Starting phenix.real_space_refine on Sun Mar 24 07:58:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpv_7974/03_2024/6dpv_7974.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpv_7974/03_2024/6dpv_7974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpv_7974/03_2024/6dpv_7974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpv_7974/03_2024/6dpv_7974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpv_7974/03_2024/6dpv_7974.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpv_7974/03_2024/6dpv_7974.pdb" } resolution = 3.3 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= -0.007 sd= 0.925 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 276 5.16 5 C 25464 2.51 5 N 6924 2.21 5 O 7806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 386": "OE1" <-> "OE2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 434": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 386": "OE1" <-> "OE2" Residue "E GLU 411": "OE1" <-> "OE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "E GLU 434": "OE1" <-> "OE2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G GLU 345": "OE1" <-> "OE2" Residue "G PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 125": "OE1" <-> "OE2" Residue "H GLU 183": "OE1" <-> "OE2" Residue "H GLU 345": "OE1" <-> "OE2" Residue "H PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 113": "OE1" <-> "OE2" Residue "I GLU 125": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I GLU 345": "OE1" <-> "OE2" Residue "I PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J GLU 71": "OE1" <-> "OE2" Residue "J GLU 77": "OE1" <-> "OE2" Residue "J ARG 79": "NH1" <-> "NH2" Residue "J GLU 196": "OE1" <-> "OE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J GLU 411": "OE1" <-> "OE2" Residue "J GLU 429": "OE1" <-> "OE2" Residue "J GLU 433": "OE1" <-> "OE2" Residue "J GLU 434": "OE1" <-> "OE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K GLU 77": "OE1" <-> "OE2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "K GLU 196": "OE1" <-> "OE2" Residue "K GLU 386": "OE1" <-> "OE2" Residue "K GLU 411": "OE1" <-> "OE2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "K GLU 433": "OE1" <-> "OE2" Residue "K GLU 434": "OE1" <-> "OE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L GLU 71": "OE1" <-> "OE2" Residue "L GLU 77": "OE1" <-> "OE2" Residue "L ARG 79": "NH1" <-> "NH2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L GLU 386": "OE1" <-> "OE2" Residue "L GLU 411": "OE1" <-> "OE2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "L GLU 433": "OE1" <-> "OE2" Residue "L GLU 434": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40506 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "E" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "G" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "H" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "I" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3340 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "J" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.79, per 1000 atoms: 0.49 Number of scatterers: 40506 At special positions: 0 Unit cell: (170.482, 86.32, 209.326, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 276 16.00 P 30 15.00 Mg 6 11.99 O 7806 8.00 N 6924 7.00 C 25464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.23 Conformation dependent library (CDL) restraints added in 6.7 seconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9492 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 30 sheets defined 56.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.635A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.594A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.093A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 206 through 218 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.584A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.991A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.706A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.846A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.562A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.750A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 3.894A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.873A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 48 removed outlier: 4.450A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 81 removed outlier: 4.574A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.745A pdb=" N PHE B 87 " --> pdb=" O GLY B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 109 through 129 removed outlier: 4.474A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.886A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 216 Processing helix chain 'B' and resid 223 through 244 removed outlier: 5.198A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 243 " --> pdb=" O THR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.631A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.075A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 436 removed outlier: 3.951A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.634A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.594A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.094A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.583A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.991A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 283 removed outlier: 3.705A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.847A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.562A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 401 removed outlier: 3.750A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.893A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.872A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 41 through 48 removed outlier: 4.450A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 71 through 81 removed outlier: 4.573A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.744A pdb=" N PHE D 87 " --> pdb=" O GLY D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 109 through 129 removed outlier: 4.473A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.886A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 216 Processing helix chain 'D' and resid 223 through 244 removed outlier: 5.198A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 384 through 401 removed outlier: 3.632A pdb=" N ARG D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 4.074A pdb=" N TYR D 408 " --> pdb=" O PHE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 436 removed outlier: 3.950A pdb=" N PHE D 418 " --> pdb=" O ASP D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.633A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.594A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.093A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 206 through 218 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.584A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.991A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 283 removed outlier: 3.706A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.846A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 removed outlier: 3.563A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 401 removed outlier: 3.750A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.894A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.873A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 Processing helix chain 'F' and resid 41 through 48 removed outlier: 4.449A pdb=" N ARG F 48 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 71 through 81 removed outlier: 4.573A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.744A pdb=" N PHE F 87 " --> pdb=" O GLY F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 109 through 129 removed outlier: 4.474A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 182 through 198 removed outlier: 3.885A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Processing helix chain 'F' and resid 223 through 244 removed outlier: 5.199A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG F 243 " --> pdb=" O THR F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 287 through 296 Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 