Starting phenix.real_space_refine on Thu Mar 21 18:43:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcw_9799/03_2024/6jcw_9799.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcw_9799/03_2024/6jcw_9799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcw_9799/03_2024/6jcw_9799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcw_9799/03_2024/6jcw_9799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcw_9799/03_2024/6jcw_9799.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jcw_9799/03_2024/6jcw_9799.pdb" } resolution = 3.04 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= -0.003 sd= 0.339 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 24 5.21 5 S 120 5.16 5 C 19889 2.51 5 N 5043 2.21 5 O 5812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 35": "NH1" <-> "NH2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 66": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 88": "OE1" <-> "OE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E GLU 66": "OE1" <-> "OE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F GLU 244": "OE1" <-> "OE2" Residue "F ARG 273": "NH1" <-> "NH2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 88": "OE1" <-> "OE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G GLU 227": "OE1" <-> "OE2" Residue "G GLU 243": "OE1" <-> "OE2" Residue "G GLU 244": "OE1" <-> "OE2" Residue "G ARG 273": "NH1" <-> "NH2" Residue "H ARG 35": "NH1" <-> "NH2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H GLU 222": "OE1" <-> "OE2" Residue "H GLU 227": "OE1" <-> "OE2" Residue "H GLU 243": "OE1" <-> "OE2" Residue "H GLU 244": "OE1" <-> "OE2" Residue "H ARG 273": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I GLU 66": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 222": "OE1" <-> "OE2" Residue "I GLU 227": "OE1" <-> "OE2" Residue "I GLU 243": "OE1" <-> "OE2" Residue "I GLU 244": "OE1" <-> "OE2" Residue "I ARG 273": "NH1" <-> "NH2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J GLU 100": "OE1" <-> "OE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J GLU 222": "OE1" <-> "OE2" Residue "J GLU 227": "OE1" <-> "OE2" Residue "J GLU 243": "OE1" <-> "OE2" Residue "J GLU 244": "OE1" <-> "OE2" Residue "J ARG 273": "NH1" <-> "NH2" Residue "K ARG 35": "NH1" <-> "NH2" Residue "K GLU 57": "OE1" <-> "OE2" Residue "K GLU 66": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K GLU 88": "OE1" <-> "OE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K GLU 222": "OE1" <-> "OE2" Residue "K GLU 227": "OE1" <-> "OE2" Residue "K GLU 233": "OE1" <-> "OE2" Residue "K GLU 236": "OE1" <-> "OE2" Residue "K GLU 243": "OE1" <-> "OE2" Residue "K GLU 244": "OE1" <-> "OE2" Residue "K ARG 273": "NH1" <-> "NH2" Residue "L ARG 35": "NH1" <-> "NH2" Residue "L GLU 36": "OE1" <-> "OE2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L GLU 66": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L GLU 222": "OE1" <-> "OE2" Residue "L GLU 227": "OE1" <-> "OE2" Residue "L GLU 243": "OE1" <-> "OE2" Residue "L GLU 244": "OE1" <-> "OE2" Residue "L ARG 273": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30888 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "B" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "D" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "E" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "F" Number of atoms: 2571 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Conformer: "B" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} bond proxies already assigned to first conformer: 2607 Chain: "G" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "H" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "I" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "J" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "K" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "L" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 17.05, per 1000 atoms: 0.55 Number of scatterers: 30888 At special positions: 0 Unit cell: (144.84, 145.52, 144.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 Mg 24 11.99 O 5812 8.00 N 5043 7.00 C 19889 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: 10.79 Conformation dependent library (CDL) restraints added in 6.1 seconds 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7130 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 12 sheets defined 55.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.783A pdb=" N ARG A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 37 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.771A pdb=" N LEU A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.816A pdb=" N ARG A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.582A pdb=" N GLU A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.714A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 108 through 113' Processing helix chain 'A' and resid 136 through 141 removed outlier: 4.240A pdb=" N LYS A 141 " --> pdb=" O MET A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.606A pdb=" N ALA A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 165 " --> pdb=" O TRP A 161 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.708A pdb=" N LEU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.717A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.509A pdb=" N PHE A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 224 through 229' Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.782A pdb=" N ALA A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.717A pdb=" N HIS A 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.692A pdb=" N VAL A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.628A pdb=" N LYS A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 removed outlier: 3.808A pdb=" N TYR A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.592A pdb=" N ALA A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 37 removed outlier: 3.783A pdb=" N ARG B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.779A pdb=" N LEU B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 removed outlier: 3.816A pdb=" N ARG B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.508A pdb=" N GLU B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.715A pdb=" N ALA B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 108 through 113' Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.607A pdb=" N ALA B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 165 " --> pdb=" O TRP B 161 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.707A pdb=" N LEU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 218 removed outlier: 3.717A pdb=" N ILE B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.552A pdb=" N PHE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 224 through 229' Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.794A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 removed outlier: 3.720A pdb=" N HIS B 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 285 removed outlier: 3.679A pdb=" N VAL B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.635A pdb=" N LYS B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.808A pdb=" N TYR B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP B 307 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 311 " --> pdb=" O TRP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 removed outlier: 3.576A pdb=" N ALA B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 37 removed outlier: 3.778A pdb=" N ARG C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET C 34 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 54 removed outlier: 3.772A pdb=" N LEU C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.814A pdb=" N ARG C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 removed outlier: 3.535A pdb=" N GLU C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 removed outlier: 3.713A pdb=" N ALA C 112 " --> pdb=" O GLY C 108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 159 through 171 removed outlier: 3.600A pdb=" N ALA C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS C 165 " --> pdb=" O TRP C 161 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 