Starting phenix.real_space_refine on Sat Feb 17 16:01:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2024/6uov_20833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2024/6uov_20833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2024/6uov_20833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2024/6uov_20833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2024/6uov_20833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uov_20833/02_2024/6uov_20833.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 161 5.16 5 C 44068 2.51 5 N 12374 2.21 5 O 13248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 82": "NH1" <-> "NH2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "F TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "H TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "J TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "L TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 82": "NH1" <-> "NH2" Residue "N TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "P TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 82": "NH1" <-> "NH2" Residue "R TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 82": "NH1" <-> "NH2" Residue "T TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "V TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 82": "NH1" <-> "NH2" Residue "X TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 82": "NH1" <-> "NH2" Residue "Z TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 82": "NH1" <-> "NH2" Residue "b TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 82": "NH1" <-> "NH2" Residue "d TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 82": "NH1" <-> "NH2" Residue "f TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 82": "NH1" <-> "NH2" Residue "h TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 82": "NH1" <-> "NH2" Residue "j TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 82": "NH1" <-> "NH2" Residue "l TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 82": "NH1" <-> "NH2" Residue "n TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 82": "NH1" <-> "NH2" Residue "p TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 82": "NH1" <-> "NH2" Residue "r TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 82": "NH1" <-> "NH2" Residue "t TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 69851 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "B" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "C" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "D" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "E" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "F" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "G" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "H" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "I" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "J" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "K" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "L" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "M" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "N" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "P" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "Q" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "R" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "S" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "T" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "U" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "V" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "W" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "X" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "Y" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "Z" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "a" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "b" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "c" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "d" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "e" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "f" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "g" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "h" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "i" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "j" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "k" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "l" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "m" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "n" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "o" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "p" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "q" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "r" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "s" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1437 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 171} Chain: "t" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1600 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Time building chain proxies: 25.77, per 1000 atoms: 0.37 Number of scatterers: 69851 At special positions: 0 Unit cell: (247.17, 246.1, 75.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 161 16.00 O 13248 8.00 N 12374 7.00 C 44068 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: 19.00 Conformation dependent library (CDL) restraints added in 9.0 seconds 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16560 Finding SS restraints... Secondary structure from input PDB file: 345 helices and 115 sheets defined 43.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 75 " --> pdb=" O TRP A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE A 89 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 167 " --> pdb=" O GLN A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 212 " --> pdb=" O ARG B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 308 Processing helix chain 'B' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 36 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 37 " --> pdb=" O ASN C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 43 No H-bonds generated for 'chain 'C' and resid 41 through 43' Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS C 73 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C 75 " --> pdb=" O TRP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 102 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP C 166 " --> pdb=" O HIS C 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 167 " --> pdb=" O GLN C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL D 210 " --> pdb=" O TRP D 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 212 " --> pdb=" O ARG D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU D 228 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS D 230 " --> pdb=" O ASN D 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D 233 " --> pdb=" O ASN D 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 308 Processing helix chain 'D' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 37 " --> pdb=" O ASN E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 43 No H-bonds generated for 'chain 'E' and resid 41 through 43' Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR E 70 " --> pdb=" O THR E 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 73 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR E 75 " --> pdb=" O TRP E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE E 89 " --> pdb=" O ALA E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU E 101 " --> pdb=" O SER E 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS E 102 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 163 through 171 removed outlier: 3.575A pdb=" N ILE E 167 " --> pdb=" O GLN E 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU F 205 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL F 210 " --> pdb=" O TRP F 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA F 212 " --> pdb=" O ARG F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU F 228 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN F 229 " --> pdb=" O GLU F 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS F 230 " --> pdb=" O ASN F 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER F 233 " --> pdb=" O ASN F 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR F 238 " --> pdb=" O ILE F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 279 removed outlier: 3.635A pdb=" N GLU F 273 " --> pdb=" O LYS F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 308 Processing helix chain 'F' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG F 340 " --> pdb=" O ILE F 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN F 341 " --> pdb=" O LEU F 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER F 345 " --> pdb=" O GLN F 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU G 34 " --> pdb=" O GLU G 30 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 43 No H-bonds generated for 'chain 'G' and resid 41 through 43' Processing helix chain 'G' and resid 52 through 54 No H-bonds generated for 'chain 'G' and resid 52 through 54' Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'G' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR G 70 " --> pdb=" O THR G 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR G 75 " --> pdb=" O TRP G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 89 removed outlier: 3.532A pdb=" N PHE G 89 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU G 101 " --> pdb=" O SER G 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS G 102 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 140 Processing helix chain 'G' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP G 166 " --> pdb=" O HIS G 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE G 167 " --> pdb=" O GLN G 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 177 Processing helix chain 'H' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU H 205 " --> pdb=" O GLU H 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL H 210 " --> pdb=" O TRP H 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA H 212 " --> pdb=" O ARG H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU H 228 " --> pdb=" O ASN H 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN H 229 " --> pdb=" O GLU H 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS H 230 " --> pdb=" O ASN H 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR H 238 " --> pdb=" O ILE H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU H 273 " --> pdb=" O LYS H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 308 Processing helix chain 'H' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG H 340 " --> pdb=" O ILE H 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN H 341 " --> pdb=" O LEU H 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER H 345 " --> pdb=" O GLN H 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR H 349 " --> pdb=" O SER H 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 52 through 54 No H-bonds generated for 'chain 'I' and resid 52 through 54' Processing helix chain 'I' and resid 61 through 63 No H-bonds generated for 'chain 'I' and resid 61 through 63' Processing helix chain 'I' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS I 73 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR I 75 " --> pdb=" O TRP I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE I 89 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 118 removed outlier: 3.671A pdb=" N GLU I 101 " --> pdb=" O SER I 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS I 102 " --> pdb=" O PRO I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 140 Processing helix chain 'I' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP I 166 " --> pdb=" O HIS I 162 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE I 167 " --> pdb=" O GLN I 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 177 Processing helix chain 'J' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU J 205 " --> pdb=" O GLU J 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL J 210 " --> pdb=" O TRP J 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA J 212 " --> pdb=" O ARG J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU J 228 " --> pdb=" O ASN J 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN J 229 " --> pdb=" O GLU J 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER J 233 " --> pdb=" O ASN J 229 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR J 238 " --> pdb=" O ILE J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU J 273 " --> pdb=" O LYS J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 308 Processing helix chain 'J' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG J 340 " --> pdb=" O ILE J 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN J 341 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER J 345 " --> pdb=" O GLN J 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR J 349 " --> pdb=" O SER J 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU K 34 " --> pdb=" O GLU K 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE K 36 " --> pdb=" O ALA K 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA K 37 " --> pdb=" O ASN K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 43 No H-bonds generated for 'chain 'K' and resid 41 through 43' Processing helix chain 'K' and resid 52 through 54 No H-bonds generated for 'chain 'K' and resid 52 through 54' Processing helix chain 'K' and resid 61 through 63 No H-bonds generated for 'chain 'K' and resid 61 through 63' Processing helix chain 'K' and resid 64 through 76 removed outlier: 3.573A pdb=" N TYR K 70 " --> pdb=" O THR K 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS K 73 " --> pdb=" O VAL K 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR K 75 " --> pdb=" O TRP K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE K 89 " --> pdb=" O ALA K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 118 removed outlier: 3.673A pdb=" N GLU K 101 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS K 102 " --> pdb=" O PRO K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 140 Processing helix chain 'K' and resid 163 through 171 removed outlier: 3.575A pdb=" N ILE K 167 " --> pdb=" O GLN K 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 177 Processing helix chain 'L' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU L 205 " --> pdb=" O GLU L 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL L 210 " --> pdb=" O TRP L 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA L 212 " --> pdb=" O ARG L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU L 228 " --> pdb=" O ASN L 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN L 229 " --> pdb=" O GLU L 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER L 233 " --> pdb=" O ASN L 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR L 238 " --> pdb=" O ILE L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU L 273 " --> pdb=" O LYS L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 308 Processing helix chain 'L' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG L 340 " --> pdb=" O ILE L 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN L 341 " --> pdb=" O LEU L 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER L 345 " --> pdb=" O GLN L 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR L 349 " --> pdb=" O SER L 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU M 34 " --> pdb=" O GLU M 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE M 36 " --> pdb=" O ALA M 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA M 37 " --> pdb=" O ASN M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 43 No H-bonds generated for 'chain 'M' and resid 41 through 43' Processing helix chain 'M' and resid 52 through 54 No H-bonds generated for 'chain 'M' and resid 52 through 54' Processing helix chain 'M' and resid 61 through 63 No H-bonds generated for 'chain 'M' and resid 61 through 63' Processing helix chain 'M' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR M 70 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR M 75 " --> pdb=" O TRP M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE M 89 " --> pdb=" O ALA M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU M 101 " --> pdb=" O SER M 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS M 102 " --> pdb=" O PRO M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 140 Processing helix chain 'M' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP M 166 " --> pdb=" O HIS M 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE M 167 " --> pdb=" O GLN M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 177 Processing helix chain 'N' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU N 205 " --> pdb=" O GLU N 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL N 210 " --> pdb=" O TRP N 206 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA N 212 " --> pdb=" O ARG N 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU N 228 " --> pdb=" O ASN N 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN N 229 " --> pdb=" O GLU N 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS N 230 " --> pdb=" O ASN N 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR N 238 " --> pdb=" O ILE N 234 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU N 273 " --> pdb=" O LYS N 269 " (cutoff:3.500A) Processing helix chain 'N' and resid 295 through 308 Processing helix chain 'N' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG N 340 " --> pdb=" O ILE N 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN N 341 " --> pdb=" O LEU N 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER N 345 " --> pdb=" O GLN N 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR N 349 " --> pdb=" O SER N 345 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU O 34 " --> pdb=" O GLU O 30 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE O 36 " --> pdb=" O ALA O 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA O 37 " --> pdb=" O ASN O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 43 No H-bonds generated for 'chain 'O' and resid 41 through 43' Processing helix chain 'O' and resid 52 through 54 No H-bonds generated for 'chain 'O' and resid 52 through 54' Processing helix chain 'O' and resid 61 through 63 No H-bonds generated for 'chain 'O' and resid 61 through 63' Processing helix chain 'O' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR O 70 " --> pdb=" O THR O 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS O 73 " --> pdb=" O VAL O 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR O 75 " --> pdb=" O TRP O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE O 89 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU O 101 " --> pdb=" O SER O 97 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS O 102 " --> pdb=" O PRO O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 140 Processing helix chain 'O' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP O 166 " --> pdb=" O HIS O 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE O 167 " --> pdb=" O GLN O 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 177 Processing helix chain 'P' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU P 205 " --> pdb=" O GLU P 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL P 210 " --> pdb=" O TRP P 206 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA P 212 " --> pdb=" O ARG P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU P 228 " --> pdb=" O ASN P 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN P 229 " --> pdb=" O GLU P 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS P 230 " --> pdb=" O ASN P 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER P 233 " --> pdb=" O ASN P 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR P 238 " --> pdb=" O ILE P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 268 through 279 removed outlier: 3.635A pdb=" N GLU P 273 " --> pdb=" O LYS P 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 308 Processing helix chain 'P' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG P 340 " --> pdb=" O ILE P 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN P 341 " --> pdb=" O LEU P 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER P 345 " --> pdb=" O GLN P 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR P 349 " --> pdb=" O SER P 345 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU Q 34 " --> pdb=" O GLU Q 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE Q 36 " --> pdb=" O ALA Q 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Q 37 " --> pdb=" O ASN Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'Q' and resid 52 through 54 No H-bonds generated for 'chain 'Q' and resid 52 through 54' Processing helix chain 'Q' and resid 61 through 63 No H-bonds generated for 'chain 'Q' and resid 61 through 63' Processing helix chain 'Q' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR Q 70 " --> pdb=" O THR Q 66 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS Q 73 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR Q 75 " --> pdb=" O TRP Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE Q 89 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU Q 101 " --> pdb=" O SER Q 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS Q 102 " --> pdb=" O PRO Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 135 through 140 Processing helix chain 'Q' and resid 163 through 171 removed outlier: 3.575A pdb=" N ILE Q 167 " --> pdb=" O GLN Q 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 177 Processing helix chain 'R' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU R 205 " --> pdb=" O GLU R 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL R 210 " --> pdb=" O TRP R 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA R 212 " --> pdb=" O ARG R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU R 228 " --> pdb=" O ASN R 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN R 229 " --> pdb=" O GLU R 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER R 233 " --> pdb=" O ASN R 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR R 238 " --> pdb=" O ILE R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 308 Processing helix chain 'R' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG R 340 " --> pdb=" O ILE R 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN R 341 " --> pdb=" O LEU R 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER R 345 " --> pdb=" O GLN R 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR R 349 " --> pdb=" O SER R 345 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU S 34 " --> pdb=" O GLU S 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA S 37 " --> pdb=" O ASN S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 43 No H-bonds generated for 'chain 'S' and resid 41 through 43' Processing helix chain 'S' and resid 52 through 54 No H-bonds generated for 'chain 'S' and resid 52 through 54' Processing helix chain 'S' and resid 61 through 63 No H-bonds generated for 'chain 'S' and resid 61 through 63' Processing helix chain 'S' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR S 70 " --> pdb=" O THR S 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS S 73 " --> pdb=" O VAL S 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR S 75 " --> pdb=" O TRP S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE S 89 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 118 removed outlier: 3.673A pdb=" N GLU S 101 " --> pdb=" O SER S 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS S 102 " --> pdb=" O PRO S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 140 Processing helix chain 'S' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP S 166 " --> pdb=" O HIS S 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE S 167 " --> pdb=" O GLN S 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 172 through 177 Processing helix chain 'T' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU T 205 " --> pdb=" O GLU T 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL T 210 " --> pdb=" O TRP T 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA T 212 " --> pdb=" O ARG T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU T 228 " --> pdb=" O ASN T 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN T 229 " --> pdb=" O GLU T 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS T 230 " --> pdb=" O ASN T 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER T 233 " --> pdb=" O ASN T 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR T 238 " --> pdb=" O ILE T 234 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU T 273 " --> pdb=" O LYS T 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 295 through 308 Processing helix chain 'T' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG T 340 " --> pdb=" O ILE T 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN T 341 " --> pdb=" O LEU T 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER T 345 " --> pdb=" O GLN T 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR T 349 " --> pdb=" O SER T 345 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE U 36 " --> pdb=" O ALA U 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA U 37 " --> pdb=" O ASN U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 43 No H-bonds generated for 'chain 'U' and resid 41 through 43' Processing helix chain 'U' and resid 52 through 54 No H-bonds generated for 'chain 'U' and resid 52 through 54' Processing helix chain 'U' and resid 61 through 63 No H-bonds generated for 'chain 'U' and resid 61 through 63' Processing helix chain 'U' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR U 70 " --> pdb=" O THR U 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS U 73 " --> pdb=" O VAL U 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR U 75 " --> pdb=" O TRP U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE U 89 " --> pdb=" O ALA U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU U 101 " --> pdb=" O SER U 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS U 102 " --> pdb=" O PRO U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 140 Processing helix chain 'U' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP U 166 " --> pdb=" O HIS U 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE U 167 " --> pdb=" O GLN U 163 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 177 Processing helix chain 'V' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU V 205 " --> pdb=" O GLU V 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL V 210 " --> pdb=" O TRP V 206 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA V 212 " --> pdb=" O ARG V 208 " (cutoff:3.500A) Processing helix chain 'V' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU V 228 " --> pdb=" O ASN V 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN V 229 " --> pdb=" O GLU V 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS V 230 " --> pdb=" O ASN V 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER V 233 " --> pdb=" O ASN V 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR V 238 " --> pdb=" O ILE V 234 " (cutoff:3.500A) Processing helix chain 'V' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU V 273 " --> pdb=" O LYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 295 through 308 Processing helix chain 'V' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG V 340 " --> pdb=" O ILE V 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN V 341 " --> pdb=" O LEU V 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER V 345 " --> pdb=" O GLN V 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR V 349 " --> pdb=" O SER V 345 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE W 36 " --> pdb=" O ALA W 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA W 37 " --> pdb=" O ASN W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 43 No H-bonds generated for 'chain 'W' and resid 41 through 43' Processing helix chain 'W' and resid 52 through 54 No H-bonds generated for 'chain 'W' and resid 52 through 54' Processing helix chain 'W' and resid 61 through 63 No H-bonds generated for 'chain 'W' and resid 61 through 63' Processing helix chain 'W' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR W 70 " --> pdb=" O THR W 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS W 73 " --> pdb=" O VAL W 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR W 75 " --> pdb=" O TRP W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE W 89 " --> pdb=" O ALA W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 118 removed outlier: 3.673A pdb=" N GLU W 101 " --> pdb=" O SER W 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS W 102 " --> pdb=" O PRO W 98 " (cutoff:3.500A) Processing helix chain 'W' and resid 135 through 140 Processing helix chain 'W' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP W 166 " --> pdb=" O HIS W 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE W 167 " --> pdb=" O GLN W 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 172 through 177 Processing helix chain 'X' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU X 205 " --> pdb=" O GLU X 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL X 210 " --> pdb=" O TRP X 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA X 212 " --> pdb=" O ARG X 208 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU X 228 " --> pdb=" O ASN X 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN X 229 " --> pdb=" O GLU X 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS X 230 " --> pdb=" O ASN X 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER X 233 " --> pdb=" O ASN X 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR X 238 " --> pdb=" O ILE X 234 " (cutoff:3.500A) Processing helix chain 'X' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU X 273 " --> pdb=" O LYS X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 295 through 308 Processing helix chain 'X' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN X 341 " --> pdb=" O LEU X 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER X 345 " --> pdb=" O GLN X 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR X 349 " --> pdb=" O SER X 345 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU Y 34 " --> pdb=" O GLU Y 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE Y 36 " --> pdb=" O ALA Y 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Y 37 " --> pdb=" O ASN Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 43 No H-bonds generated for 'chain 'Y' and resid 41 through 43' Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 61 through 63 No H-bonds generated for 'chain 'Y' and resid 61 through 63' Processing helix chain 'Y' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR Y 70 " --> pdb=" O THR Y 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS Y 73 " --> pdb=" O VAL Y 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR Y 75 " --> pdb=" O TRP Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE Y 89 " --> pdb=" O ALA Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU Y 101 " --> pdb=" O SER Y 97 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS Y 102 " --> pdb=" O PRO Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 140 Processing helix chain 'Y' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP Y 166 " --> pdb=" O HIS Y 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE Y 167 " --> pdb=" O GLN Y 163 " (cutoff:3.500A) Processing helix chain 'Z' and resid 172 through 177 Processing helix chain 'Z' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU Z 205 " --> pdb=" O GLU Z 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL Z 210 " --> pdb=" O TRP Z 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA Z 212 " --> pdb=" O ARG Z 208 " (cutoff:3.500A) Processing helix chain 'Z' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU Z 228 " --> pdb=" O ASN Z 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN Z 229 " --> pdb=" O GLU Z 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS Z 230 " --> pdb=" O ASN Z 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER Z 233 " --> pdb=" O ASN Z 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR Z 238 " --> pdb=" O ILE Z 234 " (cutoff:3.500A) Processing helix chain 'Z' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU Z 273 " --> pdb=" O LYS Z 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 295 through 308 Processing helix chain 'Z' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG Z 340 " --> pdb=" O ILE Z 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN Z 341 " --> pdb=" O LEU Z 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER Z 345 " --> pdb=" O GLN Z 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR Z 349 " --> pdb=" O SER Z 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU a 34 " --> pdb=" O GLU a 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE a 36 " --> pdb=" O ALA a 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA a 37 " --> pdb=" O ASN a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 43 No H-bonds generated for 'chain 'a' and resid 41 through 43' Processing helix chain 'a' and resid 52 through 54 No H-bonds generated for 'chain 'a' and resid 52 through 54' Processing helix chain 'a' and resid 61 through 63 No H-bonds generated for 'chain 'a' and resid 61 through 63' Processing helix chain 'a' and resid 64 through 76 removed outlier: 3.573A pdb=" N TYR a 70 " --> pdb=" O THR a 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS a 73 " --> pdb=" O VAL a 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR a 75 " --> pdb=" O TRP a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE a 89 " --> pdb=" O ALA a 86 " (cutoff:3.500A) Processing helix chain 'a' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU a 101 " --> pdb=" O SER a 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS a 102 " --> pdb=" O PRO a 98 " (cutoff:3.500A) Processing helix chain 'a' and resid 135 through 140 Processing helix chain 'a' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP a 166 " --> pdb=" O HIS a 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE a 167 " --> pdb=" O GLN a 163 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 177 Processing helix chain 'b' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU b 205 " --> pdb=" O GLU b 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL b 210 " --> pdb=" O TRP b 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA b 212 " --> pdb=" O ARG b 208 " (cutoff:3.500A) Processing helix chain 'b' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU b 228 " --> pdb=" O ASN b 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN b 229 " --> pdb=" O GLU b 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS b 230 " --> pdb=" O ASN b 226 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER b 233 " --> pdb=" O ASN b 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR b 238 " --> pdb=" O ILE b 234 " (cutoff:3.500A) Processing helix chain 'b' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU b 273 " --> pdb=" O LYS b 269 " (cutoff:3.500A) Processing helix chain 'b' and resid 295 through 308 Processing helix chain 'b' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG b 340 " --> pdb=" O ILE b 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN b 341 " --> pdb=" O LEU b 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER b 345 " --> pdb=" O GLN b 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR b 349 " --> pdb=" O SER b 345 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU c 34 " --> pdb=" O GLU c 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE c 36 " --> pdb=" O ALA c 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA c 37 " --> pdb=" O ASN c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 43 No H-bonds generated for 'chain 'c' and resid 41 through 43' Processing helix chain 'c' and resid 52 through 54 No H-bonds generated for 'chain 'c' and resid 52 through 54' Processing helix chain 'c' and resid 61 through 63 No H-bonds generated for 'chain 'c' and resid 61 through 63' Processing helix chain 'c' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR c 70 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS c 73 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR c 75 " --> pdb=" O TRP c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE c 89 " --> pdb=" O ALA c 86 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 118 removed outlier: 3.671A pdb=" N GLU c 101 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS c 102 " --> pdb=" O PRO c 98 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 140 Processing helix chain 'c' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP c 166 " --> pdb=" O HIS c 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE c 167 " --> pdb=" O GLN c 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 172 through 177 Processing helix chain 'd' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL d 210 " --> pdb=" O TRP d 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA d 212 " --> pdb=" O ARG d 208 " (cutoff:3.500A) Processing helix chain 'd' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU d 228 " --> pdb=" O ASN d 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN d 229 " --> pdb=" O GLU d 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS d 230 " --> pdb=" O ASN d 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER d 233 " --> pdb=" O ASN d 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR d 238 " --> pdb=" O ILE d 234 " (cutoff:3.500A) Processing helix chain 'd' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU d 273 " --> pdb=" O LYS d 269 " (cutoff:3.500A) Processing helix chain 'd' and resid 295 through 308 Processing helix chain 'd' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG d 340 " --> pdb=" O ILE d 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN d 341 " --> pdb=" O LEU d 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER d 345 " --> pdb=" O GLN d 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR d 349 " --> pdb=" O SER d 345 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU e 34 " --> pdb=" O GLU e 30 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE e 36 " --> pdb=" O ALA e 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA e 37 " --> pdb=" O ASN e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 43 No H-bonds generated for 'chain 'e' and resid 41 through 43' Processing helix chain 'e' and resid 52 through 54 No H-bonds generated for 'chain 'e' and resid 52 through 54' Processing helix chain 'e' and resid 61 through 63 No H-bonds generated for 'chain 'e' and resid 61 through 63' Processing helix chain 'e' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR e 70 " --> pdb=" O THR e 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS e 73 " --> pdb=" O VAL e 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR e 75 " --> pdb=" O TRP e 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 89 removed outlier: 3.532A pdb=" N PHE e 89 " --> pdb=" O ALA e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU e 101 " --> pdb=" O SER e 97 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS e 102 " --> pdb=" O PRO e 98 " (cutoff:3.500A) Processing helix chain 'e' and resid 135 through 140 Processing helix chain 'e' and resid 163 through 171 removed outlier: 3.575A pdb=" N ILE e 167 " --> pdb=" O GLN e 163 " (cutoff:3.500A) Processing helix chain 'f' and resid 172 through 177 Processing helix chain 'f' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU f 205 " --> pdb=" O GLU f 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL f 210 " --> pdb=" O TRP f 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA f 212 " --> pdb=" O ARG f 208 " (cutoff:3.500A) Processing helix chain 'f' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU f 228 " --> pdb=" O ASN f 224 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN f 229 " --> pdb=" O GLU f 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS f 230 " --> pdb=" O ASN f 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER f 233 " --> pdb=" O ASN f 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR f 238 " --> pdb=" O ILE f 234 " (cutoff:3.500A) Processing helix chain 'f' and resid 268 through 279 removed outlier: 3.635A pdb=" N GLU f 273 " --> pdb=" O LYS f 269 " (cutoff:3.500A) Processing helix chain 'f' and resid 295 through 308 Processing helix chain 'f' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG f 340 " --> pdb=" O ILE f 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN f 341 " --> pdb=" O LEU f 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER f 345 " --> pdb=" O GLN f 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR f 349 " --> pdb=" O SER f 345 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU g 34 " --> pdb=" O GLU g 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE g 36 " --> pdb=" O ALA g 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA g 37 " --> pdb=" O ASN g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 41 through 43 No H-bonds generated for 'chain 'g' and resid 41 through 43' Processing helix chain 'g' and resid 52 through 54 No H-bonds generated for 'chain 'g' and resid 52 through 54' Processing helix chain 'g' and resid 61 through 63 No H-bonds generated for 'chain 'g' and resid 61 through 63' Processing helix chain 'g' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR g 70 " --> pdb=" O THR g 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS g 73 " --> pdb=" O VAL g 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR g 75 " --> pdb=" O TRP g 71 " (cutoff:3.500A) Processing helix chain 'g' and resid 84 through 89 removed outlier: 3.534A pdb=" N PHE g 89 " --> pdb=" O ALA g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 97 through 118 removed outlier: 3.673A pdb=" N GLU g 101 " --> pdb=" O SER g 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS g 102 " --> pdb=" O PRO g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 135 through 140 Processing helix chain 'g' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP g 166 " --> pdb=" O HIS g 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE g 167 " --> pdb=" O GLN g 163 " (cutoff:3.500A) Processing helix chain 'h' and resid 172 through 177 Processing helix chain 'h' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU h 205 " --> pdb=" O GLU h 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL h 210 " --> pdb=" O TRP h 206 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA h 212 " --> pdb=" O ARG h 208 " (cutoff:3.500A) Processing helix chain 'h' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU h 228 " --> pdb=" O ASN h 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN h 229 " --> pdb=" O GLU h 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS h 230 " --> pdb=" O ASN h 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER h 233 " --> pdb=" O ASN h 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR h 238 " --> pdb=" O ILE h 234 " (cutoff:3.500A) Processing helix chain 'h' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU h 273 " --> pdb=" O LYS h 269 " (cutoff:3.500A) Processing helix chain 'h' and resid 295 through 308 Processing helix chain 'h' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG h 340 " --> pdb=" O ILE h 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN h 341 " --> pdb=" O LEU h 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER h 345 " --> pdb=" O GLN h 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR h 349 " --> pdb=" O SER h 345 " (cutoff:3.500A) Processing helix chain 'i' and resid 28 through 40 removed outlier: 3.667A pdb=" N GLU i 34 " --> pdb=" O GLU i 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE i 36 " --> pdb=" O ALA i 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA i 37 " --> pdb=" O ASN i 33 " (cutoff:3.500A) Processing helix chain 'i' and resid 41 through 43 No H-bonds generated for 'chain 'i' and resid 41 through 43' Processing helix chain 'i' and resid 52 through 54 No H-bonds generated for 'chain 'i' and resid 52 through 54' Processing helix chain 'i' and resid 61 through 63 No H-bonds generated for 'chain 'i' and resid 61 through 63' Processing helix chain 'i' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR i 70 " --> pdb=" O THR i 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS i 73 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR i 75 " --> pdb=" O TRP i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE i 89 " --> pdb=" O ALA i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU i 101 " --> pdb=" O SER i 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS i 102 " --> pdb=" O PRO i 98 " (cutoff:3.500A) Processing helix chain 'i' and resid 135 through 140 Processing helix chain 'i' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP i 166 " --> pdb=" O HIS i 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE i 167 " --> pdb=" O GLN i 163 " (cutoff:3.500A) Processing helix chain 'j' and resid 172 through 177 Processing helix chain 'j' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU j 205 " --> pdb=" O GLU j 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL j 210 " --> pdb=" O TRP j 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA j 212 " --> pdb=" O ARG j 208 " (cutoff:3.500A) Processing helix chain 'j' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU j 228 " --> pdb=" O ASN j 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN j 229 " --> pdb=" O GLU j 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS j 230 " --> pdb=" O ASN j 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER j 233 " --> pdb=" O ASN j 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR j 238 " --> pdb=" O ILE j 234 " (cutoff:3.500A) Processing helix chain 'j' and resid 268 through 279 removed outlier: 3.635A pdb=" N GLU j 273 " --> pdb=" O LYS j 269 " (cutoff:3.500A) Processing helix chain 'j' and resid 295 through 308 Processing helix chain 'j' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG j 340 " --> pdb=" O ILE j 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN j 341 " --> pdb=" O LEU j 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER j 345 " --> pdb=" O GLN j 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR j 349 " --> pdb=" O SER j 345 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU k 34 " --> pdb=" O GLU k 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE k 36 " --> pdb=" O ALA k 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA k 37 " --> pdb=" O ASN k 33 " (cutoff:3.500A) Processing helix chain 'k' and resid 41 through 43 No H-bonds generated for 'chain 'k' and resid 41 through 43' Processing helix chain 'k' and resid 52 through 54 No H-bonds generated for 'chain 'k' and resid 52 through 54' Processing helix chain 'k' and resid 61 through 63 No H-bonds generated for 'chain 'k' and resid 61 through 63' Processing helix chain 'k' and resid 64 through 76 removed outlier: 3.573A pdb=" N TYR k 70 " --> pdb=" O THR k 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS k 73 " --> pdb=" O VAL k 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR k 75 " --> pdb=" O TRP k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE k 89 " --> pdb=" O ALA k 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 97 through 118 removed outlier: 3.671A pdb=" N GLU k 101 " --> pdb=" O SER k 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS k 102 " --> pdb=" O PRO k 98 " (cutoff:3.500A) Processing helix chain 'k' and resid 135 through 140 Processing helix chain 'k' and resid 162 through 171 removed outlier: 4.177A pdb=" N ASP k 166 " --> pdb=" O HIS k 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE k 167 " --> pdb=" O GLN k 163 " (cutoff:3.500A) Processing helix chain 'l' and resid 172 through 177 Processing helix chain 'l' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU l 205 " --> pdb=" O GLU l 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL l 210 " --> pdb=" O TRP l 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA l 212 " --> pdb=" O ARG l 208 " (cutoff:3.500A) Processing helix chain 'l' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU l 228 " --> pdb=" O ASN l 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN l 229 " --> pdb=" O GLU l 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS l 230 " --> pdb=" O ASN l 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER l 233 " --> pdb=" O ASN l 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR l 238 " --> pdb=" O ILE l 234 " (cutoff:3.500A) Processing helix chain 'l' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU l 273 " --> pdb=" O LYS l 269 " (cutoff:3.500A) Processing helix chain 'l' and resid 295 through 308 Processing helix chain 'l' and resid 332 through 351 removed outlier: 3.711A pdb=" N ARG l 340 " --> pdb=" O ILE l 336 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN l 341 " --> pdb=" O LEU l 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER l 345 " --> pdb=" O GLN l 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR l 349 " --> pdb=" O SER l 345 " (cutoff:3.500A) Processing helix chain 'm' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU m 34 " --> pdb=" O GLU m 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE m 36 " --> pdb=" O ALA m 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA m 37 " --> pdb=" O ASN m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 41 through 43 No H-bonds generated for 'chain 'm' and resid 41 through 43' Processing helix chain 'm' and resid 52 through 54 No H-bonds generated for 'chain 'm' and resid 52 through 54' Processing helix chain 'm' and resid 61 through 63 No H-bonds generated for 'chain 'm' and resid 61 through 63' Processing helix chain 'm' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR m 70 " --> pdb=" O THR m 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR m 75 " --> pdb=" O TRP m 71 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 89 removed outlier: 3.533A pdb=" N PHE m 89 " --> pdb=" O ALA m 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 97 through 118 removed outlier: 3.673A pdb=" N GLU m 101 " --> pdb=" O SER m 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS m 102 " --> pdb=" O PRO m 98 " (cutoff:3.500A) Processing helix chain 'm' and resid 135 through 140 Processing helix chain 'm' and resid 163 through 171 removed outlier: 3.575A pdb=" N ILE m 167 " --> pdb=" O GLN m 163 " (cutoff:3.500A) Processing helix chain 'n' and resid 172 through 177 Processing helix chain 'n' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU n 205 " --> pdb=" O GLU n 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL n 210 " --> pdb=" O TRP n 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA n 212 " --> pdb=" O ARG n 208 " (cutoff:3.500A) Processing helix chain 'n' and resid 224 through 240 removed outlier: 3.534A pdb=" N GLU n 228 " --> pdb=" O ASN n 224 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN n 229 " --> pdb=" O GLU n 225 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS n 230 " --> pdb=" O ASN n 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER n 233 " --> pdb=" O ASN n 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR n 238 " --> pdb=" O ILE n 234 " (cutoff:3.500A) Processing helix chain 'n' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU n 273 " --> pdb=" O LYS n 269 " (cutoff:3.500A) Processing helix chain 'n' and resid 295 through 308 Processing helix chain 'n' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG n 340 " --> pdb=" O ILE n 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN n 341 " --> pdb=" O LEU n 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER n 345 " --> pdb=" O GLN n 341 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR n 349 " --> pdb=" O SER n 345 " (cutoff:3.500A) Processing helix chain 'o' and resid 28 through 40 removed outlier: 3.665A pdb=" N GLU o 34 " --> pdb=" O GLU o 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE o 36 " --> pdb=" O ALA o 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA o 37 " --> pdb=" O ASN o 33 " (cutoff:3.500A) Processing helix chain 'o' and resid 41 through 43 No H-bonds generated for 'chain 'o' and resid 41 through 43' Processing helix chain 'o' and resid 52 through 54 No H-bonds generated for 'chain 'o' and resid 52 through 54' Processing helix chain 'o' and resid 61 through 63 No H-bonds generated for 'chain 'o' and resid 61 through 63' Processing helix chain 'o' and resid 64 through 76 removed outlier: 3.571A pdb=" N TYR o 70 " --> pdb=" O THR o 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS o 73 " --> pdb=" O VAL o 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR o 75 " --> pdb=" O TRP o 71 " (cutoff:3.500A) Processing helix chain 'o' and resid 84 through 89 removed outlier: 3.534A pdb=" N PHE o 89 " --> pdb=" O ALA o 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU o 101 " --> pdb=" O SER o 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS o 102 " --> pdb=" O PRO o 98 " (cutoff:3.500A) Processing helix chain 'o' and resid 135 through 140 Processing helix chain 'o' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP o 166 " --> pdb=" O HIS o 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE o 167 " --> pdb=" O GLN o 163 " (cutoff:3.500A) Processing helix chain 'p' and resid 172 through 177 Processing helix chain 'p' and resid 200 through 214 removed outlier: 3.821A pdb=" N LEU p 205 " --> pdb=" O GLU p 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL p 210 " --> pdb=" O TRP p 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA p 212 " --> pdb=" O ARG p 208 " (cutoff:3.500A) Processing helix chain 'p' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU p 228 " --> pdb=" O ASN p 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN p 229 " --> pdb=" O GLU p 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS p 230 " --> pdb=" O ASN p 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER p 233 " --> pdb=" O ASN p 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR p 238 " --> pdb=" O ILE p 234 " (cutoff:3.500A) Processing helix chain 'p' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU p 273 " --> pdb=" O LYS p 269 " (cutoff:3.500A) Processing helix chain 'p' and resid 295 through 308 Processing helix chain 'p' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG p 340 " --> pdb=" O ILE p 336 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN p 341 " --> pdb=" O LEU p 337 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER p 345 " --> pdb=" O GLN p 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR p 349 " --> pdb=" O SER p 345 " (cutoff:3.500A) Processing helix chain 'q' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU q 34 " --> pdb=" O GLU q 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE q 36 " --> pdb=" O ALA q 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA q 37 " --> pdb=" O ASN q 33 " (cutoff:3.500A) Processing helix chain 'q' and resid 41 through 43 No H-bonds generated for 'chain 'q' and resid 41 through 43' Processing helix chain 'q' and resid 52 through 54 No H-bonds generated for 'chain 'q' and resid 52 through 54' Processing helix chain 'q' and resid 61 through 63 No H-bonds generated for 'chain 'q' and resid 61 through 63' Processing helix chain 'q' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR q 70 " --> pdb=" O THR q 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS q 73 " --> pdb=" O VAL q 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR q 75 " --> pdb=" O TRP q 71 " (cutoff:3.500A) Processing helix chain 'q' and resid 84 through 89 removed outlier: 3.534A pdb=" N PHE q 89 " --> pdb=" O ALA q 86 " (cutoff:3.500A) Processing helix chain 'q' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU q 101 " --> pdb=" O SER q 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS q 102 " --> pdb=" O PRO q 98 " (cutoff:3.500A) Processing helix chain 'q' and resid 135 through 140 Processing helix chain 'q' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP q 166 " --> pdb=" O HIS q 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE q 167 " --> pdb=" O GLN q 163 " (cutoff:3.500A) Processing helix chain 'r' and resid 172 through 177 Processing helix chain 'r' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU r 205 " --> pdb=" O GLU r 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL r 210 " --> pdb=" O TRP r 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA r 212 " --> pdb=" O ARG r 208 " (cutoff:3.500A) Processing helix chain 'r' and resid 224 through 240 removed outlier: 3.536A pdb=" N GLU r 228 " --> pdb=" O ASN r 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN r 229 " --> pdb=" O GLU r 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS r 230 " --> pdb=" O ASN r 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER r 233 " --> pdb=" O ASN r 229 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N THR r 238 " --> pdb=" O ILE r 234 " (cutoff:3.500A) Processing helix chain 'r' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU r 273 " --> pdb=" O LYS r 269 " (cutoff:3.500A) Processing helix chain 'r' and resid 295 through 308 Processing helix chain 'r' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG r 340 " --> pdb=" O ILE r 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN r 341 " --> pdb=" O LEU r 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER r 345 " --> pdb=" O GLN r 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR r 349 " --> pdb=" O SER r 345 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 40 removed outlier: 3.666A pdb=" N GLU s 34 " --> pdb=" O GLU s 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE s 36 " --> pdb=" O ALA s 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA s 37 " --> pdb=" O ASN s 33 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 43 No H-bonds generated for 'chain 's' and resid 41 through 43' Processing helix chain 's' and resid 52 through 54 No H-bonds generated for 'chain 's' and resid 52 through 54' Processing helix chain 's' and resid 61 through 63 No H-bonds generated for 'chain 's' and resid 61 through 63' Processing helix chain 's' and resid 64 through 76 removed outlier: 3.572A pdb=" N TYR s 70 " --> pdb=" O THR s 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS s 73 " --> pdb=" O VAL s 69 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR s 75 " --> pdb=" O TRP s 71 " (cutoff:3.500A) Processing helix chain 's' and resid 84 through 89 removed outlier: 3.534A pdb=" N PHE s 89 " --> pdb=" O ALA s 86 " (cutoff:3.500A) Processing helix chain 's' and resid 97 through 118 removed outlier: 3.672A pdb=" N GLU s 101 " --> pdb=" O SER s 97 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS s 102 " --> pdb=" O PRO s 98 " (cutoff:3.500A) Processing helix chain 's' and resid 135 through 140 Processing helix chain 's' and resid 162 through 171 removed outlier: 4.178A pdb=" N ASP s 166 " --> pdb=" O HIS s 162 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE s 167 " --> pdb=" O GLN s 163 " (cutoff:3.500A) Processing helix chain 't' and resid 172 through 177 Processing helix chain 't' and resid 200 through 214 removed outlier: 3.820A pdb=" N LEU t 205 " --> pdb=" O GLU t 201 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL t 210 " --> pdb=" O TRP t 206 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA t 212 " --> pdb=" O ARG t 208 " (cutoff:3.500A) Processing helix chain 't' and resid 224 through 240 removed outlier: 3.535A pdb=" N GLU t 228 " --> pdb=" O ASN t 224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN t 229 " --> pdb=" O GLU t 225 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS t 230 " --> pdb=" O ASN t 226 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER t 233 " --> pdb=" O ASN t 229 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR t 238 " --> pdb=" O ILE t 234 " (cutoff:3.500A) Processing helix chain 't' and resid 268 through 279 removed outlier: 3.634A pdb=" N GLU t 273 " --> pdb=" O LYS t 269 " (cutoff:3.500A) Processing helix chain 't' and resid 295 through 308 Processing helix chain 't' and resid 332 through 351 removed outlier: 3.712A pdb=" N ARG t 340 " --> pdb=" O ILE t 336 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN t 341 " --> pdb=" O LEU t 337 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER t 345 " --> pdb=" O GLN t 341 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR t 349 " --> pdb=" O SER t 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU A 23 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 60 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS A 25 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 58 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 59 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 130 removed outlier: 3.845A pdb=" N SER A 125 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA A 152 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 188 removed outlier: 6.712A pdb=" N LEU B 194 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE B 223 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL B 196 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR B 245 " --> pdb=" O SER B 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER B 261 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG B 247 " --> pdb=" O TRP B 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE B 258 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET B 294 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU B 260 " --> pdb=" O MET B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL B 326 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B 322 " --> pdb=" O HIS B 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU C 23 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL C 60 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS C 25 " --> pdb=" O ILE C 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE C 58 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 59 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER C 125 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 152 " --> pdb=" O VAL C 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU D 194 " --> pdb=" O ARG D 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE D 223 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL D 196 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR D 245 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER D 261 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG D 247 " --> pdb=" O TRP D 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE D 258 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET D 294 " --> pdb=" O PHE D 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU D 260 " --> pdb=" O MET D 