306 through 310 Processing helix chain 'F' and resid 324 through 339 Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 384 through 401 removed outlier: 3.632A pdb=" N ARG F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 410 removed outlier: 4.074A pdb=" N TYR F 408 " --> pdb=" O PHE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 436 removed outlier: 3.950A pdb=" N PHE F 418 " --> pdb=" O ASP F 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 29 Processing helix chain 'G' and resid 41 through 48 removed outlier: 4.449A pdb=" N ARG G 48 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 71 through 81 removed outlier: 4.573A pdb=" N MET G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.745A pdb=" N PHE G 87 " --> pdb=" O GLY G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 109 through 129 removed outlier: 4.474A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 Processing helix chain 'G' and resid 182 through 198 removed outlier: 3.885A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 223 through 244 removed outlier: 5.198A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG G 243 " --> pdb=" O THR G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 287 through 296 Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 324 through 339 Processing helix chain 'G' and resid 340 through 343 Processing helix chain 'G' and resid 384 through 401 removed outlier: 3.630A pdb=" N ARG G 401 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 410 removed outlier: 4.073A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 436 removed outlier: 3.950A pdb=" N PHE G 418 " --> pdb=" O ASP G 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 29 Processing helix chain 'H' and resid 41 through 48 removed outlier: 4.450A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 71 through 81 removed outlier: 4.574A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.744A pdb=" N PHE H 87 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 108 Processing helix chain 'H' and resid 109 through 129 removed outlier: 4.474A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 Processing helix chain 'H' and resid 182 through 198 removed outlier: 3.885A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 216 Processing helix chain 'H' and resid 223 through 244 removed outlier: 5.197A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG H 243 " --> pdb=" O THR H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 287 through 296 Processing helix chain 'H' and resid 297 through 301 Processing helix chain 'H' and resid 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 401 removed outlier: 3.631A pdb=" N ARG H 401 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 410 removed outlier: 4.073A pdb=" N TYR H 408 " --> pdb=" O PHE H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 436 removed outlier: 3.950A pdb=" N PHE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 41 through 48 removed outlier: 4.450A pdb=" N ARG I 48 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 71 through 81 removed outlier: 4.574A pdb=" N MET I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.744A pdb=" N PHE I 87 " --> pdb=" O GLY I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 109 through 129 removed outlier: 4.474A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 161 Processing helix chain 'I' and resid 182 through 198 removed outlier: 3.885A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 5.198A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG I 243 " --> pdb=" O THR I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'I' and resid 287 through 296 Processing helix chain 'I' and resid 297 through 301 Processing helix chain 'I' and resid 306 through 310 Processing helix chain 'I' and resid 324 through 339 Processing helix chain 'I' and resid 340 through 343 Processing helix chain 'I' and resid 384 through 401 removed outlier: 3.631A pdb=" N ARG I 401 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 410 removed outlier: 4.073A pdb=" N TYR I 408 " --> pdb=" O PHE I 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 436 removed outlier: 3.950A pdb=" N PHE I 418 " --> pdb=" O ASP I 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 29 Processing helix chain 'J' and resid 47 through 51 Processing helix chain 'J' and resid 72 through 81 removed outlier: 3.634A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 128 removed outlier: 3.594A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.093A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'J' and resid 206 through 218 Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.584A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 3.990A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 283 removed outlier: 3.705A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 296 removed outlier: 3.847A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 301 Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 removed outlier: 3.562A pdb=" N VAL J 328 " --> pdb=" O VAL J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 401 removed outlier: 3.750A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 3.895A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.872A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 29 Processing helix chain 'K' and resid 47 through 51 Processing helix chain 'K' and resid 72 through 81 removed outlier: 3.635A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.595A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.094A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 196 through 198 No H-bonds generated for 'chain 'K' and resid 196 through 198' Processing helix chain 'K' and resid 206 through 218 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.584A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 3.990A pdb=" N PHE K 255 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 283 removed outlier: 3.705A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 296 removed outlier: 3.846A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 301 Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 removed outlier: 3.562A pdb=" N VAL K 328 " --> pdb=" O VAL K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 401 removed outlier: 3.750A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 3.895A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.872A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'L' and resid 72 through 81 removed outlier: 3.635A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.594A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.093A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 196 through 198 No H-bonds generated for 'chain 'L' and resid 196 through 198' Processing helix chain 'L' and resid 206 through 218 Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.584A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 removed outlier: 3.990A pdb=" N PHE L 255 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 277 through 283 removed outlier: 3.704A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 296 removed outlier: 3.845A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 301 Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 removed outlier: 3.563A pdb=" N VAL L 328 " --> pdb=" O VAL L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 401 removed outlier: 3.751A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 3.893A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.873A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.051A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 171 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.622A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN B 133 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE B 135 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR B 201 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N CYS B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N PHE B 272 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 13.237A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 248 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER C 165 