Starting phenix.real_space_refine on Tue Apr 16 19:18:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evw_3961/04_2024/6evw_3961_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evw_3961/04_2024/6evw_3961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evw_3961/04_2024/6evw_3961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evw_3961/04_2024/6evw_3961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evw_3961/04_2024/6evw_3961_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evw_3961/04_2024/6evw_3961_updated.pdb" } resolution = 4.4 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= 0.013 sd= 0.039 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 36 5.49 5 Mg 12 5.21 5 S 276 5.16 5 C 25464 2.51 5 N 6918 2.21 5 O 7830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 64": "NH1" <-> "NH2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 390": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40536 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: "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: "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: "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} 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: "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: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.52, per 1000 atoms: 0.48 Number of scatterers: 40536 At special positions: 0 Unit cell: (113.98, 169.58, 216.84, 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 36 15.00 Mg 12 11.99 O 7830 8.00 N 6918 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: 14.85 Conformation dependent library (CDL) restraints added in 6.6 seconds 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 42 sheets defined 42.5% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.93 Creating SS restraints... Processing helix chain 'E' and resid 10 through 27 removed outlier: 3.503A pdb=" N GLN E 15 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 79 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE E 122 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 160 removed outlier: 4.502A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 152 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.713A pdb=" N SER E 187 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE E 188 " --> pdb=" O TYR E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 194 No H-bonds generated for 'chain 'E' and resid 191 through 194' Processing helix chain 'E' and resid 207 through 214 removed outlier: 4.292A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 212 " --> pdb=" O ALA E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 240 removed outlier: 3.746A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 258 removed outlier: 4.140A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 288 through 295 removed outlier: 4.018A pdb=" N THR E 292 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU E 386 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP E 388 " --> pdb=" O ALA E 385 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP E 392 " --> pdb=" O ALA E 389 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS E 393 " --> pdb=" O ARG E 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP E 396 " --> pdb=" O HIS E 393 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU E 397 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET E 398 " --> pdb=" O PHE E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 Processing helix chain 'E' and resid 415 through 436 removed outlier: 3.550A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 423 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP E 424 " --> pdb=" O GLU E 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 426 " --> pdb=" O ARG E 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP E 431 " --> pdb=" O ALA E 427 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 27 removed outlier: 3.502A pdb=" N GLN J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU J 22 " --> pdb=" O ASN J 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 79 Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE J 122 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG J 123 " --> pdb=" O LEU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 160 removed outlier: 4.501A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU J 155 " --> pdb=" O SER J 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER J 158 " --> pdb=" O MET J 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 189 removed outlier: 3.714A pdb=" N SER J 187 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE J 188 " --> pdb=" O TYR J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 194 No H-bonds generated for 'chain 'J' and resid 191 through 194' Processing helix chain 'J' and resid 207 through 214 removed outlier: 4.293A pdb=" N ASP J 211 " --> pdb=" O GLU J 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE J 212 " --> pdb=" O ALA J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 240 removed outlier: 3.746A pdb=" N ARG J 229 " --> pdb=" O THR J 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE J 231 " --> pdb=" O LEU J 227 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 258 removed outlier: 4.140A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 281 No H-bonds generated for 'chain 'J' and resid 279 through 281' Processing helix chain 'J' and resid 288 through 295 removed outlier: 4.017A pdb=" N THR J 292 " --> pdb=" O VAL J 288 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN J 293 " --> pdb=" O ALA J 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA J 331 " --> pdb=" O ASP J 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE J 335 " --> pdb=" O ALA J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU J 386 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP J 388 " --> pdb=" O ALA J 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP J 392 " --> pdb=" O ALA J 389 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS J 393 " --> pdb=" O ARG J 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP J 396 " --> pdb=" O HIS J 393 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU J 397 " --> pdb=" O LYS J 394 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET J 398 " --> pdb=" O PHE J 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 411 Processing helix chain 'J' and resid 415 through 436 removed outlier: 3.549A pdb=" N SER J 419 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU J 423 " --> pdb=" O SER J 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP J 424 " --> pdb=" O GLU J 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET J 425 " --> pdb=" O ALA J 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA J 426 " --> pdb=" O ARG J 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP J 431 " --> pdb=" O ALA J 427 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR J 432 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 27 removed outlier: 3.502A pdb=" N GLN C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE C 122 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 4.501A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 189 removed outlier: 3.714A pdb=" N SER C 187 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 188 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 207 through 214 removed outlier: 4.294A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 240 removed outlier: 3.747A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 removed outlier: 4.140A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 288 through 295 removed outlier: 4.018A pdb=" N THR C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU C 386 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP C 388 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP C 392 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS C 393 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP C 396 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 397 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET C 398 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 Processing helix chain 'C' and resid 415 through 436 removed outlier: 