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL D 326 " --> pdb=" O SER D 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY D 322 " --> pdb=" O HIS D 319 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU E 23 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL E 60 " --> pdb=" O LEU E 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS E 25 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE E 58 " --> pdb=" O LYS E 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR E 59 " --> pdb=" O ASN E 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER E 125 " --> pdb=" O VAL E 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA E 152 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU F 194 " --> pdb=" O ARG F 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE F 223 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL F 196 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR F 245 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER F 261 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG F 247 " --> pdb=" O TRP F 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE F 258 " --> pdb=" O THR F 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET F 294 " --> pdb=" O PHE F 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU F 260 " --> pdb=" O MET F 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL F 326 " --> pdb=" O SER F 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY F 322 " --> pdb=" O HIS F 319 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU G 23 " --> pdb=" O VAL G 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL G 60 " --> pdb=" O LEU G 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS G 25 " --> pdb=" O ILE G 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE G 58 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR G 59 " --> pdb=" O ASN G 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER G 125 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA G 152 " --> pdb=" O VAL G 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU H 194 " --> pdb=" O ARG H 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE H 223 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL H 196 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR H 245 " --> pdb=" O SER H 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER H 261 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG H 247 " --> pdb=" O TRP H 259 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE H 258 " --> pdb=" O THR H 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET H 294 " --> pdb=" O PHE H 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU H 260 " --> pdb=" O MET H 294 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL H 326 " --> pdb=" O SER H 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY H 322 " --> pdb=" O HIS H 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU I 23 " --> pdb=" O VAL I 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL I 60 " --> pdb=" O LEU I 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS I 25 " --> pdb=" O ILE I 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE I 58 " --> pdb=" O LYS I 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR I 59 " --> pdb=" O ASN I 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER I 125 " --> pdb=" O VAL I 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA I 152 " --> pdb=" O VAL I 186 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU J 194 " --> pdb=" O ARG J 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE J 223 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL J 196 " --> pdb=" O ILE J 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR J 245 " --> pdb=" O SER J 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER J 261 " --> pdb=" O TYR J 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG J 247 " --> pdb=" O TRP J 259 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE J 258 " --> pdb=" O THR J 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET J 294 " --> pdb=" O PHE J 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU J 260 " --> pdb=" O MET J 294 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL J 326 " --> pdb=" O SER J 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY J 322 " --> pdb=" O HIS J 319 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU K 23 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL K 60 " --> pdb=" O LEU K 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS K 25 " --> pdb=" O ILE K 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE K 58 " --> pdb=" O LYS K 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR K 59 " --> pdb=" O ASN K 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER K 125 " --> pdb=" O VAL K 153 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA K 152 " --> pdb=" O VAL K 186 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU L 194 " --> pdb=" O ARG L 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE L 223 " --> pdb=" O LEU L 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL L 196 " --> pdb=" O ILE L 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR L 245 " --> pdb=" O SER L 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER L 261 " --> pdb=" O TYR L 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG L 247 " --> pdb=" O TRP L 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE L 258 " --> pdb=" O THR L 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET L 294 " --> pdb=" O PHE L 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU L 260 " --> pdb=" O MET L 294 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL L 326 " --> pdb=" O SER L 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY L 322 " --> pdb=" O HIS L 319 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 21 through 27 removed outlier: 6.670A pdb=" N LEU M 23 " --> pdb=" O VAL M 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL M 60 " --> pdb=" O LEU M 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS M 25 " --> pdb=" O ILE M 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE M 58 " --> pdb=" O LYS M 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR M 59 " --> pdb=" O ASN M 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 125 through 130 removed outlier: 3.845A pdb=" N SER M 125 " --> pdb=" O VAL M 153 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA M 152 " --> pdb=" O VAL M 186 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU N 194 " --> pdb=" O ARG N 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE N 223 " --> pdb=" O LEU N 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL N 196 " --> pdb=" O ILE N 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR N 245 " --> pdb=" O SER N 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER N 261 " --> pdb=" O TYR N 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG N 247 " --> pdb=" O TRP N 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE N 258 " --> pdb=" O THR N 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET N 294 " --> pdb=" O PHE N 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU N 260 " --> pdb=" O MET N 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL N 326 " --> pdb=" O SER N 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY N 322 " --> pdb=" O HIS N 319 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU O 23 " --> pdb=" O VAL O 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL O 60 " --> pdb=" O LEU O 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS O 25 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE O 58 " --> pdb=" O LYS O 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR O 59 " --> pdb=" O ASN O 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER O 125 " --> pdb=" O VAL O 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA O 152 " --> pdb=" O VAL O 186 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU P 194 " --> pdb=" O ARG P 221 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE P 223 " --> pdb=" O LEU P 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL P 196 " --> pdb=" O ILE P 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR P 245 " --> pdb=" O SER P 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER P 261 " --> pdb=" O TYR P 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG P 247 " --> pdb=" O TRP P 259 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE P 258 " --> pdb=" O THR P 292 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET P 294 " --> pdb=" O PHE P 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU P 260 " --> pdb=" O MET P 294 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL P 326 " --> pdb=" O SER P 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY P 322 " --> pdb=" O HIS P 319 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU Q 23 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL Q 60 " --> pdb=" O LEU Q 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS Q 25 " --> pdb=" O ILE Q 58 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE Q 58 " --> pdb=" O LYS Q 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR Q 59 " --> pdb=" O ASN Q 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER Q 125 " --> pdb=" O VAL Q 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA Q 152 " --> pdb=" O VAL Q 186 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU R 194 " --> pdb=" O ARG R 221 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE R 223 " --> pdb=" O LEU R 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL R 196 " --> pdb=" O ILE R 223 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR R 245 " --> pdb=" O SER R 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER R 261 " --> pdb=" O TYR R 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG R 247 " --> pdb=" O TRP R 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE R 258 " --> pdb=" O THR R 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET R 294 " --> pdb=" O PHE R 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU R 260 " --> pdb=" O MET R 294 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL R 326 " --> pdb=" O SER R 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY R 322 " --> pdb=" O HIS R 319 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU S 23 " --> pdb=" O VAL S 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL S 60 " --> pdb=" O LEU S 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS S 25 " --> pdb=" O ILE S 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE S 58 " --> pdb=" O LYS S 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR S 59 " --> pdb=" O ASN S 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S' and resid 125 through 130 removed outlier: 3.845A pdb=" N SER S 125 " --> pdb=" O VAL S 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA S 152 " --> pdb=" O VAL S 186 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU T 194 " --> pdb=" O ARG T 221 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE T 223 " --> pdb=" O LEU T 194 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL T 196 " --> pdb=" O ILE T 223 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR T 245 " --> pdb=" O SER T 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER T 261 " --> pdb=" O TYR T 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG T 247 " --> pdb=" O TRP T 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE T 258 " --> pdb=" O THR T 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET T 294 " --> pdb=" O PHE T 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU T 260 " --> pdb=" O MET T 294 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 315 through 319 removed outlier: 3.829A pdb=" N VAL T 326 " --> pdb=" O SER T 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY T 322 " --> pdb=" O HIS T 319 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU U 23 " --> pdb=" O VAL U 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL U 60 " --> pdb=" O LEU U 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS U 25 " --> pdb=" O ILE U 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE U 58 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR U 59 " --> pdb=" O ASN U 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 125 through 130 removed outlier: 3.843A pdb=" N SER U 125 " --> pdb=" O VAL U 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA U 152 " --> pdb=" O VAL U 186 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU V 194 " --> pdb=" O ARG V 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE V 223 " --> pdb=" O LEU V 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL V 196 " --> pdb=" O ILE V 223 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR V 245 " --> pdb=" O SER V 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER V 261 " --> pdb=" O TYR V 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG V 247 " --> pdb=" O TRP V 259 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE V 258 " --> pdb=" O THR V 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET V 294 " --> pdb=" O PHE V 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU V 260 " --> pdb=" O MET V 294 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL V 326 " --> pdb=" O SER V 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY V 322 " --> pdb=" O HIS V 319 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU W 23 " --> pdb=" O VAL W 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL W 60 " --> pdb=" O LEU W 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS W 25 " --> pdb=" O ILE W 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE W 58 " --> pdb=" O LYS W 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR W 59 " --> pdb=" O ASN W 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER W 125 " --> pdb=" O VAL W 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA W 152 " --> pdb=" O VAL W 186 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU X 194 " --> pdb=" O ARG X 221 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE X 223 " --> pdb=" O LEU X 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL X 196 " --> pdb=" O ILE X 223 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 245 through 249 removed outlier: 6.533A pdb=" N TYR X 245 " --> pdb=" O SER X 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER X 261 " --> pdb=" O TYR X 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG X 247 " --> pdb=" O TRP X 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE X 258 " --> pdb=" O THR X 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET X 294 " --> pdb=" O PHE X 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU X 260 " --> pdb=" O MET X 294 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL X 326 " --> pdb=" O SER X 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY X 322 " --> pdb=" O HIS X 319 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 21 through 27 removed outlier: 6.670A pdb=" N LEU Y 23 " --> pdb=" O VAL Y 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL Y 60 " --> pdb=" O LEU Y 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS Y 25 " --> pdb=" O ILE Y 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE Y 58 " --> pdb=" O LYS Y 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR Y 59 " --> pdb=" O ASN Y 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER Y 125 " --> pdb=" O VAL Y 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA Y 152 " --> pdb=" O VAL Y 186 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU Z 194 " --> pdb=" O ARG Z 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE Z 223 " --> pdb=" O LEU Z 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL Z 196 " --> pdb=" O ILE Z 223 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 245 through 249 removed outlier: 6.533A pdb=" N TYR Z 245 " --> pdb=" O SER Z 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER Z 261 " --> pdb=" O TYR Z 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG Z 247 " --> pdb=" O TRP Z 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE Z 258 " --> pdb=" O THR Z 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET Z 294 " --> pdb=" O PHE Z 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU Z 260 " --> pdb=" O MET Z 294 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL Z 326 " --> pdb=" O SER Z 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY Z 322 " --> pdb=" O HIS Z 319 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU a 23 " --> pdb=" O VAL a 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL a 60 " --> pdb=" O LEU a 23 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS a 25 " --> pdb=" O ILE a 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE a 58 " --> pdb=" O LYS a 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR a 59 " --> pdb=" O ASN a 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER a 125 " --> pdb=" O VAL a 153 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA a 152 " --> pdb=" O VAL a 186 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU b 194 " --> pdb=" O ARG b 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE b 223 " --> pdb=" O LEU b 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL b 196 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 245 through 249 removed outlier: 6.533A pdb=" N TYR b 245 " --> pdb=" O SER b 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER b 261 " --> pdb=" O TYR b 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG b 247 " --> pdb=" O TRP b 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE b 258 " --> pdb=" O THR b 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET b 294 " --> pdb=" O PHE b 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU b 260 " --> pdb=" O MET b 294 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL b 326 " --> pdb=" O SER b 315 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY b 322 " --> pdb=" O HIS b 319 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'c' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU c 23 " --> pdb=" O VAL c 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL c 60 " --> pdb=" O LEU c 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS c 25 " --> pdb=" O ILE c 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE c 58 " --> pdb=" O LYS c 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR c 59 " --> pdb=" O ASN c 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'c' and resid 125 through 130 removed outlier: 3.845A pdb=" N SER c 125 " --> pdb=" O VAL c 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA c 152 " --> pdb=" O VAL c 186 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'd' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU d 194 " --> pdb=" O ARG d 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE d 223 " --> pdb=" O LEU d 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL d 196 " --> pdb=" O ILE d 223 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'd' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR d 245 " --> pdb=" O SER d 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER d 261 " --> pdb=" O TYR d 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG d 247 " --> pdb=" O TRP d 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE d 258 " --> pdb=" O THR d 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET d 294 " --> pdb=" O PHE d 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU d 260 " --> pdb=" O MET d 294 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'd' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL d 326 " --> pdb=" O SER d 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY d 322 " --> pdb=" O HIS d 319 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'e' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU e 23 " --> pdb=" O VAL e 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL e 60 " --> pdb=" O LEU e 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS e 25 " --> pdb=" O ILE e 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE e 58 " --> pdb=" O LYS e 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR e 59 " --> pdb=" O ASN e 47 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'e' and resid 125 through 130 removed outlier: 3.843A pdb=" N SER e 125 " --> pdb=" O VAL e 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA e 152 " --> pdb=" O VAL e 186 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'f' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU f 194 " --> pdb=" O ARG f 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE f 223 " --> pdb=" O LEU f 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL f 196 " --> pdb=" O ILE f 223 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'f' and resid 245 through 249 removed outlier: 6.533A pdb=" N TYR f 245 " --> pdb=" O SER f 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER f 261 " --> pdb=" O TYR f 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG f 247 " --> pdb=" O TRP f 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE f 258 " --> pdb=" O THR f 292 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET f 294 " --> pdb=" O PHE f 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU f 260 " --> pdb=" O MET f 294 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'f' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL f 326 " --> pdb=" O SER f 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY f 322 " --> pdb=" O HIS f 319 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'g' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU g 23 " --> pdb=" O VAL g 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL g 60 " --> pdb=" O LEU g 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS g 25 " --> pdb=" O ILE g 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE g 58 " --> pdb=" O LYS g 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR g 59 " --> pdb=" O ASN g 47 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'g' and resid 125 through 130 removed outlier: 3.845A pdb=" N SER g 125 " --> pdb=" O VAL g 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA g 152 " --> pdb=" O VAL g 186 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'h' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU h 194 " --> pdb=" O ARG h 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE h 223 " --> pdb=" O LEU h 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL h 196 " --> pdb=" O ILE h 223 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'h' and resid 245 through 249 removed outlier: 6.533A pdb=" N TYR h 245 " --> pdb=" O SER h 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER h 261 " --> pdb=" O TYR h 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG h 247 " --> pdb=" O TRP h 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE h 258 " --> pdb=" O THR h 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET h 294 " --> pdb=" O PHE h 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU h 260 " --> pdb=" O MET h 294 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL h 326 " --> pdb=" O SER h 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY h 322 " --> pdb=" O HIS h 319 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'i' and resid 21 through 27 removed outlier: 6.670A pdb=" N LEU i 23 " --> pdb=" O VAL i 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL i 60 " --> pdb=" O LEU i 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS i 25 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE i 58 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR i 59 " --> pdb=" O ASN i 47 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'i' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER i 125 " --> pdb=" O VAL i 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA i 152 " --> pdb=" O VAL i 186 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'j' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU j 194 " --> pdb=" O ARG j 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE j 223 " --> pdb=" O LEU j 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL j 196 " --> pdb=" O ILE j 223 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'j' and resid 245 through 249 removed outlier: 6.535A pdb=" N TYR j 245 " --> pdb=" O SER j 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER j 261 " --> pdb=" O TYR j 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG j 247 " --> pdb=" O TRP j 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE j 258 " --> pdb=" O THR j 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET j 294 " --> pdb=" O PHE j 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU j 260 " --> pdb=" O MET j 294 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'j' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL j 326 " --> pdb=" O SER j 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY j 322 " --> pdb=" O HIS j 319 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'k' and resid 21 through 27 removed outlier: 6.670A pdb=" N LEU k 23 " --> pdb=" O VAL k 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL k 60 " --> pdb=" O LEU k 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS k 25 " --> pdb=" O ILE k 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE k 58 " --> pdb=" O LYS k 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR k 59 " --> pdb=" O ASN k 47 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'k' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER k 125 " --> pdb=" O VAL k 153 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA k 152 " --> pdb=" O VAL k 186 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'l' and resid 186 through 188 removed outlier: 6.714A pdb=" N LEU l 194 " --> pdb=" O ARG l 221 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE l 223 " --> pdb=" O LEU l 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL l 196 " --> pdb=" O ILE l 223 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'l' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR l 245 " --> pdb=" O SER l 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER l 261 " --> pdb=" O TYR l 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG l 247 " --> pdb=" O TRP l 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE l 258 " --> pdb=" O THR l 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET l 294 " --> pdb=" O PHE l 258 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU l 260 " --> pdb=" O MET l 294 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'l' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL l 326 " --> pdb=" O SER l 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY l 322 " --> pdb=" O HIS l 319 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'm' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU m 23 " --> pdb=" O VAL m 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL m 60 " --> pdb=" O LEU m 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS m 25 " --> pdb=" O ILE m 58 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE m 58 " --> pdb=" O LYS m 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR m 59 " --> pdb=" O ASN m 47 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'm' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER m 125 " --> pdb=" O VAL m 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA m 152 " --> pdb=" O VAL m 186 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'n' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU n 194 " --> pdb=" O ARG n 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE n 223 " --> pdb=" O LEU n 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL n 196 " --> pdb=" O ILE n 223 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'n' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR n 245 " --> pdb=" O SER n 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER n 261 " --> pdb=" O TYR n 245 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG n 247 " --> pdb=" O TRP n 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE n 258 " --> pdb=" O THR n 292 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET n 294 " --> pdb=" O PHE n 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU n 260 " --> pdb=" O MET n 294 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'n' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL n 326 " --> pdb=" O SER n 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY n 322 " --> pdb=" O HIS n 319 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'o' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU o 23 " --> pdb=" O VAL o 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL o 60 " --> pdb=" O LEU o 23 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LYS o 25 " --> pdb=" O ILE o 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE o 58 " --> pdb=" O LYS o 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR o 59 " --> pdb=" O ASN o 47 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'o' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER o 125 " --> pdb=" O VAL o 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA o 152 " --> pdb=" O VAL o 186 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'p' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU p 194 " --> pdb=" O ARG p 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE p 223 " --> pdb=" O LEU p 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL p 196 " --> pdb=" O ILE p 223 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'p' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR p 245 " --> pdb=" O SER p 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER p 261 " --> pdb=" O TYR p 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG p 247 " --> pdb=" O TRP p 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE p 258 " --> pdb=" O THR p 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET p 294 " --> pdb=" O PHE p 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU p 260 " --> pdb=" O MET p 294 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'p' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL p 326 " --> pdb=" O SER p 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY p 322 " --> pdb=" O HIS p 319 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'q' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU q 23 " --> pdb=" O VAL q 60 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL q 60 " --> pdb=" O LEU q 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS q 25 " --> pdb=" O ILE q 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE q 58 " --> pdb=" O LYS q 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR q 59 " --> pdb=" O ASN q 47 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'q' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER q 125 " --> pdb=" O VAL q 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA q 152 " --> pdb=" O VAL q 186 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'r' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU r 194 " --> pdb=" O ARG r 221 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE r 223 " --> pdb=" O LEU r 194 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL r 196 " --> pdb=" O ILE r 223 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'r' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR r 245 " --> pdb=" O SER r 261 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N SER r 261 " --> pdb=" O TYR r 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG r 247 " --> pdb=" O TRP r 259 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE r 258 " --> pdb=" O THR r 292 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET r 294 " --> pdb=" O PHE r 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU r 260 " --> pdb=" O MET r 294 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'r' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL r 326 " --> pdb=" O SER r 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY r 322 " --> pdb=" O HIS r 319 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 's' and resid 21 through 27 removed outlier: 6.671A pdb=" N LEU s 23 " --> pdb=" O VAL s 60 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL s 60 " --> pdb=" O LEU s 23 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS s 25 " --> pdb=" O ILE s 58 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE s 58 " --> pdb=" O LYS s 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR s 59 " --> pdb=" O ASN s 47 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 's' and resid 125 through 130 removed outlier: 3.844A pdb=" N SER s 125 " --> pdb=" O VAL s 153 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA s 152 " --> pdb=" O VAL s 186 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 't' and resid 186 through 188 removed outlier: 6.713A pdb=" N LEU t 194 " --> pdb=" O ARG t 221 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ILE t 223 " --> pdb=" O LEU t 194 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL t 196 " --> pdb=" O ILE t 223 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 't' and resid 245 through 249 removed outlier: 6.534A pdb=" N TYR t 245 " --> pdb=" O SER t 261 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N SER t 261 " --> pdb=" O TYR t 245 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG t 247 " --> pdb=" O TRP t 259 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE t 258 " --> pdb=" O THR t 292 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N MET t 294 " --> pdb=" O PHE t 258 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU t 260 " --> pdb=" O MET t 294 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 't' and resid 315 through 319 removed outlier: 3.830A pdb=" N VAL t 326 " --> pdb=" O SER t 315 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY t 322 " --> pdb=" O HIS t 319 " (cutoff:3.500A) 2553 hydrogen bonds defined for protein. 