Starting phenix.real_space_refine on Sat Dec 9 15:42:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/12_2023/8ari_15603_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/12_2023/8ari_15603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/12_2023/8ari_15603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/12_2023/8ari_15603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/12_2023/8ari_15603_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/12_2023/8ari_15603_updated.pdb" } resolution = 3.0 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= -0.000 sd= 0.035 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 297 5.16 5 C 39655 2.51 5 N 11628 2.21 5 O 12128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 63756 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "B" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2542 Classifications: {'peptide': 330} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 321} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2546 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 321} Chain: "D" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "E" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "F" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "G" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "H" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "I" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "J" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "K" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "L" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "M" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "N" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "O" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "P" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "Q" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "R" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "S" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "T" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "U" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "V" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2546 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 321} Chain: "W" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2546 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 321} Chain: "X" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2557 Classifications: {'peptide': 331} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 321} Chain: "a" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "b" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "c" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "f" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "g" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "h" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "i" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "j" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 20} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.80, per 1000 atoms: 0.37 Number of scatterers: 63756 At special positions: 0 Unit cell: (126.15, 333.21, 119.19, 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 297 16.00 P 48 15.00 O 12128 8.00 N 11628 7.00 C 39655 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: 16.29 Conformation dependent library (CDL) restraints added in 8.4 seconds 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 336 helices and 48 sheets defined 33.5% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.00 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 211 through 215' Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN A 254 " --> pdb=" O PHE A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 254' Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.811A pdb=" N GLN A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 removed outlier: 3.836A pdb=" N ILE A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 125 through 140 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 184 through 196 removed outlier: 4.141A pdb=" N ALA B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 211 through 215' Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 249 through 254 removed outlier: 3.843A pdb=" N LYS B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN B 254 " --> pdb=" O PHE B 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 254' Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing helix chain 'B' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 159 through 165 Processing helix chain 'C' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 211 through 215' Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 249 through 254 removed outlier: 3.843A pdb=" N LYS C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 254' Processing helix chain 'C' and resid 267 through 269 No H-bonds generated for 'chain 'C' and resid 267 through 269' Processing helix chain 'C' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 339 removed outlier: 3.836A pdb=" N ILE C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 159 through 165 Processing helix chain 'D' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU D 215 " --> pdb=" O VAL D 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 211 through 215' Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS D 253 " --> pdb=" O ASP D 249 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN D 254 " --> pdb=" O PHE D 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 249 through 254' Processing helix chain 'D' and resid 267 through 269 No H-bonds generated for 'chain 'D' and resid 267 through 269' Processing helix chain 'D' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 64 through 68 Processing helix chain 'E' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 125 through 140 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 159 through 165 Processing helix chain 'E' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA E 195 " --> pdb=" O LEU E 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU E 215 " --> pdb=" O VAL E 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 211 through 215' Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN E 254 " --> pdb=" O PHE E 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 249 through 254' Processing helix chain 'E' and resid 267 through 269 No H-bonds generated for 'chain 'E' and resid 267 through 269' Processing helix chain 'E' and resid 272 through 281 removed outlier: 3.811A pdb=" N GLN E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS F 88 " --> pdb=" O GLU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 125 through 140 Processing helix chain 'F' and resid 144 through 151 Processing helix chain 'F' and resid 159 through 165 Processing helix chain 'F' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE F 196 " --> pdb=" O ARG F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU F 215 " --> pdb=" O VAL F 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 211 through 215' Processing helix chain 'F' and resid 223 through 228 Processing helix chain 'F' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN F 254 " --> pdb=" O PHE F 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 249 through 254' Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN F 277 " --> pdb=" O LYS F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 339 removed outlier: 3.836A pdb=" N ILE F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 83 through 88 removed outlier: 3.693A pdb=" N LYS G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 125 through 140 Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 159 through 165 Processing helix chain 'G' and resid 184 through 196 removed outlier: 4.141A pdb=" N ALA G 195 " --> pdb=" O LEU G 191 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE G 196 " --> pdb=" O ARG G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 removed outlier: 3.668A pdb=" N LEU G 215 " --> pdb=" O VAL G 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 211 through 215' Processing helix chain 'G' and resid 223 through 228 Processing helix chain 'G' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS G 253 " --> pdb=" O ASP G 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN G 254 " --> pdb=" O PHE G 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 249 through 254' Processing helix chain 'G' and resid 267 through 269 No H-bonds generated for 'chain 'G' and resid 267 through 269' Processing helix chain 'G' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN G 277 " --> pdb=" O LYS G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE G 325 " --> pdb=" O GLU G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 113 Processing helix chain 'H' and resid 125 through 140 Processing helix chain 'H' and resid 144 through 151 Processing helix chain 'H' and resid 159 through 165 Processing helix chain 'H' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA H 195 " --> pdb=" O LEU H 191 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE H 196 " --> pdb=" O ARG H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU H 215 " --> pdb=" O VAL H 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 211 through 215' Processing helix chain 'H' and resid 223 through 228 Processing helix chain 'H' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS H 253 " --> pdb=" O ASP H 249 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN H 254 " --> pdb=" O PHE H 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 249 through 254' Processing helix chain 'H' and resid 267 through 269 No H-bonds generated for 'chain 'H' and resid 267 through 269' Processing helix chain 'H' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN H 277 " --> pdb=" O LYS H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE H 325 " --> pdb=" O GLU H 321 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 61 No H-bonds generated for 'chain 'I' and resid 59 through 61' Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 83 through 88 removed outlier: 3.691A pdb=" N LYS I 88 " --> pdb=" O GLU I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 113 Processing helix chain 'I' and resid 125 through 140 Processing helix chain 'I' and resid 144 through 151 Processing helix chain 'I' and resid 159 through 165 Processing helix chain 'I' and resid 184 through 196 removed outlier: 4.141A pdb=" N ALA I 195 " --> pdb=" O LEU I 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE I 196 " --> pdb=" O ARG I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU I 215 " --> pdb=" O VAL I 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 211 through 215' Processing helix chain 'I' and resid 223 through 228 Processing helix chain 'I' and resid 249 through 254 removed outlier: 3.843A pdb=" N LYS I 253 " --> pdb=" O ASP I 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN I 254 " --> pdb=" O PHE I 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 249 through 254' Processing helix chain 'I' and resid 267 through 269 No H-bonds generated for 'chain 'I' and resid 267 through 269' Processing helix chain 'I' and resid 272 through 281 removed outlier: 3.811A pdb=" N GLN I 277 " --> pdb=" O LYS I 273 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 113 Processing helix chain 'J' and resid 125 through 140 Processing helix chain 'J' and resid 144 through 151 Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'J' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA J 195 " --> pdb=" O