3.550A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 424 " --> pdb=" O GLU C 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 27 removed outlier: 3.502A pdb=" N GLN L 15 " --> pdb=" O GLN L 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 22 " --> pdb=" O ASN L 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 79 Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE L 122 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 160 removed outlier: 4.502A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU L 152 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU L 155 " --> pdb=" O SER L 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL L 159 " --> pdb=" O GLU L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 removed outlier: 3.714A pdb=" N SER L 187 " --> pdb=" O PRO L 184 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE L 188 " --> pdb=" O TYR L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 194 No H-bonds generated for 'chain 'L' and resid 191 through 194' Processing helix chain 'L' and resid 207 through 214 removed outlier: 4.292A pdb=" N ASP L 211 " --> pdb=" O GLU L 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE L 212 " --> pdb=" O ALA L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 240 removed outlier: 3.746A pdb=" N ARG L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE L 231 " --> pdb=" O LEU L 227 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 258 removed outlier: 4.139A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 281 No H-bonds generated for 'chain 'L' and resid 279 through 281' Processing helix chain 'L' and resid 288 through 295 removed outlier: 4.017A pdb=" N THR L 292 " --> pdb=" O VAL L 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 309 No H-bonds generated for 'chain 'L' and resid 307 through 309' Processing helix chain 'L' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA L 331 " --> pdb=" O ASP L 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE L 335 " --> pdb=" O ALA L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU L 386 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP L 388 " --> pdb=" O ALA L 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP L 392 " --> pdb=" O ALA L 389 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS L 393 " --> pdb=" O ARG L 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP L 396 " --> pdb=" O HIS L 393 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU L 397 " --> pdb=" O LYS L 394 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET L 398 " --> pdb=" O PHE L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 411 Processing helix chain 'L' and resid 415 through 436 removed outlier: 3.550A pdb=" N SER L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU L 423 " --> pdb=" O SER L 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP L 424 " --> pdb=" O GLU L 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET L 425 " --> pdb=" O ALA L 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA L 426 " --> pdb=" O ARG L 422 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP L 431 " --> pdb=" O ALA L 427 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR L 432 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.502A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.502A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.714A pdb=" N SER A 187 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE A 188 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 194 No H-bonds generated for 'chain 'A' and resid 191 through 194' Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.293A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 240 removed outlier: 3.746A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 4.139A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 288 through 295 removed outlier: 4.017A pdb=" N THR A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU A 386 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP A 388 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS A 393 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A 396 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 397 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET A 398 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.550A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 27 removed outlier: 3.502A pdb=" N GLN K 15 " --> pdb=" O GLN K 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU K 22 " --> pdb=" O ASN K 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 79 Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE K 122 " --> pdb=" O VAL K 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG K 123 " --> pdb=" O LEU K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 160 removed outlier: 4.502A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU K 152 " --> pdb=" O GLY K 148 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU K 157 " --> pdb=" O LEU K 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER K 158 " --> pdb=" O MET K 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 189 removed outlier: 3.714A pdb=" N SER K 187 " --> pdb=" O PRO K 184 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE K 188 " --> pdb=" O TYR K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 194 No H-bonds generated for 'chain 'K' and resid 191 through 194' Processing helix chain 'K' and resid 207 through 214 removed outlier: 4.292A pdb=" N ASP K 211 " --> pdb=" O GLU K 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE K 212 " --> pdb=" O ALA K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 224 through 240 removed outlier: 3.746A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE K 231 " --> pdb=" O LEU K 227 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 258 removed outlier: 4.140A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 281 No H-bonds generated for 'chain 'K' and resid 279 through 281' Processing helix chain 'K' and resid 288 through 295 removed outlier: 4.017A pdb=" N THR K 292 " --> pdb=" O VAL K 288 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN K 293 " --> pdb=" O ALA K 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA K 331 " --> pdb=" O ASP K 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU K 386 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP K 388 " --> pdb=" O ALA K 385 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP K 392 " --> pdb=" O ALA K 389 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS K 393 " --> pdb=" O ARG K 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP K 396 " --> pdb=" O HIS K 393 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU K 397 " --> pdb=" O LYS K 394 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET K 398 " --> pdb=" O PHE K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 411 Processing helix chain 'K' and resid 415 through 436 removed outlier: 3.549A pdb=" N SER K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU K 423 " --> pdb=" O SER K 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP K 424 " --> pdb=" O GLU K 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET K 425 " --> pdb=" O ALA K 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA K 426 " --> pdb=" O ARG K 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP K 431 " --> pdb=" O ALA K 427 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR K 432 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU K 433 " --> pdb=" O GLU K 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 26 removed outlier: 4.486A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 removed outlier: 4.079A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 109 through 126 removed outlier: 3.749A pdb=" N VAL B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 4.380A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 removed outlier: 4.321A pdb=" N LEU B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 225 No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 227 through 236 Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 324 through 327 No H-bonds generated for 'chain 'B' and resid 324 through 327' Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.822A pdb=" N VAL