Starting phenix.real_space_refine on Tue Mar 12 16:57:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/03_2024/8ari_15603_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/03_2024/8ari_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_15603/03_2024/8ari_15603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/03_2024/8ari_15603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/03_2024/8ari_15603_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ari_15603/03_2024/8ari_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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 24.80, per 1000 atoms: 0.39 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: 17.41 Conformation dependent library (CDL) restraints added in 8.7 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: 8.94 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: 20.70 Time building geometry restraints manager: 19.35 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: 8.150 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: 0.050 Extract box with map and model: 30.590 Check model and map are aligned: 0.720 Set scattering table: 0.440 Process input model: 122.770 Find NCS groups from input model: 4.240 Set up NCS constraints: 0.890 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.780 ------------------------------------------------------------------------------- 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 : 5.568 Fit side-chains REVERT: B 43 PRO cc_start: 0.9354 (Cg_endo) cc_final: 0.9008 (Cg_exo) REVERT: B 75 MET cc_start: 0.8814 (ptm) cc_final: 0.8592 (ptm) REVERT: B 319 TYR cc_start: 0.9297 (t80) cc_final: 0.8425 (t80) REVERT: C 43 PRO cc_start: 0.9356 (Cg_endo) cc_final: 0.9008 (Cg_exo) REVERT: C 319 TYR cc_start: 0.9287 (t80) cc_final: 0.8364 (t80) REVERT: V 43 PRO cc_start: 0.9361 (Cg_endo) cc_final: 0.9032 (Cg_exo) REVERT: V 319 TYR cc_start: 0.9294 (t80) cc_final: 0.8384 (t80) REVERT: W 43 PRO cc_start: 0.9359 (Cg_endo) cc_final: 0.9026 (Cg_exo) REVERT: W 319 TYR cc_start: 0.9301 (t80) cc_final: 0.8425 (t80) outliers start: 25 outliers final: 4 residues processed: 316 average time/residue: 1.5763 time to fit residues: 632.5908 Evaluate side-chains 216 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 212 time to evaluate : 5.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain C residue 354 ASP Chi-restraints excluded: chain V residue 354 ASP Chi-restraints excluded: chain W residue 354 ASP 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: 0.8583 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 64802 Z= 0.226 Angle : 0.443 7.434 87883 Z= 0.244 Chirality : 0.042 0.147 10215 Planarity : 0.004 0.045 11364 Dihedral : 7.558 109.197 10170 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.20 % Allowed : 5.78 % Favored : 94.02 % 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: -0.40 (0.09), residues: 8092 helix: 1.04 (0.10), residues: 2688 sheet: 0.47 (0.20), residues: 956 loop : -1.30 (0.08), residues: 4448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.003 0.001 HIS G 355 PHE 0.009 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 229 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 216 time to evaluate : 5.495 Fit side-chains REVERT: B 43 PRO cc_start: 0.9323 (Cg_endo) cc_final: 0.9096 (Cg_exo) REVERT: B 75 MET cc_start: 0.8747 (ptm) cc_final: 0.8491 (ptm) REVERT: B 319 TYR cc_start: 0.9179 (t80) cc_final: 0.8577 (t80) REVERT: C 43 PRO cc_start: 0.9312 (Cg_endo) cc_final: 0.9082 (Cg_exo) REVERT: C 319 TYR cc_start: 0.9174 (t80) cc_final: 0.8541 (t80) REVERT: V 43 PRO cc_start: 0.9338 (Cg_endo) cc_final: 0.9114 (Cg_exo) REVERT: V 319 TYR cc_start: 0.9187 (t80) cc_final: 0.8572 (t80) REVERT: W 43 PRO cc_start: 0.9343 (Cg_endo) cc_final: 0.9117 (Cg_exo) REVERT: W 319 TYR cc_start: 0.9188 (t80) cc_final: 0.8582 (t80) REVERT: i 321 MET cc_start: 0.7706 (ttp) cc_final: 0.7357 (ttp) REVERT: i 344 ASP cc_start: 0.9021 (t0) cc_final: 0.8771 (t0) outliers start: 13 outliers final: 6 residues processed: 218 average time/residue: 1.5061 time to fit residues: 424.3468 Evaluate side-chains 202 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 5.