removed outlier: 3.707A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 218 removed outlier: 3.700A pdb=" N ILE C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.506A pdb=" N PHE C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 224 through 229' Processing helix chain 'C' and resid 238 through 245 removed outlier: 3.776A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.716A pdb=" N HIS C 252 " --> pdb=" O GLN C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.809A pdb=" N ARG C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 285 removed outlier: 3.677A pdb=" N VAL C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.635A pdb=" N LYS C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.808A pdb=" N TYR C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 305 " --> pdb=" O PRO C 301 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP C 307 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 308 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 311 " --> pdb=" O TRP C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 323 removed outlier: 3.576A pdb=" N ALA C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 37 removed outlier: 3.777A pdb=" N ARG D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D 34 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 54 removed outlier: 3.759A pdb=" N LEU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.818A pdb=" N ARG D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.509A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.714A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 108 through 113' Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.550A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 165 " --> pdb=" O TRP D 161 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 195 removed outlier: 3.706A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.726A pdb=" N ILE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP D 211 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.509A pdb=" N PHE D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 224 through 229' Processing helix chain 'D' and resid 238 through 245 removed outlier: 3.773A pdb=" N ALA D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 245 " --> pdb=" O ILE D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.717A pdb=" N HIS D 252 " --> pdb=" O GLN D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.679A pdb=" N VAL D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.636A pdb=" N LYS D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 removed outlier: 3.807A pdb=" N TYR D 304 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG D 305 " --> pdb=" O PRO D 301 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP D 307 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 308 " --> pdb=" O TYR D 304 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR D 311 " --> pdb=" O TRP D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 323 removed outlier: 3.594A pdb=" N ALA D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.781A pdb=" N ARG E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 36 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 54 removed outlier: 3.737A pdb=" N LEU E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 71 removed outlier: 3.817A pdb=" N ARG E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 88 removed outlier: 3.534A pdb=" N GLU E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.715A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E 113 " --> pdb=" O TYR E 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 108 through 113' Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.601A pdb=" N ALA E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 165 " --> pdb=" O TRP E 161 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 195 removed outlier: 3.708A pdb=" N LEU E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 218 removed outlier: 3.654A pdb=" N ILE E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY E 218 " --> pdb=" O VAL E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 229 removed outlier: 3.554A pdb=" N PHE E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 224 through 229' Processing helix chain 'E' and resid 238 through 245 removed outlier: 3.791A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.719A pdb=" N HIS E 252 " --> pdb=" O GLN E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.676A pdb=" N VAL E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE E 275 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN E 278 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 removed outlier: 3.635A pdb=" N LYS E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN E 296 " --> pdb=" O TRP E 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN E 297 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 312 removed outlier: 3.810A pdb=" N TYR E 304 " --> pdb=" O TYR E 300 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG E 305 " --> pdb=" O PRO E 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP E 307 " --> pdb=" O PHE E 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 308 " --> pdb=" O TYR E 304 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 309 " --> pdb=" O ARG E 305 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 311 " --> pdb=" O TRP E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 323 removed outlier: 3.610A pdb=" N ALA E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 37 removed outlier: 3.884A pdb=" N VAL F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN F 30 " --> pdb=" O GLN F 26 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET F 34 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 36 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN F 37 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 3.810A pdb=" N LEU F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.838A pdb=" N ARG F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 88 removed outlier: 3.521A pdb=" N GLU F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 96 removed outlier: 4.204A pdb=" N GLN F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 113 removed outlier: 3.675A pdb=" N ALA F 112 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE F 113 " --> pdb=" O TYR F 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 108 through 113' Processing helix chain 'F' and resid 136 through 141 removed outlier: 4.199A pdb=" N LYS F 141 " --> pdb=" O MET F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.598A pdb=" N ALA F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS F 165 " --> pdb=" O TRP F 161 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.583A pdb=" N ALA F 188 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 218 removed outlier: 3.724A pdb=" N ILE F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F 211 " --> pdb=" O LYS F 207 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY F 218 " --> pdb=" O VAL F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.527A pdb=" N PHE F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 224 through 229' Processing helix chain 'F' and resid 238 through 245 removed outlier: 3.802A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 245 " --> pdb=" O ILE F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.774A pdb=" N HIS F 252 " --> pdb=" O GLN F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.796A pdb=" N ARG F 264 " --> pdb=" O GLY F 260 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.634A pdb=" N VAL F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG F 274 " --> pdb=" O ASP F 270 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE F 275 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL F 276 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN F 278 " --> pdb=" O ARG F 274 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 removed outlier: 3.628A pdb=" N LYS F 290 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN F 296 " --> pdb=" O TRP F 292 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 removed outlier: 3.802A pdb=" N TYR