B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 387 removed outlier: 3.702A pdb=" N LYS B 379 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 387 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 26 removed outlier: 4.485A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 4.079A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL F 49 " --> pdb=" O GLU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 109 through 126 removed outlier: 3.749A pdb=" N VAL F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 158 removed outlier: 4.382A pdb=" N GLY F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER F 153 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS F 154 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 195 removed outlier: 4.321A pdb=" N LEU F 187 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN F 195 " --> pdb=" O GLN F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 213 Processing helix chain 'F' and resid 222 through 225 No H-bonds generated for 'chain 'F' and resid 222 through 225' Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 250 through 257 Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 296 through 298 No H-bonds generated for 'chain 'F' and resid 296 through 298' Processing helix chain 'F' and resid 305 through 307 No H-bonds generated for 'chain 'F' and resid 305 through 307' Processing helix chain 'F' and resid 324 through 327 No H-bonds generated for 'chain 'F' and resid 324 through 327' Processing helix chain 'F' and resid 329 through 336 removed outlier: 3.822A pdb=" N VAL F 333 " --> pdb=" O GLN F 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 387 removed outlier: 3.703A pdb=" N LYS F 379 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER F 382 " --> pdb=" O LYS F 379 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA F 387 " --> pdb=" O GLN F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 401 Processing helix chain 'F' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN F 424 " --> pdb=" O SER F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 26 removed outlier: 4.486A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 49 removed outlier: 4.078A pdb=" N ARG G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN G 48 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 78 Processing helix chain 'G' and resid 101 through 105 Processing helix chain 'G' and resid 109 through 126 removed outlier: 3.749A pdb=" N VAL G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 158 removed outlier: 4.381A pdb=" N GLY G 148 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER G 153 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS G 154 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 195 removed outlier: 4.321A pdb=" N LEU G 187 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU G 194 " --> pdb=" O HIS G 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN G 195 " --> pdb=" O GLN G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'G' and resid 222 through 225 No H-bonds generated for 'chain 'G' and resid 222 through 225' Processing helix chain 'G' and resid 227 through 236 Processing helix chain 'G' and resid 250 through 257 Processing helix chain 'G' and resid 286 through 291 Processing helix chain 'G' and resid 296 through 298 No H-bonds generated for 'chain 'G' and resid 296 through 298' Processing helix chain 'G' and resid 305 through 307 No H-bonds generated for 'chain 'G' and resid 305 through 307' Processing helix chain 'G' and resid 324 through 327 No H-bonds generated for 'chain 'G' and resid 324 through 327' Processing helix chain 'G' and resid 329 through 336 removed outlier: 3.822A pdb=" N VAL G 333 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 387 removed outlier: 3.703A pdb=" N LYS G 379 " --> pdb=" O GLU G 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER G 382 " --> pdb=" O LYS G 379 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA G 387 " --> pdb=" O GLN G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 401 Processing helix chain 'G' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA G 411 " --> pdb=" O GLU G 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN G 424 " --> pdb=" O SER G 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 26 removed outlier: 4.485A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 removed outlier: 4.079A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 109 through 126 removed outlier: 3.749A pdb=" N VAL D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 158 removed outlier: 4.381A pdb=" N GLY D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 4.320A pdb=" N LEU D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 236 Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'D' and resid 324 through 327 No H-bonds generated for 'chain 'D' and resid 324 through 327' Processing helix chain 'D' and resid 329 through 336 removed outlier: 3.823A pdb=" N VAL D 333 " --> pdb=" O GLN D 329 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 387 removed outlier: 3.703A pdb=" N LYS D 379 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER D 382 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA D 387 " --> pdb=" O GLN D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 26 removed outlier: 4.486A pdb=" N GLU I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 49 removed outlier: 4.079A pdb=" N ARG I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN I 48 " --> pdb=" O LEU I 44 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL I 49 " --> pdb=" O GLU I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'I' and resid 109 through 126 removed outlier: 3.750A pdb=" N VAL I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP I 118 " --> pdb=" O ASP I 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 158 removed outlier: 4.381A pdb=" N GLY I 148 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE I 152 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER I 153 " --> pdb=" O THR I 149 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS I 154 " --> pdb=" O LEU I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 195 removed outlier: 4.321A pdb=" N LEU I 187 " --> pdb=" O TYR I 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER I 188 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN I 195 " --> pdb=" O GLN I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 222 through 225 No H-bonds generated for 'chain 'I' and resid 222 through 225' Processing helix chain 'I' and resid 227 through 236 Processing helix chain 'I' and resid 250 through 257 Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 296 through 298 No H-bonds generated for 'chain 'I' and resid 296 through 298' Processing helix chain 'I' and resid 305 through 307 No H-bonds generated for 'chain 'I' and resid 305 through 307' Processing helix chain 'I' and resid 324 through 327 No H-bonds generated for 'chain 'I' and resid 324 through 327' Processing helix chain 'I' and resid 329 through 336 removed outlier: 3.822A pdb=" N VAL I 333 " --> pdb=" O GLN I 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN I 334 " --> pdb=" O MET I 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN I 335 " --> pdb=" O LEU I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 387 removed outlier: 3.703A pdb=" N LYS I 379 " --> pdb=" O GLU I 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER I 382 " --> pdb=" O LYS I 379 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA I 387 " --> pdb=" O GLN I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 401 Processing helix chain 'I' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA I 411 " --> pdb=" O GLU I 407 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN I 424 " --> pdb=" O SER I 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 removed outlier: 4.486A pdb=" N GLU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 49 removed outlier: 4.079A pdb=" N ARG H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 78 Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 109 through 126 removed outlier: 3.749A pdb=" N VAL H 113 " --> pdb=" O GLY H 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 158 removed outlier: 