7245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 25.86 Time building geometry restraints manager: 21.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23163 1.34 - 1.45: 9418 1.45 - 1.57: 38259 1.57 - 1.68: 69 1.68 - 1.80: 322 Bond restraints: 71231 Sorted by residual: bond pdb=" CB GLU h 360 " pdb=" CG GLU h 360 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.91e+00 bond pdb=" CB GLU X 360 " pdb=" CG GLU X 360 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.89e+00 bond pdb=" CB GLU l 360 " pdb=" CG GLU l 360 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CB GLU L 360 " pdb=" CG GLU L 360 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.88e+00 bond pdb=" CB GLU B 360 " pdb=" CG GLU B 360 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.88e+00 ... (remaining 71226 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.16: 1568 105.16 - 112.39: 34633 112.39 - 119.63: 25308 119.63 - 126.86: 34015 126.86 - 134.09: 915 Bond angle restraints: 96439 Sorted by residual: angle pdb=" CA GLU N 360 " pdb=" CB GLU N 360 " pdb=" CG GLU N 360 " ideal model delta sigma weight residual 114.10 129.32 -15.22 2.00e+00 2.50e-01 5.79e+01 angle pdb=" CA GLU H 360 " pdb=" CB GLU H 360 " pdb=" CG GLU H 360 " ideal model delta sigma weight residual 114.10 129.31 -15.21 2.00e+00 2.50e-01 5.79e+01 angle pdb=" CA GLU p 360 " pdb=" CB GLU p 360 " pdb=" CG GLU p 360 " ideal model delta sigma weight residual 114.10 129.31 -15.21 2.00e+00 2.50e-01 5.79e+01 angle pdb=" CA GLU f 360 " pdb=" CB GLU f 360 " pdb=" CG GLU f 360 " ideal model delta sigma weight residual 114.10 129.30 -15.20 2.00e+00 2.50e-01 5.78e+01 angle pdb=" CA GLU V 360 " pdb=" CB GLU V 360 " pdb=" CG GLU V 360 " ideal model delta sigma weight residual 114.10 129.30 -15.20 2.00e+00 2.50e-01 5.77e+01 ... (remaining 96434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.17: 37963 11.17 - 22.34: 4056 22.34 - 33.51: 1064 33.51 - 44.68: 410 44.68 - 55.85: 184 Dihedral angle restraints: 43677 sinusoidal: 18055 harmonic: 25622 Sorted by residual: dihedral pdb=" CA ASP n 215 " pdb=" C ASP n 215 " pdb=" N TYR n 216 " pdb=" CA TYR n 216 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ASP B 215 " pdb=" C ASP B 215 " pdb=" N TYR B 216 " pdb=" CA TYR B 216 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ASP F 215 " pdb=" C ASP F 215 " pdb=" N TYR F 216 " pdb=" CA TYR F 216 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 43674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 8989 0.086 - 0.172: 1350 0.172 - 0.258: 126 0.258 - 0.343: 0 0.343 - 0.429: 23 Chirality restraints: 10488 Sorted by residual: chirality pdb=" CB ILE l 359 " pdb=" CA ILE l 359 " pdb=" CG1 ILE l 359 " pdb=" CG2 ILE l 359 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CB ILE R 359 " pdb=" CA ILE R 359 " pdb=" CG1 ILE R 359 " pdb=" CG2 ILE R 359 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.60e+00 chirality pdb=" CB ILE D 359 " pdb=" CA ILE D 359 " pdb=" CG1 ILE D 359 " pdb=" CG2 ILE D 359 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 10485 not shown) Planarity restraints: 12696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 180 " 0.011 2.00e-02 2.50e+03 1.28e-02 3.27e+00 pdb=" CG TYR Q 180 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 180 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 180 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 180 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 180 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR Q 180 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR Q 180 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 180 " -0.011 2.00e-02 2.50e+03 1.27e-02 3.25e+00 pdb=" CG TYR G 180 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR G 180 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR G 180 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR G 180 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR G 180 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR G 180 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 180 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 180 " 0.011 2.00e-02 2.50e+03 1.27e-02 3.25e+00 pdb=" CG TYR a 180 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR a 180 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR a 180 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR a 180 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR a 180 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR a 180 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR a 180 " 0.002 2.00e-02 2.50e+03 ... (remaining 12693 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 14472 2.77 - 3.30: 63223 3.30 - 3.83: 113799 3.83 - 4.37: 138304 4.37 - 4.90: 235059 Nonbonded interactions: 564857 Sorted by model distance: nonbonded pdb=" OH TYR H 246 " pdb=" OD1 ASP H 296 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR Z 246 " pdb=" OD1 ASP Z 296 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR N 246 " pdb=" OD1 ASP N 296 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR l 246 " pdb=" OD1 ASP l 296 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR d 246 " pdb=" OD1 ASP d 296 " model vdw 2.233 2.440 ... (remaining 564852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 's' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'r' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 12.120 Check model and map are aligned: 0.800 Set scattering table: 0.510 Process input model: 135.070 Find NCS groups from input model: 4.060 Set up NCS constraints: 0.780 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.009 0.066 71231 Z= 0.604 Angle : 1.131 15.220 96439 Z= 0.600 Chirality : 0.063 0.429 10488 Planarity : 0.006 0.040 12696 Dihedral : 11.361 55.854 27117 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.40 % Allowed : 4.63 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -5.22 (0.07), residues: 8602 helix: -4.39 (0.04), residues: 3358 sheet: -2.84 (0.11), residues: 2162 loop : -2.35 (0.10), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP i 71 HIS 0.016 0.004 HIS a 147 PHE 0.023 0.003 PHE X 258 TYR 0.028 0.003 TYR Q 180 ARG 0.011 0.001 ARG m 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2381 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 2128 time to evaluate : 6.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8376 (mtpp) REVERT: A 40 GLN cc_start: 0.8580 (mt0) cc_final: 0.8292 (mt0) REVERT: A 44 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8093 (pt) REVERT: B 192 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7086 (pptt) REVERT: B 219 ASN cc_start: 0.8276 (m-40) cc_final: 0.8039 (m-40) REVERT: B 270 LYS cc_start: 0.9215 (ttpm) cc_final: 0.8944 (ttpp) REVERT: B 294 MET cc_start: 0.8501 (mmm) cc_final: 0.8269 (mmm) REVERT: B 362 LYS cc_start: 0.8272 (pttm) cc_final: 0.8041 (pttm) REVERT: C 25 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8276 (mtpp) REVERT: C 44 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8163 (pt) REVERT: C 76 GLN cc_start: 0.8174 (mt0) cc_final: 0.7925 (mt0) REVERT: D 192 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6946 (pptt) REVERT: D 219 ASN cc_start: 0.7925 (m-40) cc_final: 0.7578 (m-40) REVERT: D 270 LYS cc_start: 0.9260 (ttpm) cc_final: 0.9000 (ttpp) REVERT: E 25 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8022 (mtpp) REVERT: E 40 GLN cc_start: 0.8521 (mt0) cc_final: 0.8241 (mt0) REVERT: E 44 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8360 (pt) REVERT: E 156 ARG cc_start: 0.8299 (mmt180) cc_final: 0.8074 (mmt180) REVERT: F 192 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7209 (pptt) REVERT: F 213 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7762 (ttm170) REVERT: F 229 ASN cc_start: 0.9238 (t0) cc_final: 0.8856 (t0) REVERT: F 290 ASN cc_start: 0.7992 (t0) cc_final: 0.7712 (t0) REVERT: F 294 MET cc_start: 0.8337 (mmm) cc_final: 0.8076 (mmm) REVERT: F 345 SER cc_start: 0.9011 (t) cc_final: 0.8750 (p) REVERT: G 25 LYS cc_start: 0.8331 (mtpt) cc_final: 0.8059 (mtpp) REVERT: G 43 ASN cc_start: 0.8906 (t0) cc_final: 0.8554 (t0) REVERT: G 44 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8234 (pt) REVERT: G 76 GLN cc_start: 0.8062 (mt0) cc_final: 0.7764 (mt0) REVERT: G 163 GLN cc_start: 0.7993 (mp10) cc_final: 0.7649 (mp10) REVERT: H 181 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7705 (mppt) REVERT: H 192 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7048 (pptt) REVERT: H 219 ASN cc_start: 0.8207 (m-40) cc_final: 0.7859 (m110) REVERT: H 345 SER cc_start: 0.8978 (t) cc_final: 0.8727 (p) REVERT: I 44 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8065 (pt) REVERT: I 163 GLN cc_start: 0.8143 (mp10) cc_final: 0.7750 (mp10) REVERT: J 192 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6784 (pptt) REVERT: J 213 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7692 (ttm170) REVERT: J 219 ASN cc_start: 0.8170 (m-40) cc_final: 0.7805 (m-40) REVERT: J 342 PHE cc_start: 0.8874 (t80) cc_final: 0.8604 (t80) REVERT: J 345 SER cc_start: 0.8940 (t) cc_final: 0.8734 (p) REVERT: K 44 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8238 (pt) REVERT: K 99 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7889 (mtp85) REVERT: L 345 SER cc_start: 0.8799 (t) cc_final: 0.8568 (p) REVERT: M 44 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8190 (pt) REVERT: M 64 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.7109 (m-30) REVERT: M 76 GLN cc_start: 0.7712 (mt0) cc_final: 0.7203 (mt0) REVERT: M 144 LYS cc_start: 0.8640 (mttm) cc_final: 0.8220 (mmmt) REVERT: N 345 SER cc_start: 0.8978 (t) cc_final: 0.8716 (p) REVERT: O 40 GLN cc_start: 0.8434 (mt0) cc_final: 0.8160 (mt0) REVERT: O 44 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8183 (pt) REVERT: O 76 GLN cc_start: 0.8177 (mt0) cc_final: 0.7828 (mt0) REVERT: O 101 GLU cc_start: 0.8164 (mp0) cc_final: 0.7841 (mp0) REVERT: O 163 GLN cc_start: 0.8007 (mp10) cc_final: 0.7569 (mp10) REVERT: P 345 SER cc_start: 0.9008 (t) cc_final: 0.8743 (p) REVERT: Q 24 LEU cc_start: 0.9079 (mt) cc_final: 0.8833 (mt) REVERT: Q 43 ASN cc_start: 0.9023 (t0) cc_final: 0.8803 (t0) REVERT: Q 44 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8396 (pt) REVERT: Q 59 THR cc_start: 0.8856 (p) cc_final: 0.8638 (p) REVERT: R 192 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6815 (pptt) REVERT: R 219 ASN cc_start: 0.8086 (m-40) cc_final: 0.7837 (m110) REVERT: R 229 ASN cc_start: 0.9171 (t0) cc_final: 0.8839 (t0) REVERT: R 242 GLN cc_start: 0.7622 (mt0) cc_final: 0.7364 (mt0) REVERT: S 30 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: S 44 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8468 (pt) REVERT: T 192 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6774 (pptt) REVERT: T 219 ASN cc_start: 0.8080 (m-40) cc_final: 0.7389 (m-40) REVERT: T 242 GLN cc_start: 0.7883 (mt0) cc_final: 0.7577 (mt0) REVERT: T 345 SER cc_start: 0.8858 (t) cc_final: 0.8608 (p) REVERT: U 43 ASN cc_start: 0.8826 (t0) cc_final: 0.8459 (t0) REVERT: U 44 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8542 (pt) REVERT: U 101 GLU cc_start: 0.8481 (mp0) cc_final: 0.7910 (mp0) REVERT: V 192 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6661 (pptt) REVERT: V 219 ASN cc_start: 0.8198 (m-40) cc_final: 0.7800 (m-40) REVERT: V 242 GLN cc_start: 0.7896 (mt0) cc_final: 0.7425 (mt0) REVERT: V 345 SER cc_start: 0.8814 (t) cc_final: 0.8558 (p) REVERT: W 44 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8377 (pt) REVERT: W 101 GLU cc_start: 0.8447 (mp0) cc_final: 0.8053 (mp0) REVERT: X 192 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6784 (ptmt) REVERT: X 341 GLN cc_start: 0.8547 (mt0) cc_final: 0.8216 (mt0) REVERT: X 345 SER cc_start: 0.8914 (t) cc_final: 0.8571 (p) REVERT: X 362 LYS cc_start: 0.8720 (pttm) cc_final: 0.8310 (pttm) REVERT: Y 25 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7910 (mtpp) REVERT: Y 44 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8236 (pt) REVERT: Y 59 THR cc_start: 0.8787 (p) cc_final: 0.8573 (p) REVERT: Y 101 GLU cc_start: 0.8385 (mp0) cc_final: 0.7830 (mp0) REVERT: Z 242 GLN cc_start: 0.7901 (mt0) cc_final: 0.7448 (pt0) REVERT: Z 336 ILE cc_start: 0.8877 (tt) cc_final: 0.8674 (tt) REVERT: Z 342 PHE cc_start: 0.8853 (t80) cc_final: 0.8587 (t80) REVERT: Z 345 SER cc_start: 0.8918 (t) cc_final: 0.8599 (p) REVERT: a 40 GLN cc_start: 0.8600 (mt0) cc_final: 0.8338 (mt0) REVERT: a 44 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8103 (pt) REVERT: a 59 THR cc_start: 0.8677 (p) cc_final: 0.8347 (p) REVERT: b 192 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6787 (pptt) REVERT: b 242 GLN cc_start: 0.7972 (mt0) cc_final: 0.7536 (mt0) REVERT: b 270 LYS cc_start: 0.9157 (ttpm) cc_final: 0.8841 (ttpp) REVERT: b 345 SER cc_start: 0.9019 (t) cc_final: 0.8719 (p) REVERT: c 30 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7305 (tp30) REVERT: c 40 GLN cc_start: 0.8755 (mt0) cc_final: 0.8381 (mt0) REVERT: c 44 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8297 (pt) REVERT: c 99 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7610 (mtp85) REVERT: c 101 GLU cc_start: 0.8530 (mp0) cc_final: 0.8306 (mp0) REVERT: c 163 GLN cc_start: 0.8043 (mp10) cc_final: 0.7753 (mp10) REVERT: d 192 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6820 (ptmt) REVERT: d 242 GLN cc_start: 0.7909 (mt0) cc_final: 0.7567 (pt0) REVERT: d 345 SER cc_start: 0.9108 (t) cc_final: 0.8787 (p) REVERT: d 362 LYS cc_start: 0.8447 (pttm) cc_final: 0.8185 (pttm) REVERT: e 40 GLN cc_start: 0.8636 (mt0) cc_final: 0.8281 (mt0) REVERT: e 44 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8578 (pt) REVERT: e 101 GLU cc_start: 0.8482 (mp0) cc_final: 0.8211 (mp0) REVERT: f 192 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6647 (pptt) REVERT: f 242 GLN cc_start: 0.7807 (mt0) cc_final: 0.7486 (mt0) REVERT: f 341 GLN cc_start: 0.8637 (mt0) cc_final: 0.8278 (mt0) REVERT: f 345 SER cc_start: 0.8871 (t) cc_final: 0.8562 (p) REVERT: f 362 LYS cc_start: 0.8625 (pttm) cc_final: 0.8354 (pttm) REVERT: g 44 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8527 (pt) REVERT: g 101 GLU cc_start: 0.8308 (mp0) cc_final: 0.7554 (mp0) REVERT: g 156 ARG cc_start: 0.8361 (mmt180) cc_final: 0.8114 (mmt180) REVERT: g 189 GLU cc_start: 0.8292 (pt0) cc_final: 0.8062 (pt0) REVERT: h 181 LYS cc_start: 0.7915 (mmtm) cc_final: 0.7582 (mmtm) REVERT: h 219 ASN cc_start: 0.8129 (m-40) cc_final: 0.7819 (m110) REVERT: h 242 GLN cc_start: 0.7961 (mt0) cc_final: 0.7530 (pt0) REVERT: h 336 ILE cc_start: 0.8862 (tt) cc_final: 0.8520 (tt) REVERT: h 345 SER cc_start: 0.8902 (t) cc_final: 0.8641 (p) REVERT: i 40 GLN cc_start: 0.8625 (mt0) cc_final: 0.8270 (mt0) REVERT: i 44 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8500 (pt) REVERT: j 192 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6622 (pptt) REVERT: j 195 TYR cc_start: 0.8410 (m-80) cc_final: 0.8010 (m-80) REVERT: j 345 SER cc_start: 0.8968 (t) cc_final: 0.8674 (p) REVERT: k 30 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: k 44 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8301 (pt) REVERT: k 99 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7701 (mtp85) REVERT: k 121 GLU cc_start: 0.7598 (tt0) cc_final: 0.7385 (tt0) REVERT: l 192 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6858 (pptt) REVERT: l 242 GLN cc_start: 0.7758 (mt0) cc_final: 0.7300 (pt0) REVERT: l 319 HIS cc_start: 0.7649 (m90) cc_final: 0.7431 (m-70) REVERT: l 345 SER cc_start: 0.8874 (t) cc_final: 0.8633 (p) REVERT: m 44 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8433 (pt) REVERT: m 59 THR cc_start: 0.8844 (p) cc_final: 0.8595 (p) REVERT: n 219 ASN cc_start: 0.8190 (m-40) cc_final: 0.7987 (m110) REVERT: n 242 GLN cc_start: 0.7714 (mt0) cc_final: 0.7455 (mt0) REVERT: n 270 LYS cc_start: 0.9160 (ttpm) cc_final: 0.8924 (ttpp) REVERT: n 342 PHE cc_start: 0.8927 (t80) cc_final: 0.8499 (t80) REVERT: n 345 SER cc_start: 0.8935 (t) cc_final: 0.8657 (p) REVERT: o 44 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8563 (pt) REVERT: p 192 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6774 (pptt) REVERT: p 213 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7546 (ttm170) REVERT: p 242 GLN cc_start: 0.7615 (mt0) cc_final: 0.7409 (mt0) REVERT: p 336 ILE cc_start: 0.8830 (tt) cc_final: 0.8569 (tt) REVERT: q 40 GLN cc_start: 0.8501 (mt0) cc_final: 0.8146 (mt0) REVERT: q 44 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8135 (pt) REVERT: q 163 GLN cc_start: 0.7965 (mp10) cc_final: 0.7670 (mp10) REVERT: q 172 LYS cc_start: 0.8539 (tttm) cc_final: 0.8301 (tttp) REVERT: r 192 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.7028 (pptt) REVERT: r 219 ASN cc_start: 0.8209 (m-40) cc_final: 0.7836 (m110) REVERT: r 242 GLN cc_start: 0.7511 (mt0) cc_final: 0.7271 (mt0) REVERT: r 345 SER cc_start: 0.8975 (t) cc_final: 0.8732 (p) REVERT: r 362 LYS cc_start: 0.8328 (pttm) cc_final: 0.7987 (pttm) REVERT: s 40 GLN cc_start: 0.8600 (mt0) cc_final: 0.8296 (mt0) REVERT: s 44 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8085 (pt) REVERT: s 76 GLN cc_start: 0.8236 (mt0) cc_final: 0.7927 (mt0) REVERT: t 192 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.7097 (pptt) REVERT: t 219 ASN cc_start: 0.7815 (m-40) cc_final: 0.7146 (m-40) REVERT: t 345 SER cc_start: 0.8956 (t) cc_final: 0.8725 (p) outliers start: 253 outliers final: 51 residues processed: 2276 average time/residue: 0.7341 time to fit residues: 2693.7446 Evaluate side-chains 1517 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1416 time to evaluate : 5.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 213 ARG Chi-restraints excluded: chain F residue 360 GLU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 192 LYS Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 360 GLU Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain J residue 192 LYS Chi-restraints excluded: chain J residue 213 ARG Chi-restraints excluded: chain J residue 360 GLU Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 99 ARG Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 224 ASN Chi-restraints excluded: chain L residue 360 GLU Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 64 ASP Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 217 ASP Chi-restraints excluded: chain N residue 360 GLU Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 217 ASP Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain Q residue 44 ILE Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 192 LYS Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 360 GLU Chi-restraints excluded: chain S residue 30 GLU Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain T residue 192 LYS Chi-restraints excluded: chain T residue 360 GLU Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain V residue 192 LYS Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 360 GLU Chi-restraints excluded: chain W residue 44 ILE Chi-restraints excluded: chain X residue 192 LYS Chi-restraints excluded: chain X residue 196 VAL Chi-restraints excluded: chain X residue 360 GLU Chi-restraints excluded: chain Y residue 44 ILE Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain b residue 192 LYS Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 360 GLU Chi-restraints excluded: chain c residue 30 GLU Chi-restraints excluded: chain c residue 44 ILE Chi-restraints excluded: chain c residue 99 ARG Chi-restraints excluded: chain d residue 192 LYS Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 360 GLU Chi-restraints excluded: chain e residue 44 ILE Chi-restraints excluded: chain f residue 192 LYS Chi-restraints excluded: chain f residue 196 VAL Chi-restraints excluded: chain f residue 224 ASN Chi-restraints excluded: chain f residue 360 GLU Chi-restraints excluded: chain g residue 44 ILE Chi-restraints excluded: chain g residue 186 VAL Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 360 GLU Chi-restraints excluded: chain i residue 44 ILE Chi-restraints excluded: chain j residue 192 LYS Chi-restraints excluded: chain j residue 360 GLU Chi-restraints excluded: chain k residue 30 GLU Chi-restraints excluded: chain k residue 44 ILE Chi-restraints excluded: chain k residue 99 ARG Chi-restraints excluded: chain l residue 192 LYS Chi-restraints excluded: chain l residue 196 VAL Chi-restraints excluded: chain l residue 360 GLU Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain n residue 360 GLU Chi-restraints excluded: chain o residue 44 ILE Chi-restraints excluded: chain p residue 192 LYS Chi-restraints excluded: chain p residue 196 VAL Chi-restraints excluded: chain p residue 213 ARG Chi-restraints excluded: chain p residue 360 GLU Chi-restraints excluded: chain q residue 44 ILE Chi-restraints excluded: chain r residue 192 LYS Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 360 GLU Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain s residue 186 VAL Chi-restraints excluded: chain t residue 192 LYS Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 360 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 718 optimal weight: 5.9990 chunk 645 optimal weight: 0.8980 chunk 357 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 435 optimal weight: 5.9990 chunk 344 optimal weight: 1.9990 chunk 667 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 405 optimal weight: 2.9990 chunk 496 optimal weight: 0.8980 chunk 772 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN B 265 ASN C 76 GLN C 196 GLN D 224 ASN E 29 GLN E 196 GLN F 224 ASN G 29 GLN G 76 GLN G 87 GLN G 196 GLN H 242 GLN I 76 GLN I 87 GLN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN K 29 GLN K 76 GLN K 196 GLN L 224 ASN M 29 GLN ** M 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 87 GLN ** M 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 219 ASN O 29 GLN O 76 GLN ** O 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 29 GLN Q 76 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN S 76 GLN S 196 GLN U 76 GLN ** U 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 29 GLN W 33 ASN W 43 ASN W 76 GLN ** W 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 29 GLN Y 43 ASN Z 224 ASN a 43 ASN a 76 GLN b 224 ASN b 242 GLN c 29 GLN c 43 ASN c 76 GLN c 115 GLN c 196 GLN d 219 ASN d 224 ASN e 29 GLN e 43 ASN e 76 GLN e 196 GLN f 224 ASN g 29 GLN g 43 ASN g 76 GLN g 196 GLN h 224 ASN i 29 GLN i 115 GLN j 224 ASN k 29 GLN k 33 ASN k 76 GLN ** k 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 224 ASN m 29 GLN m 33 ASN m 43 ASN m 76 GLN m 196 GLN n 219 ASN n 224 ASN o 29 GLN o 76 GLN o 196 GLN p 224 ASN q 29 GLN ** q 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 87 GLN q 115 GLN ** q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 224 ASN s 76 GLN ** s 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 224 ASN t 265 ASN Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 71231 Z= 0.224 Angle : 0.654 11.901 96439 Z= 0.338 Chirality : 0.046 0.175 10488 Planarity : 0.005 0.050 12696 Dihedral : 7.427 59.954 9956 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.38 % Allowed : 11.59 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.08), residues: 8602 helix: -3.01 (0.06), residues: 3381 sheet: -2.43 (0.11), residues: 2300 loop : -1.41 (0.11), residues: 2921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP g 71 HIS 0.005 0.001 HIS e 147 PHE 0.012 0.002 PHE Z 258 TYR 0.023 0.001 TYR G 180 ARG 0.006 0.001 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1895 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1643 time to evaluate : 5.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8339 (mtpp) REVERT: A 40 GLN cc_start: 0.8719 (mt0) cc_final: 0.8444 (mt0) REVERT: B 192 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7008 (ptmt) REVERT: B 242 GLN cc_start: 0.7701 (mt0) cc_final: 0.7437 (mt0) REVERT: C 40 GLN cc_start: 0.8621 (mt0) cc_final: 0.8418 (mt0) REVERT: D 192 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7132 (ptmt) REVERT: D 270 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8994 (ttpp) REVERT: D 294 MET cc_start: 0.8317 (mmm) cc_final: 0.8076 (mtp) REVERT: E 25 LYS cc_start: 0.8402 (mtpt) cc_final: 0.7970 (mtpp) REVERT: E 29 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: E 144 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8364 (mtmm) REVERT: F 290 ASN cc_start: 0.8100 (t0) cc_final: 0.7877 (t0) REVERT: F 345 SER cc_start: 0.8953 (t) cc_final: 0.8631 (p) REVERT: G 25 LYS cc_start: 0.8400 (mtpt) cc_final: 0.7823 (mtpp) REVERT: G 43 ASN cc_start: 0.8900 (t0) cc_final: 0.8376 (t0) REVERT: G 156 ARG cc_start: 0.8076 (mmt180) cc_final: 0.7619 (mmt180) REVERT: G 163 GLN cc_start: 0.8035 (mp10) cc_final: 0.7718 (mp10) REVERT: H 192 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7190 (ptmt) REVERT: H 270 LYS cc_start: 0.9158 (ttpp) cc_final: 0.8932 (ttpp) REVERT: I 34 GLU cc_start: 0.7984 (tp30) cc_final: 0.7559 (tp30) REVERT: I 43 ASN cc_start: 0.8940 (t0) cc_final: 0.8467 (t0) REVERT: I 76 GLN cc_start: 0.8248 (mt0) cc_final: 0.8046 (mt0) REVERT: I 163 GLN cc_start: 0.8200 (mp10) cc_final: 0.7623 (mp10) REVERT: J 342 PHE cc_start: 0.8744 (t80) cc_final: 0.8382 (t80) REVERT: K 40 GLN cc_start: 0.8701 (mt0) cc_final: 0.8342 (mt0) REVERT: K 76 GLN cc_start: 0.8192 (mt0) cc_final: 0.7973 (mt0) REVERT: K 99 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7898 (mtp85) REVERT: L 345 SER cc_start: 0.8724 (t) cc_final: 0.8500 (p) REVERT: M 99 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7500 (mtp180) REVERT: M 144 LYS cc_start: 0.8586 (mttm) cc_final: 0.8234 (mmmt) REVERT: O 25 LYS cc_start: 0.8265 (mtpt) cc_final: 0.7696 (mtpp) REVERT: O 33 ASN cc_start: 0.8953 (m-40) cc_final: 0.8489 (m110) REVERT: O 40 GLN cc_start: 0.8565 (mt0) cc_final: 0.8343 (mt0) REVERT: O 41 MET cc_start: 0.7807 (mtp) cc_final: 0.7560 (ttm) REVERT: P 360 GLU cc_start: 0.7245 (pp20) cc_final: 0.6913 (pp20) REVERT: P 362 LYS cc_start: 0.8505 (pttm) cc_final: 0.8266 (pttp) REVERT: Q 40 GLN cc_start: 0.8640 (mt0) cc_final: 0.8389 (mt0) REVERT: Q 43 ASN cc_start: 0.9037 (t0) cc_final: 0.8711 (t0) REVERT: Q 101 GLU cc_start: 0.8634 (mp0) cc_final: 0.8038 (mp0) REVERT: Q 144 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8507 (mtmm) REVERT: Q 163 GLN cc_start: 0.8111 (mp10) cc_final: 0.7490 (mp10) REVERT: R 242 GLN cc_start: 0.7594 (mt0) cc_final: 0.7388 (mt0) REVERT: R 362 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8492 (pttm) REVERT: S 40 GLN cc_start: 0.8597 (mt0) cc_final: 0.8337 (mt0) REVERT: S 43 ASN cc_start: 0.9119 (t0) cc_final: 0.8773 (t0) REVERT: T 192 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6891 (ptmt) REVERT: T 219 ASN cc_start: 0.8122 (m-40) cc_final: 0.7907 (m110) REVERT: T 242 GLN cc_start: 0.7721 (mt0) cc_final: 0.7397 (mt0) REVERT: T 270 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8843 (ttpp) REVERT: T 341 GLN cc_start: 0.8687 (pt0) cc_final: 0.8460 (mt0) REVERT: T 345 SER cc_start: 0.8774 (t) cc_final: 0.8486 (p) REVERT: U 43 ASN cc_start: 0.8864 (t0) cc_final: 0.8385 (t0) REVERT: U 101 GLU cc_start: 0.8592 (mp0) cc_final: 0.8067 (mp0) REVERT: V 192 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6884 (ptmt) REVERT: V 242 GLN cc_start: 0.7844 (mt0) cc_final: 0.7464 (mt0) REVERT: W 40 GLN cc_start: 0.8713 (mt0) cc_final: 0.8445 (mt0) REVERT: W 43 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8446 (t0) REVERT: W 99 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7954 (mtp180) REVERT: W 101 GLU cc_start: 0.8654 (mp0) cc_final: 0.8314 (mp0) REVERT: X 192 LYS cc_start: 0.7074 (pttt) cc_final: 0.6651 (ptmt) REVERT: X 219 ASN cc_start: 0.8257 (m110) cc_final: 0.7881 (m110) REVERT: X 362 LYS cc_start: 0.8766 (pttm) cc_final: 0.8370 (pttm) REVERT: Y 25 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7908 (mtpp) REVERT: Y 66 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8822 (p) REVERT: Y 82 ARG cc_start: 0.7430 (tpt170) cc_final: 0.7082 (tpt170) REVERT: Y 84 GLU cc_start: 0.7710 (mp0) cc_final: 0.7422 (mm-30) REVERT: Y 101 GLU cc_start: 0.8541 (mp0) cc_final: 0.8053 (mp0) REVERT: Z 345 SER cc_start: 0.8821 (t) cc_final: 0.8496 (p) REVERT: a 40 GLN cc_start: 0.8765 (mt0) cc_final: 0.8416 (mt0) REVERT: b 181 LYS cc_start: 0.7665 (mmtm) cc_final: 0.7403 (mmtm) REVERT: b 345 SER cc_start: 0.8959 (t) cc_final: 0.8654 (p) REVERT: b 362 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8463 (pttm) REVERT: c 40 GLN cc_start: 0.8885 (mt0) cc_final: 0.8549 (mt0) REVERT: c 115 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: c 163 GLN cc_start: 0.8117 (mp10) cc_final: 0.7681 (mp10) REVERT: d 242 GLN cc_start: 0.7854 (mt0) cc_final: 0.7537 (pt0) REVERT: d 362 LYS cc_start: 0.8534 (pttm) cc_final: 0.8266 (pttm) REVERT: e 40 GLN cc_start: 0.8703 (mt0) cc_final: 0.8416 (mt0) REVERT: e 82 ARG cc_start: 0.7498 (tpt170) cc_final: 0.7283 (tpt90) REVERT: e 99 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7986 (mtp180) REVERT: e 101 GLU cc_start: 0.8595 (mp0) cc_final: 0.8230 (mp0) REVERT: f 192 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6922 (ptmt) REVERT: f 225 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7139 (tm-30) REVERT: f 242 GLN cc_start: 0.7621 (mt0) cc_final: 0.7368 (mt0) REVERT: f 341 GLN cc_start: 0.8661 (mt0) cc_final: 0.8295 (mt0) REVERT: f 345 SER cc_start: 0.8738 (t) cc_final: 0.8471 (p) REVERT: f 362 LYS cc_start: 0.8676 (pttm) cc_final: 0.8456 (pttm) REVERT: g 33 ASN cc_start: 0.8802 (m-40) cc_final: 0.8584 (m-40) REVERT: g 84 GLU cc_start: 0.7917 (mp0) cc_final: 0.7677 (mm-30) REVERT: g 88 MET cc_start: 0.8153 (mtp) cc_final: 0.7785 (mtp) REVERT: g 101 GLU cc_start: 0.8425 (mp0) cc_final: 0.7780 (mp0) REVERT: g 156 ARG cc_start: 0.7980 (mmt180) cc_final: 0.7777 (mmt180) REVERT: i 99 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7809 (mtp85) REVERT: i 115 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8434 (mt0) REVERT: i 163 GLN cc_start: 0.8115 (mp10) cc_final: 0.7736 (mp10) REVERT: k 25 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8216 (mtpt) REVERT: k 40 GLN cc_start: 0.8665 (mt0) cc_final: 0.8344 (mt0) REVERT: k 43 ASN cc_start: 0.8987 (t0) cc_final: 0.8630 (t0) REVERT: k 84 GLU cc_start: 0.7976 (mp0) cc_final: 0.7768 (mm-30) REVERT: l 294 MET cc_start: 0.8654 (mmm) cc_final: 0.8373 (mmm) REVERT: l 319 HIS cc_start: 0.7601 (m90) cc_final: 0.7309 (m-70) REVERT: l 345 SER cc_start: 0.8757 (t) cc_final: 0.8453 (p) REVERT: m 106 TYR cc_start: 0.8808 (m-80) cc_final: 0.8511 (m-80) REVERT: n 242 GLN cc_start: 0.7627 (mt0) cc_final: 0.7422 (mt0) REVERT: n 345 SER cc_start: 0.8824 (t) cc_final: 0.8550 (p) REVERT: n 362 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7928 (pttm) REVERT: o 25 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8307 (mtpp) REVERT: o 33 ASN cc_start: 0.8996 (m-40) cc_final: 0.8793 (m-40) REVERT: o 144 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8268 (mtmm) REVERT: p 192 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6852 (ptmt) REVERT: p 239 TYR cc_start: 0.8278 (m-80) cc_final: 0.7962 (m-80) REVERT: p 242 GLN cc_start: 0.7577 (mt0) cc_final: 0.7366 (mt0) REVERT: q 40 GLN cc_start: 0.8644 (mt0) cc_final: 0.8220 (mp10) REVERT: r 270 LYS cc_start: 0.9079 (ttpp) cc_final: 0.8800 (ttpp) REVERT: r 345 SER cc_start: 0.8821 (t) cc_final: 0.8580 (p) REVERT: r 362 LYS cc_start: 0.8341 (pttm) cc_final: 0.8119 (pttm) REVERT: s 25 LYS cc_start: 0.8396 (mtpt) cc_final: 0.8139 (mtpp) REVERT: s 40 GLN cc_start: 0.8676 (mt0) cc_final: 0.8335 (mt0) REVERT: s 84 GLU cc_start: 0.7766 (mp0) cc_final: 0.7558 (mp0) REVERT: s 169 ARG cc_start: 0.8564 (tpt170) cc_final: 0.8092 (tpp-160) REVERT: t 345 SER cc_start: 0.8812 (t) cc_final: 0.8603 (p) outliers start: 252 outliers final: 95 residues processed: 1823 average time/residue: 0.7064 time to fit residues: 2111.1142 Evaluate side-chains 1487 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 1374 time to evaluate : 5.