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 319 LEU Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain f residue 347 VAL Chi-restraints excluded: chain h residue 321 MET Chi-restraints excluded: chain h residue 347 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 409 optimal weight: 0.9990 chunk 228 optimal weight: 0.7980 chunk 613 optimal weight: 4.9990 chunk 502 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 738 optimal weight: 8.9990 chunk 798 optimal weight: 0.0020 chunk 657 optimal weight: 0.9980 chunk 732 optimal weight: 20.0000 chunk 251 optimal weight: 6.9990 chunk 592 optimal weight: 0.0470 overall best weight: 0.5688 ------------------------------------------------------------------------------- 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: 0.8524 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.034 64802 Z= 0.099 Angle : 0.362 7.416 87883 Z= 0.196 Chirality : 0.040 0.141 10215 Planarity : 0.003 0.040 11364 Dihedral : 6.872 46.405 10162 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.64 % Allowed : 5.40 % Favored : 93.96 % 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: -0.01 (0.09), residues: 8092 helix: 1.61 (0.10), residues: 2688 sheet: 0.54 (0.20), residues: 956 loop : -1.21 (0.08), residues: 4448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 318 HIS 0.003 0.000 HIS S 355 PHE 0.007 0.001 PHE M 53 TYR 0.004 0.001 TYR K 140 ARG 0.010 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 271 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 229 time to evaluate : 5.573 Fit side-chains REVERT: B 43 PRO cc_start: 0.9234 (Cg_endo) cc_final: 0.9016 (Cg_exo) REVERT: B 75 MET cc_start: 0.8619 (ptm) cc_final: 0.8381 (ptm) REVERT: B 319 TYR cc_start: 0.9200 (t80) cc_final: 0.8700 (t80) REVERT: C 43 PRO cc_start: 0.9245 (Cg_endo) cc_final: 0.9032 (Cg_exo) REVERT: C 319 TYR cc_start: 0.9196 (t80) cc_final: 0.8675 (t80) REVERT: V 43 PRO cc_start: 0.9273 (Cg_endo) cc_final: 0.9062 (Cg_exo) REVERT: V 319 TYR cc_start: 0.9212 (t80) cc_final: 0.8689 (t80) REVERT: W 43 PRO cc_start: 0.9272 (Cg_endo) cc_final: 0.9057 (Cg_exo) REVERT: W 319 TYR cc_start: 0.9214 (t80) cc_final: 0.8705 (t80) REVERT: i 321 MET cc_start: 0.7917 (ttp) cc_final: 0.7460 (ttp) outliers start: 42 outliers final: 22 residues processed: 261 average time/residue: 1.3748 time to fit residues: 474.0364 Evaluate side-chains 216 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 194 time to evaluate : 5.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain I residue 252 VAL Chi-restraints excluded: chain J residue 252 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain f residue 347 VAL Chi-restraints excluded: chain g residue 347 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 729 optimal weight: 6.9990 chunk 555 optimal weight: 7.9990 chunk 383 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 352 optimal weight: 4.9990 chunk 496 optimal weight: 3.9990 chunk 741 optimal weight: 10.0000 chunk 784 optimal weight: 10.0000 chunk 387 optimal weight: 6.9990 chunk 702 optimal weight: 20.0000 chunk 211 optimal weight: 0.0470 overall best weight: 3.4084 ------------------------------------------------------------------------------- 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: 0.8636 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 64802 Z= 0.377 Angle : 0.497 8.456 87883 Z= 0.271 Chirality : 0.044 0.157 10215 Planarity : 0.004 0.043 11364 Dihedral : 7.515 53.329 10162 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.86 % Allowed : 5.84 % Favored : 93.30 % 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: -0.12 (0.09), residues: 8092 helix: 1.60 (0.11), residues: 2688 sheet: 0.36 (0.20), residues: 956 loop : -1.31 (0.09), residues: 4448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 318 HIS 0.004 0.001 HIS N 147 PHE 0.014 0.002 PHE N 260 TYR 0.011 0.001 TYR J 319 ARG 0.010 0.000 ARG O 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 269 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 212 time to evaluate : 5.630 Fit side-chains REVERT: B 43 PRO cc_start: 0.9211 (Cg_endo) cc_final: 0.8976 (Cg_exo) REVERT: B 75 MET cc_start: 0.8809 (ptm) cc_final: 0.8549 (ptm) REVERT: B 319 TYR cc_start: 0.9286 (t80) cc_final: 0.8729 (t80) REVERT: C 43 PRO cc_start: 0.9213 (Cg_endo) cc_final: 0.8974 (Cg_exo) REVERT: C 319 TYR cc_start: 0.9282 (t80) cc_final: 0.8712 (t80) REVERT: D 321 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8036 (tp30) REVERT: U 321 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8059 (tp30) REVERT: V 43 PRO cc_start: 0.9237 (Cg_endo) cc_final: 0.9005 (Cg_exo) REVERT: V 319 TYR cc_start: 0.9298 (t80) cc_final: 0.8731 (t80) REVERT: W 43 PRO cc_start: 0.9234 (Cg_endo) cc_final: 0.9001 (Cg_exo) REVERT: W 319 TYR cc_start: 0.9298 (t80) cc_final: 0.8736 (t80) REVERT: i 321 MET cc_start: 0.8000 (ttp) cc_final: 0.7568 (ttp) outliers start: 57 outliers final: 30 residues processed: 258 average time/residue: 1.3818 time to fit residues: 470.8147 Evaluate side-chains 225 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 5.