LEU J 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE J 196 " --> pdb=" O ARG J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU J 215 " --> pdb=" O VAL J 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 211 through 215' Processing helix chain 'J' and resid 223 through 228 Processing helix chain 'J' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS J 253 " --> pdb=" O ASP J 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN J 254 " --> pdb=" O PHE J 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 249 through 254' Processing helix chain 'J' and resid 267 through 269 No H-bonds generated for 'chain 'J' and resid 267 through 269' Processing helix chain 'J' and resid 272 through 281 removed outlier: 3.811A pdb=" N GLN J 277 " --> pdb=" O LYS J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE J 325 " --> pdb=" O GLU J 321 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 61 No H-bonds generated for 'chain 'K' and resid 59 through 61' Processing helix chain 'K' and resid 64 through 68 Processing helix chain 'K' and resid 83 through 88 removed outlier: 3.693A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 113 Processing helix chain 'K' and resid 125 through 140 Processing helix chain 'K' and resid 144 through 151 Processing helix chain 'K' and resid 159 through 165 Processing helix chain 'K' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA K 195 " --> pdb=" O LEU K 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE K 196 " --> pdb=" O ARG K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 215 removed outlier: 3.666A pdb=" N LEU K 215 " --> pdb=" O VAL K 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 211 through 215' Processing helix chain 'K' and resid 223 through 228 Processing helix chain 'K' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS K 253 " --> pdb=" O ASP K 249 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN K 254 " --> pdb=" O PHE K 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 249 through 254' Processing helix chain 'K' and resid 267 through 269 No H-bonds generated for 'chain 'K' and resid 267 through 269' Processing helix chain 'K' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 339 removed outlier: 3.836A pdb=" N ILE K 325 " --> pdb=" O GLU K 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 61 No H-bonds generated for 'chain 'L' and resid 59 through 61' Processing helix chain 'L' and resid 64 through 68 Processing helix chain 'L' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS L 88 " --> pdb=" O GLU L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 113 Processing helix chain 'L' and resid 125 through 140 Processing helix chain 'L' and resid 144 through 151 Processing helix chain 'L' and resid 159 through 165 Processing helix chain 'L' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA L 195 " --> pdb=" O LEU L 191 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE L 196 " --> pdb=" O ARG L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU L 215 " --> pdb=" O VAL L 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 211 through 215' Processing helix chain 'L' and resid 223 through 228 Processing helix chain 'L' and resid 249 through 254 removed outlier: 3.843A pdb=" N LYS L 253 " --> pdb=" O ASP L 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN L 254 " --> pdb=" O PHE L 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 249 through 254' Processing helix chain 'L' and resid 267 through 269 No H-bonds generated for 'chain 'L' and resid 267 through 269' Processing helix chain 'L' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN L 277 " --> pdb=" O LYS L 273 " (cutoff:3.500A) Processing helix chain 'L' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE L 325 " --> pdb=" O GLU L 321 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 61 No H-bonds generated for 'chain 'M' and resid 59 through 61' Processing helix chain 'M' and resid 64 through 68 Processing helix chain 'M' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS M 88 " --> pdb=" O GLU M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 113 Processing helix chain 'M' and resid 125 through 140 Processing helix chain 'M' and resid 144 through 151 Processing helix chain 'M' and resid 159 through 165 Processing helix chain 'M' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA M 195 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE M 196 " --> pdb=" O ARG M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 215 removed outlier: 3.668A pdb=" N LEU M 215 " --> pdb=" O VAL M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 215' Processing helix chain 'M' and resid 223 through 228 Processing helix chain 'M' and resid 249 through 254 removed outlier: 3.843A pdb=" N LYS M 253 " --> pdb=" O ASP M 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN M 254 " --> pdb=" O PHE M 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 249 through 254' Processing helix chain 'M' and resid 267 through 269 No H-bonds generated for 'chain 'M' and resid 267 through 269' Processing helix chain 'M' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN M 277 " --> pdb=" O LYS M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE M 325 " --> pdb=" O GLU M 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 61 No H-bonds generated for 'chain 'N' and resid 59 through 61' Processing helix chain 'N' and resid 64 through 68 Processing helix chain 'N' and resid 83 through 88 removed outlier: 3.693A pdb=" N LYS N 88 " --> pdb=" O GLU N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 113 Processing helix chain 'N' and resid 125 through 140 Processing helix chain 'N' and resid 144 through 151 Processing helix chain 'N' and resid 159 through 165 Processing helix chain 'N' and resid 184 through 196 removed outlier: 4.141A pdb=" N ALA N 195 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE N 196 " --> pdb=" O ARG N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 211 through 215 removed outlier: 3.666A pdb=" N LEU N 215 " --> pdb=" O VAL N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 215' Processing helix chain 'N' and resid 223 through 228 Processing helix chain 'N' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS N 253 " --> pdb=" O ASP N 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN N 254 " --> pdb=" O PHE N 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 249 through 254' Processing helix chain 'N' and resid 267 through 269 No H-bonds generated for 'chain 'N' and resid 267 through 269' Processing helix chain 'N' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN N 277 " --> pdb=" O LYS N 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 339 removed outlier: 3.836A pdb=" N ILE N 325 " --> pdb=" O GLU N 321 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 64 through 68 Processing helix chain 'O' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS O 88 " --> pdb=" O GLU O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 113 Processing helix chain 'O' and resid 125 through 140 Processing helix chain 'O' and resid 144 through 151 Processing helix chain 'O' and resid 159 through 165 Processing helix chain 'O' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA O 195 " --> pdb=" O LEU O 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE O 196 " --> pdb=" O ARG O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU O 215 " --> pdb=" O VAL O 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 211 through 215' Processing helix chain 'O' and resid 223 through 228 Processing helix chain 'O' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS O 253 " --> pdb=" O ASP O 249 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN O 254 " --> pdb=" O PHE O 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 249 through 254' Processing helix chain 'O' and resid 267 through 269 No H-bonds generated for 'chain 'O' and resid 267 through 269' Processing helix chain 'O' and resid 272 through 281 removed outlier: 3.811A pdb=" N GLN O 277 " --> pdb=" O LYS O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE O 325 " --> pdb=" O GLU O 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 64 through 68 Processing helix chain 'P' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 113 Processing helix chain 'P' and resid 125 through 140 Processing helix chain 'P' and resid 144 through 151 Processing helix chain 'P' and resid 159 through 165 Processing helix chain 'P' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA P 195 " --> pdb=" O LEU P 191 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE P 196 " --> pdb=" O ARG P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU P 215 " --> pdb=" O VAL P 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 211 through 215' Processing helix chain 'P' and resid 223 through 228 Processing helix chain 'P' and resid 249 through 254 removed outlier: 3.843A pdb=" N LYS P 253 " --> pdb=" O ASP P 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN P 254 " --> pdb=" O PHE P 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 249 through 254' Processing helix chain 'P' and resid 267 through 269 No H-bonds generated for 'chain 'P' and resid 267 through 269' Processing helix chain 'P' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN P 277 " --> pdb=" O LYS P 273 " (cutoff:3.500A) Processing helix chain 'P' and resid 321 through 339 removed outlier: 3.836A pdb=" N ILE P 325 " --> pdb=" O GLU P 321 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 61 No H-bonds generated for 'chain 'Q' and resid 59 through 61' Processing helix chain 'Q' and resid 64 through 68 Processing helix chain 'Q' and resid 83 through 88 removed outlier: 3.693A pdb=" N LYS Q 88 " --> pdb=" O GLU Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 113 Processing helix chain 'Q' and resid 125 through 140 Processing helix chain 'Q' and resid 144 through 151 Processing helix chain 'Q' and resid 159 through 165 Processing helix chain 'Q' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA Q 195 " --> pdb=" O LEU Q 191 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE Q 196 " --> pdb=" O ARG Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU Q 215 " --> pdb=" O VAL Q 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 211 through 215' Processing helix chain 'Q' and resid 223 through 228 Processing helix chain 'Q' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS Q 253 " --> pdb=" O ASP Q 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN Q 254 " --> pdb=" O PHE Q 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 249 through 254' Processing helix chain 'Q' and resid 267 through 269 No H-bonds generated for 'chain 'Q' and resid 267 through 269' Processing helix chain 'Q' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN Q 277 " --> pdb=" O LYS Q 273 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 339 removed outlier: 3.836A pdb=" N ILE Q 325 " --> pdb=" O GLU Q 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 61 No H-bonds generated for 'chain 'R' and resid 59 through 61' Processing helix chain 'R' and resid 64 through 68 Processing helix chain 'R' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS R 88 " --> pdb=" O GLU R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 113 Processing helix chain 'R' and resid 125 through 140 Processing helix chain 'R' and resid 144 through 151 Processing helix chain 'R' and resid 159 through 165 Processing helix chain 'R' and resid 184 through 