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 270 LYS Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain F residue 336 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain H residue 192 LYS Chi-restraints excluded: chain H residue 255 LYS Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 217 ASP Chi-restraints excluded: chain J residue 224 ASN Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 217 ASP Chi-restraints excluded: chain L residue 248 ILE Chi-restraints excluded: chain M residue 99 ARG Chi-restraints excluded: chain M residue 101 GLU Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain N residue 217 ASP Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 217 ASP Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 217 ASP Chi-restraints excluded: chain R residue 362 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain T residue 192 LYS Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 217 ASP Chi-restraints excluded: chain T residue 270 LYS Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain V residue 192 LYS Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 217 ASP Chi-restraints excluded: chain W residue 43 ASN Chi-restraints excluded: chain X residue 333 ASP Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 186 VAL Chi-restraints excluded: chain Z residue 224 ASN Chi-restraints excluded: chain Z residue 332 ASP Chi-restraints excluded: chain Z residue 362 LYS Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain b residue 193 MET Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 200 ASN Chi-restraints excluded: chain b residue 217 ASP Chi-restraints excluded: chain b residue 224 ASN Chi-restraints excluded: chain b residue 332 ASP Chi-restraints excluded: chain b residue 362 LYS Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 115 GLN Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 217 ASP Chi-restraints excluded: chain d residue 224 ASN Chi-restraints excluded: chain f residue 192 LYS Chi-restraints excluded: chain f residue 196 VAL Chi-restraints excluded: chain f residue 332 ASP Chi-restraints excluded: chain g residue 186 VAL Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 224 ASN Chi-restraints excluded: chain i residue 38 VAL Chi-restraints excluded: chain i residue 115 GLN Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain j residue 217 ASP Chi-restraints excluded: chain j residue 224 ASN Chi-restraints excluded: chain j residue 332 ASP Chi-restraints excluded: chain k residue 181 ASP Chi-restraints excluded: chain l residue 200 ASN Chi-restraints excluded: chain l residue 217 ASP Chi-restraints excluded: chain l residue 224 ASN Chi-restraints excluded: chain m residue 66 THR Chi-restraints excluded: chain m residue 186 VAL Chi-restraints excluded: chain n residue 217 ASP Chi-restraints excluded: chain n residue 224 ASN Chi-restraints excluded: chain n residue 332 ASP Chi-restraints excluded: chain n residue 362 LYS Chi-restraints excluded: chain o residue 186 VAL Chi-restraints excluded: chain p residue 192 LYS Chi-restraints excluded: chain p residue 196 VAL Chi-restraints excluded: chain p residue 217 ASP Chi-restraints excluded: chain p residue 224 ASN Chi-restraints excluded: chain p residue 326 VAL Chi-restraints excluded: chain q residue 186 VAL Chi-restraints excluded: chain q residue 195 LEU Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 217 ASP Chi-restraints excluded: chain r residue 224 ASN Chi-restraints excluded: chain s residue 66 THR Chi-restraints excluded: chain s residue 186 VAL Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 217 ASP Chi-restraints excluded: chain t residue 224 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 429 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 643 optimal weight: 3.9990 chunk 526 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 774 optimal weight: 5.9990 chunk 836 optimal weight: 8.9990 chunk 689 optimal weight: 6.9990 chunk 767 optimal weight: 0.8980 chunk 263 optimal weight: 5.9990 chunk 621 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 87 GLN ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN C 76 GLN E 29 GLN E 33 ASN E 196 GLN G 29 GLN G 76 GLN H 224 ASN I 29 GLN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 ASN L 219 ASN M 43 ASN M 76 GLN M 87 GLN M 196 GLN ** O 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 ASN Q 76 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 ASN U 76 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN W 29 GLN W 33 ASN W 43 ASN ** W 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 224 ASN Y 43 ASN a 29 GLN a 43 ASN c 33 ASN c 43 ASN c 115 GLN e 43 ASN f 224 ASN g 43 ASN i 76 GLN i 111 GLN i 115 GLN ** k 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 29 GLN m 43 ASN m 76 GLN o 87 GLN q 76 GLN q 87 GLN q 196 GLN s 29 GLN ** s 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 71231 Z= 0.287 Angle : 0.649 12.100 96439 Z= 0.326 Chirality : 0.046 0.200 10488 Planarity : 0.004 0.040 12696 Dihedral : 5.572 46.930 9756 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.68 % Allowed : 13.84 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.08), residues: 8602 helix: -2.20 (0.07), residues: 3381 sheet: -2.16 (0.11), residues: 2300 loop : -0.93 (0.11), residues: 2921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 206 HIS 0.006 0.001 HIS U 42 PHE 0.015 0.002 PHE D 258 TYR 0.025 0.001 TYR O 180 ARG 0.010 0.001 ARG E 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1757 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1483 time to evaluate : 6.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8240 (mtpp) REVERT: A 40 GLN cc_start: 0.8784 (mt0) cc_final: 0.8460 (mt0) REVERT: B 242 GLN cc_start: 0.7737 (mt0) cc_final: 0.7504 (mt0) REVERT: C 40 GLN cc_start: 0.8814 (mt0) cc_final: 0.8573 (mt0) REVERT: D 216 TYR cc_start: 0.6883 (t80) cc_final: 0.6678 (t80) REVERT: E 25 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8003 (mtpp) REVERT: E 82 ARG cc_start: 0.7520 (tpt170) cc_final: 0.7255 (tpt90) REVERT: E 144 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8130 (mtmm) REVERT: F 290 ASN cc_start: 0.8074 (t0) cc_final: 0.7831 (t0) REVERT: F 345 SER cc_start: 0.8994 (t) cc_final: 0.8573 (p) REVERT: G 25 LYS cc_start: 0.8487 (mtpt) cc_final: 0.7994 (mtpp) REVERT: G 163 GLN cc_start: 0.8121 (mp10) cc_final: 0.7631 (mp10) REVERT: I 34 GLU cc_start: 0.7928 (tp30) cc_final: 0.7502 (tp30) REVERT: K 40 GLN cc_start: 0.8789 (mt0) cc_final: 0.8579 (mt0) REVERT: K 99 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7971 (mtp85) REVERT: L 345 SER cc_start: 0.8803 (t) cc_final: 0.8499 (p) REVERT: M 25 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7918 (mtpp) REVERT: M 43 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8644 (t0) REVERT: M 88 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7272 (mtp) REVERT: M 144 LYS cc_start: 0.8635 (mttm) cc_final: 0.8265 (mmmt) REVERT: O 25 LYS cc_start: 0.8496 (mtpt) cc_final: 0.7938 (mtpp) REVERT: O 33 ASN cc_start: 0.9017 (m-40) cc_final: 0.8568 (m-40) REVERT: O 40 GLN cc_start: 0.8640 (mt0) cc_final: 0.8363 (mt0) REVERT: O 41 MET cc_start: 0.7930 (mtp) cc_final: 0.7668 (ttm) REVERT: O 132 TYR cc_start: 0.8694 (m-80) cc_final: 0.8369 (m-80) REVERT: P 360 GLU cc_start: 0.7391 (pp20) cc_final: 0.6886 (pp20) REVERT: P 362 LYS cc_start: 0.8481 (pttm) cc_final: 0.7991 (pttm) REVERT: Q 101 GLU cc_start: 0.8637 (mp0) cc_final: 0.8001 (mp0) REVERT: Q 144 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8482 (mtmm) REVERT: R 208 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7556 (mtm110) REVERT: R 242 GLN cc_start: 0.7709 (mt0) cc_final: 0.7384 (mt0) REVERT: R 341 GLN cc_start: 0.8766 (mt0) cc_final: 0.8475 (mt0) REVERT: R 360 GLU cc_start: 0.7291 (pp20) cc_final: 0.7021 (pp20) REVERT: R 362 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8406 (pttm) REVERT: S 40 GLN cc_start: 0.8696 (mt0) cc_final: 0.8386 (mt0) REVERT: S 43 ASN cc_start: 0.9095 (t0) cc_final: 0.8735 (t0) REVERT: S 84 GLU cc_start: 0.7906 (mp0) cc_final: 0.7629 (mm-30) REVERT: T 242 GLN cc_start: 0.7645 (mt0) cc_final: 0.7312 (mt0) REVERT: T 252 GLU cc_start: 0.7267 (mp0) cc_final: 0.6922 (mp0) REVERT: T 345 SER cc_start: 0.8839 (t) cc_final: 0.8443 (p) REVERT: U 41 MET cc_start: 0.7927 (mtp) cc_final: 0.7652 (ttm) REVERT: U 43 ASN cc_start: 0.8941 (t0) cc_final: 0.8600 (t0) REVERT: U 101 GLU cc_start: 0.8564 (mp0) cc_final: 0.8017 (mp0) REVERT: V 242 GLN cc_start: 0.7867 (mt0) cc_final: 0.7550 (mt0) REVERT: W 40 GLN cc_start: 0.8780 (mt0) cc_final: 0.8435 (mt0) REVERT: W 88 MET cc_start: 0.8325 (mtp) cc_final: 0.8092 (mtp) REVERT: W 99 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7887 (mtp85) REVERT: W 101 GLU cc_start: 0.8650 (mp0) cc_final: 0.8248 (mp0) REVERT: X 362 LYS cc_start: 0.8744 (pttm) cc_final: 0.8115 (pttm) REVERT: Y 25 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8132 (mtpp) REVERT: Y 101 GLU cc_start: 0.8566 (mp0) cc_final: 0.8053 (mp0) REVERT: Z 345 SER cc_start: 0.8892 (t) cc_final: 0.8475 (p) REVERT: a 33 ASN cc_start: 0.8969 (m-40) cc_final: 0.8690 (m110) REVERT: a 40 GLN cc_start: 0.8797 (mt0) cc_final: 0.8484 (mt0) REVERT: b 181 LYS cc_start: 0.7742 (mmtm) cc_final: 0.7442 (mmtm) REVERT: b 345 SER cc_start: 0.9036 (t) cc_final: 0.8625 (p) REVERT: b 362 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8558 (pttm) REVERT: c 43 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8705 (t0) REVERT: d 242 GLN cc_start: 0.7869 (mt0) cc_final: 0.7559 (pt0) REVERT: d 362 LYS cc_start: 0.8556 (pttm) cc_final: 0.8249 (pttm) REVERT: e 40 GLN cc_start: 0.8771 (mt0) cc_final: 0.8465 (mt0) REVERT: f 341 GLN cc_start: 0.8724 (mt0) cc_final: 0.8392 (mt0) REVERT: f 345 SER cc_start: 0.8826 (t) cc_final: 0.8442 (p) REVERT: g 33 ASN cc_start: 0.8920 (m-40) cc_final: 0.8608 (m110) REVERT: g 180 TYR cc_start: 0.8938 (m-80) cc_final: 0.8657 (m-80) REVERT: h 242 GLN cc_start: 0.7790 (mt0) cc_final: 0.7572 (pt0) REVERT: i 163 GLN cc_start: 0.8193 (mp10) cc_final: 0.7808 (mp10) REVERT: j 307 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8648 (tt) REVERT: k 40 GLN cc_start: 0.8706 (mt0) cc_final: 0.8397 (mt0) REVERT: k 84 GLU cc_start: 0.8084 (mp0) cc_final: 0.7843 (mm-30) REVERT: l 319 HIS cc_start: 0.7637 (m90) cc_final: 0.7420 (m-70) REVERT: l 345 SER cc_start: 0.8762 (t) cc_final: 0.8462 (p) REVERT: l 362 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8110 (pttm) REVERT: m 106 TYR cc_start: 0.8817 (m-80) cc_final: 0.8489 (m-80) REVERT: n 242 GLN cc_start: 0.7714 (mt0) cc_final: 0.7497 (mt0) REVERT: n 345 SER cc_start: 0.8929 (t) cc_final: 0.8537 (p) REVERT: n 362 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8196 (pttm) REVERT: o 25 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8361 (mtpp) REVERT: o 33 ASN cc_start: 0.9033 (m-40) cc_final: 0.8810 (m-40) REVERT: o 41 MET cc_start: 0.7909 (mtp) cc_final: 0.7632 (ttm) REVERT: o 82 ARG cc_start: 0.7769 (tpt170) cc_final: 0.7398 (tpt170) REVERT: o 102 LYS cc_start: 0.9152 (mtpt) cc_final: 0.8934 (mtmt) REVERT: o 144 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8279 (mtmm) REVERT: q 40 GLN cc_start: 0.8780 (mt0) cc_final: 0.8356 (mp10) REVERT: q 82 ARG cc_start: 0.7647 (tpt170) cc_final: 0.7177 (tpt90) REVERT: q 163 GLN cc_start: 0.8163 (mp10) cc_final: 0.7913 (mp10) REVERT: r 213 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.6946 (ttm170) REVERT: r 345 SER cc_start: 0.8851 (t) cc_final: 0.8505 (p) REVERT: r 362 LYS cc_start: 0.8298 (pttm) cc_final: 0.8006 (pttm) REVERT: s 34 GLU cc_start: 0.7865 (tp30) cc_final: 0.7232 (tp30) REVERT: s 40 GLN cc_start: 0.8809 (mt0) cc_final: 0.8608 (mt0) REVERT: s 169 ARG cc_start: 0.8625 (tpt170) cc_final: 0.8243 (tpp-160) REVERT: t 341 GLN cc_start: 0.8779 (mt0) cc_final: 0.8477 (mt0) REVERT: t 345 SER cc_start: 0.8899 (t) cc_final: 0.8569 (p) outliers start: 274 outliers final: 171 residues processed: 1702 average time/residue: 0.7075 time to fit residues: 1972.6757 Evaluate side-chains 1525 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1344 time to evaluate : 6.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 224 ASN Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 265 ASN Chi-restraints excluded: chain H residue 336 ILE Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 41 MET Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 186 VAL Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 217 ASP Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 99 ARG Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 217 ASP Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 88 MET Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 217 ASP Chi-restraints excluded: chain N residue 336 ILE Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 217 ASP Chi-restraints excluded: chain P residue 361 LEU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 217 ASP Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 361 LEU Chi-restraints excluded: chain R residue 362 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 200 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 213 ARG Chi-restraints excluded: chain T residue 217 ASP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain V residue 193 MET Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 213 ARG Chi-restraints excluded: chain V residue 217 ASP Chi-restraints excluded: chain V residue 248 ILE Chi-restraints excluded: chain V residue 332 ASP Chi-restraints excluded: chain V residue 333 ASP Chi-restraints excluded: chain V residue 361 LEU Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain X residue 217 ASP Chi-restraints excluded: chain X residue 224 ASN Chi-restraints excluded: chain X residue 333 ASP Chi-restraints excluded: chain X residue 361 LEU Chi-restraints excluded: chain Y residue 186 VAL Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Z residue 217 ASP Chi-restraints excluded: chain Z residue 248 ILE Chi-restraints excluded: chain Z residue 268 SER Chi-restraints excluded: chain Z residue 361 LEU Chi-restraints excluded: chain Z residue 362 LYS Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 200 THR Chi-restraints excluded: chain b residue 193 MET Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 217 ASP Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 333 ASP Chi-restraints excluded: chain b residue 361 LEU Chi-restraints excluded: chain b residue 362 LYS Chi-restraints excluded: chain c residue 43 ASN Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain c residue 202 VAL Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 213 ARG Chi-restraints excluded: chain d residue 217 ASP Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 307 LEU Chi-restraints excluded: chain d residue 332 ASP Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 195 LEU Chi-restraints excluded: chain e residue 200 THR Chi-restraints excluded: chain f residue 196 VAL Chi-restraints excluded: chain f residue 217 ASP Chi-restraints excluded: chain f residue 224 ASN Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain f residue 307 LEU Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 66 THR Chi-restraints excluded: chain g residue 186 VAL Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 200 THR Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 203 ASP Chi-restraints excluded: chain h residue 217 ASP Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 276 SER Chi-restraints excluded: chain h residue 307 LEU Chi-restraints excluded: chain h residue 361 LEU Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 195 LEU Chi-restraints excluded: chain i residue 200 THR Chi-restraints excluded: chain j residue 217 ASP Chi-restraints excluded: chain j residue 307 LEU Chi-restraints excluded: chain j residue 361 LEU Chi-restraints excluded: chain k residue 181 ASP Chi-restraints excluded: chain k residue 200 THR Chi-restraints excluded: chain l residue 307 LEU Chi-restraints excluded: chain l residue 361 LEU Chi-restraints excluded: chain l residue 362 LYS Chi-restraints excluded: chain m residue 21 LYS Chi-restraints excluded: chain m residue 66 THR Chi-restraints excluded: chain m residue 186 VAL Chi-restraints excluded: chain m residue 200 THR Chi-restraints excluded: chain m residue 202 VAL Chi-restraints excluded: chain n residue 217 ASP Chi-restraints excluded: chain n residue 307 LEU Chi-restraints excluded: chain n residue 361 LEU Chi-restraints excluded: chain n residue 362 LYS Chi-restraints excluded: chain o residue 172 LYS Chi-restraints excluded: chain o residue 186 VAL Chi-restraints excluded: chain o residue 200 THR Chi-restraints excluded: chain p residue 196 VAL Chi-restraints excluded: chain p residue 217 ASP Chi-restraints excluded: chain p residue 265 ASN Chi-restraints excluded: chain p residue 307 LEU Chi-restraints excluded: chain p residue 361 LEU Chi-restraints excluded: chain q residue 120 MET Chi-restraints excluded: chain q residue 172 LYS Chi-restraints excluded: chain q residue 195 LEU Chi-restraints excluded: chain q residue 200 THR Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 213 ARG Chi-restraints excluded: chain r residue 217 ASP Chi-restraints excluded: chain r residue 307 LEU Chi-restraints excluded: chain r residue 336 ILE Chi-restraints excluded: chain r residue 361 LEU Chi-restraints excluded: chain s residue 66 THR Chi-restraints excluded: chain s residue 186 VAL Chi-restraints excluded: chain s residue 200 THR Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 217 ASP Chi-restraints excluded: chain t residue 336 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 764 optimal weight: 3.9990 chunk 582 optimal weight: 10.0000 chunk 401 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 369 optimal weight: 8.9990 chunk 519 optimal weight: 1.9990 chunk 776 optimal weight: 5.9990 chunk 822 optimal weight: 5.9990 chunk 405 optimal weight: 3.9990 chunk 736 optimal weight: 0.9990 chunk 221 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN B 224 ASN D 224 ASN F 224 ASN G 29 GLN G 76 GLN I 111 GLN ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN K 76 GLN L 219 ASN ** O 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN U 29 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN W 87 GLN W 196 GLN Y 43 ASN Z 224 ASN a 43 ASN b 224 ASN d 224 ASN e 87 GLN g 43 ASN h 224 ASN j 224 ASN ** k 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 224 ASN n 224 ASN o 87 GLN p 224 ASN q 29 GLN q 87 GLN q 196 GLN r 224 ASN s 196 GLN t 224 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 71231 Z= 0.278 Angle : 0.638 12.007 96439 Z= 0.316 Chirality : 0.045 0.215 10488 Planarity : 0.004 0.039 12696 Dihedral : 5.095 36.919 9728 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.21 % Allowed : 14.41 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.09), residues: 8602 helix: -1.67 (0.08), residues: 3404 sheet: -1.98 (0.11), residues: 2162 loop : -0.82 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP t 350 HIS 0.005 0.001 HIS Q 42 PHE 0.016 0.001 PHE j 342 TYR 0.032 0.001 TYR C 180 ARG 0.010 0.001 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1764 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 1450 time to evaluate : 5.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8769 (mt0) cc_final: 0.8508 (mt0) REVERT: B 242 GLN cc_start: 0.7682 (mt0) cc_final: 0.7471 (mt0) REVERT: B 362 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7845 (pttm) REVERT: C 171 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8784 (pt) REVERT: D 242 GLN cc_start: 0.7462 (mt0) cc_final: 0.7206 (mt0) REVERT: E 25 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8103 (mtpp) REVERT: E 144 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8181 (mtmm) REVERT: F 290 ASN cc_start: 0.8023 (t0) cc_final: 0.7754 (t0) REVERT: F 345 SER cc_start: 0.9011 (t) cc_final: 0.8627 (p) REVERT: G 25 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8137 (mtpp) REVERT: G 163 GLN cc_start: 0.8168 (mp10) cc_final: 0.7653 (mp10) REVERT: I 34 GLU cc_start: 0.8008 (tp30) cc_final: 0.7565 (tp30) REVERT: I 156 ARG cc_start: 0.8239 (mmt180) cc_final: 0.7874 (mmt180) REVERT: K 99 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7977 (mtp85) REVERT: L 345 SER cc_start: 0.8884 (t) cc_final: 0.8549 (p) REVERT: M 25 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8079 (mtpp) REVERT: M 144 LYS cc_start: 0.8664 (mttm) cc_final: 0.8294 (mmmt) REVERT: M 171 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8672 (pt) REVERT: O 25 LYS cc_start: 0.8509 (mtpt) cc_final: 0.8130 (mtpp) REVERT: O 33 ASN cc_start: 0.8935 (m-40) cc_final: 0.8368 (m-40) REVERT: O 40 GLN cc_start: 0.8630 (mt0) cc_final: 0.8378 (mt0) REVERT: O 41 MET cc_start: 0.7942 (mtp) cc_final: 0.7680 (ttm) REVERT: O 132 TYR cc_start: 0.8745 (m-80) cc_final: 0.8395 (m-80) REVERT: Q 144 LYS cc_start: 0.8791 (mtpp) cc_final: 0.8478 (mtmm) REVERT: R 242 GLN cc_start: 0.7727 (mt0) cc_final: 0.7349 (mt0) REVERT: R 360 GLU cc_start: 0.7297 (pp20) cc_final: 0.6898 (pp20) REVERT: R 362 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8143 (pttm) REVERT: S 40 GLN cc_start: 0.8736 (mt0) cc_final: 0.8421 (mt0) REVERT: S 62 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7882 (tm-30) REVERT: T 242 GLN cc_start: 0.7685 (mt0) cc_final: 0.7350 (mt0) REVERT: T 341 GLN cc_start: 0.8926 (pt0) cc_final: 0.8437 (mt0) REVERT: T 345 SER cc_start: 0.8818 (t) cc_final: 0.8364 (p) REVERT: U 41 MET cc_start: 0.7876 (mtp) cc_final: 0.7615 (ttm) REVERT: U 101 GLU cc_start: 0.8566 (mp0) cc_final: 0.8012 (mp0) REVERT: V 213 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6598 (ttm170) REVERT: V 242 GLN cc_start: 0.7844 (mt0) cc_final: 0.7527 (mt0) REVERT: V 336 ILE cc_start: 0.8936 (tt) cc_final: 0.8598 (tt) REVERT: W 40 GLN cc_start: 0.8803 (mt0) cc_final: 0.8473 (mt0) REVERT: W 88 MET cc_start: 0.8427 (mtp) cc_final: 0.8191 (mtp) REVERT: W 101 GLU cc_start: 0.8611 (mp0) cc_final: 0.8204 (mp0) REVERT: W 163 GLN cc_start: 0.8295 (mp10) cc_final: 0.7820 (mp10) REVERT: W 180 TYR cc_start: 0.8810 (m-10) cc_final: 0.8524 (m-10) REVERT: X 362 LYS cc_start: 0.8674 (pttm) cc_final: 0.8172 (pttm) REVERT: Y 25 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8003 (mtpp) REVERT: Y 144 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8358 (mmmt) REVERT: Z 213 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6125 (ttm-80) REVERT: Z 294 MET cc_start: 0.8649 (mmm) cc_final: 0.8265 (mmm) REVERT: Z 345 SER cc_start: 0.8901 (t) cc_final: 0.8468 (p) REVERT: Z 360 GLU cc_start: 0.7242 (pp20) cc_final: 0.7002 (pp20) REVERT: a 33 ASN cc_start: 0.8930 (m-40) cc_final: 0.8665 (m-40) REVERT: a 40 GLN cc_start: 0.8793 (mt0) cc_final: 0.8428 (mt0) REVERT: b 345 SER cc_start: 0.9032 (t) cc_final: 0.8599 (p) REVERT: b 362 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8472 (pttm) REVERT: c 40 GLN cc_start: 0.8815 (mt0) cc_final: 0.8465 (mt0) REVERT: c 82 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7517 (tpt90) REVERT: c 163 GLN cc_start: 0.8136 (mp10) cc_final: 0.7673 (mp10) REVERT: d 294 MET cc_start: 0.8523 (mmm) cc_final: 0.8294 (mtp) REVERT: d 333 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8476 (m-30) REVERT: d 362 LYS cc_start: 0.8547 (pttm) cc_final: 0.8218 (pttm) REVERT: e 40 GLN cc_start: 0.8754 (mt0) cc_final: 0.8442 (mt0) REVERT: e 180 TYR cc_start: 0.8906 (m-80) cc_final: 0.8663 (m-80) REVERT: f 345 SER cc_start: 0.8855 (t) cc_final: 0.8467 (p) REVERT: f 362 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8127 (pttm) REVERT: g 33 ASN cc_start: 0.8926 (m-40) cc_final: 0.8676 (m-40) REVERT: g 180 TYR cc_start: 0.8957 (m-80) cc_final: 0.8694 (m-80) REVERT: j 307 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8663 (tt) REVERT: j 342 PHE cc_start: 0.8614 (t80) cc_final: 0.8253 (t80) REVERT: k 40 GLN cc_start: 0.8732 (mt0) cc_final: 0.8430 (mt0) REVERT: l 242 GLN cc_start: 0.7648 (mt0) cc_final: 0.7179 (pt0) REVERT: l 345 SER cc_start: 0.8853 (t) cc_final: 0.8419 (p) REVERT: l 362 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8073 (pttm) REVERT: m 106 TYR cc_start: 0.8807 (m-80) cc_final: 0.8454 (m-80) REVERT: n 242 GLN cc_start: 0.7639 (mt0) cc_final: 0.7325 (mt0) REVERT: n 345 SER cc_start: 0.8910 (t) cc_final: 0.8540 (p) REVERT: n 362 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8180 (pttm) REVERT: o 25 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8345 (mtpp) REVERT: o 33 ASN cc_start: 0.9089 (m-40) cc_final: 0.8838 (m-40) REVERT: o 41 MET cc_start: 0.7940 (mtp) cc_final: 0.7684 (ttm) REVERT: o 82 ARG cc_start: 0.7732 (tpt170) cc_final: 0.7515 (tpt170) REVERT: o 144 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8231 (mtmm) REVERT: q 40 GLN cc_start: 0.8793 (mt0) cc_final: 0.8371 (mp10) REVERT: q 82 ARG cc_start: 0.7664 (tpt170) cc_final: 0.7327 (tpt90) REVERT: q 163 GLN cc_start: 0.8177 (mp10) cc_final: 0.7798 (mp10) REVERT: r 213 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6863 (ttm170) REVERT: r 345 SER cc_start: 0.8894 (t) cc_final: 0.8523 (p) REVERT: r 362 LYS cc_start: 0.8290 (pttm) cc_final: 0.8007 (pttm) REVERT: s 34 GLU cc_start: 0.7807 (tp30) cc_final: 0.7275 (tp30) REVERT: s 169 ARG cc_start: 0.8616 (tpt170) cc_final: 0.8305 (tpp-160) REVERT: t 294 MET cc_start: 0.7932 (mtp) cc_final: 0.7676 (ttm) REVERT: t 341 GLN cc_start: 0.8797 (mt0) cc_final: 0.8560 (mt0) REVERT: t 345 SER cc_start: 0.9004 (t) cc_final: 0.8589 (p) outliers start: 314 outliers final: 226 residues processed: 1693 average time/residue: 0.7160 time to fit residues: 1983.7673 Evaluate side-chains 1560 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1320 time to evaluate : 5.