F 304 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG F 305 " --> pdb=" O PRO F 301 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP F 307 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU F 308 " --> pdb=" O TYR F 304 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 309 " --> pdb=" O ARG F 305 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR F 311 " --> pdb=" O TRP F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 323 removed outlier: 3.593A pdb=" N ALA F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 removed outlier: 3.781A pdb=" N ARG G 28 " --> pdb=" O GLY G 24 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET G 34 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU G 36 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 removed outlier: 3.756A pdb=" N LEU G 53 " --> pdb=" O LYS G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 71 removed outlier: 3.817A pdb=" N ARG G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 88 removed outlier: 3.507A pdb=" N GLU G 88 " --> pdb=" O LYS G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.716A pdb=" N ALA G 112 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE G 113 " --> pdb=" O TYR G 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 108 through 113' Processing helix chain 'G' and resid 159 through 171 removed outlier: 3.547A pdb=" N ALA G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS G 165 " --> pdb=" O TRP G 161 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA G 166 " --> pdb=" O ASP G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 195 removed outlier: 3.720A pdb=" N LEU G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU G 192 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 218 removed outlier: 3.716A pdb=" N ILE G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA G 208 " --> pdb=" O GLY G 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY G 218 " --> pdb=" O VAL G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 229 removed outlier: 3.506A pdb=" N PHE G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 224 through 229' Processing helix chain 'G' and resid 238 through 245 removed outlier: 3.776A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU G 243 " --> pdb=" O ARG G 239 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY G 245 " --> pdb=" O ILE G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 253 removed outlier: 3.718A pdb=" N HIS G 252 " --> pdb=" O GLN G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE G 266 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 285 removed outlier: 3.679A pdb=" N VAL G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 274 " --> pdb=" O ASP G 270 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL G 276 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN G 278 " --> pdb=" O ARG G 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS G 281 " --> pdb=" O GLU G 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE G 283 " --> pdb=" O GLU G 279 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP G 285 " --> pdb=" O LYS G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 299 removed outlier: 3.629A pdb=" N LYS G 290 " --> pdb=" O GLY G 286 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN G 296 " --> pdb=" O TRP G 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 312 removed outlier: 3.810A pdb=" N TYR G 304 " --> pdb=" O TYR G 300 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG G 305 " --> pdb=" O PRO G 301 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP G 307 " --> pdb=" O PHE G 303 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU G 308 " --> pdb=" O TYR G 304 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR G 311 " --> pdb=" O TRP G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 323 removed outlier: 3.577A pdb=" N ALA G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU G 321 " --> pdb=" O LYS G 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 37 removed outlier: 3.783A pdb=" N ARG H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET H 34 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU H 36 " --> pdb=" O THR H 32 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 54 removed outlier: 3.764A pdb=" N LEU H 53 " --> pdb=" O LYS H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 71 removed outlier: 3.819A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 88 removed outlier: 3.521A pdb=" N GLU H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 removed outlier: 3.714A pdb=" N ALA H 112 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE H 113 " --> pdb=" O TYR H 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 108 through 113' Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 159 through 171 removed outlier: 3.551A pdb=" N ALA H 164 " --> pdb=" O ALA H 160 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS H 165 " --> pdb=" O TRP H 161 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA H 166 " --> pdb=" O ASP H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 195 removed outlier: 3.707A pdb=" N LEU H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 192 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 218 removed outlier: 3.718A pdb=" N ILE H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 208 " --> pdb=" O GLY H 204 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP H 211 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 229 removed outlier: 3.511A pdb=" N PHE H 228 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 224 through 229' Processing helix chain 'H' and resid 238 through 245 removed outlier: 3.774A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU H 243 " --> pdb=" O ARG H 239 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 253 removed outlier: 3.717A pdb=" N HIS H 252 " --> pdb=" O GLN H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG H 264 " --> pdb=" O GLY H 260 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE H 266 " --> pdb=" O LEU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 285 removed outlier: 3.679A pdb=" N VAL H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG H 274 " --> pdb=" O ASP H 270 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE H 275 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL H 276 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN H 278 " --> pdb=" O ARG H 274 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS H 281 " --> pdb=" O GLU H 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 283 " --> pdb=" O GLU H 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 removed outlier: 3.635A pdb=" N LYS H 290 " --> pdb=" O GLY H 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN H 296 " --> pdb=" O TRP H 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN H 297 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 312 removed outlier: 3.807A pdb=" N TYR H 304 " --> pdb=" O TYR H 300 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG H 305 " --> pdb=" O PRO H 301 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP H 307 " --> pdb=" O PHE H 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 308 " --> pdb=" O TYR H 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR H 311 " --> pdb=" O TRP H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 323 removed outlier: 3.576A pdb=" N ALA H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 37 removed outlier: 3.781A pdb=" N ARG I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET I 34 " --> pdb=" O GLN I 30 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU I 36 " --> pdb=" O THR I 32 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN I 37 " --> pdb=" O ILE I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.733A pdb=" N LEU I 53 " --> pdb=" O LYS I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 71 removed outlier: 3.816A pdb=" N ARG I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 88 removed outlier: 3.506A pdb=" N GLU I 88 " --> pdb=" O LYS I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 113 removed outlier: 3.715A pdb=" N ALA I 112 