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain J residue 252 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 38 CYS Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 38 CYS Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain g residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Chi-restraints excluded: chain i residue 347 VAL Chi-restraints excluded: chain j residue 346 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 653 optimal weight: 4.9990 chunk 445 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 584 optimal weight: 0.9990 chunk 323 optimal weight: 0.3980 chunk 669 optimal weight: 20.0000 chunk 542 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 400 optimal weight: 5.9990 chunk 704 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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: 0.8616 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 64802 Z= 0.255 Angle : 0.436 8.203 87883 Z= 0.238 Chirality : 0.042 0.169 10215 Planarity : 0.003 0.045 11364 Dihedral : 7.326 51.023 10162 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.83 % Allowed : 6.48 % Favored : 92.69 % 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: -0.07 (0.10), residues: 8092 helix: 1.74 (0.11), residues: 2728 sheet: 0.30 (0.20), residues: 956 loop : -1.35 (0.09), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 318 HIS 0.004 0.001 HIS G 355 PHE 0.009 0.001 PHE N 260 TYR 0.009 0.001 TYR J 319 ARG 0.010 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 257 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 202 time to evaluate : 5.592 Fit side-chains REVERT: B 75 MET cc_start: 0.8763 (ptm) cc_final: 0.8508 (ptm) REVERT: B 319 TYR cc_start: 0.9265 (t80) cc_final: 0.8691 (t80) REVERT: C 319 TYR cc_start: 0.9277 (t80) cc_final: 0.8710 (t80) REVERT: D 321 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7946 (tp30) REVERT: U 321 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7944 (tp30) REVERT: V 319 TYR cc_start: 0.9299 (t80) cc_final: 0.8738 (t80) REVERT: W 319 TYR cc_start: 0.9300 (t80) cc_final: 0.8741 (t80) REVERT: i 321 MET cc_start: 0.7999 (ttp) cc_final: 0.7589 (ttp) outliers start: 55 outliers final: 33 residues processed: 242 average time/residue: 1.3604 time to fit residues: 435.5600 Evaluate side-chains 228 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 195 time to evaluate : 5.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain J residue 252 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 38 CYS Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 38 CYS Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain a residue 347 VAL Chi-restraints excluded: chain b residue 347 VAL Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain e residue 347 VAL Chi-restraints excluded: chain g residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Chi-restraints excluded: chain j residue 346 SER Chi-restraints excluded: chain j residue 347 VAL 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: 8.9990 chunk 155 optimal weight: 6.9990 chunk 460 optimal weight: 5.9990 chunk 193 optimal weight: 0.0270 chunk 785 optimal weight: 8.9990 chunk 652 optimal weight: 6.9990 chunk 363 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 259 optimal weight: 0.1980 chunk 412 optimal weight: 2.9990 overall best weight: 3.0444 ------------------------------------------------------------------------------- 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: 0.8642 moved from start: 0.1946 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= 0.341 Angle : 0.480 8.622 87883 Z= 0.261 Chirality : 0.043 0.168 10215 Planarity : 0.004 0.055 11364 Dihedral : 7.493 52.312 10162 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.77 % Allowed : 7.19 % Favored : 92.04 % 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: -0.12 (0.10), residues: 8092 helix: 1.70 (0.11), residues: 2728 sheet: 0.50 (0.20), residues: 916 loop : -1.44 (0.09), residues: 4448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 318 HIS 0.004 0.001 HIS G 355 PHE 0.012 0.001 PHE N 260 TYR 0.011 0.001 TYR O 319 ARG 0.012 0.000 ARG N 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 