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 171 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.621A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LEU D 137 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE D 7 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N HIS D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLN D 133 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN D 167 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE D 135 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR D 201 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N CYS D 203 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N PHE D 272 " --> pdb=" O CYS D 203 " (cutoff:3.500A) removed outlier: 13.238A pdb=" N ASP D 205 " --> pdb=" O PHE D 272 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 248 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 165 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE E 171 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.622A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N HIS F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ALA F 9 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLN F 133 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN F 167 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE F 135 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE F 169 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU F 137 " --> pdb=" O PHE F 169 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL F 171 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N HIS F 139 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR F 201 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS F 203 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N PHE F 272 " --> pdb=" O CYS F 203 " (cutoff:3.500A) removed outlier: 13.237A pdb=" N ASP F 205 " --> pdb=" O PHE F 272 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU F 248 " --> pdb=" O VAL F 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AB7, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU G 3 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE G 135 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL G 5 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU G 137 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE G 7 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N HIS G 139 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA G 9 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN G 133 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASN G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE G 135 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL G 171 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N HIS G 139 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET G 166 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR G 202 " --> pdb=" O MET G 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR G 168 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE G 204 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N SER G 170 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR G 201 " --> pdb=" O PHE G 268 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS G 203 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N PHE G 272 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 13.238A pdb=" N ASP G 205 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LYS G 352 " --> pdb=" O LEU G 313 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL G 315 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA G 354 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA G 317 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS G 356 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE G 319 " --> pdb=" O CYS G 356 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU G 248 " --> pdb=" O VAL G 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLU H 3 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE H 135 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL H 5 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU H 137 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE H 7 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS H 139 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA H 9 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN H 133 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ASN H 167 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE H 135 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N PHE H 169 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU H 137 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL H 171 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N HIS H 139 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR H 201 " --> pdb=" O PHE H 268 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS H 203 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N PHE H 272 " --> pdb=" O CYS H 203 " (cutoff:3.500A) removed outlier: 13.237A pdb=" N ASP H 205 " --> pdb=" O PHE H 272 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU H 248 " --> pdb=" O VAL H 355 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.871A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU I 137 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE I 7 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS I 139 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ALA I 9 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLN I 133 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASN I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE I 135 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL I 171 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N HIS I 139 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET I 166 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N TYR I 202 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR I 168 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE I 204 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER I 170 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR I 201 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N CYS I 203 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N PHE I 272 " --> pdb=" O CYS I 203 " (cutoff:3.500A) removed outlier: 13.238A pdb=" N ASP I 205 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N LYS I 352 " --> pdb=" O LEU I 313 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL I 315 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N ALA I 354 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA I 317 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N CYS I 356 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE I 319 " --> pdb=" O CYS I 356 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU I 248 " --> pdb=" O VAL I 355 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU J 3 " --> pdb=" O LEU J 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY J 134 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER J 140 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER J 165 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE J 171 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LYS J 166 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE J 202 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.621A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.053A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU K 3 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY K 134 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER K 140 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER K 165 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE K 171 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS K 166 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE K 202 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AC9, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.621A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.052A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU L 3 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY L 134 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER L 140 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER L 165 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE L 171 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LYS L 166 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE L 202 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AD3, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.622A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) 2058 hydrogen bonds defined for protein. 