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE I 113 " --> pdb=" O TYR I 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 108 through 113' Processing helix chain 'I' and resid 136 through 141 removed outlier: 4.240A pdb=" N LYS I 141 " --> pdb=" O MET I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.601A pdb=" N ALA I 164 " --> pdb=" O ALA I 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS I 165 " --> pdb=" O TRP I 161 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA I 166 " --> pdb=" O ASP I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 195 removed outlier: 3.706A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 192 " --> pdb=" O ALA I 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER I 194 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 218 removed outlier: 3.725A pdb=" N ILE I 201 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA I 208 " --> pdb=" O GLY I 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP I 211 " --> pdb=" O LYS I 207 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY I 218 " --> pdb=" O VAL I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 229 removed outlier: 3.508A pdb=" N PHE I 228 " --> pdb=" O ALA I 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 224 through 229' Processing helix chain 'I' and resid 238 through 245 removed outlier: 3.776A pdb=" N ALA I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU I 243 " --> pdb=" O ARG I 239 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY I 245 " --> pdb=" O ILE I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 253 removed outlier: 3.718A pdb=" N HIS I 252 " --> pdb=" O GLN I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE I 266 " --> pdb=" O LEU I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 285 removed outlier: 3.679A pdb=" N VAL I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG I 274 " --> pdb=" O ASP I 270 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE I 275 " --> pdb=" O VAL I 271 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL I 276 " --> pdb=" O VAL I 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN I 278 " --> pdb=" O ARG I 274 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS I 281 " --> pdb=" O GLU I 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP I 285 " --> pdb=" O LYS I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 removed outlier: 3.636A pdb=" N LYS I 290 " --> pdb=" O GLY I 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN I 296 " --> pdb=" O TRP I 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN I 297 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 312 removed outlier: 3.809A pdb=" N TYR I 304 " --> pdb=" O TYR I 300 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG I 305 " --> pdb=" O PRO I 301 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP I 307 " --> pdb=" O PHE I 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU I 308 " --> pdb=" O TYR I 304 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU I 309 " --> pdb=" O ARG I 305 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR I 311 " --> pdb=" O TRP I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 323 removed outlier: 3.592A pdb=" N ALA I 318 " --> pdb=" O GLU I 314 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 37 removed outlier: 3.781A pdb=" N ARG J 28 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET J 34 " --> pdb=" O GLN J 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN J 37 " --> pdb=" O ILE J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 54 removed outlier: 3.746A pdb=" N LEU J 53 " --> pdb=" O LYS J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 71 removed outlier: 3.818A pdb=" N ARG J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 88 removed outlier: 3.519A pdb=" N GLU J 88 " --> pdb=" O LYS J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 113 removed outlier: 3.715A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 108 through 113' Processing helix chain 'J' and resid 136 through 140 Processing helix chain 'J' and resid 159 through 171 removed outlier: 3.551A pdb=" N ALA J 164 " --> pdb=" O ALA J 160 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS J 165 " --> pdb=" O TRP J 161 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA J 166 " --> pdb=" O ASP J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 195 removed outlier: 3.707A pdb=" N LEU J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU J 192 " --> pdb=" O ALA J 188 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 218 removed outlier: 3.702A pdb=" N ILE J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA J 208 " --> pdb=" O GLY J 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP J 211 " --> pdb=" O LYS J 207 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY J 218 " --> pdb=" O VAL J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 229 removed outlier: 3.507A pdb=" N PHE J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR J 229 " --> pdb=" O LEU J 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 224 through 229' Processing helix chain 'J' and resid 238 through 245 removed outlier: 3.776A pdb=" N ALA J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU J 243 " --> pdb=" O ARG J 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY J 245 " --> pdb=" O ILE J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 253 removed outlier: 3.716A pdb=" N HIS J 252 " --> pdb=" O GLN J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 266 removed outlier: 3.805A pdb=" N ARG J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE J 266 " --> pdb=" O LEU J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 285 removed outlier: 3.678A pdb=" N VAL J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG J 274 " --> pdb=" O ASP J 270 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE J 275 " --> pdb=" O VAL J 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL J 276 " --> pdb=" O VAL J 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN J 278 " --> pdb=" O ARG J 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS J 281 " --> pdb=" O GLU J 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP J 285 " --> pdb=" O LYS J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 299 removed outlier: 3.642A pdb=" N LYS J 290 " --> pdb=" O GLY J 286 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN J 296 " --> pdb=" O TRP J 292 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN J 297 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 312 removed outlier: 3.807A pdb=" N TYR J 304 " --> pdb=" O TYR J 300 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG J 305 " --> pdb=" O PRO J 301 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP J 307 " --> pdb=" O PHE J 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU J 308 " --> pdb=" O TYR J 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR J 311 " --> pdb=" O TRP J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 323 removed outlier: 3.576A pdb=" N ALA J 318 " --> pdb=" O GLU J 314 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU J 321 " --> pdb=" O LYS J 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 37 removed outlier: 3.782A pdb=" N ARG K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET K 34 " --> pdb=" O GLN K 30 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU K 36 " --> pdb=" O THR K 32 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN K 37 " --> pdb=" O ILE K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 54 removed outlier: 3.738A pdb=" N LEU K 53 " --> pdb=" O LYS K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 71 removed outlier: 3.816A pdb=" N ARG K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 88 removed outlier: 3.505A pdb=" N GLU K 88 " --> pdb=" O LYS K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 113 removed outlier: 3.715A pdb=" N ALA K 112 " --> pdb=" O GLY K 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE K 113 " --> pdb=" O TYR K 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 108 through 113' Processing helix chain 'K' and resid 159 through 