196 removed outlier: 4.141A pdb=" N ALA R 195 " --> pdb=" O LEU R 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE R 196 " --> pdb=" O ARG R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU R 215 " --> pdb=" O VAL R 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 211 through 215' Processing helix chain 'R' and resid 223 through 228 Processing helix chain 'R' and resid 249 through 254 removed outlier: 3.843A pdb=" N LYS R 253 " --> pdb=" O ASP R 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN R 254 " --> pdb=" O PHE R 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 249 through 254' Processing helix chain 'R' and resid 267 through 269 No H-bonds generated for 'chain 'R' and resid 267 through 269' Processing helix chain 'R' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE R 325 " --> pdb=" O GLU R 321 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 61 No H-bonds generated for 'chain 'S' and resid 59 through 61' Processing helix chain 'S' and resid 64 through 68 Processing helix chain 'S' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS S 88 " --> pdb=" O GLU S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 113 Processing helix chain 'S' and resid 125 through 140 Processing helix chain 'S' and resid 144 through 151 Processing helix chain 'S' and resid 159 through 165 Processing helix chain 'S' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA S 195 " --> pdb=" O LEU S 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE S 196 " --> pdb=" O ARG S 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU S 215 " --> pdb=" O VAL S 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 211 through 215' Processing helix chain 'S' and resid 223 through 228 Processing helix chain 'S' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS S 253 " --> pdb=" O ASP S 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN S 254 " --> pdb=" O PHE S 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 249 through 254' Processing helix chain 'S' and resid 267 through 269 No H-bonds generated for 'chain 'S' and resid 267 through 269' Processing helix chain 'S' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN S 277 " --> pdb=" O LYS S 273 " (cutoff:3.500A) Processing helix chain 'S' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE S 325 " --> pdb=" O GLU S 321 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 61 No H-bonds generated for 'chain 'T' and resid 59 through 61' Processing helix chain 'T' and resid 64 through 68 Processing helix chain 'T' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS T 88 " --> pdb=" O GLU T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 113 Processing helix chain 'T' and resid 125 through 140 Processing helix chain 'T' and resid 144 through 151 Processing helix chain 'T' and resid 159 through 165 Processing helix chain 'T' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA T 195 " --> pdb=" O LEU T 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE T 196 " --> pdb=" O ARG T 192 " (cutoff:3.500A) Processing helix chain 'T' and resid 211 through 215 removed outlier: 3.668A pdb=" N LEU T 215 " --> pdb=" O VAL T 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 211 through 215' Processing helix chain 'T' and resid 223 through 228 Processing helix chain 'T' and resid 249 through 254 removed outlier: 3.841A pdb=" N LYS T 253 " --> pdb=" O ASP T 249 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN T 254 " --> pdb=" O PHE T 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 249 through 254' Processing helix chain 'T' and resid 267 through 269 No H-bonds generated for 'chain 'T' and resid 267 through 269' Processing helix chain 'T' and resid 272 through 281 removed outlier: 3.811A pdb=" N GLN T 277 " --> pdb=" O LYS T 273 " (cutoff:3.500A) Processing helix chain 'T' and resid 321 through 339 removed outlier: 3.836A pdb=" N ILE T 325 " --> pdb=" O GLU T 321 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 61 No H-bonds generated for 'chain 'U' and resid 59 through 61' Processing helix chain 'U' and resid 64 through 68 Processing helix chain 'U' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS U 88 " --> pdb=" O GLU U 84 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 113 Processing helix chain 'U' and resid 125 through 140 Processing helix chain 'U' and resid 144 through 151 Processing helix chain 'U' and resid 159 through 165 Processing helix chain 'U' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA U 195 " --> pdb=" O LEU U 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE U 196 " --> pdb=" O ARG U 192 " (cutoff:3.500A) Processing helix chain 'U' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU U 215 " --> pdb=" O VAL U 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 211 through 215' Processing helix chain 'U' and resid 223 through 228 Processing helix chain 'U' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS U 253 " --> pdb=" O ASP U 249 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN U 254 " --> pdb=" O PHE U 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 249 through 254' Processing helix chain 'U' and resid 267 through 269 No H-bonds generated for 'chain 'U' and resid 267 through 269' Processing helix chain 'U' and resid 272 through 281 removed outlier: 3.811A pdb=" N GLN U 277 " --> pdb=" O LYS U 273 " (cutoff:3.500A) Processing helix chain 'U' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE U 325 " --> pdb=" O GLU U 321 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 61 No H-bonds generated for 'chain 'V' and resid 59 through 61' Processing helix chain 'V' and resid 64 through 68 Processing helix chain 'V' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS V 88 " --> pdb=" O GLU V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 113 Processing helix chain 'V' and resid 125 through 140 Processing helix chain 'V' and resid 144 through 151 Processing helix chain 'V' and resid 159 through 165 Processing helix chain 'V' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA V 195 " --> pdb=" O LEU V 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE V 196 " --> pdb=" O ARG V 192 " (cutoff:3.500A) Processing helix chain 'V' and resid 211 through 215 removed outlier: 3.667A pdb=" N LEU V 215 " --> pdb=" O VAL V 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 211 through 215' Processing helix chain 'V' and resid 223 through 228 Processing helix chain 'V' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS V 253 " --> pdb=" O ASP V 249 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN V 254 " --> pdb=" O PHE V 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 249 through 254' Processing helix chain 'V' and resid 267 through 269 No H-bonds generated for 'chain 'V' and resid 267 through 269' Processing helix chain 'V' and resid 272 through 281 removed outlier: 3.811A pdb=" N GLN V 277 " --> pdb=" O LYS V 273 " (cutoff:3.500A) Processing helix chain 'V' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE V 325 " --> pdb=" O GLU V 321 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 61 No H-bonds generated for 'chain 'W' and resid 59 through 61' Processing helix chain 'W' and resid 64 through 68 Processing helix chain 'W' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS W 88 " --> pdb=" O GLU W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 107 through 113 Processing helix chain 'W' and resid 125 through 140 Processing helix chain 'W' and resid 144 through 151 Processing helix chain 'W' and resid 159 through 165 Processing helix chain 'W' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA W 195 " --> pdb=" O LEU W 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE W 196 " --> pdb=" O ARG W 192 " (cutoff:3.500A) Processing helix chain 'W' and resid 211 through 215 removed outlier: 3.668A pdb=" N LEU W 215 " --> pdb=" O VAL W 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 211 through 215' Processing helix chain 'W' and resid 223 through 228 Processing helix chain 'W' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS W 253 " --> pdb=" O ASP W 249 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN W 254 " --> pdb=" O PHE W 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 249 through 254' Processing helix chain 'W' and resid 267 through 269 No H-bonds generated for 'chain 'W' and resid 267 through 269' Processing helix chain 'W' and resid 272 through 281 removed outlier: 3.811A pdb=" N GLN W 277 " --> pdb=" O LYS W 273 " (cutoff:3.500A) Processing helix chain 'W' and resid 321 through 339 removed outlier: 3.837A pdb=" N ILE W 325 " --> pdb=" O GLU W 321 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 61 No H-bonds generated for 'chain 'X' and resid 59 through 61' Processing helix chain 'X' and resid 64 through 68 Processing helix chain 'X' and resid 83 through 88 removed outlier: 3.692A pdb=" N LYS X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 113 Processing helix chain 'X' and resid 125 through 140 Processing helix chain 'X' and resid 144 through 151 Processing helix chain 'X' and resid 159 through 165 Processing helix chain 'X' and resid 184 through 196 removed outlier: 4.142A pdb=" N ALA X 195 " --> pdb=" O LEU X 191 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE X 196 " --> pdb=" O ARG X 192 " (cutoff:3.500A) Processing helix chain 'X' and resid 211 through 215 removed outlier: 3.666A pdb=" N LEU X 215 " --> pdb=" O VAL X 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 211 through 215' Processing helix chain 'X' and resid 223 through 228 Processing helix chain 'X' and resid 249 through 254 removed outlier: 3.842A pdb=" N LYS X 253 " --> pdb=" O ASP X 249 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN X 254 " --> pdb=" O PHE X 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 249 through 254' Processing helix chain 'X' and resid 267 through 269 No H-bonds generated for 'chain 'X' and resid 267 through 269' Processing helix chain 'X' and resid 272 through 281 removed outlier: 3.810A pdb=" N GLN X 277 " --> pdb=" O LYS X 273 " (cutoff:3.500A) Processing helix chain 'X' and resid 321 through 339 removed outlier: 3.836A pdb=" N ILE X 325 " --> pdb=" O GLU X 321 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA A 52 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 30 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 72 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE A 94 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET A 75 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 96 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA A 116 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG A 97 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS A 118 " --> pdb=" O ARG A 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS A 232 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE A 180 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR A 234 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE A 260 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N LEU A 235 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A 262 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A 261 " --> pdb=" O ARG A 285 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA A 287 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN A 263 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU A 289 " --> pdb=" O ASN A 263 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 50 through 