5904 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: 15.85 Time building geometry restraints manager: 17.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7181 1.32 - 1.44: 10955 1.44 - 1.57: 22820 1.57 - 1.69: 48 1.69 - 1.81: 432 Bond restraints: 41436 Sorted by residual: bond pdb=" C5 GTP E 501 " pdb=" C6 GTP E 501 " ideal model delta sigma weight residual 1.390 1.489 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C5 GTP A 501 " pdb=" C6 GTP A 501 " ideal model delta sigma weight residual 1.390 1.488 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C5 GTP C 501 " pdb=" C6 GTP C 501 " ideal model delta sigma weight residual 1.390 1.487 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C5 GTP J 501 " pdb=" C6 GTP J 501 " ideal model delta sigma weight residual 1.390 1.486 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C5 GTP L 501 " pdb=" C6 GTP L 501 " ideal model delta sigma weight residual 1.390 1.485 -0.095 2.00e-02 2.50e+03 2.24e+01 ... (remaining 41431 not shown) Histogram of bond angle deviations from ideal: 98.60 - 106.34: 1466 106.34 - 114.08: 22291 114.08 - 121.82: 21188 121.82 - 129.56: 11071 129.56 - 137.30: 288 Bond angle restraints: 56304 Sorted by residual: angle pdb=" N THR L 73 " pdb=" CA THR L 73 " pdb=" C THR L 73 " ideal model delta sigma weight residual 111.11 117.45 -6.34 1.20e+00 6.94e-01 2.79e+01 angle pdb=" N THR K 73 " pdb=" CA THR K 73 " pdb=" C THR K 73 " ideal model delta sigma weight residual 111.11 117.42 -6.31 1.20e+00 6.94e-01 2.77e+01 angle pdb=" N THR J 73 " pdb=" CA THR J 73 " pdb=" C THR J 73 " ideal model delta sigma weight residual 111.11 117.40 -6.29 1.20e+00 6.94e-01 2.75e+01 angle pdb=" N THR A 73 " pdb=" CA THR A 73 " pdb=" C THR A 73 " ideal model delta sigma weight residual 111.11 117.38 -6.27 1.20e+00 6.94e-01 2.73e+01 angle pdb=" N THR E 73 " pdb=" CA THR E 73 " pdb=" C THR E 73 " ideal model delta sigma weight residual 111.11 117.37 -6.26 1.20e+00 6.94e-01 2.73e+01 ... (remaining 56299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.60: 23772 33.60 - 67.20: 780 67.20 - 100.80: 36 100.80 - 134.41: 6 134.41 - 168.01: 18 Dihedral angle restraints: 24612 sinusoidal: 9810 harmonic: 14802 Sorted by residual: dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.72 -168.01 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.94 -167.79 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.96 -167.77 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4016 0.070 - 0.140: 1586 0.140 - 0.210: 439 0.210 - 0.280: 90 0.280 - 0.350: 25 Chirality restraints: 6156 Sorted by residual: chirality pdb=" CA PHE I 83 " pdb=" N PHE I 83 " pdb=" C PHE I 83 " pdb=" CB PHE I 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA PHE B 83 " pdb=" N PHE B 83 " pdb=" C PHE B 83 " pdb=" CB PHE B 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA PHE D 83 " pdb=" N PHE D 83 " pdb=" C PHE D 83 " pdb=" CB PHE D 83 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 6153 not shown) Planarity restraints: 7338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 288 " 0.050 5.00e-02 4.00e+02 7.64e-02 9.35e+00 pdb=" N PRO D 289 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 289 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 289 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 288 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO B 289 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL I 288 " 0.050 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO I 289 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO I 289 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 289 " 0.042 5.00e-02 4.00e+02 ... (remaining 7335 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 84 2.56 - 3.14: 30964 3.14 - 3.73: 64764 3.73 - 4.31: 89611 4.31 - 4.90: 153610 Nonbonded interactions: 339033 Sorted by model distance: nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 1.972 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.982 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 2.007 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.012 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 2.034 2.170 ... (remaining 339028 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 29.250 Check model and map are aligned: 0.600 Set scattering table: 0.370 Process input model: 101.660 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.008 0.099 41436 Z= 0.561 Angle : 1.461 9.685 56304 Z= 1.024 Chirality : 0.082 0.350 6156 Planarity : 0.007 0.076 7338 Dihedral : 16.609 168.007 15120 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.21 % Allowed : 8.99 % Favored : 88.80 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.11), residues: 5088 helix: 1.22 (0.10), residues: 2274 sheet: 0.75 (0.19), residues: 714 loop : -0.93 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP D 21 HIS 0.012 0.002 HIS E 8 PHE 0.028 0.002 PHE F 92 TYR 0.019 0.003 TYR I 224 ARG 0.018 0.001 ARG K 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1693 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1597 time to evaluate : 4.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.7824 (t0) cc_final: 0.7429 (t0) REVERT: A 71 GLU cc_start: 0.7353 (pt0) cc_final: 0.6977 (pt0) REVERT: A 76 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.7151 (m-30) REVERT: A 110 ILE cc_start: 0.8850 (mm) cc_final: 0.8594 (mm) REVERT: A 178 SER cc_start: 0.7437 (OUTLIER) cc_final: 0.7208 (p) REVERT: A 251 ASP cc_start: 0.7291 (p0) cc_final: 0.6915 (p0) REVERT: A 401 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7890 (mmtt) REVERT: B 31 ASP cc_start: 0.6891 (p0) cc_final: 0.6492 (p0) REVERT: C 27 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7633 (mt-10) REVERT: C 50 ASN cc_start: 0.7541 (t0) cc_final: 0.7104 (t0) REVERT: C 110 ILE cc_start: 0.8859 (mm) cc_final: 0.8624 (mm) REVERT: C 114 ILE cc_start: 0.8930 (tp) cc_final: 0.8723 (mt) REVERT: C 161 TYR cc_start: 0.8382 (m-80) cc_final: 0.8132 (m-80) REVERT: C 230 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8192 (tt) REVERT: C 311 LYS cc_start: 0.8321 (mtmp) cc_final: 0.8111 (mttp) REVERT: C 396 ASP cc_start: 0.6382 (m-30) cc_final: 0.6125 (m-30) REVERT: D 31 ASP cc_start: 0.6694 (p0) cc_final: 0.6459 (p0) REVERT: D 314 THR cc_start: 0.8290 (p) cc_final: 0.7957 (p) REVERT: D 398 MET cc_start: 0.8277 (mtt) cc_final: 0.8013 (mtt) REVERT: E 50 ASN cc_start: 0.7838 (t0) cc_final: 0.7358 (t0) REVERT: E 110 ILE cc_start: 0.8846 (mm) cc_final: 0.8556 (mm) REVERT: E 172 TYR cc_start: 0.8106 (t80) cc_final: 0.7519 (t80) REVERT: E 230 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7995 (mp) REVERT: F 31 ASP cc_start: 0.6701 (p0) cc_final: 0.6296 (p0) REVERT: F 224 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7252 (m-80) REVERT: F 301 MET cc_start: 0.7695 (mmp) cc_final: 0.7470 (mmp) REVERT: G 88 ARG cc_start: 0.7741 (ttp-110) cc_final: 0.7086 (tpt170) REVERT: G 349 ASN cc_start: 0.7357 (t0) cc_final: 0.7004 (t160) REVERT: H 286 LEU cc_start: 0.7776 (mt) cc_final: 0.7168 (mp) REVERT: H 287 THR cc_start: 0.8390 (p) cc_final: 0.7929 (t) REVERT: H 398 MET cc_start: 0.7603 (mtt) cc_final: 0.7262 (mtp) REVERT: I 27 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7300 (mt-10) REVERT: I 299 LYS cc_start: 0.7753 (ttpp) cc_final: 0.7371 (mtpp) REVERT: I 398 MET cc_start: 0.7791 (mtt) cc_final: 0.7391 (mtp) REVERT: J 71 GLU cc_start: 0.7301 (pt0) cc_final: 0.6937 (pt0) REVERT: J 161 TYR cc_start: 0.8467 (m-80) cc_final: 0.8159 (m-80) REVERT: J 230 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7980 (mp) REVERT: J 326 LYS cc_start: 0.7406 (ttmt) cc_final: 0.7047 (mttt) REVERT: J 396 ASP cc_start: 0.6435 (m-30) cc_final: 0.6086 (m-30) REVERT: K 161 TYR cc_start: 0.8256 (m-80) cc_final: 0.8000 (m-80) REVERT: K 230 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7994 (mp) REVERT: K 326 LYS cc_start: 0.7465 (ttmt) cc_final: 0.6779 (mttt) REVERT: L 71 GLU cc_start: 0.7068 (pt0) cc_final: 0.6837 (pt0) REVERT: L 230 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8139 (mp) REVERT: L 252 LEU cc_start: 0.8732 (mt) cc_final: 0.8317 (mt) outliers start: 96 outliers final: 24 residues processed: 1654 average time/residue: 0.5592 time to fit residues: 1470.6839 Evaluate side-chains 968 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 936 time to evaluate : 4.