40.0000 chunk 93 optimal weight: 0.0370 chunk 176 optimal weight: 7.9990 chunk 635 optimal weight: 40.0000 chunk 266 optimal weight: 9.9990 chunk 652 optimal weight: 0.0270 chunk 80 optimal weight: 0.0870 chunk 117 optimal weight: 0.0030 overall best weight: 0.0422 ------------------------------------------------------------------------------- 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 = 0.5138 r_free = 0.5138 target = 0.285721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.239170 restraints weight = 71576.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.236781 restraints weight = 123348.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.238350 restraints weight = 115905.353| |-----------------------------------------------------------------------------| r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 61664 Z= 0.102 Angle : 0.459 11.232 83088 Z= 0.226 Chirality : 0.039 0.136 10160 Planarity : 0.002 0.031 10656 Dihedral : 4.425 39.730 9040 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.81 % Favored : 95.01 % Rotamer: Outliers : 0.75 % Allowed : 12.39 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.09), residues: 8080 helix: 0.19 (0.10), residues: 3232 sheet: 1.14 (0.20), residues: 896 loop : -2.55 (0.08), residues: 3952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS L 110 PHE 0.004 0.000 PHE G 349 TYR 0.004 0.001 TYR I 118 ARG 0.007 0.000 ARG H 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9357.27 seconds wall clock time: 167 minutes 51.00 seconds (10071.00 seconds total)