171 removed outlier: 3.592A pdb=" N ALA K 164 " --> pdb=" O ALA K 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS K 165 " --> pdb=" O TRP K 161 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA K 166 " --> pdb=" O ASP K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 195 removed outlier: 3.708A pdb=" N LEU K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU K 192 " --> pdb=" O ALA K 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 218 removed outlier: 3.716A pdb=" N ILE K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA K 208 " --> pdb=" O GLY K 204 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY K 218 " --> pdb=" O VAL K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 224 through 229 removed outlier: 3.550A pdb=" N PHE K 228 " --> pdb=" O ALA K 224 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR K 229 " --> pdb=" O LEU K 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 224 through 229' Processing helix chain 'K' and resid 238 through 245 removed outlier: 3.797A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU K 243 " --> pdb=" O ARG K 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY K 245 " --> pdb=" O ILE K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 253 removed outlier: 3.713A pdb=" N HIS K 252 " --> pdb=" O GLN K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG K 264 " --> pdb=" O GLY K 260 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE K 266 " --> pdb=" O LEU K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 285 removed outlier: 3.677A pdb=" N VAL K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG K 274 " --> pdb=" O ASP K 270 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL K 276 " --> pdb=" O VAL K 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN K 278 " --> pdb=" O ARG K 274 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS K 281 " --> pdb=" O GLU K 277 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP K 285 " --> pdb=" O LYS K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 299 removed outlier: 3.636A pdb=" N LYS K 290 " --> pdb=" O GLY K 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN K 296 " --> pdb=" O TRP K 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN K 297 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 312 removed outlier: 3.807A pdb=" N TYR K 304 " --> pdb=" O TYR K 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG K 305 " --> pdb=" O PRO K 301 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP K 307 " --> pdb=" O PHE K 303 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU K 308 " --> pdb=" O TYR K 304 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR K 311 " --> pdb=" O TRP K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 323 removed outlier: 3.578A pdb=" N ALA K 318 " --> pdb=" O GLU K 314 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 37 removed outlier: 3.773A pdb=" N ARG L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET L 34 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU L 36 " --> pdb=" O THR L 32 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN L 37 " --> pdb=" O ILE L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 71 removed outlier: 3.813A pdb=" N ARG L 69 " --> pdb=" O ASP L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 88 removed outlier: 3.582A pdb=" N GLU L 88 " --> pdb=" O LYS L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 113 removed outlier: 3.716A pdb=" N ALA L 112 " --> pdb=" O GLY L 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE L 113 " --> pdb=" O TYR L 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 108 through 113' Processing helix chain 'L' and resid 136 through 140 Processing helix chain 'L' and resid 159 through 171 removed outlier: 3.602A pdb=" N ALA L 164 " --> pdb=" O ALA L 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS L 165 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA L 166 " --> pdb=" O ASP L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 195 removed outlier: 3.707A pdb=" N LEU L 190 " --> pdb=" O GLU L 186 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU L 192 " --> pdb=" O ALA L 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER L 194 " --> pdb=" O LEU L 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 218 removed outlier: 3.716A pdb=" N ILE L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA L 208 " --> pdb=" O GLY L 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP L 211 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY L 218 " --> pdb=" O VAL L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 229 removed outlier: 3.509A pdb=" N PHE L 228 " --> pdb=" O ALA L 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR L 229 " --> pdb=" O LEU L 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 224 through 229' Processing helix chain 'L' and resid 238 through 245 removed outlier: 3.773A pdb=" N ALA L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU L 243 " --> pdb=" O ARG L 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY L 245 " --> pdb=" O ILE L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 253 removed outlier: 3.717A pdb=" N HIS L 252 " --> pdb=" O GLN L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG L 264 " --> pdb=" O GLY L 260 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE L 266 " --> pdb=" O LEU L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 285 removed outlier: 3.680A pdb=" N VAL L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG L 274 " --> pdb=" O ASP L 270 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE L 275 " --> pdb=" O VAL L 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL L 276 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN L 278 " --> pdb=" O ARG L 274 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS L 281 " --> pdb=" O GLU L 277 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP L 285 " --> pdb=" O LYS L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 removed outlier: 3.635A pdb=" N LYS L 290 " --> pdb=" O GLY L 286 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN L 297 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 312 removed outlier: 3.808A pdb=" N TYR L 304 " --> pdb=" O TYR L 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG L 305 " --> pdb=" O PRO L 301 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP L 307 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU L 308 " --> pdb=" O TYR L 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR L 311 " --> pdb=" O TRP L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 323 removed outlier: 3.592A pdb=" N ALA L 318 " --> pdb=" O GLU L 314 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU L 321 " --> pdb=" O LYS L 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 9.313A pdb=" N TYR A 62 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A 124 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 removed outlier: 9.312A pdb=" N TYR B 62 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B 43 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR B 124 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 62 removed outlier: 9.312A pdb=" N TYR C 62 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL C 43 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR C 124 " --> pdb=" O LYS C 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 61 through 62 removed outlier: 9.308A pdb=" N TYR D 62 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL D 43 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR D 124 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 61 through 62 removed outlier: 9.323A pdb=" N TYR E 62 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL E 43 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 61 through 62 removed outlier: 9.303A pdb=" N TYR F 62 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL F 43 " --> pdb=" O TYR F 62 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR F 124 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 61 through 62 removed outlier: 9.321A pdb=" N TYR G 62 