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 245 ASP Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 245 ASP Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 371 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 0.5980 chunk 382 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 257 optimal weight: 4.9990 chunk 204 optimal weight: 0.5980 chunk 395 optimal weight: 0.0770 chunk 152 optimal weight: 0.6980 chunk 240 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 chunk 457 optimal weight: 4.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 18 ASN A 88 HIS A 101 ASN A 300 ASN B 37 HIS B 91 ASN B 193 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 436 GLN C 8 HIS C 15 GLN C 18 ASN C 88 HIS C 283 HIS C 300 ASN C 309 HIS D 6 HIS D 37 HIS D 91 ASN D 139 HIS D 282 GLN D 350 ASN E 15 GLN E 18 ASN E 88 HIS E 192 HIS E 285 GLN E 300 ASN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS F 37 HIS F 85 GLN F 91 ASN F 139 HIS ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 HIS G 91 ASN G 193 GLN G 331 GLN G 349 ASN G 350 ASN H 91 ASN H 349 ASN H 350 ASN I 6 HIS I 91 ASN I 331 GLN I 334 ASN I 350 ASN J 8 HIS J 15 GLN J 192 HIS J 197 HIS J 216 ASN J 285 GLN J 300 ASN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 HIS K 15 GLN K 18 ASN K 88 HIS K 101 ASN K 192 HIS K 197 HIS K 283 HIS K 300 ASN L 8 HIS L 15 GLN L 18 ASN L 88 HIS L 101 ASN L 107 HIS L 192 HIS L 197 HIS L 283 HIS L 300 ASN L 301 GLN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41436 Z= 0.189 Angle : 0.610 10.078 56304 Z= 0.320 Chirality : 0.044 0.221 6156 Planarity : 0.005 0.056 7338 Dihedral : 12.325 174.049 5771 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.67 % Allowed : 15.93 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.12), residues: 5088 helix: 2.35 (0.11), residues: 2304 sheet: 0.73 (0.17), residues: 816 loop : -0.64 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 346 HIS 0.006 0.001 HIS D 139 PHE 0.024 0.001 PHE B 388 TYR 0.018 0.001 TYR E 185 ARG 0.007 0.001 ARG H 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1045 time to evaluate : 4.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.7804 (t0) cc_final: 0.7535 (t0) REVERT: A 71 GLU cc_start: 0.7331 (pt0) cc_final: 0.7069 (pt0) REVERT: B 281 GLN cc_start: 0.7858 (pm20) cc_final: 0.7632 (pm20) REVERT: C 48 SER cc_start: 0.8039 (OUTLIER) cc_final: 0.7696 (m) REVERT: C 251 ASP cc_start: 0.7227 (p0) cc_final: 0.6911 (p0) REVERT: C 396 ASP cc_start: 0.6542 (m-30) cc_final: 0.6211 (m-30) REVERT: C 413 MET cc_start: 0.8079 (ttm) cc_final: 0.7780 (ttm) REVERT: D 37 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.7004 (m170) REVERT: E 50 ASN cc_start: 0.7946 (t0) cc_final: 0.7552 (t0) REVERT: E 413 MET cc_start: 0.8086 (ttm) cc_final: 0.7752 (ttm) REVERT: F 224 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: G 88 ARG cc_start: 0.7722 (ttp-110) cc_final: 0.7100 (tpt170) REVERT: H 125 GLU cc_start: 0.7282 (mm-30) cc_final: 0.7018 (mm-30) REVERT: H 286 LEU cc_start: 0.7752 (mt) cc_final: 0.7233 (mp) REVERT: H 398 MET cc_start: 0.7785 (mtt) cc_final: 0.7518 (mtp) REVERT: I 151 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8131 (m) REVERT: I 398 MET cc_start: 0.8054 (mtt) cc_final: 0.7629 (mtp) REVERT: J 71 GLU cc_start: 0.7295 (pt0) cc_final: 0.7092 (pt0) REVERT: J 161 TYR cc_start: 0.8367 (m-80) cc_final: 0.8152 (m-80) REVERT: J 396 ASP cc_start: 0.6573 (m-30) cc_final: 0.6211 (m-30) REVERT: K 378 LEU cc_start: 0.9014 (mm) cc_final: 0.8760 (mt) REVERT: L 309 HIS cc_start: 0.7823 (m170) cc_final: 0.7567 (m90) outliers start: 159 outliers final: 64 residues processed: 1144 average time/residue: 0.5031 time to fit residues: 949.2116 Evaluate side-chains 896 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 828 time to evaluate : 4.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain D residue 37 HIS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 37 HIS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 330 GLU Chi-restraints excluded: chain I residue 151 THR Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 178 SER Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 245 ASP Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 380 optimal weight: 7.9990 chunk 311 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 458 optimal weight: 1.9990 chunk 495 optimal weight: 0.9980 chunk 408 optimal weight: 10.0000 chunk 454 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 367 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 18 ASN A 88 HIS A 192 HIS A 256 GLN B 37 HIS B 192 HIS ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN B 433 GLN B 436 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS C 309 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 HIS E 8 HIS ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS E 88 HIS ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 192 HIS ** F 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS H 192 HIS H 293 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 192 HIS I 331 GLN I 334 ASN J 107 HIS J 300 ASN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS K 216 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN L 88 HIS L 300 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 41436 Z= 0.281 Angle : 0.584 7.721 56304 Z= 0.303 Chirality : 0.044 0.172 6156 Planarity : 0.005 0.054 7338 Dihedral : 11.675 174.218 5737 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.60 % Allowed : 18.76 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.12), residues: 5088 helix: 2.26 (0.11), residues: 2310 sheet: 1.08 (0.18), residues: 762 loop : -0.68 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 346 HIS 0.015 0.001 HIS F 37 PHE 0.014 0.002 PHE C 169 TYR 0.020 0.001 TYR I 161 ARG 0.010 0.001 ARG G 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 882 time to evaluate : 4.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8034 (mp) REVERT: B 71 GLU cc_start: 0.6327 (pt0) cc_final: 0.6107 (pt0) REVERT: C 233 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8511 (tp40) REVERT: C 357 TYR cc_start: 0.7660 (m-80) cc_final: 0.7350 (m-10) REVERT: C 413 MET cc_start: 0.8305 (ttm) cc_final: 0.8009 (ttm) REVERT: E 413 MET cc_start: 0.8218 (ttm) cc_final: 0.7867 (ttm) REVERT: G 88 ARG cc_start: 0.7831 (ttp-110) cc_final: 0.7169 (tpt170) REVERT: G 199 ASP cc_start: 0.7424 (m-30) cc_final: 0.7149 (m-30) REVERT: G 286 LEU cc_start: 0.8172 (mt) cc_final: 0.7952 (mt) REVERT: G 324 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7939 (p) REVERT: H 125 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7083 (mm-30) REVERT: H 293 GLN cc_start: 0.7400 (pt0) cc_final: 0.7049 (pt0) REVERT: H 398 MET cc_start: 0.7896 (mtt) cc_final: 0.7647 (mtp) REVERT: I 124 LYS cc_start: 0.8217 (tttt) cc_final: 0.7991 (tttp) REVERT: I 312 TYR cc_start: 0.8388 (m-80) cc_final: 0.7748 (m-80) REVERT: I 323 MET cc_start: 0.7836 (mtp) cc_final: 0.7603 (mtm) REVERT: I 398 MET cc_start: 0.8199 (mtt) cc_final: 0.7788 (mtp) REVERT: J 161 TYR cc_start: 0.8537 (m-80) cc_final: 0.8198 (m-80) REVERT: K 302 MET cc_start: 0.8097 (mmt) cc_final: 0.7874 (mmt) REVERT: L 161 TYR cc_start: 0.8191 (m-80) cc_final: 0.7766 (m-80) outliers start: 156 outliers final: 100 residues processed: 982 average time/residue: 0.5034 time to fit residues: 815.2862 Evaluate side-chains 897 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 795 time to evaluate : 4.