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain H residue 217 ASP Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 265 ASN Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 41 MET Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 217 ASP Chi-restraints excluded: chain J residue 224 ASN Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 336 ILE Chi-restraints excluded: chain K residue 99 ARG Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 217 ASP Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 307 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 217 ASP Chi-restraints excluded: chain N residue 265 ASN Chi-restraints excluded: chain N residue 336 ILE Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 217 ASP Chi-restraints excluded: chain P residue 361 LEU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain R residue 193 MET Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 213 ARG Chi-restraints excluded: chain R residue 217 ASP Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 361 LEU Chi-restraints excluded: chain R residue 362 LYS Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 181 ASP Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 200 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 213 ARG Chi-restraints excluded: chain T residue 217 ASP Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 265 ASN Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 307 LEU Chi-restraints excluded: chain T residue 333 ASP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 171 LEU Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 202 VAL Chi-restraints excluded: chain V residue 193 MET Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 213 ARG Chi-restraints excluded: chain V residue 217 ASP Chi-restraints excluded: chain V residue 248 ILE Chi-restraints excluded: chain V residue 307 LEU Chi-restraints excluded: chain V residue 333 ASP Chi-restraints excluded: chain W residue 171 LEU Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain X residue 217 ASP Chi-restraints excluded: chain X residue 333 ASP Chi-restraints excluded: chain X residue 361 LEU Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 186 VAL Chi-restraints excluded: chain Y residue 202 VAL Chi-restraints excluded: chain Z residue 213 ARG Chi-restraints excluded: chain Z residue 217 ASP Chi-restraints excluded: chain Z residue 224 ASN Chi-restraints excluded: chain Z residue 248 ILE Chi-restraints excluded: chain Z residue 268 SER Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 361 LEU Chi-restraints excluded: chain Z residue 362 LYS Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 200 THR Chi-restraints excluded: chain b residue 193 MET Chi-restraints excluded: chain b residue 217 ASP Chi-restraints excluded: chain b residue 224 ASN Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 332 ASP Chi-restraints excluded: chain b residue 361 LEU Chi-restraints excluded: chain b residue 362 LYS Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain c residue 202 VAL Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 213 ARG Chi-restraints excluded: chain d residue 217 ASP Chi-restraints excluded: chain d residue 224 ASN Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 307 LEU Chi-restraints excluded: chain d residue 333 ASP Chi-restraints excluded: chain d residue 361 LEU Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 127 ARG Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 195 LEU Chi-restraints excluded: chain e residue 200 THR Chi-restraints excluded: chain e residue 202 VAL Chi-restraints excluded: chain f residue 196 VAL Chi-restraints excluded: chain f residue 203 ASP Chi-restraints excluded: chain f residue 217 ASP Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain f residue 307 LEU Chi-restraints excluded: chain f residue 362 LYS Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 66 THR Chi-restraints excluded: chain g residue 186 VAL Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 202 VAL Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 217 ASP Chi-restraints excluded: chain h residue 224 ASN Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 269 LYS Chi-restraints excluded: chain h residue 307 LEU Chi-restraints excluded: chain h residue 361 LEU Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 195 LEU Chi-restraints excluded: chain i residue 200 THR Chi-restraints excluded: chain j residue 217 ASP Chi-restraints excluded: chain j residue 224 ASN Chi-restraints excluded: chain j residue 265 ASN Chi-restraints excluded: chain j residue 307 LEU Chi-restraints excluded: chain j residue 361 LEU Chi-restraints excluded: chain k residue 120 MET Chi-restraints excluded: chain k residue 178 VAL Chi-restraints excluded: chain k residue 181 ASP Chi-restraints excluded: chain k residue 200 THR Chi-restraints excluded: chain l residue 200 ASN Chi-restraints excluded: chain l residue 217 ASP Chi-restraints excluded: chain l residue 224 ASN Chi-restraints excluded: chain l residue 265 ASN Chi-restraints excluded: chain l residue 307 LEU Chi-restraints excluded: chain l residue 361 LEU Chi-restraints excluded: chain l residue 362 LYS Chi-restraints excluded: chain m residue 66 THR Chi-restraints excluded: chain m residue 171 LEU Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 186 VAL Chi-restraints excluded: chain m residue 200 THR Chi-restraints excluded: chain n residue 217 ASP Chi-restraints excluded: chain n residue 224 ASN Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain n residue 307 LEU Chi-restraints excluded: chain n residue 332 ASP Chi-restraints excluded: chain n residue 361 LEU Chi-restraints excluded: chain n residue 362 LYS Chi-restraints excluded: chain o residue 172 LYS Chi-restraints excluded: chain o residue 186 VAL Chi-restraints excluded: chain o residue 200 THR Chi-restraints excluded: chain p residue 195 TYR Chi-restraints excluded: chain p residue 196 VAL Chi-restraints excluded: chain p residue 217 ASP Chi-restraints excluded: chain p residue 224 ASN Chi-restraints excluded: chain p residue 265 ASN Chi-restraints excluded: chain p residue 291 ILE Chi-restraints excluded: chain p residue 307 LEU Chi-restraints excluded: chain p residue 326 VAL Chi-restraints excluded: chain p residue 333 ASP Chi-restraints excluded: chain p residue 361 LEU Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 120 MET Chi-restraints excluded: chain q residue 172 LYS Chi-restraints excluded: chain q residue 195 LEU Chi-restraints excluded: chain q residue 200 THR Chi-restraints excluded: chain r residue 193 MET Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 213 ARG Chi-restraints excluded: chain r residue 217 ASP Chi-restraints excluded: chain r residue 224 ASN Chi-restraints excluded: chain r residue 307 LEU Chi-restraints excluded: chain r residue 361 LEU Chi-restraints excluded: chain s residue 66 THR Chi-restraints excluded: chain s residue 178 VAL Chi-restraints excluded: chain s residue 186 VAL Chi-restraints excluded: chain s residue 200 THR Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 217 ASP Chi-restraints excluded: chain t residue 224 ASN Chi-restraints excluded: chain t residue 336 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 685 optimal weight: 0.0070 chunk 466 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 612 optimal weight: 9.9990 chunk 339 optimal weight: 0.9990 chunk 701 optimal weight: 5.9990 chunk 568 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 420 optimal weight: 0.9980 chunk 738 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN F 224 ASN G 29 GLN H 224 ASN I 196 GLN J 224 ASN K 87 GLN L 219 ASN ** M 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 224 ASN ** O 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 224 ASN S 29 GLN U 29 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN V 224 ASN W 29 GLN W 87 GLN X 224 ASN X 242 GLN Z 224 ASN a 43 ASN b 224 ASN c 87 GLN d 224 ASN e 87 GLN f 224 ASN g 43 ASN h 224 ASN j 224 ASN ** k 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 224 ASN n 224 ASN ** o 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 87 GLN p 224 ASN q 76 GLN q 115 GLN r 224 ASN s 196 GLN t 224 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 71231 Z= 0.216 Angle : 0.606 13.279 96439 Z= 0.298 Chirality : 0.044 0.211 10488 Planarity : 0.003 0.043 12696 Dihedral : 4.861 34.240 9726 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.11 % Allowed : 14.98 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.09), residues: 8602 helix: -1.30 (0.08), residues: 3381 sheet: -1.93 (0.11), residues: 2162 loop : -0.78 (0.11), residues: 3059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 71 HIS 0.004 0.001 HIS M 147 PHE 0.012 0.001 PHE j 342 TYR 0.027 0.001 TYR O 180 ARG 0.010 0.000 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1750 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1444 time to evaluate : 6.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8745 (mt0) cc_final: 0.8484 (mt0) REVERT: A 84 GLU cc_start: 0.7941 (mp0) cc_final: 0.7680 (mm-30) REVERT: B 272 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7604 (tt) REVERT: B 294 MET cc_start: 0.8578 (mmm) cc_final: 0.8005 (mmm) REVERT: B 362 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7854 (pttm) REVERT: C 171 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8751 (pt) REVERT: D 242 GLN cc_start: 0.7489 (mt0) cc_final: 0.7220 (mt0) REVERT: E 144 LYS cc_start: 0.8754 (mtpp) cc_final: 0.8283 (mtmm) REVERT: F 270 LYS cc_start: 0.9194 (ttpp) cc_final: 0.8968 (ttpp) REVERT: F 290 ASN cc_start: 0.8018 (t0) cc_final: 0.7774 (t0) REVERT: F 345 SER cc_start: 0.8927 (t) cc_final: 0.8541 (p) REVERT: G 25 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8122 (mtpp) REVERT: H 245 TYR cc_start: 0.8847 (p90) cc_final: 0.8624 (p90) REVERT: I 34 GLU cc_start: 0.7931 (tp30) cc_final: 0.7486 (tp30) REVERT: K 99 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7914 (mtp85) REVERT: L 345 SER cc_start: 0.8873 (t) cc_final: 0.8443 (p) REVERT: M 25 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8108 (mtpp) REVERT: M 144 LYS cc_start: 0.8660 (mttm) cc_final: 0.8317 (mmmt) REVERT: N 252 GLU cc_start: 0.7044 (mp0) cc_final: 0.6757 (mp0) REVERT: O 25 LYS cc_start: 0.8477 (mtpt) cc_final: 0.7871 (mtpp) REVERT: O 33 ASN cc_start: 0.8908 (m-40) cc_final: 0.8326 (m-40) REVERT: O 40 GLN cc_start: 0.8616 (mt0) cc_final: 0.8358 (mt0) REVERT: O 41 MET cc_start: 0.7922 (mtp) cc_final: 0.7654 (ttm) REVERT: O 132 TYR cc_start: 0.8723 (m-80) cc_final: 0.8319 (m-80) REVERT: O 144 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8342 (mtmm) REVERT: P 360 GLU cc_start: 0.7444 (pp20) cc_final: 0.6748 (pp20) REVERT: P 362 LYS cc_start: 0.8500 (pttm) cc_final: 0.7866 (pttm) REVERT: Q 25 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7713 (mtpp) REVERT: Q 101 GLU cc_start: 0.8644 (mp0) cc_final: 0.8072 (mp0) REVERT: Q 144 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8423 (mtmm) REVERT: R 335 GLU cc_start: 0.7790 (pm20) cc_final: 0.7583 (mt-10) REVERT: R 362 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8280 (pttm) REVERT: S 40 GLN cc_start: 0.8701 (mt0) cc_final: 0.8370 (mt0) REVERT: S 43 ASN cc_start: 0.9027 (t0) cc_final: 0.8743 (t0) REVERT: S 144 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8248 (mmmt) REVERT: T 242 GLN cc_start: 0.7618 (mt0) cc_final: 0.7270 (mt0) REVERT: T 345 SER cc_start: 0.8773 (t) cc_final: 0.8312 (p) REVERT: U 41 MET cc_start: 0.7886 (mtp) cc_final: 0.7608 (ttm) REVERT: U 101 GLU cc_start: 0.8578 (mp0) cc_final: 0.7989 (mp0) REVERT: V 213 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6591 (ttm170) REVERT: V 242 GLN cc_start: 0.7800 (mt0) cc_final: 0.7520 (mt0) REVERT: V 336 ILE cc_start: 0.8922 (tt) cc_final: 0.8563 (tt) REVERT: W 40 GLN cc_start: 0.8779 (mt0) cc_final: 0.8444 (mt0) REVERT: W 101 GLU cc_start: 0.8662 (mp0) cc_final: 0.8210 (mp0) REVERT: W 163 GLN cc_start: 0.8265 (mp10) cc_final: 0.7869 (mp10) REVERT: X 362 LYS cc_start: 0.8619 (pttm) cc_final: 0.8033 (pttm) REVERT: Y 25 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8144 (mtpp) REVERT: Y 87 GLN cc_start: 0.8448 (mt0) cc_final: 0.8206 (mt0) REVERT: Y 144 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8306 (mmmt) REVERT: Z 213 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6383 (ttm-80) REVERT: Z 345 SER cc_start: 0.8893 (t) cc_final: 0.8439 (p) REVERT: Z 360 GLU cc_start: 0.7188 (pp20) cc_final: 0.6926 (pp20) REVERT: a 33 ASN cc_start: 0.8923 (m-40) cc_final: 0.8650 (m-40) REVERT: a 40 GLN cc_start: 0.8748 (mt0) cc_final: 0.8415 (mt0) REVERT: b 345 SER cc_start: 0.9012 (t) cc_final: 0.8544 (p) REVERT: b 362 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8435 (pttm) REVERT: c 25 LYS cc_start: 0.8591 (mtpt) cc_final: 0.8352 (mtpp) REVERT: c 40 GLN cc_start: 0.8826 (mt0) cc_final: 0.8464 (mt0) REVERT: c 163 GLN cc_start: 0.8171 (mp10) cc_final: 0.7742 (mp10) REVERT: d 233 SER cc_start: 0.9050 (t) cc_final: 0.8794 (p) REVERT: d 333 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8461 (m-30) REVERT: d 362 LYS cc_start: 0.8431 (pttm) cc_final: 0.8132 (pttm) REVERT: e 40 GLN cc_start: 0.8722 (mt0) cc_final: 0.8400 (mt0) REVERT: f 345 SER cc_start: 0.8823 (t) cc_final: 0.8388 (p) REVERT: f 362 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7842 (pttm) REVERT: g 33 ASN cc_start: 0.8884 (m-40) cc_final: 0.8627 (m-40) REVERT: g 88 MET cc_start: 0.8368 (mtp) cc_final: 0.7934 (mtp) REVERT: g 180 TYR cc_start: 0.8958 (m-80) cc_final: 0.8711 (m-80) REVERT: h 181 LYS cc_start: 0.7989 (mmtm) cc_final: 0.7761 (mmtm) REVERT: i 147 HIS cc_start: 0.8528 (m-70) cc_final: 0.8295 (m90) REVERT: j 307 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8677 (tt) REVERT: j 342 PHE cc_start: 0.8529 (t80) cc_final: 0.8134 (t80) REVERT: k 40 GLN cc_start: 0.8719 (mt0) cc_final: 0.8415 (mt0) REVERT: l 242 GLN cc_start: 0.7610 (mt0) cc_final: 0.7174 (pt0) REVERT: l 345 SER cc_start: 0.8831 (t) cc_final: 0.8394 (p) REVERT: l 362 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8001 (pttm) REVERT: m 82 ARG cc_start: 0.7875 (tpt170) cc_final: 0.7650 (tpt90) REVERT: m 106 TYR cc_start: 0.8807 (m-80) cc_final: 0.8488 (m-80) REVERT: m 144 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8555 (mtmm) REVERT: n 242 GLN cc_start: 0.7590 (mt0) cc_final: 0.7282 (mt0) REVERT: n 255 LYS cc_start: 0.8234 (ptmm) cc_final: 0.8018 (ptpp) REVERT: n 345 SER cc_start: 0.8917 (t) cc_final: 0.8491 (p) REVERT: n 362 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8169 (pttm) REVERT: o 25 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8305 (mtpp) REVERT: o 33 ASN cc_start: 0.9122 (m-40) cc_final: 0.8884 (m-40) REVERT: o 41 MET cc_start: 0.7968 (mtp) cc_final: 0.7714 (ttm) REVERT: o 82 ARG cc_start: 0.7624 (tpt170) cc_final: 0.7306 (tpt170) REVERT: q 82 ARG cc_start: 0.7693 (tpt170) cc_final: 0.7491 (tpt170) REVERT: q 144 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8223 (mmmt) REVERT: r 213 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6903 (ttm170) REVERT: r 345 SER cc_start: 0.8818 (t) cc_final: 0.8419 (p) REVERT: r 362 LYS cc_start: 0.8267 (pttm) cc_final: 0.7968 (pttm) REVERT: s 34 GLU cc_start: 0.7768 (tp30) cc_final: 0.7256 (tp30) REVERT: s 169 ARG cc_start: 0.8585 (tpt170) cc_final: 0.8260 (tpp-160) REVERT: t 341 GLN cc_start: 0.8786 (mt0) cc_final: 0.8464 (mt0) REVERT: t 345 SER cc_start: 0.9001 (t) cc_final: 0.8532 (p) outliers start: 306 outliers final: 224 residues processed: 1672 average time/residue: 0.7588 time to fit residues: 2089.5967 Evaluate side-chains 1572 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1331 time to evaluate : 6.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 217 ASP Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain H residue 224 ASN Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 265 ASN Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 41 MET Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 99 ARG Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain L residue 176 LEU Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 307 LEU Chi-restraints excluded: chain L residue 361 LEU Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 224 ASN Chi-restraints excluded: chain N residue 265 ASN Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 181 ASP Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 361 LEU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain R residue 193 MET Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 217 ASP Chi-restraints excluded: chain R residue 224 ASN Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 265 ASN Chi-restraints excluded: chain R residue 332 ASP Chi-restraints excluded: chain R residue 361 LEU Chi-restraints excluded: chain R residue 362 LYS Chi-restraints excluded: chain S residue 144 LYS Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 200 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 213 ARG Chi-restraints excluded: chain T residue 265 ASN Chi-restraints excluded: chain T residue 307 LEU Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain U residue 29 GLN Chi-restraints excluded: chain U residue 66 THR Chi-restraints excluded: chain U residue 171 LEU Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 195 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain U residue 202 VAL Chi-restraints excluded: chain V residue 193 MET Chi-restraints excluded: chain V residue 213 ARG Chi-restraints excluded: chain V residue 217 ASP Chi-restraints excluded: chain V residue 224 ASN Chi-restraints excluded: chain V residue 248 ILE Chi-restraints excluded: chain V residue 265 ASN Chi-restraints excluded: chain V residue 307 LEU Chi-restraints excluded: chain V residue 332 ASP Chi-restraints excluded: chain V residue 333 ASP Chi-restraints excluded: chain W residue 178 VAL Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 202 VAL Chi-restraints excluded: chain X residue 193 MET Chi-restraints excluded: chain X residue 224 ASN Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 333 ASP Chi-restraints excluded: chain X residue 361 LEU Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 144 LYS Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 186 VAL Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Y residue 202 VAL Chi-restraints excluded: chain Z residue 213 ARG Chi-restraints excluded: chain Z residue 248 ILE Chi-restraints excluded: chain Z residue 265 ASN Chi-restraints excluded: chain Z residue 268 SER Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 361 LEU Chi-restraints excluded: chain Z residue 362 LYS Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 200 THR Chi-restraints excluded: chain b residue 196 VAL Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 332 ASP Chi-restraints excluded: chain b residue 333 ASP Chi-restraints excluded: chain b residue 361 LEU Chi-restraints excluded: chain b residue 362 LYS Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 144 LYS Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 217 ASP Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 307 LEU Chi-restraints excluded: chain d residue 333 ASP Chi-restraints excluded: chain d residue 361 LEU Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 127 ARG Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 195 LEU Chi-restraints excluded: chain e residue 200 THR Chi-restraints excluded: chain e residue 202 VAL Chi-restraints excluded: chain f residue 193 MET Chi-restraints excluded: chain f residue 196 VAL Chi-restraints excluded: chain f residue 217 ASP Chi-restraints excluded: chain f residue 224 ASN Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain f residue 307 LEU Chi-restraints excluded: chain f residue 361 LEU Chi-restraints excluded: chain f residue 362 LYS Chi-restraints excluded: chain g residue 60 VAL Chi-restraints excluded: chain g residue 66 THR Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 186 VAL Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 200 THR Chi-restraints excluded: chain g residue 202 VAL Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 269 LYS Chi-restraints excluded: chain h residue 307 LEU Chi-restraints excluded: chain h residue 361 LEU Chi-restraints excluded: chain i residue 171 LEU Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 195 LEU Chi-restraints excluded: chain i residue 200 THR Chi-restraints excluded: chain j residue 217 ASP Chi-restraints excluded: chain j residue 265 ASN Chi-restraints excluded: chain j residue 307 LEU Chi-restraints excluded: chain j residue 361 LEU Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 120 MET Chi-restraints excluded: chain k residue 178 VAL Chi-restraints excluded: chain k residue 181 ASP Chi-restraints excluded: chain k residue 200 THR Chi-restraints excluded: chain l residue 200 ASN Chi-restraints excluded: chain l residue 217 ASP Chi-restraints excluded: chain l residue 265 ASN Chi-restraints excluded: chain l residue 307 LEU Chi-restraints excluded: chain l residue 361 LEU Chi-restraints excluded: chain l residue 362 LYS Chi-restraints excluded: chain m residue 66 THR Chi-restraints excluded: chain m residue 171 LEU Chi-restraints excluded: chain m residue 186 VAL Chi-restraints excluded: chain m residue 200 THR Chi-restraints excluded: chain m residue 202 VAL Chi-restraints excluded: chain n residue 196 VAL Chi-restraints excluded: chain n residue 200 ASN Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain n residue 307 LEU Chi-restraints excluded: chain n residue 332 ASP Chi-restraints excluded: chain n residue 361 LEU Chi-restraints excluded: chain n residue 362 LYS Chi-restraints excluded: chain o residue 120 MET Chi-restraints excluded: chain o residue 160 LEU Chi-restraints excluded: chain o residue 172 LYS Chi-restraints excluded: chain o residue 178 VAL Chi-restraints excluded: chain o residue 186 VAL Chi-restraints excluded: chain o residue 200 THR Chi-restraints excluded: chain p residue 196 VAL Chi-restraints excluded: chain p residue 217 ASP Chi-restraints excluded: chain p residue 224 ASN Chi-restraints excluded: chain p residue 265 ASN Chi-restraints excluded: chain p residue 291 ILE Chi-restraints excluded: chain p residue 307 LEU Chi-restraints excluded: chain p residue 326 VAL Chi-restraints excluded: chain p residue 333 ASP Chi-restraints excluded: chain p residue 361 LEU Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 120 MET Chi-restraints excluded: chain q residue 144 LYS Chi-restraints excluded: chain q residue 172 LYS Chi-restraints excluded: chain q residue 178 VAL Chi-restraints excluded: chain q residue 195 LEU Chi-restraints excluded: chain q residue 200 THR Chi-restraints excluded: chain r residue 193 MET Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 213 ARG Chi-restraints excluded: chain r residue 217 ASP Chi-restraints excluded: chain r residue 224 ASN Chi-restraints excluded: chain r residue 307 LEU Chi-restraints excluded: chain s residue 66 THR Chi-restraints excluded: chain s residue 171 LEU Chi-restraints excluded: chain s residue 178 VAL Chi-restraints excluded: chain s residue 186 VAL Chi-restraints excluded: chain s residue 200 THR Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 217 ASP Chi-restraints excluded: chain t residue 361 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 276 optimal weight: 3.9990 chunk 740 optimal weight: 2.9990 chunk 162 optimal weight: 0.4980 chunk 482 optimal weight: 0.9990 chunk 203 optimal weight: 0.0980 chunk 823 optimal weight: 0.7980 chunk 683 optimal weight: 4.9990 chunk 381 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 272 optimal weight: 0.0770 chunk 432 optimal weight: 6.9990 overall best weight: 0.4940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN G 29 GLN G 76 GLN G 87 GLN ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 ASN K 76 GLN L 219 ASN ** M 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 196 GLN P 224 ASN ** Q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 224 ASN U 76 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN V 224 ASN W 29 GLN W 87 GLN ** X 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 224 ASN b 224 ASN d 224 ASN e 87 GLN ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 224 ASN j 224 ASN k 76 GLN k 196 GLN l 224 ASN n 224 ASN o 76 GLN ** o 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 196 GLN t 224 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 71231 Z= 0.139 Angle : 0.577 13.444 96439 Z= 0.281 Chirality : 0.043 0.226 10488 Planarity : 0.003 0.048 12696 Dihedral : 4.600 32.160 9721 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.33 % Allowed : 16.02 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.09), residues: 8602 helix: -0.93 (0.08), residues: 3358 sheet: -1.83 (0.11), residues: 2162 loop : -0.77 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 350 HIS 0.003 0.001 HIS Y 147 PHE 0.011 0.001 PHE j 342 TYR 0.026 0.001 TYR O 180 ARG 0.010 0.000 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1749 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1501 time to evaluate : 5.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8712 (mt0) cc_final: 0.8440 (mt0) REVERT: B 294 MET cc_start: 0.8548 (mmm) cc_final: 0.7949 (mmm) REVERT: B 362 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7826 (pttm) REVERT: D 242 GLN cc_start: 0.7279 (mt0) cc_final: 0.6974 (mt0) REVERT: E 144 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8301 (mtmm) REVERT: F 290 ASN cc_start: 0.8019 (t0) cc_final: 0.7779 (t0) REVERT: F 345 SER cc_start: 0.8919 (t) cc_final: 0.8435 (p) REVERT: G 25 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7995 (mtpp) REVERT: H 245 TYR cc_start: 0.8795 (p90) cc_final: 0.8544 (p90) REVERT: I 34 GLU cc_start: 0.7889 (tp30) cc_final: 0.7385 (tp30) REVERT: J 208 ARG cc_start: 0.7676 (mtp85) cc_final: 0.7470 (mtp180) REVERT: J 362 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8194 (pttm) REVERT: K 34 GLU cc_start: 0.7935 (tp30) cc_final: 0.7313 (tp30) REVERT: L 345 SER cc_start: 0.8831 (t) cc_final: 0.8451 (p) REVERT: M 25 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8040 (mtpp) REVERT: M 99 ARG cc_start: 0.8267 (mtp180) cc_final: 0.8020 (mtp180) REVERT: M 144 LYS cc_start: 0.8602 (mttm) cc_final: 0.8283 (mmmt) REVERT: O 25 LYS cc_start: 0.8399 (mtpt) cc_final: 0.7942 (mtpp) REVERT: O 33 ASN cc_start: 0.8887 (m-40) cc_final: 0.8291 (m-40) REVERT: O 40 GLN cc_start: 0.8564 (mt0) cc_final: 0.8283 (mt0) REVERT: O 41 MET cc_start: 0.7925 (mtp) cc_final: 0.7654 (ttm) REVERT: O 132 TYR cc_start: 0.8706 (m-80) cc_final: 0.8233 (m-80) REVERT: O 144 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8329 (mtmm) REVERT: Q 66 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8893 (p) REVERT: Q 144 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8459 (mtmm) REVERT: R 360 GLU cc_start: 0.7144 (pp20) cc_final: 0.6657 (pp20) REVERT: R 362 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7987 (pttm) REVERT: S 40 GLN cc_start: 0.8645 (mt0) cc_final: 0.8291 (mt0) REVERT: S 43 ASN cc_start: 0.9014 (t0) cc_final: 0.8670 (t0) REVERT: S 144 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8243 (mmmt) REVERT: T 242 GLN cc_start: 0.7449 (mt0) cc_final: 0.7121 (mt0) REVERT: T 341 GLN cc_start: 0.8774 (pt0) cc_final: 0.8356 (mt0) REVERT: T 345 SER cc_start: 0.8720 (t) cc_final: 0.8234 (p) REVERT: U 41 MET cc_start: 0.7808 (mtp) cc_final: 0.7552 (ttm) REVERT: U 101 GLU cc_start: 0.8574 (mp0) cc_final: 0.7970 (mp0) REVERT: V 242 GLN cc_start: 0.7681 (mt0) cc_final: 0.7382 (mt0) REVERT: W 40 GLN cc_start: 0.8744 (mt0) cc_final: 0.8435 (mt0) REVERT: X 232 ILE cc_start: 0.8905 (mt) cc_final: 0.8700 (mt) REVERT: Y 25 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7857 (mtpp) REVERT: Y 144 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8292 (mmmt) REVERT: Z 294 MET cc_start: 0.8524 (mmm) cc_final: 0.8286 (mmm) REVERT: Z 345 SER cc_start: 0.8800 (t) cc_final: 0.8303 (p) REVERT: a 33 ASN cc_start: 0.8899 (m-40) cc_final: 0.8603 (m-40) REVERT: a 40 GLN cc_start: 0.8721 (mt0) cc_final: 0.8376 (mt0) REVERT: a 144 LYS cc_start: 0.8938 (mttm) cc_final: 0.8488 (mmmt) REVERT: a 147 HIS cc_start: 0.8577 (m-70) cc_final: 0.8345 (m90) REVERT: b 345 SER cc_start: 0.8944 (t) cc_final: 0.8423 (p) REVERT: b 362 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8399 (pttm) REVERT: c 25 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8356 (mtpp) REVERT: c 40 GLN cc_start: 0.8814 (mt0) cc_final: 0.8455 (mt0) REVERT: c 163 GLN cc_start: 0.8163 (mp10) cc_final: 0.7728 (mp10) REVERT: d 233 SER cc_start: 0.9083 (t) cc_final: 0.8809 (p) REVERT: d 294 MET cc_start: 0.8431 (mmm) cc_final: 0.8185 (mtp) REVERT: d 362 LYS cc_start: 0.8387 (pttm) cc_final: 0.8085 (pttm) REVERT: e 25 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8212 (mtpp) REVERT: e 40 GLN cc_start: 0.8718 (mt0) cc_final: 0.8402 (mt0) REVERT: e 82 ARG cc_start: 0.7385 (tpt-90) cc_final: 0.6956 (tpt90) REVERT: e 144 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8460 (mmmt) REVERT: f 283 MET cc_start: 0.8953 (mtm) cc_final: 0.8706 (mtp) REVERT: f 294 MET cc_start: 0.8640 (mmm) cc_final: 0.8349 (mmm) REVERT: f 345 SER cc_start: 0.8761 (t) cc_final: 0.8283 (p) REVERT: f 362 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7901 (pttm) REVERT: g 180 TYR cc_start: 0.8992 (m-80) cc_final: 0.8724 (m-80) REVERT: h 255 LYS cc_start: 0.8081 (ptmm) cc_final: 0.7788 (ptpp) REVERT: i 25 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8264 (mtpp) REVERT: j 307 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8561 (tt) REVERT: j 342 PHE cc_start: 0.8477 (t80) cc_final: 0.8096 (t80) REVERT: k 24 LEU cc_start: 0.9022 (mt) cc_final: 0.8802 (mt) REVERT: k 25 LYS cc_start: 0.8360 (mtpp) cc_final: 0.7938 (ptpp) REVERT: k 40 GLN cc_start: 0.8683 (mt0) cc_final: 0.8353 (mt0) REVERT: k 82 ARG cc_start: 0.7188 (tpt90) cc_final: 0.6889 (tpt90) REVERT: k 163 GLN cc_start: 0.8168 (mp10) cc_final: 0.7946 (mp10) REVERT: l 242 GLN cc_start: 0.7468 (mt0) cc_final: 0.7064 (pt0) REVERT: l 345 SER cc_start: 0.8830 (t) cc_final: 0.8327 (p) REVERT: l 362 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7825 (pttm) REVERT: m 106 TYR cc_start: 0.8795 (m-80) cc_final: 0.8435 (m-80) REVERT: m 144 LYS cc_start: 0.8909 (mtpp) cc_final: 0.8608 (mtmm) REVERT: n 242 GLN cc_start: 0.7425 (mt0) cc_final: 0.7115 (mt0) REVERT: n 255 LYS cc_start: 0.8185 (ptmm) cc_final: 0.7982 (ptpp) REVERT: n 345 SER cc_start: 0.8881 (t) cc_final: 0.8450 (p) REVERT: n 348 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8219 (ttp80) REVERT: n 362 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7849 (pttm) REVERT: o 25 LYS cc_start: 0.8627 (mtpt) cc_final: 0.8222 (mtpp) REVERT: o 41 MET cc_start: 0.7893 (mtp) cc_final: 0.7597 (ttm) REVERT: o 163 GLN cc_start: 0.8210 (mp10) cc_final: 0.7758 (mp10) REVERT: p 181 LYS cc_start: 0.7936 (mmtm) cc_final: 0.7691 (mmtm) REVERT: p 192 LYS cc_start: 0.7075 (pttt) cc_final: 0.6863 (ptmt) REVERT: p 362 LYS cc_start: 0.8596 (pttm) cc_final: 0.8318 (pttm) REVERT: q 43 ASN cc_start: 0.8989 (t0) cc_final: 0.8736 (t0) REVERT: q 144 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8230 (mmmt) REVERT: r 345 SER cc_start: 0.8755 (t) cc_final: 0.8289 (p) REVERT: r 362 LYS cc_start: 0.8142 (pttm) cc_final: 0.7794 (pttm) REVERT: s 82 ARG cc_start: 0.7087 (tpt-90) cc_final: 0.6885 (mmm160) REVERT: s 169 ARG cc_start: 0.8551 (tpt170) cc_final: 0.8344 (tpp-160) REVERT: s 180 TYR cc_start: 0.8897 (m-10) cc_final: 0.8661 (m-10) REVERT: t 345 SER cc_start: 0.8860 (t) cc_final: 0.8369 (p) outliers start: 248 outliers final: 166 residues processed: 1685 average time/residue: 0.7159 time to fit residues: 1970.4924 Evaluate side-chains 1549 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1370 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 224 ASN Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 362 LYS Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 307 LEU Chi-restraints excluded: chain L residue 361 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain N residue 265 ASN Chi-restraints excluded: chain O residue 30 GLU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 361 LEU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain R residue 193 MET Chi-restraints excluded: chain R residue 217 ASP Chi-restraints excluded: chain R residue 224 ASN Chi-restraints excluded: chain R residue 265 ASN Chi-restraints excluded: chain R residue 332 ASP Chi-restraints excluded: chain R residue 361 LEU Chi-restraints excluded: chain R residue 362 LYS Chi-restraints excluded: chain S residue 144 LYS Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 200 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 265 ASN Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain U residue 195 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 265 ASN Chi-restraints excluded: chain V residue 307 LEU Chi-restraints excluded: chain V residue 332 ASP Chi-restraints excluded: chain V residue 333 ASP Chi-restraints excluded: chain W residue 29 GLN Chi-restraints excluded: chain W residue 178 VAL Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain X residue 332 ASP Chi-restraints excluded: chain X residue 333 ASP Chi-restraints excluded: chain X residue 361 LEU Chi-restraints excluded: chain Y residue 144 LYS Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 195 LEU Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Z residue 224 ASN Chi-restraints excluded: chain Z residue 248 ILE Chi-restraints excluded: chain Z residue 265 ASN Chi-restraints excluded: chain Z residue 268 SER Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 361 LEU Chi-restraints excluded: chain Z residue 362 LYS Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain b residue 224 ASN Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 361 LEU Chi-restraints excluded: chain b residue 362 LYS Chi-restraints excluded: chain c residue 144 LYS Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 195 LEU Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 217 ASP Chi-restraints excluded: chain d residue 224 ASN Chi-restraints excluded: chain d residue 307 LEU Chi-restraints excluded: chain d residue 361 LEU Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 195 LEU Chi-restraints excluded: chain f residue 193 MET Chi-restraints excluded: chain f residue 196 VAL Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain f residue 307 LEU Chi-restraints excluded: chain f residue 361 LEU Chi-restraints excluded: chain f residue 362 LYS Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 186 VAL Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 200 THR Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 224 ASN Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 307 LEU Chi-restraints excluded: chain h residue 361 LEU Chi-restraints excluded: chain h residue 362 LYS Chi-restraints excluded: chain i residue 171 LEU Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 195 LEU Chi-restraints excluded: chain j residue 224 ASN Chi-restraints excluded: chain j residue 265 ASN Chi-restraints excluded: chain j residue 307 LEU Chi-restraints excluded: chain j residue 361 LEU Chi-restraints excluded: chain k residue 120 MET Chi-restraints excluded: chain k residue 181 ASP Chi-restraints excluded: chain l residue 224 ASN Chi-restraints excluded: chain l residue 265 ASN Chi-restraints excluded: chain l residue 307 LEU Chi-restraints excluded: chain l residue 361 LEU Chi-restraints excluded: chain l residue 362 LYS Chi-restraints excluded: chain m residue 66 THR Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 186 VAL Chi-restraints excluded: chain n residue 224 ASN Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain n residue 307 LEU Chi-restraints excluded: chain n residue 332 ASP Chi-restraints excluded: chain n residue 361 LEU Chi-restraints excluded: chain n residue 362 LYS Chi-restraints excluded: chain o residue 120 MET Chi-restraints excluded: chain o residue 160 LEU Chi-restraints excluded: chain o residue 172 LYS Chi-restraints excluded: chain o residue 178 VAL Chi-restraints excluded: chain o residue 186 VAL Chi-restraints excluded: chain o residue 200 THR Chi-restraints excluded: chain p residue 196 VAL Chi-restraints excluded: chain p residue 217 ASP Chi-restraints excluded: chain p residue 265 ASN Chi-restraints excluded: chain p residue 307 LEU Chi-restraints excluded: chain p residue 333 ASP Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 120 MET Chi-restraints excluded: chain q residue 144 LYS Chi-restraints excluded: chain q residue 178 VAL Chi-restraints excluded: chain q residue 195 LEU Chi-restraints excluded: chain r residue 193 MET Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 217 ASP Chi-restraints excluded: chain r residue 307 LEU Chi-restraints excluded: chain s residue 178 VAL Chi-restraints excluded: chain s residue 186 VAL Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 224 ASN Chi-restraints excluded: chain t residue 361 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 793 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 469 optimal weight: 5.9990 chunk 601 optimal weight: 5.9990 chunk 465 optimal weight: 6.9990 chunk 693 optimal weight: 0.9990 chunk 459 optimal weight: 0.0980 chunk 820 optimal weight: 2.9990 chunk 513 optimal weight: 0.8980 chunk 500 optimal weight: 4.9990 chunk 378 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN D 224 ASN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 GLN G 43 ASN G 87 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN ** K 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 162 HIS N 224 ASN P 224 ASN Q 29 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 224 ASN S 76 GLN S 87 GLN U 29 GLN ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN V 224 ASN W 29 GLN W 43 ASN ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 87 GLN Z 224 ASN ** b 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 87 GLN ** d 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 224 ASN ** h 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 224 ASN ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 GLN ** k 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 29 GLN q 87 GLN s 196 GLN ** t 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 71231 Z= 0.155 Angle : 0.581 12.578 96439 Z= 0.283 Chirality : 0.043 0.188 10488 Planarity : 0.003 0.056 12696 Dihedral : 4.464 29.356 9718 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.35 % Allowed : 16.64 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.09), residues: 8602 helix: -0.65 (0.08), residues: 3335 sheet: -1.73 (0.11), residues: 2162 loop : -0.82 (0.11), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP f 206 HIS 0.005 0.001 HIS K 147 PHE 0.014 0.001 PHE f 342 TYR 0.048 0.001 TYR W 180 ARG 0.012 0.000 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1701 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1451 time to evaluate : 5.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8727 (mt0) cc_final: 0.8454 (mt0) REVERT: B 294 MET cc_start: 0.8527 (mmm) cc_final: 0.8095 (mmt) REVERT: B 362 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7829 (pttm) REVERT: C 102 LYS cc_start: 0.9082 (mtmt) cc_final: 0.8850 (mtpt) REVERT: D 242 GLN cc_start: 0.7252 (mt0) cc_final: 0.6950 (mt0) REVERT: E 82 ARG cc_start: 0.7339 (tpt170) cc_final: 0.7121 (tpt90) REVERT: E 144 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8314 (mtmm) REVERT: F 290 ASN cc_start: 0.8002 (t0) cc_final: 0.7778 (t0) REVERT: F 345 SER cc_start: 0.8917 (t) cc_final: 0.8422 (p) REVERT: G 25 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8018 (mtpp) REVERT: G 144 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8294 (mmmt) REVERT: H 245 TYR cc_start: 0.8750 (p90) cc_final: 0.8488 (p90) REVERT: I 34 GLU cc_start: 0.7892 (tp30) cc_final: 0.7408 (tp30) REVERT: J 362 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8115 (pttm) REVERT: K 163 GLN cc_start: 0.8172 (mp10) cc_final: 0.7962 (mp10) REVERT: L 252 GLU cc_start: 0.7471 (mp0) cc_final: 0.6984 (mp0) REVERT: L 341 GLN cc_start: 0.8803 (pt0) cc_final: 0.8380 (mt0) REVERT: L 345 SER cc_start: 0.8794 (t) cc_final: 0.8418 (p) REVERT: M 25 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8094 (mtpp) REVERT: M 34 GLU cc_start: 0.7802 (tp30) cc_final: 0.7442 (tp30) REVERT: M 144 LYS cc_start: 0.8644 (mttm) cc_final: 0.8276 (mmmt) REVERT: N 252 GLU cc_start: 0.6980 (mp0) cc_final: 0.6673 (mp0) REVERT: O 25 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7984 (mtpp) REVERT: O 33 ASN cc_start: 0.8913 (m-40) cc_final: 0.8290 (m-40) REVERT: O 40 GLN cc_start: 0.8573 (mt0) cc_final: 0.8298 (mt0) REVERT: O 41 MET cc_start: 0.7946 (mtp) cc_final: 0.7654 (ttm) REVERT: O 132 TYR cc_start: 0.8739 (m-80) cc_final: 0.8281 (m-80) REVERT: O 144 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8336 (mtmm) REVERT: Q 66 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8890 (p) REVERT: R 360 GLU cc_start: 0.7180 (pp20) cc_final: 0.6928 (pp20) REVERT: S 40 GLN cc_start: 0.8639 (mt0) cc_final: 0.8300 (mt0) REVERT: S 43 ASN cc_start: 0.9025 (t0) cc_final: 0.8669 (t0) REVERT: S 144 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8245 (mmmt) REVERT: T 242 GLN cc_start: 0.7430 (mt0) cc_final: 0.7093 (mt0) REVERT: T 341 GLN cc_start: 0.8720 (pt0) cc_final: 0.8346 (mt0) REVERT: T 345 SER cc_start: 0.8712 (t) cc_final: 0.8216 (p) REVERT: U 41 MET cc_start: 0.7913 (mtp) cc_final: 0.7566 (ttm) REVERT: U 101 GLU cc_start: 0.8594 (mp0) cc_final: 0.7993 (mp0) REVERT: V 242 GLN cc_start: 0.7668 (mt0) cc_final: 0.7367 (mt0) REVERT: V 294 MET cc_start: 0.7956 (ttm) cc_final: 0.7555 (ttp) REVERT: W 40 GLN cc_start: 0.8764 (mt0) cc_final: 0.8472 (mt0) REVERT: X 242 GLN cc_start: 0.7655 (mt0) cc_final: 0.7360 (pt0) REVERT: Y 25 LYS cc_start: 0.8412 (mtpt) cc_final: 0.7929 (mtpp) REVERT: Y 101 GLU cc_start: 0.8544 (mp0) cc_final: 0.7862 (mp0) REVERT: Y 144 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8312 (mmmt) REVERT: Y 163 GLN cc_start: 0.8307 (mp10) cc_final: 0.8023 (mp10) REVERT: Z 345 SER cc_start: 0.8770 (t) cc_final: 0.8257 (p) REVERT: a 33 ASN cc_start: 0.8893 (m-40) cc_final: 0.8606 (m-40) REVERT: a 40 GLN cc_start: 0.8720 (mt0) cc_final: 0.8378 (mt0) REVERT: a 144 LYS cc_start: 0.8876 (mttm) cc_final: 0.8328 (mmmt) REVERT: b 345 SER cc_start: 0.8964 (t) cc_final: 0.8435 (p) REVERT: c 40 GLN cc_start: 0.8811 (mt0) cc_final: 0.8433 (mt0) REVERT: c 88 MET cc_start: 0.8147 (mtp) cc_final: 0.7942 (mtp) REVERT: c 163 GLN cc_start: 0.8171 (mp10) cc_final: 0.7760 (mp10) REVERT: d 233 SER cc_start: 0.9017 (t) cc_final: 0.8758 (p) REVERT: d 294 MET cc_start: 0.8373 (mmm) cc_final: 0.8087 (mtp) REVERT: d 362 LYS cc_start: 0.8365 (pttm) cc_final: 0.8047 (pttm) REVERT: e 25 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8206 (mtpp) REVERT: e 101 GLU cc_start: 0.8552 (mp0) cc_final: 0.8085 (mp0) REVERT: e 144 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8448 (mmmt) REVERT: f 345 SER cc_start: 0.8750 (t) cc_final: 0.8238 (p) REVERT: f 362 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.7979 (pttm) REVERT: g 29 GLN cc_start: 0.7415 (tt0) cc_final: 0.7137 (tt0) REVERT: g 180 TYR cc_start: 0.9029 (m-80) cc_final: 0.8737 (m-80) REVERT: h 255 LYS cc_start: 0.8030 (ptmm) cc_final: 0.7783 (ptpp) REVERT: i 25 LYS cc_start: 0.8583 (mtmt) cc_final: 0.7890 (mtpp) REVERT: i 29 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: j 307 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8509 (tt) REVERT: j 342 PHE cc_start: 0.8495 (t80) cc_final: 0.8096 (t80) REVERT: k 40 GLN cc_start: 0.8682 (mt0) cc_final: 0.8381 (mt0) REVERT: k 144 LYS cc_start: 0.8651 (mttm) cc_final: 0.8185 (mmmt) REVERT: k 163 GLN cc_start: 0.8172 (mp10) cc_final: 0.7945 (mp10) REVERT: l 242 GLN cc_start: 0.7426 (mt0) cc_final: 0.7123 (pt0) REVERT: l 345 SER cc_start: 0.8844 (t) cc_final: 0.8311 (p) REVERT: l 362 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7817 (pttm) REVERT: m 106 TYR cc_start: 0.8799 (m-80) cc_final: 0.8457 (m-80) REVERT: m 144 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8545 (mtmm) REVERT: n 242 GLN cc_start: 0.7427 (mt0) cc_final: 0.7124 (mt0) REVERT: n 345 SER cc_start: 0.8874 (t) cc_final: 0.8437 (p) REVERT: n 348 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8258 (ttp80) REVERT: n 362 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7704 (pttm) REVERT: o 25 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8231 (mtpp) REVERT: o 41 MET cc_start: 0.7920 (mtp) cc_final: 0.7589 (ttm) REVERT: p 181 LYS cc_start: 0.7931 (mmtm) cc_final: 0.7696 (mmtm) REVERT: p 192 LYS cc_start: 0.7201 (pttt) cc_final: 0.6990 (ptmt) REVERT: q 43 ASN cc_start: 0.9015 (t0) cc_final: 0.8765 (t0) REVERT: q 163 GLN cc_start: 0.8215 (mp10) cc_final: 0.7782 (mp10) REVERT: r 345 SER cc_start: 0.8748 (t) cc_final: 0.8280 (p) REVERT: r 362 LYS cc_start: 0.8114 (pttm) cc_final: 0.7753 (pttm) REVERT: s 101 GLU cc_start: 0.8676 (mp0) cc_final: 0.7867 (mp0) REVERT: t 345 SER cc_start: 0.8879 (t) cc_final: 0.8376 (p) outliers start: 250 outliers final: 192 residues processed: 1642 average time/residue: 0.7000 time to fit residues: 1888.7409 Evaluate side-chains 1528 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1324 time to evaluate : 5.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 362 LYS Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 307 LEU Chi-restraints excluded: chain L residue 336 ILE Chi-restraints excluded: chain L residue 361 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 224 ASN Chi-restraints excluded: chain N residue 265 ASN Chi-restraints excluded: chain O residue 30 GLU Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 265 ASN Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 332 ASP Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain R residue 193 MET Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 217 ASP Chi-restraints excluded: chain R residue 224 ASN Chi-restraints excluded: chain R residue 265 ASN Chi-restraints excluded: chain R residue 332 ASP Chi-restraints excluded: chain R residue 361 LEU Chi-restraints excluded: chain R residue 362 LYS Chi-restraints excluded: chain S residue 144 LYS Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 181 ASP Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 200 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 265 ASN Chi-restraints excluded: chain T residue 333 ASP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain U residue 171 LEU Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 195 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain V residue 224 ASN Chi-restraints excluded: chain V residue 265 ASN Chi-restraints excluded: chain V residue 307 LEU Chi-restraints excluded: chain V residue 332 ASP Chi-restraints excluded: chain V residue 333 ASP Chi-restraints excluded: chain V residue 336 ILE Chi-restraints excluded: chain V residue 361 LEU Chi-restraints excluded: chain W residue 29 GLN Chi-restraints excluded: chain W residue 171 LEU Chi-restraints excluded: chain W residue 178 VAL Chi-restraints excluded: chain X residue 332 ASP Chi-restraints excluded: chain X residue 333 ASP Chi-restraints excluded: chain X residue 361 LEU Chi-restraints excluded: chain Y residue 144 LYS Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 186 VAL Chi-restraints excluded: chain Y residue 195 LEU Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Z residue 248 ILE Chi-restraints excluded: chain Z residue 265 ASN Chi-restraints excluded: chain Z residue 268 SER Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 361 LEU Chi-restraints excluded: chain Z residue 362 LYS Chi-restraints excluded: chain a residue 88 MET Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 200 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 332 ASP Chi-restraints excluded: chain b residue 361 LEU Chi-restraints excluded: chain c residue 144 LYS Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 195 LEU Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 217 ASP Chi-restraints excluded: chain d residue 307 LEU Chi-restraints excluded: chain d residue 361 LEU Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 195 LEU Chi-restraints excluded: chain e residue 200 THR Chi-restraints excluded: chain f residue 193 MET Chi-restraints excluded: chain f residue 196 VAL Chi-restraints excluded: chain f residue 217 ASP Chi-restraints excluded: chain f residue 224 ASN Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain f residue 307 LEU Chi-restraints excluded: chain f residue 332 ASP Chi-restraints excluded: chain f residue 361 LEU Chi-restraints excluded: chain f residue 362 LYS Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 186 VAL Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 200 THR Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 307 LEU Chi-restraints excluded: chain h residue 361 LEU Chi-restraints excluded: chain i residue 29 GLN Chi-restraints excluded: chain i residue 171 LEU Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 195 LEU Chi-restraints excluded: chain i residue 200 THR Chi-restraints excluded: chain j residue 265 ASN Chi-restraints excluded: chain j residue 307 LEU Chi-restraints excluded: chain j residue 332 ASP Chi-restraints excluded: chain j residue 336 ILE Chi-restraints excluded: chain j residue 361 LEU Chi-restraints excluded: chain k residue 120 MET Chi-restraints excluded: chain k residue 178 VAL Chi-restraints excluded: chain k residue 181 ASP Chi-restraints excluded: chain k residue 200 THR Chi-restraints excluded: chain l residue 200 ASN Chi-restraints excluded: chain l residue 265 ASN Chi-restraints excluded: chain l residue 307 LEU Chi-restraints excluded: chain l residue 362 LYS Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 186 VAL Chi-restraints excluded: chain m residue 200 THR Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain n residue 307 LEU Chi-restraints excluded: chain n residue 332 ASP Chi-restraints excluded: chain n residue 361 LEU Chi-restraints excluded: chain n residue 362 LYS Chi-restraints excluded: chain o residue 120 MET Chi-restraints excluded: chain o residue 160 LEU Chi-restraints excluded: chain o residue 178 VAL Chi-restraints excluded: chain o residue 186 VAL Chi-restraints excluded: chain o residue 200 THR Chi-restraints excluded: chain p residue 196 VAL Chi-restraints excluded: chain p residue 217 ASP Chi-restraints excluded: chain p residue 265 ASN Chi-restraints excluded: chain p residue 307 LEU Chi-restraints excluded: chain p residue 361 LEU Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 120 MET Chi-restraints excluded: chain q residue 178 VAL Chi-restraints excluded: chain q residue 195 LEU Chi-restraints excluded: chain q residue 200 THR Chi-restraints excluded: chain r residue 193 MET Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 217 ASP Chi-restraints excluded: chain r residue 307 LEU Chi-restraints excluded: chain s residue 171 LEU Chi-restraints excluded: chain s residue 178 VAL Chi-restraints excluded: chain s residue 186 VAL Chi-restraints excluded: chain s residue 200 THR Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 361 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 507 optimal weight: 5.9990 chunk 327 optimal weight: 6.9990 chunk 489 optimal weight: 0.9980 chunk 247 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 521 optimal weight: 0.8980 chunk 558 optimal weight: 6.9990 chunk 405 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 644 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN C 87 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN G 29 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN J 224 ASN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 GLN P 224 ASN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 GLN S 87 GLN S 111 GLN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN V 224 ASN W 29 GLN W 87 GLN X 224 ASN ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 87 GLN Z 224 ASN a 29 GLN a 43 ASN b 224 ASN c 87 GLN d 224 ASN e 87 GLN f 224 ASN g 76 GLN g 87 GLN h 224 ASN j 224 ASN k 76 GLN ** k 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 224 ASN n 224 ASN o 29 GLN ** o 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 224 ASN q 29 GLN r 224 ASN s 29 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 71231 Z= 0.181 Angle : 0.591 12.832 96439 Z= 0.287 Chirality : 0.043 0.265 10488 Planarity : 0.004 0.078 12696 Dihedral : 4.429 28.774 9718 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.38 % Allowed : 16.84 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.09), residues: 8602 helix: -0.55 (0.08), residues: 3381 sheet: -1.67 (0.11), residues: 2162 loop : -0.87 (0.11), residues: 3059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP f 206 HIS 0.004 0.001 HIS q 147 PHE 0.012 0.001 PHE f 342 TYR 0.028 0.001 TYR S 180 ARG 0.013 0.000 ARG G 141 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1633 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1381 time to evaluate : 7.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8749 (mt0) cc_final: 0.8467 (mt0) REVERT: B 294 MET cc_start: 0.8549 (mmm) cc_final: 0.8106 (mmt) REVERT: B 362 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7793 (pttm) REVERT: D 242 GLN cc_start: 0.7266 (mt0) cc_final: 0.6960 (mt0) REVERT: E 144 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8357 (mtmm) REVERT: F 290 ASN cc_start: 0.8005 (t0) cc_final: 0.7793 (t0) REVERT: F 345 SER cc_start: 0.8939 (t) cc_final: 0.8420 (p) REVERT: G 25 LYS cc_start: 0.8325 (mtpt) cc_final: 0.8020 (mtpp) REVERT: G 144 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8298 (mmmt) REVERT: H 245 TYR cc_start: 0.8740 (p90) cc_final: 0.8451 (p90) REVERT: I 34 GLU cc_start: 0.7923 (tp30) cc_final: 0.7449 (tp30) REVERT: I 163 GLN cc_start: 0.8282 (mp10) cc_final: 0.7706 (mp10) REVERT: L 341 GLN cc_start: 0.8812 (pt0) cc_final: 0.8383 (mt0) REVERT: L 345 SER cc_start: 0.8809 (t) cc_final: 0.8416 (p) REVERT: M 25 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8103 (mtpp) REVERT: M 34 GLU cc_start: 0.7817 (tp30) cc_final: 0.7575 (tp30) REVERT: M 144 LYS cc_start: 0.8659 (mttm) cc_final: 0.8284 (mmmt) REVERT: O 25 LYS cc_start: 0.8544 (mtpt) cc_final: 0.7979 (mtpp) REVERT: O 40 GLN cc_start: 0.8587 (mt0) cc_final: 0.8324 (mt0) REVERT: O 41 MET cc_start: 0.7960 (mtp) cc_final: 0.7639 (ttm) REVERT: O 132 TYR cc_start: 0.8746 (m-80) cc_final: 0.8305 (m-80) REVERT: P 362 LYS cc_start: 0.8182 (pttm) cc_final: 0.7672 (pttm) REVERT: Q 66 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8915 (p) REVERT: R 360 GLU cc_start: 0.7180 (pp20) cc_final: 0.6896 (pp20) REVERT: S 40 GLN cc_start: 0.8673 (mt0) cc_final: 0.8324 (mt0) REVERT: S 43 ASN cc_start: 0.9049 (t0) cc_final: 0.8671 (t0) REVERT: S 144 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8234 (mmmt) REVERT: T 242 GLN cc_start: 0.7433 (mt0) cc_final: 0.7103 (mt0) REVERT: T 319 HIS cc_start: 0.7665 (m-70) cc_final: 0.7388 (m-70) REVERT: T 341 GLN cc_start: 0.8701 (pt0) cc_final: 0.8368 (mt0) REVERT: T 345 SER cc_start: 0.8713 (t) cc_final: 0.8249 (p) REVERT: U 101 GLU cc_start: 0.8676 (mp0) cc_final: 0.8001 (mp0) REVERT: V 242 GLN cc_start: 0.7680 (mt0) cc_final: 0.7371 (mt0) REVERT: W 40 GLN cc_start: 0.8818 (mt0) cc_final: 0.8469 (mt0) REVERT: W 180 TYR cc_start: 0.8456 (m-80) cc_final: 0.8217 (m-10) REVERT: X 242 GLN cc_start: 0.7686 (mt0) cc_final: 0.7411 (pt0) REVERT: Y 25 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8121 (mtpp) REVERT: Y 144 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8271 (mmmt) REVERT: Z 345 SER cc_start: 0.8796 (t) cc_final: 0.8252 (p) REVERT: a 33 ASN cc_start: 0.8874 (m-40) cc_final: 0.8606 (m-40) REVERT: a 76 GLN cc_start: 0.8067 (mt0) cc_final: 0.7821 (mt0) REVERT: a 144 LYS cc_start: 0.8869 (mttm) cc_final: 0.8332 (mmmt) REVERT: a 163 GLN cc_start: 0.8268 (mp10) cc_final: 0.7954 (mp10) REVERT: b 345 SER cc_start: 0.9025 (t) cc_final: 0.8467 (p) REVERT: b 362 LYS cc_start: 0.8498 (pttm) cc_final: 0.7783 (pttm) REVERT: c 40 GLN cc_start: 0.8806 (mt0) cc_final: 0.8446 (mt0) REVERT: c 163 GLN cc_start: 0.8184 (mp10) cc_final: 0.7769 (mp10) REVERT: d 233 SER cc_start: 0.9002 (t) cc_final: 0.8752 (p) REVERT: d 362 LYS cc_start: 0.8373 (pttm) cc_final: 0.8044 (pttm) REVERT: e 25 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8217 (mtpp) REVERT: e 118 GLN cc_start: 0.8778 (tt0) cc_final: 0.8572 (mt0) REVERT: e 144 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8431 (mmmt) REVERT: f 294 MET cc_start: 0.8610 (mmm) cc_final: 0.8193 (tpp) REVERT: f 345 SER cc_start: 0.8757 (t) cc_final: 0.8224 (p) REVERT: f 362 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7896 (pttm) REVERT: g 101 GLU cc_start: 0.8530 (mp0) cc_final: 0.7713 (mp0) REVERT: g 180 TYR cc_start: 0.9022 (m-80) cc_final: 0.8734 (m-80) REVERT: h 255 LYS cc_start: 0.7990 (ptmm) cc_final: 0.7728 (ptpp) REVERT: h 294 MET cc_start: 0.8438 (mmt) cc_final: 0.7676 (mmt) REVERT: i 25 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8292 (mtpp) REVERT: i 29 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: i 34 GLU cc_start: 0.7548 (tp30) cc_final: 0.7258 (tm-30) REVERT: j 307 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8379 (tt) REVERT: j 342 PHE cc_start: 0.8547 (t80) cc_final: 0.8165 (t80) REVERT: k 25 LYS cc_start: 0.8445 (mtpp) cc_final: 0.8035 (ptpp) REVERT: k 144 LYS cc_start: 0.8662 (mttm) cc_final: 0.8186 (mmmt) REVERT: l 242 GLN cc_start: 0.7467 (mt0) cc_final: 0.7093 (pt0) REVERT: l 345 SER cc_start: 0.8866 (t) cc_final: 0.8312 (p) REVERT: l 362 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7718 (pttm) REVERT: m 106 TYR cc_start: 0.8822 (m-80) cc_final: 0.8393 (m-80) REVERT: m 144 LYS cc_start: 0.8868 (mtpp) cc_final: 0.8353 (mmmt) REVERT: n 242 GLN cc_start: 0.7427 (mt0) cc_final: 0.7126 (mt0) REVERT: n 345 SER cc_start: 0.8849 (t) cc_final: 0.8430 (p) REVERT: n 348 ARG cc_start: 0.8599 (ttp-110) cc_final: 0.8263 (ttp80) REVERT: n 362 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7729 (pttm) REVERT: o 25 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8245 (mtpp) REVERT: o 41 MET cc_start: 0.7931 (mtp) cc_final: 0.7615 (ttm) REVERT: p 181 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7702 (mmtm) REVERT: p 192 LYS cc_start: 0.7266 (pttt) cc_final: 0.7055 (ptmt) REVERT: q 43 ASN cc_start: 0.9024 (t0) cc_final: 0.8769 (t0) REVERT: q 163 GLN cc_start: 0.8254 (mp10) cc_final: 0.8026 (mp10) REVERT: r 345 SER cc_start: 0.8709 (t) cc_final: 0.8231 (p) REVERT: r 362 LYS cc_start: 0.8114 (pttm) cc_final: 0.7717 (pttm) REVERT: s 101 GLU cc_start: 0.8696 (mp0) cc_final: 0.7875 (mp0) REVERT: t 345 SER cc_start: 0.8904 (t) cc_final: 0.8386 (p) outliers start: 252 outliers final: 208 residues processed: 1565 average time/residue: 0.7068 time to fit residues: 1821.7887 Evaluate side-chains 1564 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1345 time to evaluate : 6.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 224 ASN Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 248 ILE Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 307 LEU Chi-restraints excluded: chain L residue 333 ASP Chi-restraints excluded: chain L residue 361 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 265 ASN Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain O residue 30 GLU Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 265 ASN Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 332 ASP Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain R residue 193 MET Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 217 ASP Chi-restraints excluded: chain R residue 265 ASN Chi-restraints excluded: chain R residue 332 ASP Chi-restraints excluded: chain R residue 361 LEU Chi-restraints excluded: chain R residue 362 LYS Chi-restraints excluded: chain S residue 144 LYS Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 200 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 265 ASN Chi-restraints excluded: chain T residue 332 ASP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain U residue 144 LYS Chi-restraints excluded: chain U residue 171 LEU Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 195 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 224 ASN Chi-restraints excluded: chain V residue 265 ASN Chi-restraints excluded: chain V residue 307 LEU Chi-restraints excluded: chain V residue 332 ASP Chi-restraints excluded: chain V residue 333 ASP Chi-restraints excluded: chain V residue 361 LEU Chi-restraints excluded: chain W residue 171 LEU Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain X residue 224 ASN Chi-restraints excluded: chain X residue 332 ASP Chi-restraints excluded: chain X residue 333 ASP Chi-restraints excluded: chain X residue 361 LEU Chi-restraints excluded: chain Y residue 144 LYS Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 186 VAL Chi-restraints excluded: chain Y residue 195 LEU Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Z residue 224 ASN Chi-restraints excluded: chain Z residue 248 ILE Chi-restraints excluded: chain Z residue 265 ASN Chi-restraints excluded: chain Z residue 268 SER Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 336 ILE Chi-restraints excluded: chain Z residue 361 LEU Chi-restraints excluded: chain Z residue 362 LYS Chi-restraints excluded: chain a residue 88 MET Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 200 THR Chi-restraints excluded: chain b residue 224 ASN Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 361 LEU Chi-restraints excluded: chain c residue 87 GLN Chi-restraints excluded: chain c residue 144 LYS Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 195 LEU Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 217 ASP Chi-restraints excluded: chain d residue 224 ASN Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 275 LEU Chi-restraints excluded: chain d residue 307 LEU Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 195 LEU Chi-restraints excluded: chain e residue 200 THR Chi-restraints excluded: chain f residue 193 MET Chi-restraints excluded: chain f residue 196 VAL Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain f residue 307 LEU Chi-restraints excluded: chain f residue 332 ASP Chi-restraints excluded: chain f residue 361 LEU Chi-restraints excluded: chain f residue 362 LYS Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 186 VAL Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 200 THR Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 224 ASN Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 307 LEU Chi-restraints excluded: chain h residue 332 ASP Chi-restraints excluded: chain h residue 361 LEU Chi-restraints excluded: chain i residue 29 GLN Chi-restraints excluded: chain i residue 171 LEU Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 195 LEU Chi-restraints excluded: chain i residue 200 THR Chi-restraints excluded: chain j residue 224 ASN Chi-restraints excluded: chain j residue 265 ASN Chi-restraints excluded: chain j residue 307 LEU Chi-restraints excluded: chain j residue 332 ASP Chi-restraints excluded: chain j residue 361 LEU Chi-restraints excluded: chain k residue 120 MET Chi-restraints excluded: chain k residue 178 VAL Chi-restraints excluded: chain k residue 181 ASP Chi-restraints excluded: chain k residue 200 THR Chi-restraints excluded: chain l residue 200 ASN Chi-restraints excluded: chain l residue 224 ASN Chi-restraints excluded: chain l residue 265 ASN Chi-restraints excluded: chain l residue 307 LEU Chi-restraints excluded: chain l residue 361 LEU Chi-restraints excluded: chain l residue 362 LYS Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 186 VAL Chi-restraints excluded: chain m residue 200 THR Chi-restraints excluded: chain n residue 224 ASN Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain n residue 307 LEU Chi-restraints excluded: chain n residue 332 ASP Chi-restraints excluded: chain n residue 362 LYS Chi-restraints excluded: chain o residue 120 MET Chi-restraints excluded: chain o residue 178 VAL Chi-restraints excluded: chain o residue 186 VAL Chi-restraints excluded: chain o residue 200 THR Chi-restraints excluded: chain p residue 196 VAL Chi-restraints excluded: chain p residue 217 ASP Chi-restraints excluded: chain p residue 224 ASN Chi-restraints excluded: chain p residue 265 ASN Chi-restraints excluded: chain p residue 307 LEU Chi-restraints excluded: chain p residue 332 ASP Chi-restraints excluded: chain p residue 361 LEU Chi-restraints excluded: chain q residue 29 GLN Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 120 MET Chi-restraints excluded: chain q residue 178 VAL Chi-restraints excluded: chain q residue 195 LEU Chi-restraints excluded: chain q residue 200 THR Chi-restraints excluded: chain r residue 193 MET Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 217 ASP Chi-restraints excluded: chain r residue 224 ASN Chi-restraints excluded: chain r residue 307 LEU Chi-restraints excluded: chain s residue 29 GLN Chi-restraints excluded: chain s residue 171 LEU Chi-restraints excluded: chain s residue 178 VAL Chi-restraints excluded: chain s residue 186 VAL Chi-restraints excluded: chain s residue 200 THR Chi-restraints excluded: chain t residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 746 optimal weight: 0.7980 chunk 785 optimal weight: 0.9980 chunk 716 optimal weight: 2.9990 chunk 764 optimal weight: 3.9990 chunk 460 optimal weight: 4.9990 chunk 332 optimal weight: 9.9990 chunk 600 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 690 optimal weight: 4.9990 chunk 722 optimal weight: 4.9990 chunk 761 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 GLN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 GLN N 224 ASN O 29 GLN O 87 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 224 ASN S 87 GLN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN V 224 ASN ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 87 GLN ** X 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 ASN e 43 ASN e 87 GLN f 224 ASN ** g 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 87 GLN m 87 GLN o 29 GLN o 76 GLN p 224 ASN q 29 GLN r 224 ASN ** s 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 76 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 71231 Z= 0.262 Angle : 0.628 12.623 96439 Z= 0.305 Chirality : 0.045 0.263 10488 Planarity : 0.004 0.065 12696 Dihedral : 4.497 28.513 9718 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.49 % Allowed : 16.61 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.09), residues: 8602 helix: -0.51 (0.08), residues: 3404 sheet: -1.67 (0.11), residues: 2162 loop : -0.86 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Z 350 HIS 0.008 0.001 HIS C 147 PHE 0.012 0.001 PHE f 342 TYR 0.032 0.001 TYR s 180 ARG 0.015 0.001 ARG s 141 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1333 time to evaluate : 6.