4.381A pdb=" N GLY H 148 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER H 153 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS H 154 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 195 removed outlier: 4.320A pdb=" N LEU H 187 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER H 188 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 195 " --> pdb=" O GLN H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 222 through 225 No H-bonds generated for 'chain 'H' and resid 222 through 225' Processing helix chain 'H' and resid 227 through 236 Processing helix chain 'H' and resid 250 through 257 Processing helix chain 'H' and resid 286 through 291 Processing helix chain 'H' and resid 296 through 298 No H-bonds generated for 'chain 'H' and resid 296 through 298' Processing helix chain 'H' and resid 305 through 307 No H-bonds generated for 'chain 'H' and resid 305 through 307' Processing helix chain 'H' and resid 324 through 327 No H-bonds generated for 'chain 'H' and resid 324 through 327' Processing helix chain 'H' and resid 329 through 336 removed outlier: 3.822A pdb=" N VAL H 333 " --> pdb=" O GLN H 329 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN H 335 " --> pdb=" O LEU H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 387 removed outlier: 3.703A pdb=" N LYS H 379 " --> pdb=" O GLU H 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER H 382 " --> pdb=" O LYS H 379 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA H 387 " --> pdb=" O GLN H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 401 Processing helix chain 'H' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA H 411 " --> pdb=" O GLU H 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN H 424 " --> pdb=" O SER H 420 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 135 through 139 removed outlier: 7.116A pdb=" N ILE E 5 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE E 138 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE E 7 " --> pdb=" O PHE E 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'E' and resid 167 through 169 removed outlier: 7.229A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET E 203 " --> pdb=" O PRO E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'E' and resid 270 through 273 removed outlier: 6.034A pdb=" N LYS E 352 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR E 319 " --> pdb=" O LYS E 352 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY E 354 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 135 through 139 removed outlier: 7.116A pdb=" N ILE J 5 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE J 138 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE J 7 " --> pdb=" O PHE J 138 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= G, first strand: chain 'J' and resid 167 through 169 removed outlier: 7.230A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET J 203 " --> pdb=" O PRO J 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'J' and resid 270 through 273 removed outlier: 6.035A pdb=" N LYS J 352 " --> pdb=" O LEU J 317 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR J 319 " --> pdb=" O LYS J 352 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY J 354 " --> pdb=" O TYR J 319 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 135 through 139 removed outlier: 7.115A pdb=" N ILE C 5 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE C 138 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE C 7 " --> pdb=" O PHE C 138 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= K, first strand: chain 'C' and resid 167 through 169 removed outlier: 7.229A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET C 203 " --> pdb=" O PRO C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 270 through 273 removed outlier: 6.034A pdb=" N LYS C 352 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR C 319 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY C 354 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'L' and resid 135 through 139 removed outlier: 7.116A pdb=" N ILE L 5 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE L 138 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE L 7 " --> pdb=" O PHE L 138 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'L' and resid 167 through 169 removed outlier: 7.229A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET L 203 " --> pdb=" O PRO L 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'L' and resid 270 through 273 removed outlier: 6.034A pdb=" N LYS L 352 " --> pdb=" O LEU L 317 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR L 319 " --> pdb=" O LYS L 352 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY L 354 " --> pdb=" O TYR L 319 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 135 through 139 removed outlier: 7.115A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= S, first strand: chain 'A' and resid 167 through 169 removed outlier: 7.230A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 203 " --> pdb=" O PRO A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'A' and resid 270 through 273 removed outlier: 6.035A pdb=" N LYS A 352 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR A 319 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY A 354 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 135 through 139 removed outlier: 7.115A pdb=" N ILE K 5 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE K 138 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE K 7 " --> pdb=" O PHE K 138 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'K' and resid 167 through 169 removed outlier: 7.230A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET K 203 " --> pdb=" O PRO K 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'K' and resid 270 through 273 removed outlier: 6.034A pdb=" N LYS K 352 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR K 319 " --> pdb=" O LYS K 352 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY K 354 " --> pdb=" O TYR K 319 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.880A pdb=" N ASP B 67 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.773A pdb=" N THR B 166 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 202 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 267 through 271 removed outlier: 3.897A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.879A pdb=" N ASP F 67 " --> pdb=" O VAL F 91 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 198 through 202 removed outlier: 3.774A pdb=" N THR F 166 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE F 202 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 163 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 267 through 271 removed outlier: 3.896A pdb=" N THR F 312 " --> pdb=" O ASN F 370 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.880A pdb=" N ASP G 67 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 198 through 202 removed outlier: 3.774A pdb=" N THR G 166 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE G 202 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE G 163 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 267 through 271 removed outlier: 3.897A pdb=" N THR G 312 " --> pdb=" O ASN G 370 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.879A pdb=" N ASP D 67 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 198 through 202 removed outlier: 3.774A pdb=" N THR D 166 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 202 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 267 through 271 removed outlier: 3.897A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 65 through 67 removed outlier: 3.879A pdb=" N ASP I 67 " --> pdb=" O VAL I 91 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 198 through 202 removed outlier: 3.774A pdb=" N THR I 166 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE I 202 " --> pdb=" O SER I 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE I 163 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 267 through 271 removed outlier: 3.897A pdb=" N THR I 312 " --> pdb=" O ASN I 370 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.880A pdb=" N ASP H 67 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 198 through 202 removed outlier: 3.774A pdb=" N THR H 166 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE H 202 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE H 163 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 267 through 271 removed outlier: 3.896A pdb=" N THR H 312 " --> pdb=" O ASN H 370 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 3132 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: 14.97 Time building geometry restraints manager: 16.