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 330 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain I residue 338 LYS Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 245 ASP Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain K residue 158 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 194 THR Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 300 ASN Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 433 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 0.4980 chunk 344 optimal weight: 0.9990 chunk 237 optimal weight: 0.0970 chunk 50 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 307 optimal weight: 7.9990 chunk 460 optimal weight: 0.9990 chunk 487 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 436 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 37 HIS B 206 ASN B 258 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 37 HIS ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN E 88 HIS E 301 GLN F 11 GLN F 37 HIS F 258 ASN F 282 GLN ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN G 334 ASN H 107 HIS H 206 ASN ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN I 258 ASN I 334 ASN J 285 GLN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN K 283 HIS ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 41436 Z= 0.157 Angle : 0.525 8.656 56304 Z= 0.269 Chirality : 0.042 0.255 6156 Planarity : 0.004 0.054 7338 Dihedral : 11.396 177.370 5730 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.79 % Allowed : 20.26 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.12), residues: 5088 helix: 2.13 (0.11), residues: 2346 sheet: 1.08 (0.18), residues: 762 loop : -0.68 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 346 HIS 0.008 0.001 HIS F 37 PHE 0.012 0.001 PHE C 169 TYR 0.015 0.001 TYR I 161 ARG 0.006 0.000 ARG K 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 848 time to evaluate : 4.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 149 PHE cc_start: 0.8388 (t80) cc_final: 0.8176 (t80) REVERT: C 357 TYR cc_start: 0.7541 (m-80) cc_final: 0.7312 (m-10) REVERT: C 413 MET cc_start: 0.8130 (ttm) cc_final: 0.7849 (ttm) REVERT: E 413 MET cc_start: 0.8069 (ttm) cc_final: 0.7695 (ttm) REVERT: G 88 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7068 (tpt170) REVERT: G 199 ASP cc_start: 0.7248 (m-30) cc_final: 0.7016 (m-30) REVERT: H 398 MET cc_start: 0.7993 (mtt) cc_final: 0.7747 (mtp) REVERT: I 312 TYR cc_start: 0.8238 (m-80) cc_final: 0.7467 (m-80) REVERT: I 398 MET cc_start: 0.8249 (mtt) cc_final: 0.7930 (mtp) REVERT: J 161 TYR cc_start: 0.8429 (m-80) cc_final: 0.8142 (m-80) REVERT: L 71 GLU cc_start: 0.7065 (pt0) cc_final: 0.6706 (pt0) REVERT: L 161 TYR cc_start: 0.8171 (m-80) cc_final: 0.7900 (m-80) REVERT: L 309 HIS cc_start: 0.7825 (m170) cc_final: 0.7543 (m90) outliers start: 121 outliers final: 71 residues processed: 920 average time/residue: 0.5007 time to fit residues: 757.9240 Evaluate side-chains 846 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 775 time to evaluate : 4.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 422 ARG Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 163 LYS Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 10.0000 chunk 276 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 362 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 415 optimal weight: 5.9990 chunk 336 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 437 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 28 HIS A 101 ASN A 309 HIS B 6 HIS B 8 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS C 107 HIS ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 61 HIS ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 258 ASN F 282 GLN F 293 GLN ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 ASN G 336 GLN H 258 ASN H 293 GLN H 331 GLN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 334 ASN ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 HIS J 101 ASN J 285 GLN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS K 101 ASN K 107 HIS K 133 GLN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 41436 Z= 0.521 Angle : 0.688 7.698 56304 Z= 0.358 Chirality : 0.050 0.264 6156 Planarity : 0.006 0.054 7338 Dihedral : 11.530 174.615 5726 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.26 % Allowed : 20.33 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.12), residues: 5088 helix: 1.73 (0.11), residues: 2334 sheet: 0.74 (0.18), residues: 798 loop : -1.08 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 346 HIS 0.022 0.002 HIS F 37 PHE 0.023 0.003 PHE F 20 TYR 0.022 0.002 TYR B 52 ARG 0.008 0.001 ARG H 400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 807 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: A 422 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6271 (tpp-160) REVERT: C 127 ASP cc_start: 0.7446 (m-30) cc_final: 0.7214 (m-30) REVERT: C 254 GLU cc_start: 0.7367 (mm-30) cc_final: 0.7014 (mm-30) REVERT: C 357 TYR cc_start: 0.8075 (m-80) cc_final: 0.7730 (m-10) REVERT: E 327 ASP cc_start: 0.7716 (p0) cc_final: 0.7356 (p0) REVERT: E 413 MET cc_start: 0.8465 (ttm) cc_final: 0.8048 (ttm) REVERT: F 37 HIS cc_start: 0.7383 (OUTLIER) cc_final: 0.7177 (m170) REVERT: G 88 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7236 (tpt170) REVERT: G 165 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8865 (tp) REVERT: G 324 SER cc_start: 0.8399 (OUTLIER) cc_final: 0.8078 (p) REVERT: I 110 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6624 (mt-10) REVERT: I 398 MET cc_start: 0.8215 (mtt) cc_final: 0.7953 (mtp) REVERT: J 161 TYR cc_start: 0.8624 (m-80) cc_final: 0.8315 (m-80) REVERT: J 290 GLU cc_start: 0.6653 (tm-30) cc_final: 0.5905 (tm-30) REVERT: J 422 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6912 (tpp-160) REVERT: K 309 HIS cc_start: 0.7803 (m170) cc_final: 0.7504 (m90) REVERT: K 413 MET cc_start: 0.8402 (ttm) cc_final: 0.8109 (ttm) REVERT: L 91 GLN cc_start: 0.8139 (mt0) cc_final: 0.7930 (mt0) REVERT: L 172 TYR cc_start: 0.7489 (t80) cc_final: 0.7207 (t80) REVERT: L 212 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8971 (mp) REVERT: L 338 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7679 (ttpt) REVERT: L 413 MET cc_start: 0.8188 (ttm) cc_final: 0.7980 (ttm) REVERT: L 422 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6740 (tpp-160) outliers start: 185 outliers final: 127 residues processed: 932 average time/residue: 0.5229 time to fit residues: 797.1579 Evaluate side-chains 881 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 745 time to evaluate : 4.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 336 LYS Chi-restraints excluded: chain E residue 361 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 94 PHE Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 331 GLN Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 381 SER Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 293 GLN Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 254 GLU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 378 LEU Chi-restraints excluded: chain J residue 422 ARG Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 133 GLN Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 158 SER Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 371 VAL Chi-restraints excluded: chain L residue 422 ARG Chi-restraints excluded: chain L residue 433 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 2.9990 chunk 438 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 487 optimal weight: 0.9990 chunk 404 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 256 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 309 HIS ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 206 ASN F 258 ASN ** F 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN J 285 GLN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN L 342 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 41436 Z= 0.262 Angle : 0.579 8.876 56304 Z= 0.297 Chirality : 0.044 0.286 6156 Planarity : 0.005 0.051 7338 Dihedral : 11.378 179.249 5726 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.60 % Allowed : 22.11 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.12), residues: 5088 helix: 1.83 (0.11), residues: 2346 sheet: 0.66 (0.18), residues: 798 loop : -1.05 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 21 HIS 0.008 0.001 HIS L 309 PHE 0.022 0.001 PHE L 49 TYR 0.015 0.001 TYR I 161 ARG 0.009 0.001 ARG E 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 775 time to evaluate : 4.