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL G 43 " --> pdb=" O TYR G 62 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR G 124 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 61 through 62 removed outlier: 9.311A pdb=" N TYR H 62 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL H 43 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR H 124 " --> pdb=" O LYS H 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 61 through 62 removed outlier: 9.311A pdb=" N TYR I 62 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL I 43 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR I 124 " --> pdb=" O LYS I 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 61 through 62 removed outlier: 9.321A pdb=" N TYR J 62 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL J 43 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR J 124 " --> pdb=" O LYS J 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 61 through 62 removed outlier: 9.322A pdb=" N TYR K 62 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL K 43 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR K 124 " --> pdb=" O LYS K 153 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 61 through 62 removed outlier: 9.343A pdb=" N TYR L 62 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL L 43 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR L 124 " --> pdb=" O LYS L 153 " (cutoff:3.500A) 1051 hydrogen bonds defined for protein. 3063 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: 9.02 Time building geometry restraints manager: 11.68 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: 9780 1.34 - 1.45: 4771 1.45 - 1.57: 16622 1.57 - 1.69: 0 1.69 - 1.80: 228 Bond restraints: 31401 Sorted by residual: bond pdb=" N ARG L 35 " pdb=" CA ARG L 35 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.88e+00 bond pdb=" CB PRO D 200 " pdb=" CG PRO D 200 " ideal model delta sigma weight residual 1.492 1.400 0.092 5.00e-02 4.00e+02 3.41e+00 bond pdb=" CB PRO B 200 " pdb=" CG PRO B 200 " ideal model delta sigma weight residual 1.492 1.400 0.092 5.00e-02 4.00e+02 3.40e+00 bond pdb=" CB PRO I 200 " pdb=" CG PRO I 200 " ideal model delta sigma weight residual 1.492 1.400 0.092 5.00e-02 4.00e+02 3.37e+00 bond pdb=" CB PRO G 200 " pdb=" CG PRO G 200 " ideal model delta sigma weight residual 1.492 1.400 0.092 5.00e-02 4.00e+02 3.36e+00 ... (remaining 31396 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.11: 645 106.11 - 113.16: 16181 113.16 - 120.20: 12956 120.20 - 127.24: 12326 127.24 - 134.29: 301 Bond angle restraints: 42409 Sorted by residual: angle pdb=" N VAL J 111 " pdb=" CA VAL J 111 " pdb=" C VAL J 111 " ideal model delta sigma weight residual 112.96 109.03 3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N VAL E 111 " pdb=" CA VAL E 111 " pdb=" C VAL E 111 " ideal model delta sigma weight residual 112.96 109.03 3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N VAL C 111 " pdb=" CA VAL C 111 " pdb=" C VAL C 111 " ideal model delta sigma weight residual 112.96 109.04 3.92 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N VAL D 111 " pdb=" CA VAL D 111 " pdb=" C VAL D 111 " ideal model delta sigma weight residual 112.96 109.04 3.92 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N VAL A 111 " pdb=" CA VAL A 111 " pdb=" C VAL A 111 " ideal model delta sigma weight residual 112.96 109.04 3.92 1.00e+00 1.00e+00 1.54e+01 ... (remaining 42404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 16716 18.14 - 36.29: 1637 36.29 - 54.43: 347 54.43 - 72.57: 26 72.57 - 90.72: 51 Dihedral angle restraints: 18777 sinusoidal: 7529 harmonic: 11248 Sorted by residual: dihedral pdb=" CA SER G 157 " pdb=" C SER G 157 " pdb=" N GLY G 158 " pdb=" CA GLY G 158 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA SER F 157 " pdb=" C SER F 157 " pdb=" N GLY F 158 " pdb=" CA GLY F 158 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA SER A 157 " pdb=" C SER A 157 " pdb=" N GLY A 158 " pdb=" CA GLY A 158 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 18774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2548 0.038 - 0.076: 1449 0.076 - 0.114: 438 0.114 - 0.152: 168 0.152 - 0.190: 42 Chirality restraints: 4645 Sorted by residual: chirality pdb=" CA ASP H 11 " pdb=" N ASP H 11 " pdb=" C ASP H 11 " pdb=" CB ASP H 11 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA ASP D 11 " pdb=" N ASP D 11 " pdb=" C ASP D 11 " pdb=" CB ASP D 11 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA ASP G 11 " pdb=" N ASP G 11 " pdb=" C ASP G 11 " pdb=" CB ASP G 11 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 4642 not shown) Planarity restraints: 5390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 11 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO G 12 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 12 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 12 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 11 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.67e+00 pdb=" N PRO H 12 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO H 12 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 12 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 11 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO J 12 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO J 12 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO J 12 " -0.039 5.00e-02 4.00e+02 ... (remaining 5387 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1223 2.71 - 3.26: 25322 3.26 - 3.81: 44566 3.81 - 4.35: 60408 4.35 - 4.90: 104257 Nonbonded interactions: 235776 Sorted by model distance: nonbonded pdb=" OE2 GLU F 227 " pdb="MG MG F 401 " model vdw 2.168 2.170 nonbonded pdb=" OE2 GLU E 227 " pdb="MG MG E 402 " model vdw 2.172 2.170 nonbonded pdb=" OE2 GLU K 227 " pdb="MG MG K 402 " model vdw 2.175 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 401 " model vdw 2.176 2.170 nonbonded pdb=" OE2 GLU C 227 " pdb="MG MG C 402 " model vdw 2.206 2.170 ... (remaining 235771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) selection = (chain 'B' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) selection = (chain 'C' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) selection = (chain 'D' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) selection = (chain 'E' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) selection = (chain 'F' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) selection = (chain 'G' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) selection = (chain 'H' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) selection = (chain 'I' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) selection = (chain 'J' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) selection = (chain 'K' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) selection = (chain 'L' and (resid 3 through 27 or resid 29 through 328 or resid 401 through \ 402)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.280 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: 0.020 Extract box with map and model: 19.500 Check model and map are aligned: 0.620 Set scattering table: 0.300 Process input model: 76.390 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 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 : 0.007 0.092 31401 Z= 0.461 Angle : 0.883 11.483 42409 Z= 0.475 Chirality : 0.054 0.190 4645 Planarity : 0.007 0.069 5390 Dihedral : 15.375 90.716 11647 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.35 % Allowed : 5.25 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -6.55 (0.08), residues: 3889 helix: -5.10 (0.03), residues: 2161 sheet: -2.32 (0.17), residues: 564 loop : -3.15 (0.14), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 284 HIS 0.004 0.001 HIS J 140 PHE 0.015 0.003 PHE F 184 TYR 0.017 0.003 TYR B 217 ARG 0.006 0.001 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 472 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 GLN cc_start: 0.9031 (mm110) cc_final: 0.8810 (mp10) REVERT: C 142 GLN cc_start: 0.9037 (mm110) cc_final: 0.8819 (mp10) REVERT: E 142 GLN cc_start: 0.9042 (mm110) cc_final: 0.8814 (mp10) REVERT: H 142 GLN cc_start: 0.8796 (mp10) cc_final: 0.8546 (mp10) REVERT: K 142 GLN cc_start: 0.9033 (mm110) cc_final: 0.8832 (mp10) outliers start: 11 outliers final: 0 residues processed: 483 average time/residue: 0.4058 time to fit residues: 311.2258 Evaluate side-chains 378 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 348 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS B 110 ASN B 196 HIS C 110 ASN C 196 HIS D 110 ASN D 196 HIS E 110 ASN E 196 HIS F 110 ASN F 196 HIS G 110 ASN G 196 HIS H 110 ASN H 196 HIS I 110 ASN I 196 HIS J 110 ASN J 196 HIS K 110 ASN K 196 HIS L 196 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31401 Z= 0.336 Angle : 0.633 9.044 42409 Z= 0.331 Chirality : 0.046 0.148 4645 Planarity : 0.005 0.051 5390 Dihedral : 4.562 17.955 4263 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.88 % Allowed : 10.47 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -4.60 (0.11), residues: 3889 helix: -3.42 (0.08), residues: 2101 sheet: -1.69 (0.19), residues: 540 loop : -2.51 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 198 HIS 0.004 0.001 HIS C 140 PHE 0.007 0.001 PHE F 113 TYR 0.016 0.001 TYR A 217 ARG 0.004 0.000 ARG F 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 355 time to evaluate : 3.633 Fit side-chains REVERT: B 142 GLN cc_start: 0.9184 (mm110) cc_final: 0.8887 (mp10) REVERT: C 142 GLN cc_start: 0.9193 (mm110) cc_final: 0.8891 (mp10) REVERT: E 142 GLN cc_start: 0.9203 (mm110) cc_final: 0.8899 (mp10) REVERT: F 26 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8811 (mm-40) REVERT: G 142 GLN cc_start: 0.9179 (mm110) cc_final: 0.8883 (mp10) REVERT: H 142 GLN cc_start: 0.8988 (mp10) cc_final: 0.8668 (mp10) REVERT: K 142 GLN cc_start: 0.9182 (mm110) cc_final: 0.8887 (mp10) outliers start: 28 outliers final: 23 residues processed: 373 average time/residue: 0.4078 time to fit residues: 244.0726 Evaluate side-chains 349 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 326 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 290 optimal weight: 9.9990 chunk 237 optimal weight: 0.4980 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 0.5980 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 346 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN F 96 GLN L 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 31401 Z= 0.330 Angle : 0.602 8.715 42409 Z= 0.308 Chirality : 0.046 0.150 4645 Planarity : 0.004 0.044 5390 Dihedral : 4.209 15.706 4263 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.75 % Allowed : 11.51 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -3.39 (0.12), residues: 3889 helix: -2.26 (0.10), residues: 2089 sheet: -1.40 (0.19), residues: 540 loop : -2.21 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 198 HIS 0.004 0.001 HIS J 140 PHE 0.007 0.001 PHE F 113 TYR 0.014 0.001 TYR A 217 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 327 time to evaluate : 3.705 Fit side-chains REVERT: B 142 GLN cc_start: 0.9270 (mm110) cc_final: 0.8922 (mp10) REVERT: C 142 GLN cc_start: 0.9279 (mm110) cc_final: 0.8924 (mp10) REVERT: E 142 GLN cc_start: 0.9285 (mm110) cc_final: 0.8927 (mp10) REVERT: G 142 GLN cc_start: 0.9271 (mm110) cc_final: 0.8902 (mp10) REVERT: K 142 GLN cc_start: 0.9277 (mm110) cc_final: 0.8925 (mp10) outliers start: 24 outliers final: 21 residues processed: 341 average time/residue: 0.4016 time to fit residues: 218.0402 Evaluate side-chains 332 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 311 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 6.9990 chunk 262 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 350 optimal weight: 3.9990 chunk 371 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 31401 Z= 0.291 Angle : 0.563 8.876 42409 Z= 0.287 Chirality : 0.045 0.151 4645 Planarity : 0.003 0.039 5390 Dihedral : 3.956 14.365 4263 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.16 % Allowed : 12.70 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.12), residues: 3889 helix: -1.67 (0.10), residues: 2113 sheet: -1.21 (0.19), residues: 552 loop : -1.95 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 198 HIS 0.003 0.000 HIS H 140 PHE 0.006 0.001 PHE L 113 TYR 0.013 0.001 TYR I 217 ARG 0.003 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 328 time to evaluate : 3.889 Fit side-chains REVERT: B 142 GLN cc_start: 0.9302 (mm110) cc_final: 0.8947 (mp10) REVERT: C 142 GLN cc_start: 0.9314 (mm110) cc_final: 0.8949 (mp10) REVERT: E 142 GLN cc_start: 0.9325 (mm110) cc_final: 0.8952 (mp10) REVERT: G 142 GLN cc_start: 0.9286 (mm110) cc_final: 0.8921 (mp10) REVERT: K 142 GLN cc_start: 0.9311 (mm110) cc_final: 0.8950 (mp10) outliers start: 37 outliers final: 24 residues processed: 355 average time/residue: 0.4010 time to fit residues: 231.4267 Evaluate side-chains 345 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 321 time to evaluate : 3.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.9990 chunk 210 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 276 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 316 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.9980 chunk 333 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 GLN F 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31401 Z= 0.137 Angle : 0.490 8.931 42409 Z= 0.242 Chirality : 0.042 0.129 4645 Planarity : 0.003 0.036 5390 Dihedral : 3.614 12.703 4263 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.38 % Allowed : 14.37 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -2.05 (0.13), residues: 3889 helix: -1.10 (0.11), residues: 2173 sheet: -0.86 (0.20), residues: 552 loop : -1.74 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 198 HIS 0.002 0.000 HIS F 140 PHE 0.004 0.001 PHE F 184 TYR 0.010 0.001 TYR F 217 ARG 0.003 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 331 time to evaluate : 3.683 Fit side-chains REVERT: B 142 GLN cc_start: 0.9278 (mm110) cc_final: 0.8973 (mp10) REVERT: C 142 GLN cc_start: 0.9294 (mm110) cc_final: 0.8974 (mp10) REVERT: E 142 GLN cc_start: 0.9302 (mm110) cc_final: 0.8979 (mp10) REVERT: F 26 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8438 (mm-40) REVERT: F 30 GLN cc_start: 0.9092 (mt0) cc_final: 0.8761 (mp10) REVERT: G 142 GLN cc_start: 0.9276 (mm110) cc_final: 0.8954 (mp10) REVERT: H 142 GLN cc_start: 0.9215 (mp10) cc_final: 0.8758 (mp10) REVERT: I 142 GLN cc_start: 0.8563 (mp10) cc_final: 0.8295 (pm20) REVERT: K 142 GLN cc_start: 0.9289 (mm110) cc_final: 0.8981 (mp10) outliers start: 12 outliers final: 12 residues processed: 343 average time/residue: 0.4096 time to fit residues: 226.7640 Evaluate side-chains 335 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 323 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain K residue 80 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 1.9990 chunk 334 optimal weight: 7.9990 chunk 73 optimal weight: 0.0040 chunk 217 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 371 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN C 96 GLN E 96 GLN L 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 31401 Z= 0.276 Angle : 0.543 8.499 42409 Z= 0.274 Chirality : 0.045 0.148 4645 Planarity : 0.003 0.033 5390 Dihedral : 3.650 13.267 4263 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.91 % Allowed : 14.52 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.13), residues: 3889 helix: -0.63 (0.11), residues: 2113 sheet: -0.20 (0.22), residues: 444 loop : -1.51 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 198 HIS 0.002 0.000 HIS B 140 PHE 0.006 0.001 PHE D 113 TYR 0.012 0.001 TYR F 217 ARG 0.004 0.000 ARG K 274 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 317 time to evaluate : 4.087 Fit side-chains REVERT: B 142 GLN cc_start: 0.9298 (mm110) cc_final: 0.8976 (mp10) REVERT: C 142 GLN cc_start: 0.9300 (mm110) cc_final: 0.8988 (mp10) REVERT: E 142 GLN cc_start: 0.9314 (mm110) cc_final: 0.8989 (mp10) REVERT: F 26 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8212 (mm-40) REVERT: F 30 GLN cc_start: 0.9105 (mt0) cc_final: 0.8778 (mp10) REVERT: G 142 GLN cc_start: 0.9281 (mm110) cc_final: 0.8953 (mp10) REVERT: H 142 GLN cc_start: 0.9262 (mp10) cc_final: 0.8808 (mp10) REVERT: K 142 GLN cc_start: 0.9306 (mm110) cc_final: 0.8985 (mp10) outliers start: 29 outliers final: 28 residues processed: 340 average time/residue: 0.4078 time to fit residues: 224.3116 Evaluate side-chains 340 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 312 time to evaluate : 3.