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13215 1.34 - 1.46: 7322 1.46 - 1.57: 20437 1.57 - 1.69: 36 1.69 - 1.81: 444 Bond restraints: 41454 Sorted by residual: bond pdb=" O3B G2P D 501 " pdb=" PG G2P D 501 " ideal model delta sigma weight residual 1.716 1.590 0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" O3B G2P F 501 " pdb=" PG G2P F 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" O3B G2P H 501 " pdb=" PG G2P H 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" O3B G2P G 501 " pdb=" PG G2P G 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 41449 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 1351 106.29 - 113.22: 22060 113.22 - 120.16: 15294 120.16 - 127.09: 17137 127.09 - 134.03: 486 Bond angle restraints: 56328 Sorted by residual: angle pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " pdb=" PB GTP L 501 " ideal model delta sigma weight residual 120.50 132.39 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " pdb=" PB GTP C 501 " ideal model delta sigma weight residual 120.50 132.05 -11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sigma weight residual 120.50 131.99 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " pdb=" PB GTP K 501 " ideal model delta sigma weight residual 120.50 131.95 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " pdb=" PB GTP E 501 " ideal model delta sigma weight residual 120.50 131.66 -11.16 3.00e+00 1.11e-01 1.38e+01 ... (remaining 56323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 24529 34.54 - 69.08: 178 69.08 - 103.62: 31 103.62 - 138.16: 0 138.16 - 172.70: 18 Dihedral angle restraints: 24756 sinusoidal: 9972 harmonic: 14784 Sorted by residual: dihedral pdb=" C8 GTP L 501 " pdb=" C1' GTP L 501 " pdb=" N9 GTP L 501 " pdb=" O4' GTP L 501 " ideal model delta sinusoidal sigma weight residual 104.59 -68.10 172.70 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP J 501 " pdb=" C1' GTP J 501 " pdb=" N9 GTP J 501 " pdb=" O4' GTP J 501 " ideal model delta sinusoidal sigma weight residual 104.59 -67.62 172.22 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP K 501 " pdb=" C1' GTP K 501 " pdb=" N9 GTP K 501 " pdb=" O4' GTP K 501 " ideal model delta sinusoidal sigma weight residual 104.59 -66.88 171.47 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 24753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4131 0.045 - 0.091: 1544 0.091 - 0.136: 433 0.136 - 0.182: 24 0.182 - 0.227: 30 Chirality restraints: 6162 Sorted by residual: chirality pdb=" C2' GTP C 501 " pdb=" C1' GTP C 501 " pdb=" C3' GTP C 501 " pdb=" O2' GTP C 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C2' GTP A 501 " pdb=" C1' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" O2' GTP A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2' GTP J 501 " pdb=" C1' GTP J 501 " pdb=" C3' GTP J 501 " pdb=" O2' GTP J 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 6159 not shown) Planarity restraints: 7326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G2P G 501 " 0.119 2.00e-02 2.50e+03 4.92e-02 7.27e+01 pdb=" C2 G2P G 501 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G2P G 501 " -0.040 2.00e-02 2.50e+03 pdb=" C5 G2P G 501 " -0.035 2.00e-02 2.50e+03 pdb=" C6 G2P G 501 " 0.013 2.00e-02 2.50e+03 pdb=" C8 G2P G 501 " -0.035 2.00e-02 2.50e+03 pdb=" N1 G2P G 501 " 0.018 2.00e-02 2.50e+03 pdb=" N2 G2P G 501 " -0.011 2.00e-02 2.50e+03 pdb=" N3 G2P G 501 " -0.039 2.00e-02 2.50e+03 pdb=" N7 G2P G 501 " -0.043 2.00e-02 2.50e+03 pdb=" N9 G2P G 501 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G2P G 501 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G2P I 501 " -0.119 2.00e-02 2.50e+03 4.91e-02 7.22e+01 pdb=" C2 G2P I 501 " 0.012 2.00e-02 2.50e+03 pdb=" C4 G2P I 501 " 0.043 2.00e-02 2.50e+03 pdb=" C5 G2P I 501 " 0.036 2.00e-02 2.50e+03 pdb=" C6 G2P I 501 " -0.013 2.00e-02 2.50e+03 pdb=" C8 G2P I 501 " 0.032 2.00e-02 2.50e+03 pdb=" N1 G2P I 501 " -0.020 2.00e-02 2.50e+03 pdb=" N2 G2P I 501 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G2P I 501 " 0.043 2.00e-02 2.50e+03 pdb=" N7 G2P I 501 " 0.041 2.00e-02 2.50e+03 pdb=" N9 G2P I 501 " 0.016 2.00e-02 2.50e+03 pdb=" O6 G2P I 501 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G2P D 501 " -0.118 2.00e-02 2.50e+03 4.87e-02 7.13e+01 pdb=" C2 G2P D 501 " 0.013 2.00e-02 2.50e+03 pdb=" C4 G2P D 501 " 0.042 2.00e-02 2.50e+03 pdb=" C5 G2P D 501 " 0.035 2.00e-02 2.50e+03 pdb=" C6 G2P D 501 " -0.014 2.00e-02 2.50e+03 pdb=" C8 G2P D 501 " 0.033 2.00e-02 2.50e+03 pdb=" N1 G2P D 501 " -0.019 2.00e-02 2.50e+03 pdb=" N2 G2P D 501 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G2P D 501 " 0.042 2.00e-02 2.50e+03 pdb=" N7 G2P D 501 " 0.040 2.00e-02 2.50e+03 pdb=" N9 G2P D 501 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G2P D 501 " -0.078 2.00e-02 2.50e+03 ... (remaining 7323 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 720 2.65 - 3.21: 36721 3.21 - 3.78: 62822 3.78 - 4.34: 88685 4.34 - 4.90: 139979 Nonbonded interactions: 328927 Sorted by model distance: nonbonded pdb=" O2B GTP C 501 " pdb="MG MG C 502 " model vdw 2.091 2.170 nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 2.092 2.170 nonbonded pdb=" O2B GTP J 501 " pdb="MG MG J 502 " model vdw 2.095 2.170 nonbonded pdb=" OE1 GLN G 11 " pdb="MG MG G 502 " model vdw 2.099 2.170 nonbonded pdb=" O1B G2P G 501 " pdb="MG MG G 502 " model vdw 2.101 2.170 ... (remaining 328922 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 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: 0.030 Extract box with map and model: 2.820 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 99.060 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.390 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.005 0.126 41454 Z= 0.334 Angle : 0.838 11.892 56328 Z= 0.431 Chirality : 0.051 0.227 6162 Planarity : 0.006 0.056 7326 Dihedral : 11.536 172.697 15264 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -4.53 (0.09), residues: 5064 helix: -3.66 (0.06), residues: 2052 sheet: -1.81 (0.18), residues: 762 loop : -2.64 (0.11), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP G 101 HIS 0.010 0.002 HIS A 8 PHE 0.018 0.002 PHE J 202 TYR 0.022 0.002 TYR K 24 ARG 0.006 0.001 ARG I 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1439 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1439 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.7252 (ptm) cc_final: 0.6367 (tmm) REVERT: E 120 ASP cc_start: 0.8512 (t70) cc_final: 0.8285 (t70) REVERT: E 172 TYR cc_start: 0.7727 (t80) cc_final: 0.6357 (t80) REVERT: E 192 HIS cc_start: 0.7682 (t-90) cc_final: 0.7331 (t-90) REVERT: E 205 ASP cc_start: 0.7674 (t0) cc_final: 0.6236 (m-30) REVERT: E 301 GLN cc_start: 0.8369 (mt0) cc_final: 0.8162 (mt0) REVERT: E 302 MET cc_start: 0.8303 (mtt) cc_final: 0.7993 (mtt) REVERT: E 313 MET cc_start: 0.8051 (mtm) cc_final: 0.6895 (mtp) REVERT: E 351 PHE cc_start: 0.8166 (m-80) cc_final: 0.7388 (m-80) REVERT: E 391 LEU cc_start: 0.9167 (tp) cc_final: 0.8788 (tp) REVERT: E 398 MET cc_start: 0.7519 (mtp) cc_final: 0.7194 (mtm) REVERT: E 425 MET cc_start: 0.8679 (tpp) cc_final: 0.7975 (mmm) REVERT: J 124 LYS cc_start: 0.8316 (mttm) cc_final: 0.8022 (tptp) REVERT: J 149 PHE cc_start: 0.8577 (t80) cc_final: 0.8270 (t80) REVERT: J 172 TYR cc_start: 0.7670 (t80) cc_final: 0.6202 (t80) REVERT: J 183 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8053 (pp20) REVERT: J 205 ASP cc_start: 0.7452 (t0) cc_final: 0.6383 (m-30) REVERT: J 221 ARG cc_start: 0.8700 (mtt90) cc_final: 0.8447 (mpp-170) REVERT: J 267 PHE cc_start: 0.9043 (m-80) cc_final: 0.8745 (m-80) REVERT: J 313 MET cc_start: 0.7410 (mtm) cc_final: 0.6239 (mtp) REVERT: J 316 CYS cc_start: 0.8439 (t) cc_final: 0.7765 (t) REVERT: J 391 LEU cc_start: 0.9117 (tp) cc_final: 0.8612 (tp) REVERT: J 398 MET cc_start: 0.7304 (mtp) cc_final: 0.6968 (mtm) REVERT: J 425 MET cc_start: 0.8545 (tpp) cc_final: 0.7896 (mmm) REVERT: C 24 TYR cc_start: 0.8374 (m-80) cc_final: 0.8151 (m-80) REVERT: C 36 MET cc_start: 0.7276 (ptm) cc_final: 0.6614 (tmm) REVERT: C 136 LEU cc_start: 0.8533 (mt) cc_final: 0.8332 (mp) REVERT: C 149 PHE cc_start: 0.7882 (t80) cc_final: 0.7568 (t80) REVERT: C 182 VAL cc_start: 0.8535 (m) cc_final: 0.7968 (p) REVERT: C 192 HIS cc_start: 0.8135 (t-90) cc_final: 0.7843 (t-90) REVERT: C 205 ASP cc_start: 0.8280 (t0) cc_final: 0.6866 (m-30) REVERT: C 301 GLN cc_start: 0.8446 (mt0) cc_final: 0.8042 (pt0) REVERT: C 313 MET cc_start: 0.7803 (mtm) cc_final: 0.6548 (mtp) REVERT: C 377 MET cc_start: 0.7876 (ttp) cc_final: 0.7413 (tmm) REVERT: C 425 MET cc_start: 0.8389 (tpp) cc_final: 0.7624 (mmm) REVERT: L 36 MET cc_start: 0.7183 (ptm) cc_final: 0.6238 (tmm) REVERT: L 136 LEU cc_start: 0.8800 (mt) cc_final: 0.8521 (mp) REVERT: L 149 PHE cc_start: 0.8298 (t80) cc_final: 0.8040 (t80) REVERT: L 205 ASP cc_start: 0.8002 (t0) cc_final: 0.6459 (m-30) REVERT: L 301 GLN cc_start: 0.8678 (mt0) cc_final: 0.8007 (pt0) REVERT: L 313 MET cc_start: 0.7719 (mtm) cc_final: 0.6386 (mtp) REVERT: L 377 MET cc_start: 0.7485 (ttp) cc_final: 0.7248 (tmm) REVERT: L 395 PHE cc_start: 0.8848 (t80) cc_final: 0.8165 (t80) REVERT: L 425 MET cc_start: 0.8511 (tpp) cc_final: 0.7604 (mmm) REVERT: A 24 TYR cc_start: 0.8486 (m-80) cc_final: 0.8277 (m-80) REVERT: A 36 MET cc_start: 0.7028 (ptm) cc_final: 0.6398 (tmm) REVERT: A 54 SER cc_start: 0.7385 (p) cc_final: 0.6867 (t) REVERT: A 149 PHE cc_start: 0.8296 (t80) cc_final: 0.8055 (t80) REVERT: A 172 TYR cc_start: 0.7521 (t80) cc_final: 0.6304 (t80) REVERT: A 182 VAL cc_start: 0.8502 (m) cc_final: 0.7815 (p) REVERT: A 196 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8060 (tm-30) REVERT: A 205 ASP cc_start: 0.8003 (t0) cc_final: 0.6276 (m-30) REVERT: A 260 VAL cc_start: 0.8860 (t) cc_final: 0.8621 (t) REVERT: A 267 PHE cc_start: 0.8917 (m-80) cc_final: 0.8550 (m-80) REVERT: A 377 MET cc_start: 0.7915 (ttp) cc_final: 0.7219 (tmm) REVERT: A 380 ASN cc_start: 0.8414 (t0) cc_final: 0.8042 (t0) REVERT: A 391 LEU cc_start: 0.9095 (tp) cc_final: 0.8804 (tp) REVERT: A 398 MET cc_start: 0.7276 (mtp) cc_final: 0.6711 (mtm) REVERT: K 36 MET cc_start: 0.7261 (ptm) cc_final: 0.6639 (tmm) REVERT: K 136 LEU cc_start: 0.8480 (mt) cc_final: 0.8103 (mp) REVERT: K 149 PHE cc_start: 0.8319 (t80) cc_final: 0.7912 (t80) REVERT: K 172 TYR cc_start: 0.7755 (t80) cc_final: 0.6497 (t80) REVERT: K 205 ASP cc_start: 0.8220 (t0) cc_final: 0.6359 (m-30) REVERT: K 212 ILE cc_start: 0.9261 (mt) cc_final: 0.8940 (mt) REVERT: K 316 CYS cc_start: 0.8287 (t) cc_final: 0.7313 (t) REVERT: K 319 TYR cc_start: 0.8183 (m-80) cc_final: 0.7961 (m-10) REVERT: K 377 MET cc_start: 0.7564 (ttp) cc_final: 0.7311 (tmm) REVERT: B 14 ASN cc_start: 0.8491 (m-40) cc_final: 0.8260 (t0) REVERT: B 51 TYR cc_start: 0.8071 (m-80) cc_final: 0.7634 (m-10) REVERT: B 163 ILE cc_start: 0.8678 (pp) cc_final: 0.8214 (mt) REVERT: B 181 GLU cc_start: 0.8938 (pt0) cc_final: 0.8520 (pp20) REVERT: B 200 TYR cc_start: 0.7995 (m-80) cc_final: 0.7519 (m-80) REVERT: B 293 MET cc_start: 0.7126 (mtm) cc_final: 0.6759 (mmm) REVERT: B 297 LYS cc_start: 0.8754 (ptpt) cc_final: 0.8497 (mtmm) REVERT: B 317 PHE cc_start: 0.8738 (m-80) cc_final: 0.8497 (m-80) REVERT: B 355 ASP cc_start: 0.8482 (m-30) cc_final: 0.8109 (m-30) REVERT: B 379 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8079 (mtmm) REVERT: B 383 GLU cc_start: 0.8980 (tt0) cc_final: 0.8732 (mm-30) REVERT: F 6 HIS cc_start: 0.8754 (t70) cc_final: 0.8084 (t-170) REVERT: F 51 TYR cc_start: 0.7823 (m-80) cc_final: 0.7398 (m-10) REVERT: F 117 LEU cc_start: 0.8072 (mt) cc_final: 0.7864 (mm) REVERT: F 163 ILE cc_start: 0.8709 (pp) cc_final: 0.7900 (tp) REVERT: F 197 ASP cc_start: 0.7853 (m-30) cc_final: 0.7651 (m-30) REVERT: F 210 ILE cc_start: 0.9025 (mt) cc_final: 0.8762 (tt) REVERT: F 216 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7784 (mmtm) REVERT: F 233 MET cc_start: 0.9393 (mtp) cc_final: 0.8960 (mtm) REVERT: F 330 MET cc_start: 0.8434 (mmp) cc_final: 0.8090 (mmm) REVERT: F 379 LYS cc_start: 0.9088 (mtpt) cc_final: 0.8621 (pttp) REVERT: G 73 MET cc_start: 0.8235 (mmt) cc_final: 0.8014 (mmt) REVERT: G 163 ILE cc_start: 0.8653 (pp) cc_final: 0.7946 (mt) REVERT: G 178 THR cc_start: 0.8475 (m) cc_final: 0.8249 (m) REVERT: G 233 MET cc_start: 0.9306 (mtp) cc_final: 0.8832 (mtm) REVERT: G 288 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7598 (tm-30) REVERT: G 332 ASN cc_start: 0.8023 (t0) cc_final: 0.7705 (p0) REVERT: D 6 HIS cc_start: 0.8701 (t70) cc_final: 0.8132 (t70) REVERT: D 14 ASN cc_start: 0.8421 (m-40) cc_final: 0.8161 (t0) REVERT: D 21 TRP cc_start: 0.8776 (m100) cc_final: 0.8282 (m100) REVERT: D 51 TYR cc_start: 0.8049 (m-80) cc_final: 0.7147 (m-10) REVERT: D 60 VAL cc_start: 0.8936 (m) cc_final: 0.8736 (m) REVERT: D 163 ILE cc_start: 0.8814 (pp) cc_final: 0.8229 (mt) REVERT: D 181 GLU cc_start: 0.8928 (pt0) cc_final: 0.8642 (pp20) REVERT: D 200 TYR cc_start: 0.8095 (m-80) cc_final: 0.7151 (m-80) REVERT: D 293 MET cc_start: 0.7408 (mtm) cc_final: 0.6882 (mmm) REVERT: D 317 PHE cc_start: 0.8794 (m-80) cc_final: 0.8540 (m-80) REVERT: D 355 ASP cc_start: 0.8403 (m-30) cc_final: 0.8096 (m-30) REVERT: D 379 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8836 (mtmm) REVERT: I 14 ASN cc_start: 0.8403 (m-40) cc_final: 0.8069 (t0) REVERT: I 163 ILE cc_start: 0.8943 (pp) cc_final: 0.8342 (mt) REVERT: I 200 TYR cc_start: 0.7981 (m-80) cc_final: 0.7536 (m-80) REVERT: I 242 PHE cc_start: 0.7765 (m-80) cc_final: 0.7553 (m-10) REVERT: I 250 LEU cc_start: 0.8634 (mt) cc_final: 0.8403 (mp) REVERT: I 297 LYS cc_start: 0.8073 (ptpt) cc_final: 0.7784 (mmtt) REVERT: I 306 ARG cc_start: 0.7348 (mtt90) cc_final: 0.7080 (mpt-90) REVERT: I 353 VAL cc_start: 0.8735 (t) cc_final: 0.8529 (p) REVERT: I 379 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8896 (mttp) REVERT: H 6 HIS cc_start: 0.8621 (t70) cc_final: 0.7975 (t70) REVERT: H 163 ILE cc_start: 0.8682 (pp) cc_final: 0.8222 (mt) REVERT: H 216 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8366 (mtmm) REVERT: H 242 PHE cc_start: 0.8071 (m-80) cc_final: 0.7685 (m-10) REVERT: H 281 TYR cc_start: 0.7661 (m-80) cc_final: 0.7449 (m-80) REVERT: H 293 MET cc_start: 0.7373 (mtm) cc_final: 0.6914 (mmm) REVERT: H 332 ASN cc_start: 0.7871 (t0) cc_final: 0.7575 (p0) REVERT: H 379 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8522 (mttt) outliers start: 0 outliers final: 0 residues processed: 1439 average time/residue: 0.5219 time to fit residues: 1202.8290 Evaluate side-chains 715 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 715 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 20.0000 chunk 382 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 257 optimal weight: 30.0000 chunk 204 optimal weight: 4.9990 chunk 395 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 294 optimal weight: 30.0000 chunk 457 optimal weight: 0.3980 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS E 258 ASN E 300 ASN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS J 283 HIS J 300 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 372 GLN C 88 HIS C 258 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 258 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 256 ASN B 291 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS B 423 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 131 GLN F 256 ASN F 292 GLN F 396 HIS F 423 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN G 256 ASN G 292 GLN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 256 ASN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN I 256 ASN ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN H 256 ASN H 291 GLN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 41454 Z= 0.246 Angle : 0.602 8.558 56328 Z= 0.319 Chirality : 0.044 0.164 6162 Planarity : 0.005 0.044 7326 Dihedral : 12.590 176.927 5826 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.09 % Allowed : 2.78 % Favored : 97.13 % 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: -2.84 (0.10), residues: 5064 helix: -1.98 (0.09), residues: 2058 sheet: -1.04 (0.19), residues: 714 loop : -1.95 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 397 HIS 0.013 0.001 HIS I 28 PHE 0.033 0.002 PHE D 212 TYR 0.048 0.002 TYR J 108 ARG 0.004 0.000 ARG H 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 972 time to evaluate : 4.