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6989 (m-30) REVERT: C 127 ASP cc_start: 0.7358 (m-30) cc_final: 0.7113 (m-30) REVERT: C 149 PHE cc_start: 0.8506 (t80) cc_final: 0.8282 (t80) REVERT: C 254 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7116 (mm-30) REVERT: C 339 ARG cc_start: 0.7681 (tpm170) cc_final: 0.7423 (tpp-160) REVERT: E 327 ASP cc_start: 0.7498 (p0) cc_final: 0.7124 (p0) REVERT: E 413 MET cc_start: 0.8318 (ttm) cc_final: 0.7996 (ttm) REVERT: G 88 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7221 (tpt170) REVERT: I 110 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6630 (mt-10) REVERT: I 199 ASP cc_start: 0.7734 (m-30) cc_final: 0.7466 (m-30) REVERT: I 398 MET cc_start: 0.8270 (mtt) cc_final: 0.8047 (mtp) REVERT: J 161 TYR cc_start: 0.8484 (m-80) cc_final: 0.8164 (m-80) REVERT: J 290 GLU cc_start: 0.6400 (tm-30) cc_final: 0.5835 (tm-30) REVERT: J 422 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7123 (tpp-160) REVERT: K 413 MET cc_start: 0.8247 (ttm) cc_final: 0.7927 (ttm) REVERT: L 91 GLN cc_start: 0.8050 (mt0) cc_final: 0.7841 (mt0) REVERT: L 161 TYR cc_start: 0.8336 (m-80) cc_final: 0.8030 (m-80) REVERT: L 172 TYR cc_start: 0.7561 (t80) cc_final: 0.7262 (t80) REVERT: L 212 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8940 (mp) REVERT: L 413 MET cc_start: 0.8054 (ttm) cc_final: 0.7838 (ttm) outliers start: 156 outliers final: 111 residues processed: 869 average time/residue: 0.5180 time to fit residues: 733.6874 Evaluate side-chains 867 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 752 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 293 GLN Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 330 GLU Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 254 GLU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 306 ASP Chi-restraints excluded: chain J residue 422 ARG Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 339 ARG Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 0.0470 chunk 54 optimal weight: 0.5980 chunk 277 optimal weight: 1.9990 chunk 356 optimal weight: 6.9990 chunk 275 optimal weight: 7.9990 chunk 410 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 chunk 485 optimal weight: 5.9990 chunk 304 optimal weight: 9.9990 chunk 296 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 overall best weight: 2.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 GLN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 41436 Z= 0.242 Angle : 0.556 7.267 56304 Z= 0.284 Chirality : 0.043 0.282 6156 Planarity : 0.005 0.051 7338 Dihedral : 11.160 176.463 5726 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.73 % Allowed : 21.69 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.12), residues: 5088 helix: 1.89 (0.11), residues: 2340 sheet: 0.64 (0.18), residues: 798 loop : -1.05 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 346 HIS 0.005 0.001 HIS L 309 PHE 0.019 0.001 PHE K 49 TYR 0.014 0.001 TYR I 161 ARG 0.007 0.000 ARG H 400 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 777 time to evaluate : 4.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.7048 (m-30) REVERT: A 393 HIS cc_start: 0.8102 (t70) cc_final: 0.7823 (t70) REVERT: C 127 ASP cc_start: 0.7345 (m-30) cc_final: 0.7129 (m-30) REVERT: C 149 PHE cc_start: 0.8432 (t80) cc_final: 0.8209 (t80) REVERT: C 339 ARG cc_start: 0.7742 (tpm170) cc_final: 0.7522 (tpp-160) REVERT: E 259 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8624 (mp) REVERT: E 413 MET cc_start: 0.8265 (ttm) cc_final: 0.7950 (ttm) REVERT: G 88 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7209 (tpt170) REVERT: I 110 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6513 (mt-10) REVERT: I 199 ASP cc_start: 0.7658 (m-30) cc_final: 0.7394 (m-30) REVERT: I 312 TYR cc_start: 0.8201 (m-80) cc_final: 0.7396 (m-80) REVERT: I 398 MET cc_start: 0.8295 (mtt) cc_final: 0.8087 (mtp) REVERT: J 161 TYR cc_start: 0.8476 (m-80) cc_final: 0.8174 (m-80) REVERT: J 290 GLU cc_start: 0.6421 (tm-30) cc_final: 0.5956 (tm-30) REVERT: J 422 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7290 (tpp-160) REVERT: K 413 MET cc_start: 0.8178 (ttm) cc_final: 0.7868 (ttm) REVERT: L 172 TYR cc_start: 0.7475 (t80) cc_final: 0.7202 (t80) REVERT: L 212 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8937 (mp) REVERT: L 306 ASP cc_start: 0.7911 (t0) cc_final: 0.7434 (t0) REVERT: L 309 HIS cc_start: 0.7941 (m170) cc_final: 0.7400 (m-70) outliers start: 162 outliers final: 126 residues processed: 877 average time/residue: 0.5252 time to fit residues: 743.6965 Evaluate side-chains 866 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 735 time to evaluate : 4.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 420 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 37 HIS Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 373 MET Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 254 GLU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 422 ARG Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 254 GLU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 339 ARG Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 290 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 308 optimal weight: 10.0000 chunk 330 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 381 optimal weight: 6.9990 overall best weight: 1.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 GLN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41436 Z= 0.212 Angle : 0.552 7.912 56304 Z= 0.280 Chirality : 0.043 0.303 6156 Planarity : 0.005 0.056 7338 Dihedral : 11.037 179.493 5726 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.46 % Allowed : 22.18 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.12), residues: 5088 helix: 1.91 (0.11), residues: 2340 sheet: 0.65 (0.18), residues: 798 loop : -1.06 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 346 HIS 0.021 0.001 HIS F 37 PHE 0.020 0.001 PHE K 49 TYR 0.013 0.001 TYR I 161 ARG 0.014 0.000 ARG E 390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 761 time to evaluate : 4.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: A 393 HIS cc_start: 0.8103 (t70) cc_final: 0.7825 (t70) REVERT: B 299 LYS cc_start: 0.7891 (tttp) cc_final: 0.7580 (tttm) REVERT: C 127 ASP cc_start: 0.7338 (m-30) cc_final: 0.7091 (m-30) REVERT: C 149 PHE cc_start: 0.8397 (t80) cc_final: 0.8193 (t80) REVERT: C 339 ARG cc_start: 0.7712 (tpm170) cc_final: 0.7509 (tpp-160) REVERT: E 259 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8611 (mp) REVERT: E 413 MET cc_start: 0.8166 (ttm) cc_final: 0.7854 (ttm) REVERT: G 88 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7209 (tpt170) REVERT: I 110 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6581 (mt-10) REVERT: I 199 ASP cc_start: 0.7613 (m-30) cc_final: 0.7317 (m-30) REVERT: I 312 TYR cc_start: 0.8122 (m-80) cc_final: 0.7214 (m-80) REVERT: I 398 MET cc_start: 0.8302 (mtt) cc_final: 0.8093 (mtp) REVERT: J 161 TYR cc_start: 0.8463 (m-80) cc_final: 0.8146 (m-80) REVERT: J 290 GLU cc_start: 0.6296 (tm-30) cc_final: 0.5997 (tm-30) REVERT: J 422 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7323 (tpp-160) REVERT: K 309 HIS cc_start: 0.7813 (m90) cc_final: 0.7358 (m90) REVERT: K 357 TYR cc_start: 0.7859 (m-80) cc_final: 0.7482 (m-10) REVERT: K 413 MET cc_start: 0.8108 (ttm) cc_final: 0.7792 (ttm) REVERT: L 172 TYR cc_start: 0.7492 (t80) cc_final: 0.7220 (t80) REVERT: L 212 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8901 (mp) REVERT: L 306 ASP cc_start: 0.7925 (t0) cc_final: 0.7532 (t0) REVERT: L 309 HIS cc_start: 0.7953 (m170) cc_final: 0.7637 (m170) outliers start: 150 outliers final: 121 residues processed: 854 average time/residue: 0.5101 time to fit residues: 712.4358 Evaluate side-chains 869 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 743 time to evaluate : 4.