254 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 203 time to evaluate : 5.597 Fit side-chains REVERT: A 321 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8038 (tp30) REVERT: B 75 MET cc_start: 0.8814 (ptm) cc_final: 0.8529 (ptm) REVERT: B 319 TYR cc_start: 0.9281 (t80) cc_final: 0.8756 (t80) REVERT: C 319 TYR cc_start: 0.9286 (t80) cc_final: 0.8766 (t80) REVERT: D 321 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8128 (tp30) REVERT: U 321 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8142 (tp30) REVERT: V 319 TYR cc_start: 0.9309 (t80) cc_final: 0.8799 (t80) REVERT: W 319 TYR cc_start: 0.9306 (t80) cc_final: 0.8794 (t80) REVERT: X 321 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8070 (tp30) REVERT: i 321 MET cc_start: 0.8112 (ttp) cc_final: 0.7728 (ttp) REVERT: j 344 ASP cc_start: 0.9164 (t0) cc_final: 0.8884 (t0) REVERT: j 346 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8874 (p) outliers start: 51 outliers final: 25 residues processed: 240 average time/residue: 1.4141 time to fit residues: 446.2929 Evaluate side-chains 221 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 5.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain J residue 252 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 38 CYS Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 38 CYS Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain g residue 321 MET Chi-restraints excluded: chain g residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Chi-restraints excluded: chain j residue 346 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 757 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 447 optimal weight: 3.9990 chunk 573 optimal weight: 1.9990 chunk 444 optimal weight: 4.9990 chunk 661 optimal weight: 5.9990 chunk 438 optimal weight: 6.9990 chunk 782 optimal weight: 10.0000 chunk 489 optimal weight: 4.9990 chunk 477 optimal weight: 3.9990 chunk 361 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.8662 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 64802 Z= 0.443 Angle : 0.534 9.265 87883 Z= 0.289 Chirality : 0.045 0.167 10215 Planarity : 0.004 0.060 11364 Dihedral : 7.702 53.300 10162 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.76 % Allowed : 7.81 % Favored : 91.43 % 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: -0.25 (0.10), residues: 8092 helix: 1.60 (0.11), residues: 2728 sheet: 0.34 (0.20), residues: 916 loop : -1.50 (0.09), residues: 4448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 318 HIS 0.004 0.001 HIS G 355 PHE 0.014 0.002 PHE O 260 TYR 0.012 0.002 TYR N 319 ARG 0.012 0.000 ARG O 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 253 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 5.643 Fit side-chains REVERT: A 321 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8135 (tp30) REVERT: B 75 MET cc_start: 0.8880 (ptm) cc_final: 0.8568 (ptm) REVERT: B 319 TYR cc_start: 0.9299 (t80) cc_final: 0.8831 (t80) REVERT: C 319 TYR cc_start: 0.9302 (t80) cc_final: 0.8842 (t80) REVERT: U 321 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8200 (tp30) REVERT: V 319 TYR cc_start: 0.9324 (t80) cc_final: 0.8866 (t80) REVERT: W 319 TYR cc_start: 0.9326 (t80) cc_final: 0.8870 (t80) REVERT: X 321 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8154 (tp30) REVERT: i 321 MET cc_start: 0.8148 (ttp) cc_final: 0.7712 (ttp) REVERT: j 346 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8819 (p) outliers start: 50 outliers final: 32 residues processed: 240 average time/residue: 1.4132 time to fit residues: 444.7044 Evaluate side-chains 228 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 195 time to evaluate : 5.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 38 CYS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain J residue 252 VAL Chi-restraints excluded: chain J residue 306 ASP Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 306 ASP Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain N residue 306 ASP Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain O residue 306 ASP Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 38 CYS Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 38 CYS Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain a residue 321 MET Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain g residue 321 MET Chi-restraints excluded: chain g residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Chi-restraints excluded: chain j residue 346 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 484 optimal weight: 1.9990 chunk 312 optimal weight: 0.9980 chunk 467 optimal weight: 5.9990 chunk 235 optimal weight: 0.2980 chunk 153 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 497 optimal weight: 4.9990 chunk 533 optimal weight: 0.8980 chunk 386 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 615 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8578 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 64802 Z= 0.113 Angle : 0.394 9.380 87883 Z= 0.212 Chirality : 0.040 0.162 10215 Planarity : 0.003 0.056 11364 Dihedral : 7.068 52.776 10162 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.39 % Allowed : 8.32 % Favored : 91.28 % 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: 0.02 (0.10), residues: 8092 helix: 1.93 (0.11), residues: 2728 sheet: 0.20 (0.20), residues: 956 loop : -1.35 (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 F 355 PHE 0.009 0.001 PHE S 202 TYR 0.007 0.001 TYR J 319 ARG 0.013 0.000 ARG J 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 233 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 5.620 Fit side-chains REVERT: A 321 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7874 (tp30) REVERT: B 75 MET cc_start: 0.8701 (ptm) cc_final: 0.8415 (ptm) REVERT: B 319 TYR cc_start: 0.9263 (t80) cc_final: 0.8765 (t80) REVERT: C 319 TYR cc_start: 0.9267 (t80) cc_final: 0.8781 (t80) REVERT: U 321 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7918 (tp30) REVERT: V 319 TYR cc_start: 0.9293 (t80) cc_final: 0.8816 (t80) REVERT: W 319 TYR cc_start: 0.9293 (t80) cc_final: 0.8821 (t80) REVERT: X 321 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7898 (tp30) REVERT: i 321 MET cc_start: 0.8103 (ttp) cc_final: 0.7757 (ttp) REVERT: j 346 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.8738 (p) outliers start: 26 outliers final: 18 residues processed: 228 average time/residue: 1.4245 time to fit residues: 426.1760 Evaluate side-chains 212 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 193 time to evaluate : 5.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain g residue 321 MET Chi-restraints excluded: chain h residue 347 VAL Chi-restraints excluded: chain j residue 346 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 711 optimal weight: 9.9990 chunk 749 optimal weight: 10.0000 chunk 684 optimal weight: 9.9990 chunk 729 optimal weight: 6.9990 chunk 438 optimal weight: 2.9990 chunk 317 optimal weight: 0.0870 chunk 572 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 659 optimal weight: 4.9990 chunk 689 optimal weight: 2.9990 chunk 726 optimal weight: 20.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- 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: 0.8633 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 64802 Z= 0.292 Angle : 0.463 10.129 87883 Z= 0.248 Chirality : 0.042 0.176 10215 Planarity : 0.004 0.063 11364 Dihedral : 7.339 53.142 10162 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.56 % Allowed : 8.34 % Favored : 91.10 % 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: -0.02 (0.10), residues: 8092 helix: 1.84 (0.11), residues: 2752 sheet: 0.15 (0.20), residues: 956 loop : -1.34 (0.09), residues: 4384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 318 HIS 0.004 0.001 HIS F 355 PHE 0.010 0.001 PHE P 202 TYR 0.010 0.001 TYR N 319 ARG 0.014 0.000 ARG S 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 221 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 5.568 Fit side-chains REVERT: A 321 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8053 (tp30) REVERT: B 75 MET cc_start: 0.8761 (ptm) cc_final: 0.8440 (ptm) REVERT: B 319 TYR cc_start: 0.9287 (t80) cc_final: 0.8767 (t80) REVERT: C 319 TYR cc_start: 0.9301 (t80) cc_final: 0.8709 (t80) REVERT: U 321 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8061 (tp30) REVERT: V 319 TYR cc_start: 0.9328 (t80) cc_final: 0.8833 (t80) REVERT: W 319 TYR cc_start: 0.9323 (t80) cc_final: 0.8749 (t80) REVERT: X 321 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8078 (tp30) REVERT: i 321 MET cc_start: 0.8125 (ttp) cc_final: 0.7826 (ttp) REVERT: j 346 SER cc_start: 0.9007 (p) cc_final: 0.8750 (p) outliers start: 37 outliers final: 28 residues processed: 219 average time/residue: 1.4065 time to fit residues: 405.4155 Evaluate side-chains 211 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 183 time to evaluate : 5.