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 16 ILE cc_start: 0.9202 (mt) cc_final: 0.8873 (mm) REVERT: E 36 MET cc_start: 0.7185 (ptm) cc_final: 0.6263 (tmm) REVERT: E 54 SER cc_start: 0.7617 (p) cc_final: 0.7293 (t) REVERT: E 119 LEU cc_start: 0.9327 (mt) cc_final: 0.9073 (mt) REVERT: E 123 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8031 (mtp85) REVERT: E 135 PHE cc_start: 0.8859 (m-80) cc_final: 0.8576 (m-10) REVERT: E 136 LEU cc_start: 0.8683 (mp) cc_final: 0.8427 (mp) REVERT: E 253 THR cc_start: 0.8274 (p) cc_final: 0.7525 (t) REVERT: E 267 PHE cc_start: 0.9019 (m-80) cc_final: 0.8755 (m-80) REVERT: E 301 GLN cc_start: 0.8601 (mt0) cc_final: 0.8348 (mt0) REVERT: E 313 MET cc_start: 0.8230 (mtm) cc_final: 0.7070 (mtp) REVERT: E 351 PHE cc_start: 0.8020 (m-80) cc_final: 0.7438 (m-80) REVERT: J 14 VAL cc_start: 0.9170 (t) cc_final: 0.8890 (p) REVERT: J 16 ILE cc_start: 0.9101 (mt) cc_final: 0.8827 (mt) REVERT: J 124 LYS cc_start: 0.8684 (mttm) cc_final: 0.8213 (tptp) REVERT: J 195 LEU cc_start: 0.8015 (mm) cc_final: 0.7745 (mm) REVERT: J 221 ARG cc_start: 0.8704 (mtt90) cc_final: 0.8438 (mpp-170) REVERT: J 267 PHE cc_start: 0.8990 (m-80) cc_final: 0.8780 (m-80) REVERT: J 313 MET cc_start: 0.7793 (mtm) cc_final: 0.6435 (mtp) REVERT: C 36 MET cc_start: 0.7070 (ptm) cc_final: 0.6193 (tmm) REVERT: C 78 VAL cc_start: 0.9171 (t) cc_final: 0.8736 (p) REVERT: C 149 PHE cc_start: 0.7908 (t80) cc_final: 0.7335 (t80) REVERT: C 165 SER cc_start: 0.6660 (t) cc_final: 0.6346 (t) REVERT: C 182 VAL cc_start: 0.8633 (m) cc_final: 0.8123 (p) REVERT: C 192 HIS cc_start: 0.8035 (t-90) cc_final: 0.7658 (p90) REVERT: C 301 GLN cc_start: 0.8842 (mt0) cc_final: 0.8065 (pt0) REVERT: C 313 MET cc_start: 0.7894 (mtm) cc_final: 0.6622 (mtp) REVERT: C 377 MET cc_start: 0.7809 (ttp) cc_final: 0.7257 (tmm) REVERT: L 36 MET cc_start: 0.7172 (ptm) cc_final: 0.6361 (tmm) REVERT: L 149 PHE cc_start: 0.8422 (t80) cc_final: 0.7942 (t80) REVERT: L 195 LEU cc_start: 0.8050 (mm) cc_final: 0.7845 (mm) REVERT: L 256 GLN cc_start: 0.8314 (pt0) cc_final: 0.7603 (tt0) REVERT: L 301 GLN cc_start: 0.8838 (mt0) cc_final: 0.8102 (pt0) REVERT: L 313 MET cc_start: 0.7642 (mtm) cc_final: 0.6333 (mtp) REVERT: L 377 MET cc_start: 0.7271 (ttp) cc_final: 0.7044 (tmm) REVERT: L 395 PHE cc_start: 0.8801 (t80) cc_final: 0.8053 (t80) REVERT: A 36 MET cc_start: 0.6920 (ptm) cc_final: 0.5953 (tmm) REVERT: A 52 PHE cc_start: 0.8494 (m-80) cc_final: 0.8148 (m-10) REVERT: A 119 LEU cc_start: 0.9325 (mt) cc_final: 0.9122 (mm) REVERT: A 149 PHE cc_start: 0.8161 (t80) cc_final: 0.7721 (t80) REVERT: A 192 HIS cc_start: 0.7631 (t-90) cc_final: 0.7291 (p90) REVERT: A 212 ILE cc_start: 0.8959 (mt) cc_final: 0.8662 (mt) REVERT: A 267 PHE cc_start: 0.9101 (m-80) cc_final: 0.8690 (m-80) REVERT: A 316 CYS cc_start: 0.8569 (t) cc_final: 0.8263 (t) REVERT: A 377 MET cc_start: 0.7602 (ttp) cc_final: 0.7085 (tmm) REVERT: K 33 ASP cc_start: 0.7336 (m-30) cc_final: 0.6985 (p0) REVERT: K 36 MET cc_start: 0.7293 (ptm) cc_final: 0.6166 (tmm) REVERT: K 54 SER cc_start: 0.7387 (p) cc_final: 0.6942 (t) REVERT: K 267 PHE cc_start: 0.8984 (m-80) cc_final: 0.8589 (m-80) REVERT: K 301 GLN cc_start: 0.8277 (mt0) cc_final: 0.7519 (pt0) REVERT: K 313 MET cc_start: 0.7381 (mtm) cc_final: 0.6196 (mtp) REVERT: K 377 MET cc_start: 0.7750 (ttp) cc_final: 0.7117 (tmm) REVERT: K 413 MET cc_start: 0.7140 (tpp) cc_final: 0.6555 (tpp) REVERT: K 425 MET cc_start: 0.8627 (mmm) cc_final: 0.8381 (tpp) REVERT: B 6 HIS cc_start: 0.8679 (t70) cc_final: 0.8441 (t70) REVERT: B 51 TYR cc_start: 0.7944 (m-80) cc_final: 0.7319 (m-10) REVERT: B 73 MET cc_start: 0.8420 (mmt) cc_final: 0.8142 (mmt) REVERT: B 163 ILE cc_start: 0.8935 (pt) cc_final: 0.8229 (mt) REVERT: B 164 MET cc_start: 0.7991 (mpp) cc_final: 0.7756 (mpp) REVERT: B 181 GLU cc_start: 0.9115 (pt0) cc_final: 0.8612 (pp20) REVERT: B 257 MET cc_start: 0.8318 (mtm) cc_final: 0.8062 (mtp) REVERT: B 297 LYS cc_start: 0.8944 (ptpt) cc_final: 0.8634 (mtmm) REVERT: B 379 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8109 (mtmm) REVERT: F 51 TYR cc_start: 0.7835 (m-80) cc_final: 0.7129 (m-10) REVERT: F 85 PHE cc_start: 0.8275 (m-80) cc_final: 0.7697 (m-80) REVERT: F 163 ILE cc_start: 0.8623 (pt) cc_final: 0.8009 (mt) REVERT: F 197 ASP cc_start: 0.8052 (m-30) cc_final: 0.7803 (t70) REVERT: F 216 LYS cc_start: 0.8277 (mmtp) cc_final: 0.7858 (mmtm) REVERT: F 233 MET cc_start: 0.9275 (mtp) cc_final: 0.8932 (mtm) REVERT: F 242 PHE cc_start: 0.8058 (m-80) cc_final: 0.7455 (m-10) REVERT: F 250 LEU cc_start: 0.8674 (mt) cc_final: 0.8223 (mp) REVERT: F 267 MET cc_start: 0.7408 (mtm) cc_final: 0.7007 (mtm) REVERT: F 300 MET cc_start: 0.8585 (mtt) cc_final: 0.8216 (mtt) REVERT: G 6 HIS cc_start: 0.8702 (t70) cc_final: 0.8480 (t-170) REVERT: G 83 GLN cc_start: 0.8382 (mp10) cc_final: 0.7950 (mm110) REVERT: G 163 ILE cc_start: 0.8638 (pt) cc_final: 0.8428 (tp) REVERT: G 233 MET cc_start: 0.9169 (mtp) cc_final: 0.8763 (mtm) REVERT: D 51 TYR cc_start: 0.8019 (m-80) cc_final: 0.7113 (m-10) REVERT: D 73 MET cc_start: 0.8375 (mmt) cc_final: 0.8103 (mmt) REVERT: D 163 ILE cc_start: 0.9062 (pt) cc_final: 0.8409 (mt) REVERT: D 164 MET cc_start: 0.7796 (mpp) cc_final: 0.7469 (mpp) REVERT: D 181 GLU cc_start: 0.9031 (pt0) cc_final: 0.8793 (pp20) REVERT: D 200 TYR cc_start: 0.8017 (m-80) cc_final: 0.7687 (m-80) REVERT: D 250 LEU cc_start: 0.8634 (mt) cc_final: 0.8249 (mp) REVERT: D 288 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7943 (tm-30) REVERT: D 317 PHE cc_start: 0.8896 (m-80) cc_final: 0.8538 (m-80) REVERT: D 355 ASP cc_start: 0.8358 (m-30) cc_final: 0.7918 (m-30) REVERT: D 379 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8923 (mtmm) REVERT: I 118 ASP cc_start: 0.8324 (m-30) cc_final: 0.7505 (t0) REVERT: I 163 ILE cc_start: 0.8873 (pt) cc_final: 0.8462 (tp) REVERT: I 164 MET cc_start: 0.7659 (mpp) cc_final: 0.7278 (mpp) REVERT: I 200 TYR cc_start: 0.7896 (m-80) cc_final: 0.7295 (m-80) REVERT: I 228 LEU cc_start: 0.9280 (mm) cc_final: 0.9037 (tt) REVERT: I 242 PHE cc_start: 0.7978 (m-80) cc_final: 0.7531 (m-10) REVERT: I 297 LYS cc_start: 0.8406 (ptpt) cc_final: 0.7981 (mmtm) REVERT: I 306 ARG cc_start: 0.7556 (mtt90) cc_final: 0.7174 (mpt-90) REVERT: I 323 MET cc_start: 0.7731 (mpp) cc_final: 0.7464 (mpp) REVERT: I 328 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8512 (mm-30) REVERT: I 363 MET cc_start: 0.8038 (ptp) cc_final: 0.7705 (ptm) REVERT: I 425 TYR cc_start: 0.8450 (m-80) cc_final: 0.8203 (m-80) REVERT: H 118 ASP cc_start: 0.8514 (m-30) cc_final: 0.8216 (m-30) REVERT: H 147 MET cc_start: 0.8093 (tmm) cc_final: 0.7868 (tmm) REVERT: H 163 ILE cc_start: 0.8927 (pt) cc_final: 0.8483 (mt) REVERT: H 250 LEU cc_start: 0.8283 (mm) cc_final: 0.7739 (mp) REVERT: H 266 PHE cc_start: 0.8387 (m-10) cc_final: 0.8166 (m-10) REVERT: H 363 MET cc_start: 0.8100 (mtp) cc_final: 0.7836 (mtp) REVERT: H 395 LEU cc_start: 0.7259 (tp) cc_final: 0.7056 (tp) REVERT: H 403 MET cc_start: 0.6881 (mtt) cc_final: 0.6351 (mtm) outliers start: 4 outliers final: 1 residues processed: 972 average time/residue: 0.5374 time to fit residues: 850.3053 Evaluate side-chains 654 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 653 time to evaluate : 4.