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 182 SER Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 271 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 207 optimal weight: 0.1980 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31401 Z= 0.227 Angle : 0.521 9.224 42409 Z= 0.260 Chirality : 0.044 0.143 4645 Planarity : 0.003 0.033 5390 Dihedral : 3.577 12.431 4263 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.10 % Allowed : 14.43 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 3889 helix: -0.09 (0.11), residues: 2173 sheet: -0.01 (0.23), residues: 444 loop : -1.52 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 198 HIS 0.002 0.000 HIS L 140 PHE 0.006 0.001 PHE C 113 TYR 0.012 0.001 TYR F 217 ARG 0.004 0.000 ARG K 274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 316 time to evaluate : 4.177 Fit side-chains REVERT: B 142 GLN cc_start: 0.9296 (mm110) cc_final: 0.8981 (mp10) REVERT: C 142 GLN cc_start: 0.9302 (mm110) cc_final: 0.8975 (mp10) REVERT: E 142 GLN cc_start: 0.9315 (mm110) cc_final: 0.8979 (mp10) REVERT: F 26 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8559 (mm-40) REVERT: F 30 GLN cc_start: 0.9098 (mt0) cc_final: 0.8781 (mp10) REVERT: G 142 GLN cc_start: 0.9290 (mm110) cc_final: 0.8964 (mp10) REVERT: H 142 GLN cc_start: 0.9272 (mp10) cc_final: 0.8817 (mp10) REVERT: J 142 GLN cc_start: 0.8552 (mp10) cc_final: 0.8207 (pm20) REVERT: K 142 GLN cc_start: 0.9308 (mm110) cc_final: 0.8990 (mp10) outliers start: 35 outliers final: 26 residues processed: 344 average time/residue: 0.3975 time to fit residues: 221.9270 Evaluate side-chains 341 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 315 time to evaluate : 3.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 182 SER Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 221 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 72 optimal weight: 0.2980 chunk 71 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 252 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 290 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN D 96 GLN H 96 GLN J 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31401 Z= 0.232 Angle : 0.530 9.203 42409 Z= 0.265 Chirality : 0.045 0.140 4645 Planarity : 0.003 0.032 5390 Dihedral : 3.556 13.413 4263 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.82 % Allowed : 14.68 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 3889 helix: 0.24 (0.11), residues: 2173 sheet: 0.13 (0.23), residues: 444 loop : -1.46 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 198 HIS 0.002 0.000 HIS I 140 PHE 0.006 0.001 PHE L 113 TYR 0.011 0.001 TYR F 217 ARG 0.003 0.000 ARG I 274 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 315 time to evaluate : 3.834 Fit side-chains REVERT: B 142 GLN cc_start: 0.9288 (mm110) cc_final: 0.8970 (mp10) REVERT: C 142 GLN cc_start: 0.9300 (mm110) cc_final: 0.8965 (mp10) REVERT: E 142 GLN cc_start: 0.9308 (mm110) cc_final: 0.8969 (mp10) REVERT: F 26 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8563 (mm-40) REVERT: F 30 GLN cc_start: 0.9096 (mt0) cc_final: 0.8787 (mp10) REVERT: G 142 GLN cc_start: 0.9287 (mm110) cc_final: 0.8968 (mp10) REVERT: K 142 GLN cc_start: 0.9294 (mm110) cc_final: 0.8976 (mp10) outliers start: 26 outliers final: 26 residues processed: 336 average time/residue: 0.4049 time to fit residues: 220.0215 Evaluate side-chains 331 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 305 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 182 SER Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 6.9990 chunk 354 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 270 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 311 optimal weight: 0.8980 chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 96 GLN I 96 GLN K 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 31401 Z= 0.387 Angle : 0.603 9.643 42409 Z= 0.305 Chirality : 0.047 0.161 4645 Planarity : 0.003 0.033 5390 Dihedral : 3.783 13.821 4263 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.82 % Allowed : 14.68 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 3889 helix: 0.25 (0.11), residues: 2137 sheet: 0.23 (0.24), residues: 444 loop : -1.51 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 198 HIS 0.003 0.001 HIS J 140 PHE 0.008 0.001 PHE I 228 TYR 0.014 0.001 TYR F 217 ARG 0.004 0.000 ARG K 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 312 time to evaluate : 3.765 Fit side-chains REVERT: B 142 GLN cc_start: 0.9295 (mm110) cc_final: 0.8944 (mp10) REVERT: C 142 GLN cc_start: 0.9313 (mm110) cc_final: 0.8944 (mp10) REVERT: E 142 GLN cc_start: 0.9320 (mm110) cc_final: 0.8944 (mp10) REVERT: G 142 GLN cc_start: 0.9305 (mm110) cc_final: 0.8940 (mp10) REVERT: K 142 GLN cc_start: 0.9307 (mm110) cc_final: 0.8954 (mp10) outliers start: 26 outliers final: 16 residues processed: 333 average time/residue: 0.3983 time to fit residues: 214.5810 Evaluate side-chains 327 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 311 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 10.0000 chunk 364 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 173 optimal weight: 0.0070 chunk 253 optimal weight: 1.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 304 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 235 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 31401 Z= 0.141 Angle : 0.519 10.807 42409 Z= 0.253 Chirality : 0.043 0.130 4645 Planarity : 0.003 0.035 5390 Dihedral : 3.504 13.700 4263 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.41 % Allowed : 15.28 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3889 helix: 0.79 (0.12), residues: 2077 sheet: 0.33 (0.24), residues: 444 loop : -1.29 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 198 HIS 0.001 0.000 HIS F 140 PHE 0.004 0.001 PHE F 184 TYR 0.009 0.001 TYR F 217 ARG 0.004 0.000 ARG D 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 312 time to evaluate : 3.628 Fit side-chains REVERT: B 142 GLN cc_start: 0.9290 (mm110) cc_final: 0.8981 (mp10) REVERT: C 142 GLN cc_start: 0.9306 (mm110) cc_final: 0.8979 (mp10) REVERT: E 142 GLN cc_start: 0.9321 (mm110) cc_final: 0.8990 (mp10) REVERT: F 26 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8626 (tp40) REVERT: F 30 GLN cc_start: 0.9035 (mt0) cc_final: 0.8784 (mp10) REVERT: G 142 GLN cc_start: 0.9289 (mm110) cc_final: 0.8974 (mp10) REVERT: K 142 GLN cc_start: 0.9300 (mm110) cc_final: 0.8984 (mp10) outliers start: 13 outliers final: 13 residues processed: 322 average time/residue: 0.4083 time to fit residues: 212.1382 Evaluate side-chains 325 residues out of total 3179 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 312 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 280 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 0.2980 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.075488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.051513 restraints weight = 115433.736| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 4.39 r_work: 0.2448 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2447 r_free = 0.2447 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 31401 Z= 0.397 Angle : 0.608 10.822 42409 Z= 0.304 Chirality : 0.048 0.158 4645 Planarity : 0.003 0.034 5390 Dihedral : 3.696 13.574 4263 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.50 % Allowed : 15.00 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3889 helix: 0.48 (0.11), residues: 2209 sheet: 0.39 (0.24), residues: 444 loop : -1.41 (0.18), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 198 HIS 0.003 0.001 HIS L 140 PHE 0.009 0.001 PHE C 113 TYR 0.014 0.001 TYR F 217 ARG 0.004 0.000 ARG A 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6357.92 seconds wall clock time: 115 minutes 56.15 seconds (6956.15 seconds total)