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8768 (mt0) cc_final: 0.8474 (mt0) REVERT: B 362 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7851 (pttm) REVERT: D 242 GLN cc_start: 0.7329 (mt0) cc_final: 0.7062 (mt0) REVERT: E 144 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8275 (mtmm) REVERT: F 290 ASN cc_start: 0.8033 (t0) cc_final: 0.7797 (t0) REVERT: G 25 LYS cc_start: 0.8430 (mtpt) cc_final: 0.8092 (mtpp) REVERT: G 40 GLN cc_start: 0.8677 (mt0) cc_final: 0.8363 (mp10) REVERT: G 144 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8237 (mmmt) REVERT: H 245 TYR cc_start: 0.8772 (p90) cc_final: 0.8339 (p90) REVERT: I 34 GLU cc_start: 0.7974 (tp30) cc_final: 0.7507 (tp30) REVERT: I 163 GLN cc_start: 0.8293 (mp10) cc_final: 0.8052 (mp10) REVERT: J 362 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8167 (pttm) REVERT: L 325 PHE cc_start: 0.8805 (m-10) cc_final: 0.8530 (m-80) REVERT: L 341 GLN cc_start: 0.8843 (pt0) cc_final: 0.8588 (mt0) REVERT: L 345 SER cc_start: 0.8904 (t) cc_final: 0.8493 (p) REVERT: M 25 LYS cc_start: 0.8572 (mtpt) cc_final: 0.8179 (mtpp) REVERT: M 144 LYS cc_start: 0.8694 (mttm) cc_final: 0.8298 (mmmt) REVERT: O 25 LYS cc_start: 0.8634 (mtpt) cc_final: 0.7980 (mtpp) REVERT: O 33 ASN cc_start: 0.9072 (m-40) cc_final: 0.8559 (m-40) REVERT: O 40 GLN cc_start: 0.8627 (mt0) cc_final: 0.8377 (mt0) REVERT: O 41 MET cc_start: 0.7954 (mtp) cc_final: 0.7598 (ttm) REVERT: O 132 TYR cc_start: 0.8823 (m-80) cc_final: 0.8389 (m-80) REVERT: P 362 LYS cc_start: 0.8248 (pttm) cc_final: 0.7709 (pttm) REVERT: R 362 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8013 (pttm) REVERT: S 40 GLN cc_start: 0.8725 (mt0) cc_final: 0.8367 (mt0) REVERT: S 43 ASN cc_start: 0.9082 (t0) cc_final: 0.8697 (t0) REVERT: S 144 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8247 (mmmt) REVERT: T 242 GLN cc_start: 0.7479 (mt0) cc_final: 0.7158 (mt0) REVERT: T 319 HIS cc_start: 0.7692 (m-70) cc_final: 0.7413 (m-70) REVERT: T 341 GLN cc_start: 0.8734 (pt0) cc_final: 0.8383 (mt0) REVERT: T 345 SER cc_start: 0.8762 (t) cc_final: 0.8263 (p) REVERT: U 101 GLU cc_start: 0.8673 (mp0) cc_final: 0.7981 (mp0) REVERT: V 242 GLN cc_start: 0.7753 (mt0) cc_final: 0.7447 (mt0) REVERT: W 40 GLN cc_start: 0.8850 (mt0) cc_final: 0.8498 (mt0) REVERT: X 242 GLN cc_start: 0.7793 (mt0) cc_final: 0.7504 (pt0) REVERT: Y 25 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8159 (mtpp) REVERT: Y 101 GLU cc_start: 0.8572 (mp0) cc_final: 0.7883 (mp0) REVERT: Y 144 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8265 (mmmt) REVERT: Z 233 SER cc_start: 0.9048 (t) cc_final: 0.8757 (p) REVERT: Z 345 SER cc_start: 0.8862 (t) cc_final: 0.8316 (p) REVERT: a 29 GLN cc_start: 0.7616 (tt0) cc_final: 0.7260 (tt0) REVERT: a 33 ASN cc_start: 0.8875 (m-40) cc_final: 0.8570 (m-40) REVERT: a 144 LYS cc_start: 0.8895 (mttm) cc_final: 0.8348 (mmmt) REVERT: a 147 HIS cc_start: 0.8700 (m-70) cc_final: 0.8341 (m90) REVERT: b 345 SER cc_start: 0.9077 (t) cc_final: 0.8490 (p) REVERT: b 362 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7773 (pttm) REVERT: c 163 GLN cc_start: 0.8209 (mp10) cc_final: 0.7760 (mp10) REVERT: d 233 SER cc_start: 0.9016 (t) cc_final: 0.8759 (p) REVERT: d 362 LYS cc_start: 0.8328 (pttm) cc_final: 0.8001 (pttm) REVERT: e 144 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8412 (mmmt) REVERT: f 345 SER cc_start: 0.8761 (t) cc_final: 0.8264 (p) REVERT: f 362 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8060 (pttm) REVERT: g 101 GLU cc_start: 0.8565 (mp0) cc_final: 0.7750 (mp0) REVERT: g 163 GLN cc_start: 0.8338 (mp10) cc_final: 0.8077 (mp10) REVERT: g 180 TYR cc_start: 0.9061 (m-80) cc_final: 0.8782 (m-80) REVERT: h 194 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8066 (tt) REVERT: h 255 LYS cc_start: 0.7999 (ptmm) cc_final: 0.7744 (ptpp) REVERT: i 25 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8286 (mtpp) REVERT: j 307 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8483 (tt) REVERT: k 25 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8082 (ptpp) REVERT: k 163 GLN cc_start: 0.8286 (mp10) cc_final: 0.7992 (mp10) REVERT: l 242 GLN cc_start: 0.7572 (mt0) cc_final: 0.7207 (pt0) REVERT: l 345 SER cc_start: 0.8907 (t) cc_final: 0.8336 (p) REVERT: l 362 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7802 (pttm) REVERT: m 106 TYR cc_start: 0.8852 (m-80) cc_final: 0.8437 (m-80) REVERT: m 144 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8356 (mmmt) REVERT: n 242 GLN cc_start: 0.7541 (mt0) cc_final: 0.7225 (mt0) REVERT: n 345 SER cc_start: 0.8915 (t) cc_final: 0.8438 (p) REVERT: n 362 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7780 (pttm) REVERT: o 25 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8322 (mtpp) REVERT: o 41 MET cc_start: 0.7974 (mtp) cc_final: 0.7687 (ttm) REVERT: p 181 LYS cc_start: 0.7950 (mmtm) cc_final: 0.7724 (mmtm) REVERT: p 192 LYS cc_start: 0.7340 (pttt) cc_final: 0.7123 (ptmt) REVERT: r 345 SER cc_start: 0.8657 (t) cc_final: 0.8209 (p) REVERT: r 362 LYS cc_start: 0.8230 (pttm) cc_final: 0.7903 (pttm) REVERT: s 101 GLU cc_start: 0.8732 (mp0) cc_final: 0.7867 (mp0) REVERT: t 345 SER cc_start: 0.8952 (t) cc_final: 0.8405 (p) outliers start: 260 outliers final: 222 residues processed: 1535 average time/residue: 0.7261 time to fit residues: 1844.7814 Evaluate side-chains 1532 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1297 time to evaluate : 5.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 332 ASP Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 362 LYS Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 248 ILE Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 307 LEU Chi-restraints excluded: chain L residue 333 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 217 ASP Chi-restraints excluded: chain N residue 224 ASN Chi-restraints excluded: chain N residue 265 ASN Chi-restraints excluded: chain O residue 29 GLN Chi-restraints excluded: chain O residue 30 GLU Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 178 VAL Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 265 ASN Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain P residue 332 ASP Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain R residue 193 MET Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 217 ASP Chi-restraints excluded: chain R residue 224 ASN Chi-restraints excluded: chain R residue 265 ASN Chi-restraints excluded: chain R residue 332 ASP Chi-restraints excluded: chain R residue 361 LEU Chi-restraints excluded: chain R residue 362 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 144 LYS Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 181 ASP Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 200 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 265 ASN Chi-restraints excluded: chain T residue 332 ASP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain U residue 171 LEU Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 181 ASP Chi-restraints excluded: chain U residue 195 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 217 ASP Chi-restraints excluded: chain V residue 265 ASN Chi-restraints excluded: chain V residue 307 LEU Chi-restraints excluded: chain V residue 332 ASP Chi-restraints excluded: chain V residue 333 ASP Chi-restraints excluded: chain V residue 361 LEU Chi-restraints excluded: chain W residue 88 MET Chi-restraints excluded: chain W residue 171 LEU Chi-restraints excluded: chain W residue 178 VAL Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 332 ASP Chi-restraints excluded: chain X residue 333 ASP Chi-restraints excluded: chain X residue 360 GLU Chi-restraints excluded: chain X residue 361 LEU Chi-restraints excluded: chain Y residue 144 LYS Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 186 VAL Chi-restraints excluded: chain Y residue 195 LEU Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Z residue 248 ILE Chi-restraints excluded: chain Z residue 265 ASN Chi-restraints excluded: chain Z residue 268 SER Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 361 LEU Chi-restraints excluded: chain Z residue 362 LYS Chi-restraints excluded: chain a residue 88 MET Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 181 ASP Chi-restraints excluded: chain a residue 200 THR Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 361 LEU Chi-restraints excluded: chain b residue 362 LYS Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 195 LEU Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 217 ASP Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 307 LEU Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 87 GLN Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 178 VAL Chi-restraints excluded: chain e residue 195 LEU Chi-restraints excluded: chain e residue 200 THR Chi-restraints excluded: chain f residue 193 MET Chi-restraints excluded: chain f residue 196 VAL Chi-restraints excluded: chain f residue 217 ASP Chi-restraints excluded: chain f residue 224 ASN Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain f residue 307 LEU Chi-restraints excluded: chain f residue 332 ASP Chi-restraints excluded: chain f residue 361 LEU Chi-restraints excluded: chain f residue 362 LYS Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 186 VAL Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 200 THR Chi-restraints excluded: chain h residue 194 LEU Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 307 LEU Chi-restraints excluded: chain h residue 332 ASP Chi-restraints excluded: chain h residue 361 LEU Chi-restraints excluded: chain i residue 171 LEU Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 195 LEU Chi-restraints excluded: chain i residue 200 THR Chi-restraints excluded: chain j residue 217 ASP Chi-restraints excluded: chain j residue 265 ASN Chi-restraints excluded: chain j residue 307 LEU Chi-restraints excluded: chain j residue 332 ASP Chi-restraints excluded: chain j residue 361 LEU Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 120 MET Chi-restraints excluded: chain k residue 178 VAL Chi-restraints excluded: chain k residue 181 ASP Chi-restraints excluded: chain k residue 200 THR Chi-restraints excluded: chain l residue 265 ASN Chi-restraints excluded: chain l residue 307 LEU Chi-restraints excluded: chain l residue 361 LEU Chi-restraints excluded: chain l residue 362 LYS Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 186 VAL Chi-restraints excluded: chain m residue 200 THR Chi-restraints excluded: chain n residue 196 VAL Chi-restraints excluded: chain n residue 200 ASN Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain n residue 307 LEU Chi-restraints excluded: chain n residue 332 ASP Chi-restraints excluded: chain n residue 362 LYS Chi-restraints excluded: chain o residue 120 MET Chi-restraints excluded: chain o residue 172 LYS Chi-restraints excluded: chain o residue 178 VAL Chi-restraints excluded: chain o residue 186 VAL Chi-restraints excluded: chain o residue 200 THR Chi-restraints excluded: chain p residue 196 VAL Chi-restraints excluded: chain p residue 217 ASP Chi-restraints excluded: chain p residue 224 ASN Chi-restraints excluded: chain p residue 265 ASN Chi-restraints excluded: chain p residue 307 LEU Chi-restraints excluded: chain p residue 332 ASP Chi-restraints excluded: chain p residue 361 LEU Chi-restraints excluded: chain q residue 29 GLN Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 120 MET Chi-restraints excluded: chain q residue 178 VAL Chi-restraints excluded: chain q residue 195 LEU Chi-restraints excluded: chain q residue 200 THR Chi-restraints excluded: chain r residue 193 MET Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 217 ASP Chi-restraints excluded: chain r residue 307 LEU Chi-restraints excluded: chain s residue 29 GLN Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 171 LEU Chi-restraints excluded: chain s residue 178 VAL Chi-restraints excluded: chain s residue 186 VAL Chi-restraints excluded: chain s residue 200 THR Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 361 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 501 optimal weight: 6.9990 chunk 808 optimal weight: 3.9990 chunk 493 optimal weight: 0.9990 chunk 383 optimal weight: 0.9980 chunk 561 optimal weight: 0.1980 chunk 847 optimal weight: 2.9990 chunk 780 optimal weight: 5.9990 chunk 675 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 521 optimal weight: 0.7980 chunk 413 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 224 ASN ** C 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 29 GLN J 224 ASN K 29 GLN ** N 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 GLN P 224 ASN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 224 ASN ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 87 GLN X 224 ASN ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 224 ASN a 43 ASN b 224 ASN d 224 ASN f 224 ASN g 76 GLN g 115 GLN h 224 ASN i 29 GLN j 224 ASN l 224 ASN n 224 ASN o 76 GLN q 29 GLN q 87 GLN r 224 ASN ** s 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 224 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 71231 Z= 0.161 Angle : 0.604 14.789 96439 Z= 0.290 Chirality : 0.043 0.264 10488 Planarity : 0.004 0.064 12696 Dihedral : 4.420 27.453 9718 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.27 % Allowed : 17.28 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.09), residues: 8602 helix: -0.36 (0.09), residues: 3404 sheet: -1.58 (0.11), residues: 2162 loop : -0.87 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 235 HIS 0.006 0.001 HIS C 147 PHE 0.011 0.001 PHE f 342 TYR 0.028 0.001 TYR i 180 ARG 0.015 0.000 ARG A 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17204 Ramachandran restraints generated. 8602 Oldfield, 0 Emsley, 8602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1621 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1377 time to evaluate : 5.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8746 (mt0) cc_final: 0.8455 (mt0) REVERT: B 294 MET cc_start: 0.8363 (mmm) cc_final: 0.7846 (mmm) REVERT: B 362 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7814 (pttm) REVERT: E 144 LYS cc_start: 0.8839 (mtpp) cc_final: 0.8305 (mtmm) REVERT: F 290 ASN cc_start: 0.8020 (t0) cc_final: 0.7806 (t0) REVERT: G 25 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8023 (mtpp) REVERT: G 40 GLN cc_start: 0.8617 (mt0) cc_final: 0.8328 (mp10) REVERT: G 144 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8268 (mmmt) REVERT: H 245 TYR cc_start: 0.8736 (p90) cc_final: 0.8384 (p90) REVERT: I 34 GLU cc_start: 0.7890 (tp30) cc_final: 0.7402 (tp30) REVERT: I 163 GLN cc_start: 0.8270 (mp10) cc_final: 0.8036 (mp10) REVERT: K 34 GLU cc_start: 0.7905 (tp30) cc_final: 0.7302 (tp30) REVERT: L 255 LYS cc_start: 0.8131 (ptmm) cc_final: 0.7852 (ptpp) REVERT: L 325 PHE cc_start: 0.8757 (m-10) cc_final: 0.8508 (m-80) REVERT: L 341 GLN cc_start: 0.8791 (pt0) cc_final: 0.8365 (mt0) REVERT: L 345 SER cc_start: 0.8839 (t) cc_final: 0.8427 (p) REVERT: M 25 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8019 (mtpp) REVERT: M 34 GLU cc_start: 0.7753 (tp30) cc_final: 0.7399 (tp30) REVERT: M 144 LYS cc_start: 0.8627 (mttm) cc_final: 0.8281 (mmmt) REVERT: N 325 PHE cc_start: 0.8857 (m-10) cc_final: 0.8630 (m-80) REVERT: O 40 GLN cc_start: 0.8604 (mt0) cc_final: 0.8311 (mt0) REVERT: O 132 TYR cc_start: 0.8786 (m-80) cc_final: 0.8341 (m-80) REVERT: O 144 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8331 (mtmm) REVERT: P 362 LYS cc_start: 0.8163 (pttm) cc_final: 0.7691 (pttm) REVERT: Q 66 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8887 (p) REVERT: R 360 GLU cc_start: 0.7101 (pp20) cc_final: 0.6280 (pp20) REVERT: R 362 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7876 (pttm) REVERT: S 40 GLN cc_start: 0.8653 (mt0) cc_final: 0.8303 (mt0) REVERT: S 43 ASN cc_start: 0.9050 (t0) cc_final: 0.8648 (t0) REVERT: S 87 GLN cc_start: 0.8428 (mt0) cc_final: 0.8204 (mt0) REVERT: S 144 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8159 (mmmt) REVERT: T 242 GLN cc_start: 0.7415 (mt0) cc_final: 0.7089 (mt0) REVERT: T 341 GLN cc_start: 0.8642 (pt0) cc_final: 0.8350 (mt0) REVERT: T 345 SER cc_start: 0.8721 (t) cc_final: 0.8235 (p) REVERT: V 242 GLN cc_start: 0.7676 (mt0) cc_final: 0.7370 (mt0) REVERT: W 40 GLN cc_start: 0.8830 (mt0) cc_final: 0.8492 (mt0) REVERT: W 101 GLU cc_start: 0.8770 (mp0) cc_final: 0.8148 (mp0) REVERT: X 242 GLN cc_start: 0.7782 (mt0) cc_final: 0.7497 (pt0) REVERT: X 335 GLU cc_start: 0.7689 (pm20) cc_final: 0.7440 (mt-10) REVERT: Y 25 LYS cc_start: 0.8492 (mtpt) cc_final: 0.8057 (mtpp) REVERT: Y 82 ARG cc_start: 0.7205 (tpt-90) cc_final: 0.6742 (tpt90) REVERT: Y 144 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8249 (mmmt) REVERT: Z 233 SER cc_start: 0.8934 (t) cc_final: 0.8717 (p) REVERT: Z 345 SER cc_start: 0.8797 (t) cc_final: 0.8259 (p) REVERT: a 29 GLN cc_start: 0.7503 (tt0) cc_final: 0.7171 (tt0) REVERT: a 33 ASN cc_start: 0.8848 (m-40) cc_final: 0.8531 (m-40) REVERT: a 101 GLU cc_start: 0.8484 (mp0) cc_final: 0.8132 (mp0) REVERT: a 144 LYS cc_start: 0.8863 (mttm) cc_final: 0.8290 (mmmt) REVERT: a 147 HIS cc_start: 0.8613 (m-70) cc_final: 0.8266 (m90) REVERT: b 345 SER cc_start: 0.8995 (t) cc_final: 0.8422 (p) REVERT: b 362 LYS cc_start: 0.8418 (pttm) cc_final: 0.7642 (pttm) REVERT: c 163 GLN cc_start: 0.8199 (mp10) cc_final: 0.7798 (mp10) REVERT: d 233 SER cc_start: 0.8997 (t) cc_final: 0.8725 (p) REVERT: d 362 LYS cc_start: 0.8223 (pttm) cc_final: 0.7902 (pttm) REVERT: e 144 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8414 (mmmt) REVERT: f 294 MET cc_start: 0.8585 (mmm) cc_final: 0.8155 (tpp) REVERT: f 345 SER cc_start: 0.8738 (t) cc_final: 0.8199 (p) REVERT: f 362 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7954 (pttm) REVERT: g 101 GLU cc_start: 0.8533 (mp0) cc_final: 0.7694 (mp0) REVERT: g 163 GLN cc_start: 0.8258 (mp10) cc_final: 0.8007 (mp10) REVERT: g 180 TYR cc_start: 0.9011 (m-80) cc_final: 0.8735 (m-80) REVERT: h 181 LYS cc_start: 0.7718 (mmtm) cc_final: 0.7496 (mmtm) REVERT: h 255 LYS cc_start: 0.7969 (ptmm) cc_final: 0.7712 (ptpp) REVERT: h 294 MET cc_start: 0.8401 (mmt) cc_final: 0.7684 (mmt) REVERT: i 25 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8210 (mtpp) REVERT: i 34 GLU cc_start: 0.7511 (tp30) cc_final: 0.7227 (tm-30) REVERT: j 307 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8480 (tt) REVERT: j 342 PHE cc_start: 0.8492 (t80) cc_final: 0.8120 (t80) REVERT: k 25 LYS cc_start: 0.8417 (mtpp) cc_final: 0.8083 (ptpp) REVERT: k 163 GLN cc_start: 0.8245 (mp10) cc_final: 0.7954 (mp10) REVERT: l 242 GLN cc_start: 0.7494 (mt0) cc_final: 0.7165 (pt0) REVERT: l 345 SER cc_start: 0.8831 (t) cc_final: 0.8253 (p) REVERT: l 362 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7602 (pttm) REVERT: m 106 TYR cc_start: 0.8801 (m-80) cc_final: 0.8381 (m-80) REVERT: m 144 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8347 (mmmt) REVERT: n 345 SER cc_start: 0.8852 (t) cc_final: 0.8383 (p) REVERT: n 362 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7605 (pttm) REVERT: o 25 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8254 (mtpp) REVERT: o 41 MET cc_start: 0.7923 (mtp) cc_final: 0.7605 (ttm) REVERT: o 163 GLN cc_start: 0.8235 (mp10) cc_final: 0.7744 (mp10) REVERT: p 181 LYS cc_start: 0.7932 (mmtm) cc_final: 0.7708 (mmtm) REVERT: p 192 LYS cc_start: 0.7334 (pttt) cc_final: 0.7115 (ptmt) REVERT: q 43 ASN cc_start: 0.9007 (t0) cc_final: 0.8752 (t0) REVERT: q 163 GLN cc_start: 0.8295 (mp10) cc_final: 0.8052 (mp10) REVERT: r 335 GLU cc_start: 0.7594 (pm20) cc_final: 0.7281 (mt-10) REVERT: r 345 SER cc_start: 0.8638 (t) cc_final: 0.8195 (p) REVERT: r 346 TYR cc_start: 0.9048 (t80) cc_final: 0.8839 (t80) REVERT: r 362 LYS cc_start: 0.8093 (pttm) cc_final: 0.7747 (pttm) REVERT: s 101 GLU cc_start: 0.8695 (mp0) cc_final: 0.7830 (mp0) REVERT: t 345 SER cc_start: 0.8904 (t) cc_final: 0.8364 (p) outliers start: 244 outliers final: 211 residues processed: 1554 average time/residue: 0.6953 time to fit residues: 1781.6708 Evaluate side-chains 1547 residues out of total 7452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1325 time to evaluate : 5.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 224 ASN Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 224 ASN Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain G residue 144 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 307 LEU Chi-restraints excluded: chain H residue 332 ASP Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 200 THR Chi-restraints excluded: chain J residue 193 MET Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 224 ASN Chi-restraints excluded: chain J residue 292 THR Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 200 THR Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain L residue 196 VAL Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 248 ILE Chi-restraints excluded: chain L residue 265 ASN Chi-restraints excluded: chain L residue 307 LEU Chi-restraints excluded: chain L residue 333 ASP Chi-restraints excluded: chain L residue 361 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 186 VAL Chi-restraints excluded: chain M residue 200 THR Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain N residue 265 ASN Chi-restraints excluded: chain O residue 30 GLU Chi-restraints excluded: chain O residue 171 LEU Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 217 ASP Chi-restraints excluded: chain P residue 224 ASN Chi-restraints excluded: chain P residue 265 ASN Chi-restraints excluded: chain P residue 283 MET Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 178 VAL Chi-restraints excluded: chain Q residue 186 VAL Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain R residue 193 MET Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain R residue 217 ASP Chi-restraints excluded: chain R residue 265 ASN Chi-restraints excluded: chain R residue 332 ASP Chi-restraints excluded: chain R residue 361 LEU Chi-restraints excluded: chain R residue 362 LYS Chi-restraints excluded: chain S residue 29 GLN Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 144 LYS Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 186 VAL Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 200 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 265 ASN Chi-restraints excluded: chain T residue 332 ASP Chi-restraints excluded: chain T residue 361 LEU Chi-restraints excluded: chain U residue 178 VAL Chi-restraints excluded: chain U residue 181 ASP Chi-restraints excluded: chain U residue 195 LEU Chi-restraints excluded: chain U residue 200 THR Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 224 ASN Chi-restraints excluded: chain V residue 265 ASN Chi-restraints excluded: chain V residue 307 LEU Chi-restraints excluded: chain V residue 332 ASP Chi-restraints excluded: chain V residue 333 ASP Chi-restraints excluded: chain V residue 361 LEU Chi-restraints excluded: chain W residue 171 LEU Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain X residue 224 ASN Chi-restraints excluded: chain X residue 332 ASP Chi-restraints excluded: chain X residue 333 ASP Chi-restraints excluded: chain X residue 360 GLU Chi-restraints excluded: chain X residue 361 LEU Chi-restraints excluded: chain Y residue 66 THR Chi-restraints excluded: chain Y residue 144 LYS Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 186 VAL Chi-restraints excluded: chain Y residue 195 LEU Chi-restraints excluded: chain Y residue 200 THR Chi-restraints excluded: chain Z residue 224 ASN Chi-restraints excluded: chain Z residue 248 ILE Chi-restraints excluded: chain Z residue 265 ASN Chi-restraints excluded: chain Z residue 268 SER Chi-restraints excluded: chain Z residue 307 LEU Chi-restraints excluded: chain Z residue 361 LEU Chi-restraints excluded: chain Z residue 362 LYS Chi-restraints excluded: chain a residue 88 MET Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 200 THR Chi-restraints excluded: chain b residue 224 ASN Chi-restraints excluded: chain b residue 265 ASN Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 332 ASP Chi-restraints excluded: chain b residue 361 LEU Chi-restraints excluded: chain c residue 144 LYS Chi-restraints excluded: chain c residue 178 VAL Chi-restraints excluded: chain c residue 186 VAL Chi-restraints excluded: chain c residue 195 LEU Chi-restraints excluded: chain c residue 200 THR Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 217 ASP Chi-restraints excluded: chain d residue 224 ASN Chi-restraints excluded: chain d residue 248 ILE Chi-restraints excluded: chain d residue 275 LEU Chi-restraints excluded: chain d residue 307 LEU Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 83 VAL Chi-restraints excluded: chain e residue 144 LYS Chi-restraints excluded: chain e residue 195 LEU Chi-restraints excluded: chain f residue 196 VAL Chi-restraints excluded: chain f residue 265 ASN Chi-restraints excluded: chain f residue 307 LEU Chi-restraints excluded: chain f residue 361 LEU Chi-restraints excluded: chain f residue 362 LYS Chi-restraints excluded: chain g residue 178 VAL Chi-restraints excluded: chain g residue 186 VAL Chi-restraints excluded: chain g residue 195 LEU Chi-restraints excluded: chain g residue 200 THR Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 224 ASN Chi-restraints excluded: chain h residue 268 SER Chi-restraints excluded: chain h residue 307 LEU Chi-restraints excluded: chain h residue 361 LEU Chi-restraints excluded: chain i residue 29 GLN Chi-restraints excluded: chain i residue 171 LEU Chi-restraints excluded: chain i residue 186 VAL Chi-restraints excluded: chain i residue 195 LEU Chi-restraints excluded: chain j residue 224 ASN Chi-restraints excluded: chain j residue 265 ASN Chi-restraints excluded: chain j residue 307 LEU Chi-restraints excluded: chain j residue 361 LEU Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 120 MET Chi-restraints excluded: chain k residue 178 VAL Chi-restraints excluded: chain k residue 181 ASP Chi-restraints excluded: chain k residue 200 THR Chi-restraints excluded: chain l residue 200 ASN Chi-restraints excluded: chain l residue 224 ASN Chi-restraints excluded: chain l residue 265 ASN Chi-restraints excluded: chain l residue 275 LEU Chi-restraints excluded: chain l residue 307 LEU Chi-restraints excluded: chain l residue 361 LEU Chi-restraints excluded: chain l residue 362 LYS Chi-restraints excluded: chain m residue 178 VAL Chi-restraints excluded: chain m residue 186 VAL Chi-restraints excluded: chain m residue 200 THR Chi-restraints excluded: chain n residue 196 VAL Chi-restraints excluded: chain n residue 200 ASN Chi-restraints excluded: chain n residue 224 ASN Chi-restraints excluded: chain n residue 265 ASN Chi-restraints excluded: chain n residue 307 LEU Chi-restraints excluded: chain n residue 332 ASP Chi-restraints excluded: chain n residue 362 LYS Chi-restraints excluded: chain o residue 120 MET Chi-restraints excluded: chain o residue 178 VAL Chi-restraints excluded: chain o residue 186 VAL Chi-restraints excluded: chain o residue 200 THR Chi-restraints excluded: chain p residue 196 VAL Chi-restraints excluded: chain p residue 217 ASP Chi-restraints excluded: chain p residue 265 ASN Chi-restraints excluded: chain p residue 307 LEU Chi-restraints excluded: chain p residue 332 ASP Chi-restraints excluded: chain p residue 361 LEU Chi-restraints excluded: chain q residue 29 GLN Chi-restraints excluded: chain q residue 66 THR Chi-restraints excluded: chain q residue 120 MET Chi-restraints excluded: chain q residue 178 VAL Chi-restraints excluded: chain q residue 195 LEU Chi-restraints excluded: chain q residue 200 THR Chi-restraints excluded: chain r residue 193 MET Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 217 ASP Chi-restraints excluded: chain r residue 224 ASN Chi-restraints excluded: chain r residue 307 LEU Chi-restraints excluded: chain s residue 69 VAL Chi-restraints excluded: chain s residue 171 LEU Chi-restraints excluded: chain s residue 178 VAL Chi-restraints excluded: chain s residue 186 VAL Chi-restraints excluded: chain s residue 200 THR Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 224 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 536 optimal weight: 4.9990 chunk 719 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 622 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 187 optimal weight: 0.5980 chunk 676 optimal weight: 1.9990 chunk 282 optimal weight: 10.0000 chunk 694 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN G 29 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN K 29 GLN N 224 ASN ** O 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 GLN P 224 ASN Q 29 GLN ** Q 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN ** U 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 87 GLN ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 87 GLN a 29 GLN a 43 ASN c 43 ASN e 87 GLN f 224 ASN i 29 GLN ** j 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 29 GLN o 76 GLN p 224 ASN q 29 GLN ** s 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 224 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.112858 restraints weight = 106407.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116143 restraints weight = 59480.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118330 restraints weight = 41048.363| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 71231 Z= 0.295 Angle : 0.645 12.570 96439 Z= 0.313 Chirality : 0.045 0.295 10488 Planarity : 0.004 0.070 12696 Dihedral : 4.507 27.796 9718 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.27 % Allowed : 17.47 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.09), residues: 8602 helix: -0.38 (0.09), residues: 3404 sheet: -1.60 (0.11), residues: 2162 loop : -0.81 (0.12), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP X 350 HIS 0.006 0.001 HIS q 147 PHE 0.014 0.001 PHE X 342 TYR 0.035 0.001 TYR i 180 ARG 0.016 0.001 ARG s 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24985.96 seconds wall clock time: 433 minutes 49.72 seconds (26029.72 seconds total)