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 252 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain P residue 48 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain T residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain e residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 478 optimal weight: 0.8980 chunk 771 optimal weight: 9.9990 chunk 470 optimal weight: 0.9990 chunk 365 optimal weight: 1.9990 chunk 536 optimal weight: 7.9990 chunk 808 optimal weight: 20.0000 chunk 744 optimal weight: 6.9990 chunk 644 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 497 optimal weight: 0.8980 chunk 394 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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: 0.8591 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 64802 Z= 0.149 Angle : 0.410 11.422 87883 Z= 0.217 Chirality : 0.040 0.200 10215 Planarity : 0.003 0.063 11364 Dihedral : 7.042 54.126 10162 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.39 % Allowed : 8.54 % Favored : 91.07 % 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: 0.10 (0.10), residues: 8092 helix: 2.01 (0.11), residues: 2728 sheet: 0.22 (0.20), residues: 956 loop : -1.30 (0.09), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 318 HIS 0.004 0.000 HIS F 355 PHE 0.008 0.001 PHE P 202 TYR 0.008 0.001 TYR O 319 ARG 0.015 0.000 ARG N 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 218 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 5.571 Fit side-chains REVERT: A 321 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7918 (tp30) REVERT: B 75 MET cc_start: 0.8688 (ptm) cc_final: 0.8395 (ptm) REVERT: B 319 TYR cc_start: 0.9261 (t80) cc_final: 0.8768 (t80) REVERT: C 319 TYR cc_start: 0.9281 (t80) cc_final: 0.8802 (t80) REVERT: U 321 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7927 (tp30) REVERT: V 319 TYR cc_start: 0.9301 (t80) cc_final: 0.8834 (t80) REVERT: W 319 TYR cc_start: 0.9296 (t80) cc_final: 0.8757 (t80) REVERT: X 321 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7937 (tp30) REVERT: i 321 MET cc_start: 0.8118 (ttp) cc_final: 0.7852 (ttp) REVERT: j 346 SER cc_start: 0.8893 (p) cc_final: 0.8629 (p) outliers start: 26 outliers final: 26 residues processed: 217 average time/residue: 1.4175 time to fit residues: 403.2570 Evaluate side-chains 216 residues out of total 6680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 5.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 38 CYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain J residue 252 VAL Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain N residue 252 VAL Chi-restraints excluded: chain O residue 252 VAL Chi-restraints excluded: chain Q residue 252 VAL Chi-restraints excluded: chain R residue 252 VAL Chi-restraints excluded: chain S residue 252 VAL Chi-restraints excluded: chain U residue 252 VAL Chi-restraints excluded: chain V residue 252 VAL Chi-restraints excluded: chain W residue 252 VAL Chi-restraints excluded: chain X residue 252 VAL Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain d residue 347 VAL Chi-restraints excluded: chain e residue 347 VAL Chi-restraints excluded: chain h residue 347 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 812 random chunks: chunk 511 optimal weight: 0.0770 chunk 686 optimal weight: 8.9990 chunk 197 optimal weight: 1.9990 chunk 593 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 645 optimal weight: 4.9990 chunk 270 optimal weight: 0.9990 chunk 662 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 0.0270 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.107721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.073245 restraints weight = 130595.868| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.69 r_work: 0.2638 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 64802 Z= 0.102 Angle : 0.382 11.792 87883 Z= 0.200 Chirality : 0.040 0.201 10215 Planarity : 0.003 0.062 11364 Dihedral : 6.587 55.676 10162 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.36 % Allowed : 8.61 % Favored : 91.03 % 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: 0.25 (0.10), residues: 8092 helix: 2.15 (0.11), residues: 2728 sheet: 0.29 (0.20), residues: 956 loop : -1.22 (0.09), residues: 4408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 318 HIS 0.004 0.000 HIS F 355 PHE 0.008 0.001 PHE O 202 TYR 0.006 0.001 TYR N 319 ARG 0.017 0.000 ARG O 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11543.48 seconds wall clock time: 204 minutes 44.34 seconds (12284.34 seconds total)