53 removed outlier: 6.680A pdb=" N GLY B 72 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE B 94 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET B 75 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL B 96 " --> pdb=" O MET B 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA B 116 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ARG B 97 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS B 118 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS B 232 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE B 180 " --> pdb=" O CYS B 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR B 234 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE B 260 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU B 235 " --> pdb=" O PHE B 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 262 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU B 261 " --> pdb=" O ARG B 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA B 287 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN B 263 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU B 289 " --> pdb=" O ASN B 263 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 50 through 53 removed outlier: 6.680A pdb=" N GLY C 72 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE C 94 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET C 75 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 96 " --> pdb=" O MET C 75 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA C 116 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ARG C 97 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS C 118 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 199 through 203 removed outlier: 6.287A pdb=" N CYS C 232 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE C 180 " --> pdb=" O CYS C 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C 234 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE C 260 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU C 235 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL C 262 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU C 261 " --> pdb=" O ARG C 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA C 287 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN C 263 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU C 289 " --> pdb=" O ASN C 263 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 49 through 53 removed outlier: 7.833A pdb=" N ALA D 52 " --> pdb=" O PRO D 28 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL D 30 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY D 72 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE D 94 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET D 75 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL D 96 " --> pdb=" O MET D 75 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA D 116 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG D 97 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS D 118 " --> pdb=" O ARG D 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS D 232 " --> pdb=" O GLY D 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE D 180 " --> pdb=" O CYS D 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR D 234 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE D 260 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU D 235 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL D 262 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU D 261 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA D 287 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN D 263 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU D 289 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA E 52 " --> pdb=" O PRO E 28 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL E 30 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY E 72 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE E 94 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET E 75 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL E 96 " --> pdb=" O MET E 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA E 116 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ARG E 97 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS E 118 " --> pdb=" O ARG E 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS E 232 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE E 180 " --> pdb=" O CYS E 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR E 234 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE E 260 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU E 235 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL E 262 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU E 261 " --> pdb=" O ARG E 285 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA E 287 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN E 263 " --> pdb=" O ALA E 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU E 289 " --> pdb=" O ASN E 263 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA F 52 " --> pdb=" O PRO F 28 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL F 30 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY F 72 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE F 94 " --> pdb=" O ALA F 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET F 75 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL F 96 " --> pdb=" O MET F 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA F 116 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG F 97 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS F 118 " --> pdb=" O ARG F 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 199 through 203 removed outlier: 6.289A pdb=" N CYS F 232 " --> pdb=" O GLY F 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE F 180 " --> pdb=" O CYS F 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR F 234 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE F 260 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU F 235 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL F 262 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU F 261 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA F 287 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN F 263 " --> pdb=" O ALA F 287 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU F 289 " --> pdb=" O ASN F 263 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA G 52 " --> pdb=" O PRO G 28 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL G 30 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY G 72 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE G 94 " --> pdb=" O ALA G 73 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N MET G 75 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL G 96 " --> pdb=" O MET G 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA G 116 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG G 97 " --> pdb=" O ALA G 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS G 118 " --> pdb=" O ARG G 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'G' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS G 232 " --> pdb=" O GLY G 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE G 180 " --> pdb=" O CYS G 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR G 234 " --> pdb=" O ILE G 180 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE G 260 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU G 235 " --> pdb=" O PHE G 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL G 262 " --> pdb=" O LEU G 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU G 261 " --> pdb=" O ARG G 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA G 287 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN G 263 " --> pdb=" O ALA G 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU G 289 " --> pdb=" O ASN G 263 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA H 52 " --> pdb=" O PRO H 28 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL H 30 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY H 72 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE H 94 " --> pdb=" O ALA H 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET H 75 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL H 96 " --> pdb=" O MET H 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA H 116 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG H 97 " --> pdb=" O ALA H 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS H 118 " --> pdb=" O ARG H 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS H 232 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE H 180 " --> pdb=" O CYS H 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR H 234 " --> pdb=" O ILE H 180 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE H 260 " --> pdb=" O VAL H 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU H 235 " --> pdb=" O PHE H 260 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL H 262 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU H 261 " --> pdb=" O ARG H 285 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA H 287 " --> pdb=" O LEU H 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN H 263 " --> pdb=" O ALA H 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU H 289 " --> pdb=" O ASN H 263 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 49 through 53 removed outlier: 7.833A pdb=" N ALA I 52 " --> pdb=" O PRO I 28 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL I 30 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY I 72 " --> pdb=" O ALA I 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE I 94 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET I 75 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL I 96 " --> pdb=" O MET I 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA I 116 " --> pdb=" O ILE I 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG I 97 " --> pdb=" O ALA I 116 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS I 118 " --> pdb=" O ARG I 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'I' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS I 232 " --> pdb=" O GLY I 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE I 180 " --> pdb=" O CYS I 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR I 234 " --> pdb=" O ILE I 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE I 260 " --> pdb=" O VAL I 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU I 235 " --> pdb=" O PHE I 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL I 262 " --> pdb=" O LEU I 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU I 261 " --> pdb=" O ARG I 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA I 287 " --> pdb=" O LEU I 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN I 263 " --> pdb=" O ALA I 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU I 289 " --> pdb=" O ASN I 263 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA J 52 " --> pdb=" O PRO J 28 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL J 30 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY J 72 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE J 94 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET J 75 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL J 96 " --> pdb=" O MET J 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA J 116 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ARG J 97 " --> pdb=" O ALA J 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS J 118 " --> pdb=" O ARG J 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'J' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS J 232 " --> pdb=" O GLY J 178 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE J 180 " --> pdb=" O CYS J 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR J 234 " --> pdb=" O ILE J 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE J 260 " --> pdb=" O VAL J 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU J 235 " --> pdb=" O PHE J 260 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL J 262 " --> pdb=" O LEU J 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU J 261 " --> pdb=" O ARG J 285 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA J 287 " --> pdb=" O LEU J 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN J 263 " --> pdb=" O ALA J 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU J 289 " --> pdb=" O ASN J 263 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 49 through 53 removed outlier: 7.833A pdb=" N ALA K 52 " --> pdb=" O PRO K 28 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL K 30 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY K 72 " --> pdb=" O ALA K 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE K 94 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET K 75 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL K 96 " --> pdb=" O MET K 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA K 116 " --> pdb=" O ILE K 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG K 97 " --> pdb=" O ALA K 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS K 118 " --> pdb=" O ARG K 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'K' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS K 232 " --> pdb=" O GLY K 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE K 180 " --> pdb=" O CYS K 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR K 234 " --> pdb=" O ILE K 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE K 260 " --> pdb=" O VAL K 233 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU K 235 " --> pdb=" O PHE K 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL K 262 " --> pdb=" O LEU K 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU K 261 " --> pdb=" O ARG K 285 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA K 287 " --> pdb=" O LEU K 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN K 263 " --> pdb=" O ALA K 287 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU K 289 " --> pdb=" O ASN K 263 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA L 52 " --> pdb=" O PRO L 28 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL L 30 " --> pdb=" O ALA L 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY L 72 " --> pdb=" O ALA L 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE L 94 " --> pdb=" O ALA L 73 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N MET L 75 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL L 96 " --> pdb=" O MET L 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA L 116 " --> pdb=" O ILE L 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG L 97 " --> pdb=" O ALA L 116 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS L 118 " --> pdb=" O ARG L 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS L 232 " --> pdb=" O GLY L 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE L 180 " --> pdb=" O CYS L 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR L 234 " --> pdb=" O ILE L 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE L 260 " --> pdb=" O VAL L 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU L 235 " --> pdb=" O PHE L 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL L 262 " --> pdb=" O LEU L 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU L 261 " --> pdb=" O ARG L 285 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA L 287 " --> pdb=" O LEU L 261 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN L 263 " --> pdb=" O ALA L 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU L 289 " --> pdb=" O ASN L 263 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 49 through 53 removed outlier: 7.833A pdb=" N ALA M 52 " --> pdb=" O PRO M 28 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL M 30 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY M 72 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE M 94 " --> pdb=" O ALA M 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET M 75 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL M 96 " --> pdb=" O MET M 75 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA M 116 " --> pdb=" O ILE M 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG M 97 " --> pdb=" O ALA M 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS M 118 " --> pdb=" O ARG M 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'M' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS M 232 " --> pdb=" O GLY M 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE M 180 " --> pdb=" O CYS M 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR M 234 " --> pdb=" O ILE M 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE M 260 " --> pdb=" O VAL M 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU M 235 " --> pdb=" O PHE M 260 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL M 262 " --> pdb=" O LEU M 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU M 261 " --> pdb=" O ARG M 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA M 287 " --> pdb=" O LEU M 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN M 263 " --> pdb=" O ALA M 287 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU M 289 " --> pdb=" O ASN M 263 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'N' and resid 49 through 53 removed outlier: 7.833A pdb=" N ALA N 52 " --> pdb=" O PRO N 28 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL N 30 " --> pdb=" O ALA N 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY N 72 " --> pdb=" O ALA N 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE N 94 " --> pdb=" O ALA N 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET N 75 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL N 96 " --> pdb=" O MET N 75 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA N 116 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ARG N 97 " --> pdb=" O ALA N 116 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS N 118 " --> pdb=" O ARG N 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'N' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS N 232 " --> pdb=" O GLY N 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE N 180 " --> pdb=" O CYS N 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR N 234 " --> pdb=" O ILE N 180 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE N 260 " --> pdb=" O VAL N 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU N 235 " --> pdb=" O PHE N 260 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL N 262 " --> pdb=" O LEU N 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU N 261 " --> pdb=" O ARG N 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA N 287 " --> pdb=" O LEU N 261 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN N 263 " --> pdb=" O ALA N 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU N 289 " --> pdb=" O ASN N 263 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 49 through 53 removed outlier: 7.833A pdb=" N ALA O 52 " --> pdb=" O PRO O 28 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL O 30 " --> pdb=" O ALA O 52 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY O 72 " --> pdb=" O ALA O 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE O 94 " --> pdb=" O ALA O 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET O 75 " --> pdb=" O ILE O 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL O 96 " --> pdb=" O MET O 75 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA O 116 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG O 97 " --> pdb=" O ALA O 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS O 118 " --> pdb=" O ARG O 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'O' and resid 199 through 203 removed outlier: 6.287A pdb=" N CYS O 232 " --> pdb=" O GLY O 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE O 180 " --> pdb=" O CYS O 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR O 234 " --> pdb=" O ILE O 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE O 260 " --> pdb=" O VAL O 233 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU O 235 " --> pdb=" O PHE O 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL O 262 " --> pdb=" O LEU O 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU O 261 " --> pdb=" O ARG O 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA O 287 " --> pdb=" O LEU O 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN O 263 " --> pdb=" O ALA O 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU O 289 " --> pdb=" O ASN O 263 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'P' and resid 49 through 53 removed outlier: 7.833A pdb=" N ALA P 52 " --> pdb=" O PRO P 28 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL P 30 " --> pdb=" O ALA P 52 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY P 72 " --> pdb=" O ALA P 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE P 94 " --> pdb=" O ALA P 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET P 75 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL P 96 " --> pdb=" O MET P 75 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA P 116 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG P 97 " --> pdb=" O ALA P 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS P 118 " --> pdb=" O ARG P 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'P' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS P 232 " --> pdb=" O GLY P 178 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE P 180 " --> pdb=" O CYS P 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR P 234 " --> pdb=" O ILE P 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE P 260 " --> pdb=" O VAL P 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU P 235 " --> pdb=" O PHE P 260 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL P 262 " --> pdb=" O LEU P 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU P 261 " --> pdb=" O ARG P 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA P 287 " --> pdb=" O LEU P 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN P 263 " --> pdb=" O ALA P 287 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU P 289 " --> pdb=" O ASN P 263 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Q' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA Q 52 " --> pdb=" O PRO Q 28 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL Q 30 " --> pdb=" O ALA Q 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY Q 72 " --> pdb=" O ALA Q 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE Q 94 " --> pdb=" O ALA Q 73 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N MET Q 75 " --> pdb=" O ILE Q 94 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL Q 96 " --> pdb=" O MET Q 75 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA Q 116 " --> pdb=" O ILE Q 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG Q 97 " --> pdb=" O ALA Q 116 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS Q 118 " --> pdb=" O ARG Q 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'Q' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS Q 232 " --> pdb=" O GLY Q 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE Q 180 " --> pdb=" O CYS Q 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR Q 234 " --> pdb=" O ILE Q 180 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE Q 260 " --> pdb=" O VAL Q 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU Q 235 " --> pdb=" O PHE Q 260 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL Q 262 " --> pdb=" O LEU Q 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU Q 261 " --> pdb=" O ARG Q 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA Q 287 " --> pdb=" O LEU Q 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN Q 263 " --> pdb=" O ALA Q 287 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU Q 289 " --> pdb=" O ASN Q 263 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'R' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA R 52 " --> pdb=" O PRO R 28 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL R 30 " --> pdb=" O ALA R 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY R 72 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE R 94 " --> pdb=" O ALA R 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET R 75 " --> pdb=" O ILE R 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL R 96 " --> pdb=" O MET R 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA R 116 " --> pdb=" O ILE R 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG R 97 " --> pdb=" O ALA R 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS R 118 " --> pdb=" O ARG R 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'R' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS R 232 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE R 180 " --> pdb=" O CYS R 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR R 234 " --> pdb=" O ILE R 180 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE R 260 " --> pdb=" O VAL R 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU R 235 " --> pdb=" O PHE R 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL R 262 " --> pdb=" O LEU R 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU R 261 " --> pdb=" O ARG R 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA R 287 " --> pdb=" O LEU R 261 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN R 263 " --> pdb=" O ALA R 287 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU R 289 " --> pdb=" O ASN R 263 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'S' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA S 52 " --> pdb=" O PRO S 28 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL S 30 " --> pdb=" O ALA S 52 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY S 72 " --> pdb=" O ALA S 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE S 94 " --> pdb=" O ALA S 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET S 75 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL S 96 " --> pdb=" O MET S 75 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA S 116 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG S 97 " --> pdb=" O ALA S 116 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS S 118 " --> pdb=" O ARG S 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'S' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS S 232 " --> pdb=" O GLY S 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE S 180 " --> pdb=" O CYS S 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR S 234 " --> pdb=" O ILE S 180 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE S 260 " --> pdb=" O VAL S 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU S 235 " --> pdb=" O PHE S 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL S 262 " --> pdb=" O LEU S 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU S 261 " --> pdb=" O ARG S 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA S 287 " --> pdb=" O LEU S 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN S 263 " --> pdb=" O ALA S 287 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU S 289 " --> pdb=" O ASN S 263 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'T' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA T 52 " --> pdb=" O PRO T 28 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL T 30 " --> pdb=" O ALA T 52 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY T 72 " --> pdb=" O ALA T 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE T 94 " --> pdb=" O ALA T 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET T 75 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL T 96 " --> pdb=" O MET T 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA T 116 " --> pdb=" O ILE T 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG T 97 " --> pdb=" O ALA T 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS T 118 " --> pdb=" O ARG T 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'T' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS T 232 " --> pdb=" O GLY T 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE T 180 " --> pdb=" O CYS T 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR T 234 " --> pdb=" O ILE T 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE T 260 " --> pdb=" O VAL T 233 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU T 235 " --> pdb=" O PHE T 260 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL T 262 " --> pdb=" O LEU T 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU T 261 " --> pdb=" O ARG T 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA T 287 " --> pdb=" O LEU T 261 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN T 263 " --> pdb=" O ALA T 287 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU T 289 " --> pdb=" O ASN T 263 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'U' and resid 49 through 53 removed outlier: 7.833A pdb=" N ALA U 52 " --> pdb=" O PRO U 28 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL U 30 " --> pdb=" O ALA U 52 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY U 72 " --> pdb=" O ALA U 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE U 94 " --> pdb=" O ALA U 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET U 75 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL U 96 " --> pdb=" O MET U 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA U 116 " --> pdb=" O ILE U 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG U 97 " --> pdb=" O ALA U 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS U 118 " --> pdb=" O ARG U 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'U' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS U 232 " --> pdb=" O GLY U 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE U 180 " --> pdb=" O CYS U 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR U 234 " --> pdb=" O ILE U 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE U 260 " --> pdb=" O VAL U 233 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU U 235 " --> pdb=" O PHE U 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL U 262 " --> pdb=" O LEU U 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU U 261 " --> pdb=" O ARG U 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA U 287 " --> pdb=" O LEU U 261 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN U 263 " --> pdb=" O ALA U 287 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU U 289 " --> pdb=" O ASN U 263 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'V' and resid 50 through 53 removed outlier: 6.679A pdb=" N GLY V 72 " --> pdb=" O ALA V 31 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE V 94 " --> pdb=" O ALA V 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET V 75 " --> pdb=" O ILE V 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL V 96 " --> pdb=" O MET V 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA V 116 " --> pdb=" O ILE V 95 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ARG V 97 " --> pdb=" O ALA V 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS V 118 " --> pdb=" O ARG V 97 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'V' and resid 199 through 203 removed outlier: 6.288A pdb=" N CYS V 232 " --> pdb=" O GLY V 178 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE V 180 " --> pdb=" O CYS V 232 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR V 234 " --> pdb=" O ILE V 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE V 260 " --> pdb=" O VAL V 233 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU V 235 " --> pdb=" O PHE V 260 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL V 262 " --> pdb=" O LEU V 235 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU V 261 " --> pdb=" O ARG V 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA V 287 " --> pdb=" O LEU V 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN V 263 " --> pdb=" O ALA V 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU V 289 " --> pdb=" O ASN V 263 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'W' and resid 50 through 53 removed outlier: 6.679A pdb=" N GLY W 72 " --> pdb=" O ALA W 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE W 94 " --> pdb=" O ALA W 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET W 75 " --> pdb=" O ILE W 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL W 96 " --> pdb=" O MET W 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA W 116 " --> pdb=" O ILE W 95 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ARG W 97 " --> pdb=" O ALA W 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS W 118 " --> pdb=" O ARG W 97 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'W' and resid 199 through 203 removed outlier: 6.289A pdb=" N CYS W 232 " --> pdb=" O GLY W 178 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE W 180 " --> pdb=" O CYS W 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR W 234 " --> pdb=" O ILE W 180 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE W 260 " --> pdb=" O VAL W 233 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N LEU W 235 " --> pdb=" O PHE W 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL W 262 " --> pdb=" O LEU W 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU W 261 " --> pdb=" O ARG W 285 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA W 287 " --> pdb=" O LEU W 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN W 263 " --> pdb=" O ALA W 287 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU W 289 " --> pdb=" O ASN W 263 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'X' and resid 49 through 53 removed outlier: 7.832A pdb=" N ALA X 52 " --> pdb=" O PRO X 28 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL X 30 " --> pdb=" O ALA X 52 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY X 72 " --> pdb=" O ALA X 31 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE X 94 " --> pdb=" O ALA X 73 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N MET X 75 " --> pdb=" O ILE X 94 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL X 96 " --> pdb=" O MET X 75 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA X 116 " --> pdb=" O ILE X 95 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ARG X 97 " --> pdb=" O ALA X 116 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS X 118 " --> pdb=" O ARG X 97 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'X' and resid 199 through 203 removed outlier: 6.289A pdb=" N CYS X 232 " --> pdb=" O GLY X 178 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE X 180 " --> pdb=" O CYS X 232 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR X 234 " --> pdb=" O ILE X 180 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE X 260 " --> pdb=" O VAL X 233 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU X 235 " --> pdb=" O PHE X 260 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL X 262 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N LEU X 261 " --> pdb=" O ARG X 285 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA X 287 " --> pdb=" O LEU X 261 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN X 263 " --> pdb=" O ALA X 287 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU X 289 " --> pdb=" O ASN X 263 " (cutoff:3.500A) 1428 hydrogen bonds defined for protein. 4284 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: 25.56 Time building geometry restraints manager: 18.12 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: 21998 1.34 - 1.46: 10022 1.46 - 1.57: 32283 1.57 - 1.69: 96 1.69 - 1.81: 403 Bond restraints: 64802 Sorted by residual: bond pdb=" O3 NAD A 501 " pdb=" PA NAD A 501 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" O3 NAD P 501 " pdb=" PA NAD P 501 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" O3 NAD L 501 " pdb=" PA NAD L 501 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.01e+00 bond pdb=" O3 NAD B 501 " pdb=" PA NAD B 501 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" O3 NAD I 501 " pdb=" PA NAD I 501 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 5.98e+00 ... (remaining 64797 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.55: 1618 106.55 - 113.61: 36490 113.61 - 120.66: 27058 120.66 - 127.72: 22203 127.72 - 134.78: 514 Bond angle restraints: 87883 Sorted by residual: angle pdb=" N PRO b 325 " pdb=" CA PRO b 325 " pdb=" CB PRO b 325 " ideal model delta sigma weight residual 103.25 110.80 -7.55 1.05e+00 9.07e-01 5.17e+01 angle pdb=" N PRO e 325 " pdb=" CA PRO e 325 " pdb=" CB PRO e 325 " ideal model delta sigma weight residual 103.25 110.79 -7.54 1.05e+00 9.07e-01 5.16e+01 angle pdb=" N PRO d 325 " pdb=" CA PRO d 325 " pdb=" CB PRO d 325 " ideal model delta sigma weight residual 103.25 110.78 -7.53 1.05e+00 9.07e-01 5.15e+01 angle pdb=" N PRO g 325 " pdb=" CA PRO g 325 " pdb=" CB PRO g 325 " ideal model delta sigma weight residual 103.25 110.78 -7.53 1.05e+00 9.07e-01 5.15e+01 angle pdb=" N PRO c 325 " pdb=" CA PRO c 325 " pdb=" CB PRO c 325 " ideal model delta sigma weight residual 103.25 110.78 -7.53 1.05e+00 9.07e-01 5.14e+01 ... (remaining 87878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.26: 36384 11.26 - 22.52: 2454 22.52 - 33.78: 771 33.78 - 45.05: 145 45.05 - 56.31: 123 Dihedral angle restraints: 39877 sinusoidal: 16483 harmonic: 23394 Sorted by residual: dihedral pdb=" N PRO g 325 " pdb=" C PRO g 325 " pdb=" CA PRO g 325 " pdb=" CB PRO g 325 " ideal model delta harmonic sigma weight residual 115.10 123.34 -8.24 0 2.50e+00 1.60e-01 1.09e+01 dihedral pdb=" N PRO b 325 " pdb=" C PRO b 325 " pdb=" CA PRO b 325 " pdb=" CB PRO b 325 " ideal model delta harmonic sigma weight residual 115.10 123.33 -8.23 0 2.50e+00 1.60e-01 1.08e+01 dihedral pdb=" N PRO e 325 " pdb=" C PRO e 325 " pdb=" CA PRO e 325 " pdb=" CB PRO e 325 " ideal model delta harmonic sigma weight residual 115.10 123.33 -8.23 0 2.50e+00 1.60e-01 1.08e+01 ... (remaining 39874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 8292 0.048 - 0.097: 1391 0.097 - 0.145: 497 0.145 - 0.194: 1 0.194 - 0.242: 34 Chirality restraints: 10215 Sorted by residual: chirality pdb=" C1D NAD J 501 " pdb=" C2D NAD J 501 " pdb=" N1N NAD J 501 " pdb=" O4D NAD J 501 " both_signs ideal model delta sigma weight residual False 2.41 2.66 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C1D NAD E 501 " pdb=" C2D NAD E 501 " pdb=" N1N NAD E 501 " pdb=" O4D NAD E 501 " both_signs ideal model delta sigma weight residual False 2.41 2.66 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1D NAD U 501 " pdb=" C2D NAD U 501 " pdb=" N1N NAD U 501 " pdb=" O4D NAD U 501 " both_signs ideal model delta sigma weight residual False 2.41 2.66 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 10212 not shown) Planarity restraints: 11364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE Q 343 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO Q 344 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO Q 344 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO Q 344 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 343 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO K 344 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO K 344 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 344 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE S 343 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO S 344 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO S 344 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO S 344 " -0.021 5.00e-02 4.00e+02 ... (remaining 11361 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 12669 2.78 - 3.31: 53624 3.31 - 3.84: 92819 3.84 - 4.37: 114561 4.37 - 4.90: 205563 Nonbonded interactions: 479236 Sorted by model distance: nonbonded pdb=" OD1 ASP Q 290 " pdb=" OG1 THR Q 313 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP U 290 " pdb=" OG1 THR U 313 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP A 290 " pdb=" OG1 THR A 313 " model vdw 2.255 2.440 nonbonded pdb=" OD1 ASP J 290 " pdb=" OG1 THR J 313 " model vdw 2.255 2.440 nonbonded pdb=" OD1 ASP V 290 " pdb=" OG1 THR V 313 " model vdw 2.255 2.440 ... (remaining 479231 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' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = chain 'B' selection = (chain 'C' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'D' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'E' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'F' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'G' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'H' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'I' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'J' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'K' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'L' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'M' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'N' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'O' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'P' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'Q' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'R' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'S' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'T' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'U' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'V' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'W' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) selection = (chain 'X' and (resid 28 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 357 or resid 501)) } 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 28.260 Check model and map are aligned: 0.680 Set scattering table: 0.430 Process input model: 125.330 Find NCS groups from input model: 4.650 Set up NCS constraints: 0.980 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 177.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 0.049 64802 Z= 0.206 Angle : 0.499 8.280 87883 Z= 0.259 Chirality : 0.043 0.242 10215 Planarity : 0.003 0.041 11364 Dihedral : 9.097 56.307 24729 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.18 % Favored : 95.70 % Rotamer: Outliers : 0.38 % Allowed : 2.95 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.09), residues: 8092 helix: -0.02 (0.09), residues: 2640 sheet: 0.97 (0.21), residues: 908 loop : -1.36 (0.08), residues: 4544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 318 HIS 0.002 0.000 HIS K 236 PHE 0.009 0.001 PHE D 198 TYR 0.005 0.001 TYR O 319 ARG 0.003 0.000 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 295 time to evaluate : 5.492 Fit side-chains outliers start: 25 outliers final: 4 residues processed: 316 average time/residue: 1.5925 time to fit residues: 639.4542 Evaluate side-chains 216 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 5.416 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 7.2206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 685 optimal weight: 7.9990 chunk 615 optimal weight: 0.6980 chunk 341 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 415 optimal weight: 5.9990 chunk 328 optimal weight: 1.9990 chunk 636 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 386 optimal weight: 0.9980 chunk 473 optimal weight: 4.9990 chunk 737 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN G 199 ASN R 199 ASN S 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 64802 Z= 0.227 Angle : 0.444 7.807 87883 Z= 0.244 Chirality : 0.042 0.147 10215 Planarity : 0.004 0.041 11364 Dihedral : 7.457 51.673 10162 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.21 % Allowed : 5.74 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.09), residues: 8092 helix: 1.00 (0.10), residues: 2688 sheet: 0.47 (0.20), residues: 956 loop : -1.31 (0.08), residues: 4448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.004 0.001 HIS B 63 PHE 0.010 0.001 PHE T 198 TYR 0.009 0.001 TYR A 140 ARG 0.010 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 219 time to evaluate : 5.677 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 221 average time/residue: 1.5520 time to fit residues: 443.2334 Evaluate side-chains 205 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 5.404 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 1 residues processed: 6 average time/residue: 0.7234 time to fit residues: 13.9838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 409 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 chunk 613 optimal weight: 4.9990 chunk 502 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 738 optimal weight: 9.9990 chunk 798 optimal weight: 9.9990 chunk 657 optimal weight: 0.9990 chunk 732 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 592 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN G 199 ASN J 57 GLN K 57 GLN N 57 GLN O 57 GLN R 199 ASN S 199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 64802 Z= 0.332 Angle : 0.481 6.264 87883 Z= 0.263 Chirality : 0.043 0.150 10215 Planarity : 0.004 0.038 11364 Dihedral : 7.533 52.835 10162 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.94 % Allowed : 5.30 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.09), residues: 8092 helix: 1.34 (0.10), residues: 2688 sheet: 0.64 (0.20), residues: 916 loop : -1.38 (0.08), residues: 4488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 318 HIS 0.004 0.001 HIS N 147 PHE 0.013 0.001 PHE N 260 TYR 0.010 0.001 TYR O 319 ARG 0.009 0.000 ARG O 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 216 time to evaluate : 5.581 Fit side-chains outliers start: 62 outliers final: 27 residues processed: 263 average time/residue: 1.3944 time to fit residues: 492.6314 Evaluate side-chains 227 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 200 time to evaluate : 5.449 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 6 average time/residue: 0.4737 time to fit residues: 12.9397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 729 optimal weight: 7.9990 chunk 555 optimal weight: 5.9990 chunk 383 optimal weight: 3.9990 chunk 81 optimal weight: 0.0570 chunk 352 optimal weight: 2.9990 chunk 496 optimal weight: 3.9990 chunk 741 optimal weight: 9.9990 chunk 784 optimal weight: 8.9990 chunk 387 optimal weight: 4.9990 chunk 702 optimal weight: 20.0000 chunk 211 optimal weight: 0.6980 overall best weight: 2.3504 ------------------------------------------------------------------------------- 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: 0.8619 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 64802 Z= 0.263 Angle : 0.438 7.666 87883 Z= 0.240 Chirality : 0.042 0.162 10215 Planarity : 0.003 0.041 11364 Dihedral : 7.369 51.065 10162 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.12 % Allowed : 5.67 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.09), residues: 8092 helix: 1.56 (0.11), residues: 2728 sheet: 0.59 (0.20), residues: 916 loop : -1.42 (0.09), residues: 4448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 318 HIS 0.004 0.001 HIS S 355 PHE 0.010 0.001 PHE I 202 TYR 0.008 0.001 TYR K 319 ARG 0.010 0.000 ARG J 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 209 time to evaluate : 6.641 Fit side-chains outliers start: 74 outliers final: 28 residues processed: 265 average time/residue: 1.4128 time to fit residues: 500.4144 Evaluate side-chains 225 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 5.752 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.4825 time to fit residues: 11.2778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 653 optimal weight: 6.9990 chunk 445 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 584 optimal weight: 3.9990 chunk 323 optimal weight: 0.7980 chunk 669 optimal weight: 2.9990 chunk 542 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 400 optimal weight: 7.9990 chunk 704 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 199 ASN R 199 ASN S 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 64802 Z= 0.204 Angle : 0.411 8.255 87883 Z= 0.225 Chirality : 0.041 0.170 10215 Planarity : 0.003 0.043 11364 Dihedral : 7.209 49.361 10162 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.67 % Allowed : 7.05 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.10), residues: 8092 helix: 1.77 (0.11), residues: 2728 sheet: 0.28 (0.20), residues: 956 loop : -1.34 (0.09), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 318 HIS 0.004 0.000 HIS R 355 PHE 0.009 0.001 PHE M 202 TYR 0.008 0.001 TYR K 319 ARG 0.011 0.000 ARG N 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 199 time to evaluate : 5.614 Fit side-chains outliers start: 44 outliers final: 29 residues processed: 236 average time/residue: 1.3984 time to fit residues: 440.2707 Evaluate side-chains 220 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 5.678 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 1 average time/residue: 1.5458 time to fit residues: 9.9119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 264 optimal weight: 6.9990 chunk 706 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 460 optimal weight: 4.9990 chunk 193 optimal weight: 0.4980 chunk 785 optimal weight: 0.0570 chunk 652 optimal weight: 7.9990 chunk 363 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 259 optimal weight: 0.1980 chunk 412 optimal weight: 2.9990 overall best weight: 0.9300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN G 199 ASN R 199 ASN S 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 64802 Z= 0.123 Angle : 0.373 8.781 87883 Z= 0.203 Chirality : 0.040 0.159 10215 Planarity : 0.003 0.049 11364 Dihedral : 6.865 50.621 10162 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.67 % Allowed : 7.32 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.10), residues: 8092 helix: 1.99 (0.11), residues: 2728 sheet: 0.34 (0.20), residues: 956 loop : -1.26 (0.09), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 318 HIS 0.004 0.000 HIS R 355 PHE 0.008 0.001 PHE N 202 TYR 0.006 0.001 TYR K 319 ARG 0.012 0.000 ARG J 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 200 time to evaluate : 5.517 Fit side-chains outliers start: 44 outliers final: 34 residues processed: 239 average time/residue: 1.3646 time to fit residues: 437.0802 Evaluate side-chains 226 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 5.500 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 33 residues processed: 1 average time/residue: 1.3484 time to fit residues: 9.0791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 757 optimal weight: 0.3980 chunk 88 optimal weight: 9.9990 chunk 447 optimal weight: 2.9990 chunk 573 optimal weight: 3.9990 chunk 444 optimal weight: 5.9990 chunk 661 optimal weight: 0.0570 chunk 438 optimal weight: 2.9990 chunk 782 optimal weight: 8.9990 chunk 489 optimal weight: 5.9990 chunk 477 optimal weight: 5.9990 chunk 361 optimal weight: 0.7980 overall best weight: 1.4502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN G 199 ASN R 199 ASN S 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 64802 Z= 0.172 Angle : 0.400 9.258 87883 Z= 0.215 Chirality : 0.041 0.160 10215 Planarity : 0.003 0.054 11364 Dihedral : 6.939 50.889 10162 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.59 % Allowed : 7.76 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.10), residues: 8092 helix: 2.05 (0.11), residues: 2728 sheet: 0.36 (0.20), residues: 956 loop : -1.23 (0.09), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 318 HIS 0.004 0.000 HIS G 355 PHE 0.008 0.001 PHE L 53 TYR 0.008 0.001 TYR N 319 ARG 0.013 0.000 ARG G 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 5.601 Fit side-chains outliers start: 39 outliers final: 32 residues processed: 226 average time/residue: 1.4299 time to fit residues: 432.4977 Evaluate side-chains 224 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 5.457 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 1.3153 time to fit residues: 8.9824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 484 optimal weight: 2.9990 chunk 312 optimal weight: 5.9990 chunk 467 optimal weight: 6.9990 chunk 235 optimal weight: 0.0970 chunk 153 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 497 optimal weight: 0.0470 chunk 533 optimal weight: 4.9990 chunk 386 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 615 optimal weight: 3.9990 overall best weight: 2.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN G 199 ASN R 199 ASN S 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 64802 Z= 0.256 Angle : 0.442 9.676 87883 Z= 0.237 Chirality : 0.042 0.161 10215 Planarity : 0.003 0.062 11364 Dihedral : 7.183 50.857 10162 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.73 % Allowed : 7.78 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.10), residues: 8092 helix: 1.97 (0.11), residues: 2728 sheet: 0.32 (0.20), residues: 956 loop : -1.26 (0.09), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 318 HIS 0.004 0.001 HIS R 355 PHE 0.009 0.001 PHE N 260 TYR 0.008 0.001 TYR O 319 ARG 0.015 0.000 ARG O 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 191 time to evaluate : 5.736 Fit side-chains outliers start: 48 outliers final: 31 residues processed: 234 average time/residue: 1.4231 time to fit residues: 443.5990 Evaluate side-chains 212 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 5.489 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 8.2839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 711 optimal weight: 10.0000 chunk 749 optimal weight: 10.0000 chunk 684 optimal weight: 6.9990 chunk 729 optimal weight: 8.9990 chunk 438 optimal weight: 0.0040 chunk 317 optimal weight: 2.9990 chunk 572 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 659 optimal weight: 4.9990 chunk 689 optimal weight: 5.9990 chunk 726 optimal weight: 20.0000 overall best weight: 2.7998 ------------------------------------------------------------------------------- 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: 0.8637 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 64802 Z= 0.312 Angle : 0.477 10.381 87883 Z= 0.255 Chirality : 0.043 0.181 10215 Planarity : 0.004 0.065 11364 Dihedral : 7.385 51.713 10162 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.53 % Allowed : 8.13 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.10), residues: 8092 helix: 1.88 (0.11), residues: 2728 sheet: 0.25 (0.20), residues: 956 loop : -1.31 (0.09), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 318 HIS 0.004 0.001 HIS F 355 PHE 0.010 0.001 PHE J 260 TYR 0.010 0.001 TYR N 319 ARG 0.014 0.000 ARG F 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 5.628 Fit side-chains outliers start: 35 outliers final: 30 residues processed: 218 average time/residue: 1.5056 time to fit residues: 434.1128 Evaluate side-chains 211 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 5.469 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 0 time to fit residues: 7.2704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 478 optimal weight: 0.9990 chunk 771 optimal weight: 9.9990 chunk 470 optimal weight: 0.8980 chunk 365 optimal weight: 3.9990 chunk 536 optimal weight: 7.9990 chunk 808 optimal weight: 20.0000 chunk 744 optimal weight: 7.9990 chunk 644 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 497 optimal weight: 1.9990 chunk 394 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8602 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 64802 Z= 0.184 Angle : 0.425 11.605 87883 Z= 0.225 Chirality : 0.041 0.199 10215 Planarity : 0.003 0.064 11364 Dihedral : 7.128 52.471 10162 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.45 % Allowed : 8.37 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.10), residues: 8092 helix: 2.00 (0.11), residues: 2728 sheet: 0.28 (0.20), residues: 956 loop : -1.27 (0.09), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 318 HIS 0.004 0.000 HIS R 355 PHE 0.008 0.001 PHE I 202 TYR 0.007 0.001 TYR X 76 ARG 0.015 0.000 ARG O 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16184 Ramachandran restraints generated. 8092 Oldfield, 0 Emsley, 8092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 189 time to evaluate : 5.504 Fit side-chains outliers start: 30 outliers final: 30 residues processed: 219 average time/residue: 1.4648 time to fit residues: 423.7406 Evaluate side-chains 212 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 5.585 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 0 time to fit residues: 7.1966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 511 optimal weight: 3.9990 chunk 686 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 593 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 645 optimal weight: 6.9990 chunk 270 optimal weight: 0.9990 chunk 662 optimal weight: 0.0020 chunk 81 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 199 ASN G 199 ASN R 199 ASN S 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.069863 restraints weight = 131072.519| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.71 r_work: 0.2547 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2410 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 64802 Z= 0.249 Angle : 0.450 11.742 87883 Z= 0.238 Chirality : 0.042 0.202 10215 Planarity : 0.003 0.065 11364 Dihedral : 7.219 52.911 10162 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.45 % Allowed : 8.43 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.10), residues: 8092 helix: 1.96 (0.11), residues: 2728 sheet: 0.24 (0.20), residues: 956 loop : -1.28 (0.09), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 318 HIS 0.004 0.001 HIS F 355 PHE 0.008 0.001 PHE L 202 TYR 0.008 0.001 TYR N 319 ARG 0.015 0.000 ARG K 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11902.63 seconds wall clock time: 210 minutes 29.33 seconds (12629.33 seconds total)