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain I residue 330 GLU Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 254 GLU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 422 ARG Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 254 GLU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 339 ARG Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 0.7980 chunk 465 optimal weight: 1.9990 chunk 424 optimal weight: 2.9990 chunk 452 optimal weight: 3.9990 chunk 272 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 355 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 409 optimal weight: 7.9990 chunk 428 optimal weight: 0.1980 chunk 451 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 406 HIS ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 285 GLN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41436 Z= 0.177 Angle : 0.541 8.787 56304 Z= 0.273 Chirality : 0.042 0.313 6156 Planarity : 0.004 0.054 7338 Dihedral : 10.825 179.861 5726 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.04 % Allowed : 22.75 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.12), residues: 5088 helix: 1.95 (0.11), residues: 2340 sheet: 0.89 (0.18), residues: 804 loop : -1.04 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 346 HIS 0.012 0.001 HIS J 309 PHE 0.018 0.001 PHE K 49 TYR 0.013 0.001 TYR K 161 ARG 0.014 0.000 ARG E 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 778 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.7052 (m-30) REVERT: A 77 GLU cc_start: 0.6887 (tp30) cc_final: 0.6537 (tp30) REVERT: A 393 HIS cc_start: 0.8114 (t70) cc_final: 0.7856 (t70) REVERT: B 282 GLN cc_start: 0.7722 (mm110) cc_final: 0.7511 (mt0) REVERT: C 127 ASP cc_start: 0.7315 (m-30) cc_final: 0.7095 (m-30) REVERT: C 149 PHE cc_start: 0.8329 (t80) cc_final: 0.8110 (t80) REVERT: C 425 MET cc_start: 0.7646 (mmm) cc_final: 0.7402 (mmm) REVERT: E 259 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8595 (mp) REVERT: E 413 MET cc_start: 0.8080 (ttm) cc_final: 0.7784 (ttm) REVERT: G 88 ARG cc_start: 0.8104 (ttp-110) cc_final: 0.7114 (tpt170) REVERT: I 110 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6654 (mt-10) REVERT: I 157 ILE cc_start: 0.9081 (mm) cc_final: 0.8762 (mt) REVERT: I 199 ASP cc_start: 0.7419 (m-30) cc_final: 0.7162 (m-30) REVERT: I 259 MET cc_start: 0.7954 (mmm) cc_final: 0.7522 (mmm) REVERT: I 312 TYR cc_start: 0.8078 (m-80) cc_final: 0.7246 (m-80) REVERT: J 161 TYR cc_start: 0.8442 (m-80) cc_final: 0.8134 (m-80) REVERT: J 290 GLU cc_start: 0.6358 (tm-30) cc_final: 0.6156 (tm-30) REVERT: K 357 TYR cc_start: 0.7787 (m-80) cc_final: 0.7419 (m-10) REVERT: K 413 MET cc_start: 0.7995 (ttm) cc_final: 0.7657 (ttm) REVERT: L 172 TYR cc_start: 0.7479 (t80) cc_final: 0.7194 (t80) REVERT: L 212 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8837 (mp) REVERT: L 309 HIS cc_start: 0.7974 (m170) cc_final: 0.7672 (m170) outliers start: 132 outliers final: 105 residues processed: 856 average time/residue: 0.5205 time to fit residues: 727.9300 Evaluate side-chains 856 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 747 time to evaluate : 4.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 339 ARG Chi-restraints excluded: chain L residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 3.9990 chunk 478 optimal weight: 3.9990 chunk 292 optimal weight: 8.9990 chunk 227 optimal weight: 0.1980 chunk 332 optimal weight: 1.9990 chunk 502 optimal weight: 5.9990 chunk 462 optimal weight: 10.0000 chunk 399 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 308 optimal weight: 20.0000 chunk 245 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 GLN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN K 133 GLN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41436 Z= 0.248 Angle : 0.568 8.856 56304 Z= 0.288 Chirality : 0.044 0.322 6156 Planarity : 0.005 0.057 7338 Dihedral : 10.755 178.800 5725 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.77 % Allowed : 23.28 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.12), residues: 5088 helix: 1.93 (0.11), residues: 2340 sheet: 0.74 (0.18), residues: 822 loop : -1.08 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 346 HIS 0.006 0.001 HIS J 309 PHE 0.024 0.001 PHE E 49 TYR 0.014 0.001 TYR J 357 ARG 0.014 0.000 ARG E 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 756 time to evaluate : 4.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: A 77 GLU cc_start: 0.6846 (tp30) cc_final: 0.6564 (tp30) REVERT: A 393 HIS cc_start: 0.8059 (t70) cc_final: 0.7786 (t70) REVERT: C 127 ASP cc_start: 0.7303 (m-30) cc_final: 0.7039 (m-30) REVERT: C 285 GLN cc_start: 0.3389 (mm-40) cc_final: 0.2874 (pt0) REVERT: E 259 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8603 (mp) REVERT: E 367 ASP cc_start: 0.7655 (m-30) cc_final: 0.7294 (m-30) REVERT: E 413 MET cc_start: 0.8191 (ttm) cc_final: 0.7909 (ttm) REVERT: G 88 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7206 (tpt170) REVERT: G 312 TYR cc_start: 0.8321 (m-80) cc_final: 0.7956 (m-80) REVERT: I 110 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6600 (mt-10) REVERT: I 199 ASP cc_start: 0.7463 (m-30) cc_final: 0.7159 (m-30) REVERT: I 259 MET cc_start: 0.7910 (mmm) cc_final: 0.7556 (mmm) REVERT: J 161 TYR cc_start: 0.8465 (m-80) cc_final: 0.8173 (m-80) REVERT: J 290 GLU cc_start: 0.6313 (tm-30) cc_final: 0.6075 (tm-30) REVERT: K 357 TYR cc_start: 0.7849 (m-80) cc_final: 0.7486 (m-10) REVERT: K 413 MET cc_start: 0.8105 (ttm) cc_final: 0.7805 (ttm) REVERT: L 172 TYR cc_start: 0.7543 (t80) cc_final: 0.7272 (t80) REVERT: L 212 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8880 (mp) REVERT: L 220 GLU cc_start: 0.7581 (pm20) cc_final: 0.7359 (pm20) REVERT: L 309 HIS cc_start: 0.8002 (m170) cc_final: 0.7519 (m-70) outliers start: 120 outliers final: 109 residues processed: 828 average time/residue: 0.5116 time to fit residues: 690.0300 Evaluate side-chains 859 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 746 time to evaluate : 4.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 71 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 166 MET Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 430 SER Chi-restraints excluded: chain G residue 129 CYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 324 SER Chi-restraints excluded: chain G residue 330 GLU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 129 CYS Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 387 LEU Chi-restraints excluded: chain H residue 430 SER Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 129 CYS Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 324 SER Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 76 ASP Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 196 GLU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 305 CYS Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 158 SER Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 36 MET Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 339 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 10.0000 chunk 425 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 368 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 400 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 411 optimal weight: 0.0060 chunk 50 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 overall best weight: 1.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 309 HIS ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 ASN ** H 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 285 GLN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109990 restraints weight = 53514.213| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.25 r_work: 0.3327 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41436 Z= 0.208 Angle : 0.554 9.042 56304 Z= 0.280 Chirality : 0.043 0.326 6156 Planarity : 0.005 0.061 7338 Dihedral : 10.602 177.514 5725 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.97 % Allowed : 23.21 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.12), residues: 5088 helix: 1.92 (0.11), residues: 2346 sheet: 0.83 (0.18), residues: 804 loop : -1.07 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 346 HIS 0.005 0.001 HIS J 309 PHE 0.026 0.001 PHE E 49 TYR 0.015 0.001 TYR J 357 ARG 0.015 0.000 ARG A 390 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13009.67 seconds wall clock time: 232 minutes 35.05 seconds (13955.05 seconds total)