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 380 optimal weight: 20.0000 chunk 311 optimal weight: 30.0000 chunk 126 optimal weight: 40.0000 chunk 458 optimal weight: 0.0670 chunk 495 optimal weight: 20.0000 chunk 408 optimal weight: 7.9990 chunk 454 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 367 optimal weight: 20.0000 overall best weight: 10.8130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 226 ASN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 256 GLN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 300 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 ASN ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN K 283 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN G 256 ASN ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN I 292 GLN I 307 HIS ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 ASN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 41454 Z= 0.358 Angle : 0.674 9.046 56328 Z= 0.357 Chirality : 0.046 0.176 6162 Planarity : 0.005 0.043 7326 Dihedral : 12.526 178.009 5826 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.02 % Allowed : 3.08 % Favored : 96.90 % 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: -2.47 (0.11), residues: 5064 helix: -1.45 (0.10), residues: 2148 sheet: -1.05 (0.19), residues: 762 loop : -1.92 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP D 397 HIS 0.014 0.002 HIS F 28 PHE 0.037 0.002 PHE H 81 TYR 0.030 0.003 TYR E 172 ARG 0.006 0.001 ARG D 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 858 time to evaluate : 4.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.7401 (ptm) cc_final: 0.6104 (tmm) REVERT: E 54 SER cc_start: 0.7902 (p) cc_final: 0.7521 (t) REVERT: E 123 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8247 (mtp85) REVERT: E 135 PHE cc_start: 0.8907 (m-80) cc_final: 0.8459 (m-10) REVERT: E 149 PHE cc_start: 0.8271 (t80) cc_final: 0.8026 (t80) REVERT: E 267 PHE cc_start: 0.9048 (m-80) cc_final: 0.8740 (m-80) REVERT: E 313 MET cc_start: 0.8324 (mtm) cc_final: 0.7124 (mtp) REVERT: E 351 PHE cc_start: 0.7938 (m-80) cc_final: 0.7318 (m-80) REVERT: J 14 VAL cc_start: 0.9233 (t) cc_final: 0.9030 (p) REVERT: J 16 ILE cc_start: 0.9370 (mt) cc_final: 0.8914 (mm) REVERT: J 124 LYS cc_start: 0.8691 (mttm) cc_final: 0.8265 (tptp) REVERT: J 203 MET cc_start: 0.8713 (tpt) cc_final: 0.8492 (tpp) REVERT: J 260 VAL cc_start: 0.8835 (t) cc_final: 0.8498 (p) REVERT: J 267 PHE cc_start: 0.9040 (m-80) cc_final: 0.8721 (m-80) REVERT: J 301 GLN cc_start: 0.8191 (mt0) cc_final: 0.7415 (pt0) REVERT: J 313 MET cc_start: 0.7866 (mtm) cc_final: 0.6521 (mtp) REVERT: J 425 MET cc_start: 0.8598 (tpt) cc_final: 0.7802 (tpt) REVERT: J 428 LEU cc_start: 0.8934 (tt) cc_final: 0.8638 (tt) REVERT: C 36 MET cc_start: 0.7275 (ptm) cc_final: 0.6315 (tmm) REVERT: C 149 PHE cc_start: 0.8132 (t80) cc_final: 0.7847 (t80) REVERT: C 192 HIS cc_start: 0.8161 (t-90) cc_final: 0.7756 (p90) REVERT: C 203 MET cc_start: 0.8765 (tpp) cc_final: 0.8534 (tpp) REVERT: C 301 GLN cc_start: 0.8906 (mt0) cc_final: 0.8147 (pt0) REVERT: C 313 MET cc_start: 0.7999 (mtm) cc_final: 0.6797 (mtp) REVERT: C 377 MET cc_start: 0.7737 (ttp) cc_final: 0.6837 (tmm) REVERT: L 36 MET cc_start: 0.7473 (ptm) cc_final: 0.6351 (tmm) REVERT: L 123 ARG cc_start: 0.8911 (mtm-85) cc_final: 0.8586 (mtp85) REVERT: L 149 PHE cc_start: 0.8517 (t80) cc_final: 0.8105 (t80) REVERT: L 301 GLN cc_start: 0.8824 (mt0) cc_final: 0.8346 (pt0) REVERT: L 313 MET cc_start: 0.7716 (mtm) cc_final: 0.6387 (mtp) REVERT: L 395 PHE cc_start: 0.9018 (t80) cc_final: 0.8598 (t80) REVERT: A 24 TYR cc_start: 0.8823 (m-80) cc_final: 0.8483 (m-80) REVERT: A 36 MET cc_start: 0.7036 (ptm) cc_final: 0.6017 (tmm) REVERT: A 192 HIS cc_start: 0.7976 (t-90) cc_final: 0.7555 (p90) REVERT: A 255 PHE cc_start: 0.7725 (m-80) cc_final: 0.7505 (m-80) REVERT: A 267 PHE cc_start: 0.9104 (m-80) cc_final: 0.8748 (m-80) REVERT: A 358 GLN cc_start: 0.7912 (pm20) cc_final: 0.7696 (pm20) REVERT: A 377 MET cc_start: 0.7847 (ttp) cc_final: 0.6652 (tmm) REVERT: A 413 MET cc_start: 0.7707 (tpp) cc_final: 0.7179 (mmm) REVERT: K 33 ASP cc_start: 0.7643 (m-30) cc_final: 0.7196 (p0) REVERT: K 36 MET cc_start: 0.7146 (ptm) cc_final: 0.6001 (tmm) REVERT: K 54 SER cc_start: 0.7411 (p) cc_final: 0.6912 (t) REVERT: K 149 PHE cc_start: 0.8390 (t80) cc_final: 0.8119 (t80) REVERT: K 267 PHE cc_start: 0.8988 (m-80) cc_final: 0.8613 (m-80) REVERT: K 313 MET cc_start: 0.7573 (mtm) cc_final: 0.6262 (mtp) REVERT: K 358 GLN cc_start: 0.7804 (pm20) cc_final: 0.7564 (pm20) REVERT: K 377 MET cc_start: 0.7750 (ttp) cc_final: 0.7006 (tmm) REVERT: K 390 ARG cc_start: 0.9128 (tmm160) cc_final: 0.8618 (tmm160) REVERT: K 391 LEU cc_start: 0.9449 (tp) cc_final: 0.9194 (tp) REVERT: B 51 TYR cc_start: 0.7881 (m-80) cc_final: 0.7171 (m-80) REVERT: B 73 MET cc_start: 0.8455 (mmt) cc_final: 0.8240 (mmt) REVERT: B 147 MET cc_start: 0.8561 (tmm) cc_final: 0.8314 (tmm) REVERT: B 163 ILE cc_start: 0.8870 (pt) cc_final: 0.8252 (mp) REVERT: B 164 MET cc_start: 0.7975 (mpp) cc_final: 0.7678 (mpp) REVERT: B 181 GLU cc_start: 0.9145 (pt0) cc_final: 0.8637 (pp20) REVERT: B 200 TYR cc_start: 0.8096 (m-80) cc_final: 0.7796 (m-80) REVERT: B 242 PHE cc_start: 0.8464 (m-10) cc_final: 0.8237 (m-10) REVERT: B 267 MET cc_start: 0.7685 (mtp) cc_final: 0.7423 (mtp) REVERT: B 297 LYS cc_start: 0.8949 (ptpt) cc_final: 0.8589 (mtmm) REVERT: B 379 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8628 (mtmm) REVERT: F 51 TYR cc_start: 0.7823 (m-80) cc_final: 0.6841 (m-80) REVERT: F 85 PHE cc_start: 0.8326 (m-80) cc_final: 0.7810 (m-80) REVERT: F 163 ILE cc_start: 0.8704 (pt) cc_final: 0.8093 (mt) REVERT: F 197 ASP cc_start: 0.8099 (m-30) cc_final: 0.7882 (t70) REVERT: F 198 GLU cc_start: 0.8072 (pt0) cc_final: 0.7745 (pt0) REVERT: F 216 LYS cc_start: 0.8336 (mmtp) cc_final: 0.7921 (mmtm) REVERT: F 233 MET cc_start: 0.9388 (mtp) cc_final: 0.8950 (mtm) REVERT: F 253 LEU cc_start: 0.8955 (pp) cc_final: 0.8730 (pp) REVERT: F 267 MET cc_start: 0.7742 (mtm) cc_final: 0.7328 (mtm) REVERT: F 300 MET cc_start: 0.8619 (mtt) cc_final: 0.8360 (mtm) REVERT: G 6 HIS cc_start: 0.8805 (t70) cc_final: 0.8497 (t-170) REVERT: G 83 GLN cc_start: 0.8472 (mp10) cc_final: 0.7950 (mm110) REVERT: G 163 ILE cc_start: 0.8794 (pt) cc_final: 0.8508 (tp) REVERT: G 164 MET cc_start: 0.7933 (mpp) cc_final: 0.7463 (mpp) REVERT: G 197 ASP cc_start: 0.7840 (m-30) cc_final: 0.6829 (m-30) REVERT: G 216 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7889 (mmtm) REVERT: G 233 MET cc_start: 0.9284 (mtp) cc_final: 0.8807 (mtm) REVERT: G 321 MET cc_start: 0.8447 (ptp) cc_final: 0.7040 (ptp) REVERT: D 57 ASN cc_start: 0.7798 (m110) cc_final: 0.7542 (m110) REVERT: D 73 MET cc_start: 0.8402 (mmt) cc_final: 0.8164 (mmt) REVERT: D 163 ILE cc_start: 0.9033 (pt) cc_final: 0.8529 (mp) REVERT: D 164 MET cc_start: 0.7876 (mpp) cc_final: 0.7451 (mpp) REVERT: D 181 GLU cc_start: 0.8982 (pt0) cc_final: 0.8632 (pp20) REVERT: D 200 TYR cc_start: 0.8147 (m-80) cc_final: 0.7933 (m-80) REVERT: D 288 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8056 (tm-30) REVERT: D 379 LYS cc_start: 0.9135 (mtpt) cc_final: 0.8922 (mtmm) REVERT: D 388 MET cc_start: 0.7373 (mtt) cc_final: 0.7027 (mtt) REVERT: I 22 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7480 (tm-30) REVERT: I 23 VAL cc_start: 0.8131 (t) cc_final: 0.7406 (t) REVERT: I 149 THR cc_start: 0.9536 (p) cc_final: 0.9269 (p) REVERT: I 163 ILE cc_start: 0.9002 (pt) cc_final: 0.8420 (mt) REVERT: I 164 MET cc_start: 0.7964 (mpp) cc_final: 0.7295 (mpp) REVERT: I 242 PHE cc_start: 0.8006 (m-80) cc_final: 0.7534 (m-10) REVERT: I 257 MET cc_start: 0.8477 (mtp) cc_final: 0.8229 (mtp) REVERT: I 297 LYS cc_start: 0.8509 (ptpt) cc_final: 0.7992 (mptt) REVERT: I 306 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7161 (mpt-90) REVERT: I 425 TYR cc_start: 0.8356 (m-80) cc_final: 0.8125 (m-10) REVERT: H 147 MET cc_start: 0.8241 (tmm) cc_final: 0.8023 (tmm) REVERT: H 163 ILE cc_start: 0.8887 (pt) cc_final: 0.8673 (tt) REVERT: H 210 ILE cc_start: 0.9141 (tp) cc_final: 0.8880 (tt) REVERT: H 262 ARG cc_start: 0.7404 (mmp80) cc_final: 0.6564 (mmp80) REVERT: H 266 PHE cc_start: 0.8447 (m-10) cc_final: 0.8200 (m-10) outliers start: 1 outliers final: 1 residues processed: 858 average time/residue: 0.5232 time to fit residues: 730.0033 Evaluate side-chains 582 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 581 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 9.9990 chunk 344 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 50 optimal weight: 0.0270 chunk 218 optimal weight: 20.0000 chunk 307 optimal weight: 9.9990 chunk 460 optimal weight: 6.9990 chunk 487 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 436 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 overall best weight: 5.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: