Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 22:24:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlv_3527/04_2023/5mlv_3527_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlv_3527/04_2023/5mlv_3527.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlv_3527/04_2023/5mlv_3527_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlv_3527/04_2023/5mlv_3527_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlv_3527/04_2023/5mlv_3527_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlv_3527/04_2023/5mlv_3527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlv_3527/04_2023/5mlv_3527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlv_3527/04_2023/5mlv_3527_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlv_3527/04_2023/5mlv_3527_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.016 sd= 0.046 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 48 5.49 5 Mg 6 5.21 5 S 342 5.16 5 C 35478 2.51 5 N 9882 2.21 5 O 11172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "G ARG 266": "NH1" <-> "NH2" Residue "I ARG 122": "NH1" <-> "NH2" Residue "I ARG 391": "NH1" <-> "NH2" Residue "O ARG 266": "NH1" <-> "NH2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "J ARG 266": "NH1" <-> "NH2" Residue "P ARG 266": "NH1" <-> "NH2" Residue "M PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 434": "NH1" <-> "NH2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 434": "NH1" <-> "NH2" Residue "K PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 434": "NH1" <-> "NH2" Residue "Q PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 434": "NH1" <-> "NH2" Residue "N ARG 122": "NH1" <-> "NH2" Residue "N ARG 391": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "F ARG 122": "NH1" <-> "NH2" Residue "F ARG 391": "NH1" <-> "NH2" Residue "L ARG 122": "NH1" <-> "NH2" Residue "L ARG 391": "NH1" <-> "NH2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 391": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 56928 Number of models: 1 Model: "" Number of chains: 36 Chain: "E" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3374 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Chain: "G" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2668 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 336} Chain breaks: 1 Chain: "I" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3319 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 412} Chain: "O" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2668 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 336} Chain breaks: 1 Chain: "A" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2668 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 336} Chain breaks: 1 Chain: "D" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2668 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 336} Chain breaks: 1 Chain: "J" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2668 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 336} Chain breaks: 1 Chain: "P" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2668 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 336} Chain breaks: 1 Chain: "M" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3374 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3374 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Chain: "H" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3374 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Chain: "K" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3374 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Chain: "Q" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3374 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 407} Chain breaks: 1 Chain: "N" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3319 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 412} Chain: "C" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3319 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 412} Chain: "F" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3319 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 412} Chain: "L" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3319 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 412} Chain: "R" Number of atoms: 3319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3319 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 412} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'EPB': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'EPB': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'EPB': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'EPB': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'EPB': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'EPB': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.42, per 1000 atoms: 0.38 Number of scatterers: 56928 At special positions: 0 Unit cell: (172.36, 180.7, 218.23, 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 342 16.00 P 48 15.00 Mg 6 11.99 O 11172 8.00 N 9882 7.00 C 35478 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.55 Conformation dependent library (CDL) restraints added in 6.6 seconds 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 270 helices and 42 sheets defined 35.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'E' and resid 10 through 27 removed outlier: 3.563A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 82 Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'E' and resid 113 through 121 removed outlier: 3.835A pdb=" N GLU E 117 " --> pdb=" O THR E 113 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N SER E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 131 removed outlier: 3.524A pdb=" N MET E 129 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 165 removed outlier: 3.752A pdb=" N GLY E 154 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU E 159 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET E 163 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU E 164 " --> pdb=" O ARG E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 195 through 200 removed outlier: 4.002A pdb=" N ASP E 200 " --> pdb=" O HIS E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 218 removed outlier: 3.520A pdb=" N ILE E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N CYS E 217 " --> pdb=" O CYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 240 removed outlier: 4.063A pdb=" N LEU E 234 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 246 No H-bonds generated for 'chain 'E' and resid 243 through 246' Processing helix chain 'E' and resid 256 through 262 removed outlier: 3.908A pdb=" N GLN E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 285 No H-bonds generated for 'chain 'E' and resid 282 through 285' Processing helix chain 'E' and resid 292 through 299 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 330 through 340 removed outlier: 3.582A pdb=" N ALA E 335 " --> pdb=" O ASP E 331 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR E 337 " --> pdb=" O GLN E 333 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER E 338 " --> pdb=" O ALA E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 403 removed outlier: 3.752A pdb=" N GLU E 390 " --> pdb=" O SER E 387 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP E 392 " --> pdb=" O ALA E 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER E 393 " --> pdb=" O GLU E 390 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP E 396 " --> pdb=" O SER E 393 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS E 397 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE E 399 " --> pdb=" O ASP E 396 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP E 400 " --> pdb=" O HIS E 397 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET E 402 " --> pdb=" O PHE E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 413 No H-bonds generated for 'chain 'E' and resid 410 through 413' Processing helix chain 'E' and resid 419 through 439 removed outlier: 3.791A pdb=" N ALA E 425 " --> pdb=" O PHE E 422 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU E 427 " --> pdb=" O GLU E 424 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU E 429 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA E 430 " --> pdb=" O GLU E 427 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU E 437 " --> pdb=" O ARG E 434 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL E 439 " --> pdb=" O TYR E 436 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 123 removed outlier: 3.911A pdb=" N ARG G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 169 Processing helix chain 'G' and resid 174 through 181 removed outlier: 3.990A pdb=" N GLN G 179 " --> pdb=" O PRO G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 202 removed outlier: 3.829A pdb=" N MET G 202 " --> pdb=" O LYS G 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 198 through 202' Processing helix chain 'G' and resid 219 through 233 removed outlier: 3.749A pdb=" N LEU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER G 230 " --> pdb=" O GLN G 226 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN G 233 " --> pdb=" O SER G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 303 removed outlier: 5.133A pdb=" N LEU G 294 " --> pdb=" O GLY G 291 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG G 295 " --> pdb=" O ASP G 292 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG G 298 " --> pdb=" O ARG G 295 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU G 299 " --> pdb=" O LEU G 296 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER G 301 " --> pdb=" O ARG G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 395 removed outlier: 3.968A pdb=" N ARG G 378 " --> pdb=" O ASN G 374 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU G 379 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE G 383 " --> pdb=" O GLU G 379 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE G 394 " --> pdb=" O LEU G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 414 removed outlier: 3.643A pdb=" N LEU G 414 " --> pdb=" O LYS G 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 410 through 414' Processing helix chain 'G' and resid 445 through 450 Processing helix chain 'I' and resid 11 through 28 removed outlier: 3.899A pdb=" N ALA I 19 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 45 removed outlier: 3.729A pdb=" N GLU I 45 " --> pdb=" O ALA I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 77 No H-bonds generated for 'chain 'I' and resid 74 through 77' Processing helix chain 'I' and resid 101 through 104 No H-bonds generated for 'chain 'I' and resid 101 through 104' Processing helix chain 'I' and resid 109 through 125 removed outlier: 6.163A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL I 119 " --> pdb=" O ALA I 115 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG I 122 " --> pdb=" O ASP I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 158 removed outlier: 3.678A pdb=" N GLY I 148 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU I 150 " --> pdb=" O GLY I 146 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU I 152 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE I 155 " --> pdb=" O LEU I 151 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG I 156 " --> pdb=" O LEU I 152 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU I 157 " --> pdb=" O SER I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 194 removed outlier: 3.852A pdb=" N THR I 186 " --> pdb=" O PRO I 182 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER I 188 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 211 removed outlier: 3.679A pdb=" N SER I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE I 211 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 222 through 236 removed outlier: 3.600A pdb=" N LEU I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER I 230 " --> pdb=" O ASN I 226 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA I 231 " --> pdb=" O HIS I 227 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL I 232 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 254 removed outlier: 3.580A pdb=" N ALA I 254 " --> pdb=" O LEU I 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 250 through 254' Processing helix chain 'I' and resid 286 through 293 removed outlier: 3.624A pdb=" N GLN I 291 " --> pdb=" O PRO I 287 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) 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 323 through 336 removed outlier: 3.614A pdb=" N ASP I 327 " --> pdb=" O MET I 323 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLN I 329 " --> pdb=" O GLU I 325 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE I 330 " --> pdb=" O VAL I 326 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER I 332 " --> pdb=" O GLU I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 390 removed outlier: 3.661A pdb=" N ALA I 387 " --> pdb=" O ASP I 383 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET I 388 " --> pdb=" O GLN I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 396 through 399 No H-bonds generated for 'chain 'I' and resid 396 through 399' Processing helix chain 'I' and resid 407 through 419 Processing helix chain 'I' and resid 422 through 424 No H-bonds generated for 'chain 'I' and resid 422 through 424' Processing helix chain 'O' and resid 117 through 123 removed outlier: 3.910A pdb=" N ARG O 121 " --> pdb=" O ASP O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 169 Processing helix chain 'O' and resid 174 through 181 removed outlier: 3.990A pdb=" N GLN O 179 " --> pdb=" O PRO O 175 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 202 removed outlier: 3.828A pdb=" N MET O 202 " --> pdb=" O LYS O 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 198 through 202' Processing helix chain 'O' and resid 219 through 233 removed outlier: 3.749A pdb=" N LEU O 227 " --> pdb=" O ALA O 223 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER O 230 " --> pdb=" O GLN O 226 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN O 233 " --> pdb=" O SER O 229 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 303 removed outlier: 5.132A pdb=" N LEU O 294 " --> pdb=" O GLY O 291 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG O 295 " --> pdb=" O ASP O 292 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG O 298 " --> pdb=" O ARG O 295 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU O 299 " --> pdb=" O LEU O 296 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER O 301 " --> pdb=" O ARG O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 374 through 395 removed outlier: 3.968A pdb=" N ARG O 378 " --> pdb=" O ASN O 374 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU O 379 " --> pdb=" O LYS O 375 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE O 383 " --> pdb=" O GLU O 379 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE O 394 " --> pdb=" O LEU O 390 " (cutoff:3.500A) Processing helix chain 'O' and resid 410 through 414 removed outlier: 3.642A pdb=" N LEU O 414 " --> pdb=" O LYS O 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 410 through 414' Processing helix chain 'O' and resid 445 through 450 Processing helix chain 'A' and resid 117 through 123 removed outlier: 3.910A pdb=" N ARG A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 174 through 181 removed outlier: 3.989A pdb=" N GLN A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.828A pdb=" N MET A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 202' Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.749A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN A 233 " --> pdb=" O SER A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 303 removed outlier: 5.132A pdb=" N LEU A 294 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 295 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG A 298 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU A 299 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 301 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 395 removed outlier: 3.968A pdb=" N ARG A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE A 383 " --> pdb=" O GLU A 379 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.642A pdb=" N LEU A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'D' and resid 117 through 123 removed outlier: 3.910A pdb=" N ARG D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 174 through 181 removed outlier: 3.989A pdb=" N GLN D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.829A pdb=" N MET D 202 " --> pdb=" O LYS D 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 202' Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.749A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER D 230 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN D 233 " --> pdb=" O SER D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 303 removed outlier: 5.133A pdb=" N LEU D 294 " --> pdb=" O GLY D 291 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG D 295 " --> pdb=" O ASP D 292 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG D 298 " --> pdb=" O ARG D 295 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU D 299 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER D 301 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 395 removed outlier: 3.968A pdb=" N ARG D 378 " --> pdb=" O ASN D 374 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU D 379 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 414 removed outlier: 3.644A pdb=" N LEU D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 410 through 414' Processing helix chain 'D' and resid 445 through 450 Processing helix chain 'J' and resid 117 through 123 removed outlier: 3.910A pdb=" N ARG J 121 " --> pdb=" O ASP J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 174 through 181 removed outlier: 3.990A pdb=" N GLN J 179 " --> pdb=" O PRO J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 202 removed outlier: 3.828A pdb=" N MET J 202 " --> pdb=" O LYS J 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 198 through 202' Processing helix chain 'J' and resid 219 through 233 removed outlier: 3.749A pdb=" N LEU J 227 " --> pdb=" O ALA J 223 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER J 230 " --> pdb=" O GLN J 226 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN J 233 " --> pdb=" O SER J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 290 through 303 removed outlier: 5.132A pdb=" N LEU J 294 " --> pdb=" O GLY J 291 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG J 295 " --> pdb=" O ASP J 292 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG J 298 " --> pdb=" O ARG J 295 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU J 299 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER J 301 " --> pdb=" O ARG J 298 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 395 removed outlier: 3.967A pdb=" N ARG J 378 " --> pdb=" O ASN J 374 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU J 379 " --> pdb=" O LYS J 375 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE J 383 " --> pdb=" O GLU J 379 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE J 394 " --> pdb=" O LEU J 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 414 removed outlier: 3.643A pdb=" N LEU J 414 " --> pdb=" O LYS J 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 410 through 414' Processing helix chain 'J' and resid 445 through 450 Processing helix chain 'P' and resid 117 through 123 removed outlier: 3.911A pdb=" N ARG P 121 " --> pdb=" O ASP P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 169 Processing helix chain 'P' and resid 174 through 181 removed outlier: 3.989A pdb=" N GLN P 179 " --> pdb=" O PRO P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 202 removed outlier: 3.828A pdb=" N MET P 202 " --> pdb=" O LYS P 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 198 through 202' Processing helix chain 'P' and resid 219 through 233 removed outlier: 3.750A pdb=" N LEU P 227 " --> pdb=" O ALA P 223 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER P 230 " --> pdb=" O GLN P 226 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN P 233 " --> pdb=" O SER P 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 290 through 303 removed outlier: 5.133A pdb=" N LEU P 294 " --> pdb=" O GLY P 291 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG P 295 " --> pdb=" O ASP P 292 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG P 298 " --> pdb=" O ARG P 295 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU P 299 " --> pdb=" O LEU P 296 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER P 301 " --> pdb=" O ARG P 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 374 through 395 removed outlier: 3.968A pdb=" N ARG P 378 " --> pdb=" O ASN P 374 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU P 379 " --> pdb=" O LYS P 375 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE P 383 " --> pdb=" O GLU P 379 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE P 394 " --> pdb=" O LEU P 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 410 through 414 removed outlier: 3.643A pdb=" N LEU P 414 " --> pdb=" O LYS P 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 410 through 414' Processing helix chain 'P' and resid 445 through 450 Processing helix chain 'M' and resid 10 through 27 removed outlier: 3.563A pdb=" N GLU M 22 " --> pdb=" O ASN M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 82 Processing helix chain 'M' and resid 107 through 111 Processing helix chain 'M' and resid 113 through 121 removed outlier: 3.834A pdb=" N GLU M 117 " --> pdb=" O THR M 113 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP M 120 " --> pdb=" O LYS M 116 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER M 121 " --> pdb=" O GLU M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 131 removed outlier: 3.524A pdb=" N MET M 129 " --> pdb=" O ARG M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 165 removed outlier: 3.752A pdb=" N GLY M 154 " --> pdb=" O GLY M 150 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA M 155 " --> pdb=" O SER M 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU M 159 " --> pdb=" O ALA M 155 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU M 161 " --> pdb=" O LEU M 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET M 163 " --> pdb=" O GLU M 159 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU M 164 " --> pdb=" O ARG M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 192 Processing helix chain 'M' and resid 195 through 200 removed outlier: 4.001A pdb=" N ASP M 200 " --> pdb=" O HIS M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 218 removed outlier: 3.520A pdb=" N ILE M 216 " --> pdb=" O ALA M 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS M 217 " --> pdb=" O CYS M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 240 removed outlier: 4.063A pdb=" N LEU M 234 " --> pdb=" O ASN M 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL M 238 " --> pdb=" O LEU M 234 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL M 239 " --> pdb=" O ILE M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 246 No H-bonds generated for 'chain 'M' and resid 243 through 246' Processing helix chain 'M' and resid 256 through 262 removed outlier: 3.907A pdb=" N GLN M 260 " --> pdb=" O LEU M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 285 No H-bonds generated for 'chain 'M' and resid 282 through 285' Processing helix chain 'M' and resid 292 through 299 Processing helix chain 'M' and resid 302 through 304 No H-bonds generated for 'chain 'M' and resid 302 through 304' Processing helix chain 'M' and resid 330 through 340 removed outlier: 3.583A pdb=" N ALA M 335 " --> pdb=" O ASP M 331 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR M 337 " --> pdb=" O GLN M 333 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER M 338 " --> pdb=" O ALA M 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 403 removed outlier: 3.752A pdb=" N GLU M 390 " --> pdb=" O SER M 387 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP M 392 " --> pdb=" O ALA M 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER M 393 " --> pdb=" O GLU M 390 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP M 396 " --> pdb=" O SER M 393 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS M 397 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE M 399 " --> pdb=" O ASP M 396 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP M 400 " --> pdb=" O HIS M 397 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET M 402 " --> pdb=" O PHE M 399 " (cutoff:3.500A) Processing helix chain 'M' and resid 410 through 413 No H-bonds generated for 'chain 'M' and resid 410 through 413' Processing helix chain 'M' and resid 419 through 439 removed outlier: 3.791A pdb=" N ALA M 425 " --> pdb=" O PHE M 422 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU M 427 " --> pdb=" O GLU M 424 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU M 429 " --> pdb=" O ARG M 426 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA M 430 " --> pdb=" O GLU M 427 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU M 437 " --> pdb=" O ARG M 434 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL M 439 " --> pdb=" O TYR M 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 removed outlier: 3.563A pdb=" N GLU B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 113 through 121 removed outlier: 3.836A pdb=" N GLU B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 131 removed outlier: 3.524A pdb=" N MET B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 165 removed outlier: 3.752A pdb=" N GLY B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 Processing helix chain 'B' and resid 195 through 200 removed outlier: 4.003A pdb=" N ASP B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 218 removed outlier: 3.520A pdb=" N ILE B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 240 removed outlier: 4.063A pdb=" N LEU B 234 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 246 No H-bonds generated for 'chain 'B' and resid 243 through 246' Processing helix chain 'B' and resid 256 through 262 removed outlier: 3.907A pdb=" N GLN B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 285 No H-bonds generated for 'chain 'B' and resid 282 through 285' Processing helix chain 'B' and resid 292 through 299 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.582A pdb=" N ALA B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 337 " --> pdb=" O GLN B 333 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 403 removed outlier: 3.752A pdb=" N GLU B 390 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 392 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER B 393 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 396 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS B 397 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 400 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET B 402 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 413 No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 419 through 439 removed outlier: 3.792A pdb=" N ALA B 425 " --> pdb=" O PHE B 422 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 427 " --> pdb=" O GLU B 424 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 429 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 430 " --> pdb=" O GLU B 427 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU B 437 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 439 " --> pdb=" O TYR B 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 27 removed outlier: 3.563A pdb=" N GLU H 22 " --> pdb=" O ASN H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 82 Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 113 through 121 removed outlier: 3.835A pdb=" N GLU H 117 " --> pdb=" O THR H 113 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N SER H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 131 removed outlier: 3.524A pdb=" N MET H 129 " --> pdb=" O ARG H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 165 removed outlier: 3.752A pdb=" N GLY H 154 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 155 " --> pdb=" O SER H 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU H 159 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU H 164 " --> pdb=" O ARG H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 192 Processing helix chain 'H' and resid 195 through 200 removed outlier: 4.002A pdb=" N ASP H 200 " --> pdb=" O HIS H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 218 removed outlier: 3.520A pdb=" N ILE H 216 " --> pdb=" O ALA H 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS H 217 " --> pdb=" O CYS H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 240 removed outlier: 4.062A pdb=" N LEU H 234 " --> pdb=" O ASN H 230 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN H 237 " --> pdb=" O ARG H 233 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL H 238 " --> pdb=" O LEU H 234 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL H 239 " --> pdb=" O ILE H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 246 No H-bonds generated for 'chain 'H' and resid 243 through 246' Processing helix chain 'H' and resid 256 through 262 removed outlier: 3.907A pdb=" N GLN H 260 " --> pdb=" O LEU H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 285 No H-bonds generated for 'chain 'H' and resid 282 through 285' Processing helix chain 'H' and resid 292 through 299 Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 330 through 340 removed outlier: 3.582A pdb=" N ALA H 335 " --> pdb=" O ASP H 331 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR H 337 " --> pdb=" O GLN H 333 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER H 338 " --> pdb=" O ALA H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 403 removed outlier: 3.753A pdb=" N GLU H 390 " --> pdb=" O SER H 387 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP H 392 " --> pdb=" O ALA H 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER H 393 " --> pdb=" O GLU H 390 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP H 396 " --> pdb=" O SER H 393 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS H 397 " --> pdb=" O ARG H 394 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE H 399 " --> pdb=" O ASP H 396 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP H 400 " --> pdb=" O HIS H 397 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET H 402 " --> pdb=" O PHE H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 413 No H-bonds generated for 'chain 'H' and resid 410 through 413' Processing helix chain 'H' and resid 419 through 439 removed outlier: 3.791A pdb=" N ALA H 425 " --> pdb=" O PHE H 422 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU H 427 " --> pdb=" O GLU H 424 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU H 429 " --> pdb=" O ARG H 426 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA H 430 " --> pdb=" O GLU H 427 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU H 437 " --> pdb=" O ARG H 434 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL H 439 " --> pdb=" O TYR H 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 27 removed outlier: 3.563A pdb=" N GLU K 22 " --> pdb=" O ASN K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 82 Processing helix chain 'K' and resid 107 through 111 Processing helix chain 'K' and resid 113 through 121 removed outlier: 3.835A pdb=" N GLU K 117 " --> pdb=" O THR K 113 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP K 120 " --> pdb=" O LYS K 116 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER K 121 " --> pdb=" O GLU K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 131 removed outlier: 3.525A pdb=" N MET K 129 " --> pdb=" O ARG K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 165 removed outlier: 3.752A pdb=" N GLY K 154 " --> pdb=" O GLY K 150 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU K 159 " --> pdb=" O ALA K 155 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET K 163 " --> pdb=" O GLU K 159 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU K 164 " --> pdb=" O ARG K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 192 Processing helix chain 'K' and resid 195 through 200 removed outlier: 4.001A pdb=" N ASP K 200 " --> pdb=" O HIS K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 212 through 218 removed outlier: 3.521A pdb=" N ILE K 216 " --> pdb=" O ALA K 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS K 217 " --> pdb=" O CYS K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 240 removed outlier: 4.064A pdb=" N LEU K 234 " --> pdb=" O ASN K 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN K 237 " --> pdb=" O ARG K 233 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL K 238 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL K 239 " --> pdb=" O ILE K 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 246 No H-bonds generated for 'chain 'K' and resid 243 through 246' Processing helix chain 'K' and resid 256 through 262 removed outlier: 3.907A pdb=" N GLN K 260 " --> pdb=" O LEU K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 285 No H-bonds generated for 'chain 'K' and resid 282 through 285' Processing helix chain 'K' and resid 292 through 299 Processing helix chain 'K' and resid 302 through 304 No H-bonds generated for 'chain 'K' and resid 302 through 304' Processing helix chain 'K' and resid 330 through 340 removed outlier: 3.582A pdb=" N ALA K 335 " --> pdb=" O ASP K 331 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR K 337 " --> pdb=" O GLN K 333 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER K 338 " --> pdb=" O ALA K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 403 removed outlier: 3.752A pdb=" N GLU K 390 " --> pdb=" O SER K 387 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP K 392 " --> pdb=" O ALA K 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER K 393 " --> pdb=" O GLU K 390 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP K 396 " --> pdb=" O SER K 393 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS K 397 " --> pdb=" O ARG K 394 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE K 399 " --> pdb=" O ASP K 396 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP K 400 " --> pdb=" O HIS K 397 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET K 402 " --> pdb=" O PHE K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 413 No H-bonds generated for 'chain 'K' and resid 410 through 413' Processing helix chain 'K' and resid 419 through 439 removed outlier: 3.791A pdb=" N ALA K 425 " --> pdb=" O PHE K 422 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU K 427 " --> pdb=" O GLU K 424 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU K 429 " --> pdb=" O ARG K 426 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA K 430 " --> pdb=" O GLU K 427 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU K 437 " --> pdb=" O ARG K 434 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL K 439 " --> pdb=" O TYR K 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 27 removed outlier: 3.563A pdb=" N GLU Q 22 " --> pdb=" O ASN Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 82 Processing helix chain 'Q' and resid 107 through 111 Processing helix chain 'Q' and resid 113 through 121 removed outlier: 3.835A pdb=" N GLU Q 117 " --> pdb=" O THR Q 113 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP Q 120 " --> pdb=" O LYS Q 116 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER Q 121 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 removed outlier: 3.524A pdb=" N MET Q 129 " --> pdb=" O ARG Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 165 removed outlier: 3.752A pdb=" N GLY Q 154 " --> pdb=" O GLY Q 150 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA Q 155 " --> pdb=" O SER Q 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU Q 159 " --> pdb=" O ALA Q 155 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU Q 161 " --> pdb=" O LEU Q 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET Q 163 " --> pdb=" O GLU Q 159 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLU Q 164 " --> pdb=" O ARG Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 192 Processing helix chain 'Q' and resid 195 through 200 removed outlier: 4.003A pdb=" N ASP Q 200 " --> pdb=" O HIS Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 218 removed outlier: 3.521A pdb=" N ILE Q 216 " --> pdb=" O ALA Q 212 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS Q 217 " --> pdb=" O CYS Q 213 " (cutoff:3.500A) Processing helix chain 'Q' and resid 228 through 240 removed outlier: 4.063A pdb=" N LEU Q 234 " --> pdb=" O ASN Q 230 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN Q 237 " --> pdb=" O ARG Q 233 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL Q 238 " --> pdb=" O LEU Q 234 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL Q 239 " --> pdb=" O ILE Q 235 " (cutoff:3.500A) Processing helix chain 'Q' and resid 243 through 246 No H-bonds generated for 'chain 'Q' and resid 243 through 246' Processing helix chain 'Q' and resid 256 through 262 removed outlier: 3.907A pdb=" N GLN Q 260 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 282 through 285 No H-bonds generated for 'chain 'Q' and resid 282 through 285' Processing helix chain 'Q' and resid 292 through 299 Processing helix chain 'Q' and resid 302 through 304 No H-bonds generated for 'chain 'Q' and resid 302 through 304' Processing helix chain 'Q' and resid 330 through 340 removed outlier: 3.582A pdb=" N ALA Q 335 " --> pdb=" O ASP Q 331 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR Q 337 " --> pdb=" O GLN Q 333 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER Q 338 " --> pdb=" O ALA Q 334 " (cutoff:3.500A) Processing helix chain 'Q' and resid 387 through 403 removed outlier: 3.752A pdb=" N GLU Q 390 " --> pdb=" O SER Q 387 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP Q 392 " --> pdb=" O ALA Q 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER Q 393 " --> pdb=" O GLU Q 390 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP Q 396 " --> pdb=" O SER Q 393 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS Q 397 " --> pdb=" O ARG Q 394 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE Q 399 " --> pdb=" O ASP Q 396 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP Q 400 " --> pdb=" O HIS Q 397 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET Q 402 " --> pdb=" O PHE Q 399 " (cutoff:3.500A) Processing helix chain 'Q' and resid 410 through 413 No H-bonds generated for 'chain 'Q' and resid 410 through 413' Processing helix chain 'Q' and resid 419 through 439 removed outlier: 3.792A pdb=" N ALA Q 425 " --> pdb=" O PHE Q 422 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU Q 427 " --> pdb=" O GLU Q 424 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU Q 429 " --> pdb=" O ARG Q 426 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA Q 430 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU Q 437 " --> pdb=" O ARG Q 434 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL Q 439 " --> pdb=" O TYR Q 436 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 28 removed outlier: 3.899A pdb=" N ALA N 19 " --> pdb=" O GLN N 15 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 45 removed outlier: 3.730A pdb=" N GLU N 45 " --> pdb=" O ALA N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 77 No H-bonds generated for 'chain 'N' and resid 74 through 77' Processing helix chain 'N' and resid 101 through 104 No H-bonds generated for 'chain 'N' and resid 101 through 104' Processing helix chain 'N' and resid 109 through 125 removed outlier: 6.161A pdb=" N ASP N 114 " --> pdb=" O ALA N 110 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA N 115 " --> pdb=" O GLU N 111 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL N 119 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG N 122 " --> pdb=" O ASP N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 158 removed outlier: 3.677A pdb=" N GLY N 148 " --> pdb=" O GLY N 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU N 150 " --> pdb=" O GLY N 146 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU N 152 " --> pdb=" O GLY N 148 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE N 155 " --> pdb=" O LEU N 151 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG N 156 " --> pdb=" O LEU N 152 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU N 157 " --> pdb=" O SER N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 194 removed outlier: 3.852A pdb=" N THR N 186 " --> pdb=" O PRO N 182 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER N 188 " --> pdb=" O ASN N 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN N 191 " --> pdb=" O LEU N 187 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU N 194 " --> pdb=" O HIS N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 211 removed outlier: 3.681A pdb=" N SER N 209 " --> pdb=" O GLU N 205 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE N 210 " --> pdb=" O ALA N 206 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE N 211 " --> pdb=" O LEU N 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 236 removed outlier: 3.600A pdb=" N LEU N 228 " --> pdb=" O ASP N 224 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL N 229 " --> pdb=" O LEU N 225 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER N 230 " --> pdb=" O ASN N 226 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA N 231 " --> pdb=" O HIS N 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL N 232 " --> pdb=" O LEU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 254 removed outlier: 3.581A pdb=" N ALA N 254 " --> pdb=" O LEU N 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 250 through 254' Processing helix chain 'N' and resid 286 through 293 removed outlier: 3.625A pdb=" N GLN N 291 " --> pdb=" O PRO N 287 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN N 292 " --> pdb=" O GLU N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 296 through 298 No H-bonds generated for 'chain 'N' and resid 296 through 298' Processing helix chain 'N' and resid 323 through 336 removed outlier: 3.613A pdb=" N ASP N 327 " --> pdb=" O MET N 323 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN N 329 " --> pdb=" O GLU N 325 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE N 330 " --> pdb=" O VAL N 326 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER N 332 " --> pdb=" O GLU N 328 " (cutoff:3.500A) Processing helix chain 'N' and resid 374 through 390 removed outlier: 3.660A pdb=" N ALA N 387 " --> pdb=" O ASP N 383 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET N 388 " --> pdb=" O GLN N 384 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 399 No H-bonds generated for 'chain 'N' and resid 396 through 399' Processing helix chain 'N' and resid 407 through 419 Processing helix chain 'N' and resid 422 through 424 No H-bonds generated for 'chain 'N' and resid 422 through 424' Processing helix chain 'C' and resid 11 through 28 removed outlier: 3.899A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.729A pdb=" N GLU C 45 " --> pdb=" O ALA C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 77 No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing helix chain 'C' and resid 101 through 104 No H-bonds generated for 'chain 'C' and resid 101 through 104' Processing helix chain 'C' and resid 109 through 125 removed outlier: 6.162A pdb=" N ASP C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 158 removed outlier: 3.678A pdb=" N GLY C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.852A pdb=" N THR C 186 " --> pdb=" O PRO C 182 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU C 194 " --> pdb=" O HIS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 211 removed outlier: 3.680A pdb=" N SER C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 236 removed outlier: 3.600A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA C 231 " --> pdb=" O HIS C 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.580A pdb=" N ALA C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 254' Processing helix chain 'C' and resid 286 through 293 removed outlier: 3.623A pdb=" N GLN C 291 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 298 No H-bonds generated for 'chain 'C' and resid 296 through 298' Processing helix chain 'C' and resid 323 through 336 removed outlier: 3.614A pdb=" N ASP C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 330 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 332 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 390 removed outlier: 3.661A pdb=" N ALA C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 399 No H-bonds generated for 'chain 'C' and resid 396 through 399' Processing helix chain 'C' and resid 407 through 419 Processing helix chain 'C' and resid 422 through 424 No H-bonds generated for 'chain 'C' and resid 422 through 424' Processing helix chain 'F' and resid 11 through 28 removed outlier: 3.899A pdb=" N ALA F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 45 removed outlier: 3.729A pdb=" N GLU F 45 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 77 No H-bonds generated for 'chain 'F' and resid 74 through 77' Processing helix chain 'F' and resid 101 through 104 No H-bonds generated for 'chain 'F' and resid 101 through 104' Processing helix chain 'F' and resid 109 through 125 removed outlier: 6.162A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 158 removed outlier: 3.677A pdb=" N GLY F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG F 156 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.852A pdb=" N THR F 186 " --> pdb=" O PRO F 182 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 211 removed outlier: 3.680A pdb=" N SER F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE F 211 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 236 removed outlier: 3.600A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER F 230 " --> pdb=" O ASN F 226 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA F 231 " --> pdb=" O HIS F 227 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 254 removed outlier: 3.581A pdb=" N ALA F 254 " --> pdb=" O LEU F 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 250 through 254' Processing helix chain 'F' and resid 286 through 293 removed outlier: 3.625A pdb=" N GLN F 291 " --> pdb=" O PRO F 287 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN F 292 " --> pdb=" O GLU F 288 " (cutoff:3.500A) 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 323 through 336 removed outlier: 3.614A pdb=" N ASP F 327 " --> pdb=" O MET F 323 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE F 330 " --> pdb=" O VAL F 326 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 390 removed outlier: 3.661A pdb=" N ALA F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET F 388 " --> pdb=" O GLN F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 399 No H-bonds generated for 'chain 'F' and resid 396 through 399' Processing helix chain 'F' and resid 407 through 419 Processing helix chain 'F' and resid 422 through 424 No H-bonds generated for 'chain 'F' and resid 422 through 424' Processing helix chain 'L' and resid 11 through 28 removed outlier: 3.898A pdb=" N ALA L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER L 22 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 45 removed outlier: 3.730A pdb=" N GLU L 45 " --> pdb=" O ALA L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 77 No H-bonds generated for 'chain 'L' and resid 74 through 77' Processing helix chain 'L' and resid 101 through 104 No H-bonds generated for 'chain 'L' and resid 101 through 104' Processing helix chain 'L' and resid 109 through 125 removed outlier: 6.162A pdb=" N ASP L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL L 119 " --> pdb=" O ALA L 115 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG L 122 " --> pdb=" O ASP L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 158 removed outlier: 3.677A pdb=" N GLY L 148 " --> pdb=" O GLY L 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU L 152 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE L 155 " --> pdb=" O LEU L 151 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU L 157 " --> pdb=" O SER L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 194 removed outlier: 3.852A pdb=" N THR L 186 " --> pdb=" O PRO L 182 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER L 188 " --> pdb=" O ASN L 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN L 191 " --> pdb=" O LEU L 187 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU L 194 " --> pdb=" O HIS L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 211 removed outlier: 3.680A pdb=" N SER L 209 " --> pdb=" O GLU L 205 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE L 210 " --> pdb=" O ALA L 206 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE L 211 " --> pdb=" O LEU L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 222 through 236 removed outlier: 3.600A pdb=" N LEU L 228 " --> pdb=" O ASP L 224 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL L 229 " --> pdb=" O LEU L 225 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA L 231 " --> pdb=" O HIS L 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL L 232 " --> pdb=" O LEU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 254 removed outlier: 3.581A pdb=" N ALA L 254 " --> pdb=" O LEU L 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 250 through 254' Processing helix chain 'L' and resid 286 through 293 removed outlier: 3.624A pdb=" N GLN L 291 " --> pdb=" O PRO L 287 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN L 292 " --> pdb=" O GLU L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 298 No H-bonds generated for 'chain 'L' and resid 296 through 298' Processing helix chain 'L' and resid 323 through 336 removed outlier: 3.615A pdb=" N ASP L 327 " --> pdb=" O MET L 323 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN L 329 " --> pdb=" O GLU L 325 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE L 330 " --> pdb=" O VAL L 326 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER L 332 " --> pdb=" O GLU L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 390 removed outlier: 3.660A pdb=" N ALA L 387 " --> pdb=" O ASP L 383 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET L 388 " --> pdb=" O GLN L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 396 through 399 No H-bonds generated for 'chain 'L' and resid 396 through 399' Processing helix chain 'L' and resid 407 through 419 Processing helix chain 'L' and resid 422 through 424 No H-bonds generated for 'chain 'L' and resid 422 through 424' Processing helix chain 'R' and resid 11 through 28 removed outlier: 3.899A pdb=" N ALA R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER R 22 " --> pdb=" O ALA R 18 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR R 23 " --> pdb=" O ALA R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 45 removed outlier: 3.729A pdb=" N GLU R 45 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 77 No H-bonds generated for 'chain 'R' and resid 74 through 77' Processing helix chain 'R' and resid 101 through 104 No H-bonds generated for 'chain 'R' and resid 101 through 104' Processing helix chain 'R' and resid 109 through 125 removed outlier: 6.162A pdb=" N ASP R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ALA R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG R 122 " --> pdb=" O ASP R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 158 removed outlier: 3.677A pdb=" N GLY R 148 " --> pdb=" O GLY R 144 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU R 152 " --> pdb=" O GLY R 148 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG R 156 " --> pdb=" O LEU R 152 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU R 157 " --> pdb=" O SER R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 194 removed outlier: 3.852A pdb=" N THR R 186 " --> pdb=" O PRO R 182 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER R 188 " --> pdb=" O ASN R 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN R 191 " --> pdb=" O LEU R 187 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU R 194 " --> pdb=" O HIS R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 211 removed outlier: 3.680A pdb=" N SER R 209 " --> pdb=" O GLU R 205 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE R 210 " --> pdb=" O ALA R 206 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 236 removed outlier: 3.601A pdb=" N LEU R 228 " --> pdb=" O ASP R 224 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL R 229 " --> pdb=" O LEU R 225 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER R 230 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA R 231 " --> pdb=" O HIS R 227 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL R 232 " --> pdb=" O LEU R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 250 through 254 removed outlier: 3.582A pdb=" N ALA R 254 " --> pdb=" O LEU R 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 250 through 254' Processing helix chain 'R' and resid 286 through 293 removed outlier: 3.624A pdb=" N GLN R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN R 292 " --> pdb=" O GLU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 298 No H-bonds generated for 'chain 'R' and resid 296 through 298' Processing helix chain 'R' and resid 323 through 336 removed outlier: 3.614A pdb=" N ASP R 327 " --> pdb=" O MET R 323 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN R 329 " --> pdb=" O GLU R 325 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE R 330 " --> pdb=" O VAL R 326 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER R 332 " --> pdb=" O GLU R 328 " (cutoff:3.500A) Processing helix chain 'R' and resid 374 through 390 removed outlier: 3.661A pdb=" N ALA R 387 " --> pdb=" O ASP R 383 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET R 388 " --> pdb=" O GLN R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 399 No H-bonds generated for 'chain 'R' and resid 396 through 399' Processing helix chain 'R' and resid 407 through 419 Processing helix chain 'R' and resid 422 through 424 No H-bonds generated for 'chain 'R' and resid 422 through 424' Processing sheet with id= A, first strand: chain 'E' and resid 6 through 8 removed outlier: 8.989A pdb=" N VAL E 7 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU E 140 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER E 169 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL E 141 " --> pdb=" O SER E 169 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU E 171 " --> pdb=" O VAL E 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'E' and resid 273 through 277 Processing sheet with id= C, first strand: chain 'G' and resid 107 through 110 removed outlier: 3.608A pdb=" N ALA G 190 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL G 240 " --> pdb=" O ILE G 287 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 245 through 247 Processing sheet with id= E, first strand: chain 'I' and resid 7 through 9 removed outlier: 6.880A pdb=" N VAL I 64 " --> pdb=" O GLN I 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'I' and resid 163 through 165 removed outlier: 3.588A pdb=" N ALA I 165 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'I' and resid 267 through 271 removed outlier: 3.708A pdb=" N THR I 312 " --> pdb=" O ASN I 370 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'O' and resid 107 through 110 removed outlier: 3.607A pdb=" N ALA O 190 " --> pdb=" O VAL O 359 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL O 240 " --> pdb=" O ILE O 287 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'O' and resid 245 through 247 Processing sheet with id= J, first strand: chain 'A' and resid 107 through 110 removed outlier: 3.608A pdb=" N ALA A 190 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 240 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 245 through 247 Processing sheet with id= L, first strand: chain 'D' and resid 107 through 110 removed outlier: 3.607A pdb=" N ALA D 190 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 240 " --> pdb=" O ILE D 287 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 245 through 247 Processing sheet with id= N, first strand: chain 'J' and resid 107 through 110 removed outlier: 3.607A pdb=" N ALA J 190 " --> pdb=" O VAL J 359 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL J 240 " --> pdb=" O ILE J 287 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 245 through 247 Processing sheet with id= P, first strand: chain 'P' and resid 107 through 110 removed outlier: 3.607A pdb=" N ALA P 190 " --> pdb=" O VAL P 359 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL P 240 " --> pdb=" O ILE P 287 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 245 through 247 Processing sheet with id= R, first strand: chain 'M' and resid 6 through 8 removed outlier: 8.988A pdb=" N VAL M 7 " --> pdb=" O GLY M 138 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU M 140 " --> pdb=" O VAL M 7 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER M 169 " --> pdb=" O PHE M 139 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL M 141 " --> pdb=" O SER M 169 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU M 171 " --> pdb=" O VAL M 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= T, first strand: chain 'B' and resid 6 through 8 removed outlier: 8.989A pdb=" N VAL B 7 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU B 140 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER B 169 " --> pdb=" O PHE B 139 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL B 141 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU B 171 " --> pdb=" O VAL B 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'B' and resid 273 through 277 Processing sheet with id= V, first strand: chain 'H' and resid 6 through 8 removed outlier: 8.988A pdb=" N VAL H 7 " --> pdb=" O GLY H 138 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU H 140 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER H 169 " --> pdb=" O PHE H 139 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL H 141 " --> pdb=" O SER H 169 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU H 171 " --> pdb=" O VAL H 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'H' and resid 273 through 277 Processing sheet with id= X, first strand: chain 'K' and resid 6 through 8 removed outlier: 8.989A pdb=" N VAL K 7 " --> pdb=" O GLY K 138 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU K 140 " --> pdb=" O VAL K 7 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER K 169 " --> pdb=" O PHE K 139 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL K 141 " --> pdb=" O SER K 169 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU K 171 " --> pdb=" O VAL K 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'K' and resid 273 through 277 Processing sheet with id= Z, first strand: chain 'Q' and resid 6 through 8 removed outlier: 8.988A pdb=" N VAL Q 7 " --> pdb=" O GLY Q 138 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU Q 140 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N SER Q 169 " --> pdb=" O PHE Q 139 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL Q 141 " --> pdb=" O SER Q 169 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU Q 171 " --> pdb=" O VAL Q 141 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'Q' and resid 273 through 277 Processing sheet with id= AB, first strand: chain 'N' and resid 7 through 9 removed outlier: 6.879A pdb=" N VAL N 64 " --> pdb=" O GLN N 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'N' and resid 163 through 165 removed outlier: 3.589A pdb=" N ALA N 165 " --> pdb=" O PHE N 133 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLU N 3 " --> pdb=" O GLN N 131 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE N 133 " --> pdb=" O GLU N 3 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL N 5 " --> pdb=" O PHE N 133 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'N' and resid 267 through 271 removed outlier: 3.708A pdb=" N THR N 312 " --> pdb=" O ASN N 370 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 7 through 9 removed outlier: 6.880A pdb=" N VAL C 64 " --> pdb=" O GLN C 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'C' and resid 163 through 165 removed outlier: 3.589A pdb=" N ALA C 165 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLU C 3 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE C 133 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL C 5 " --> pdb=" O PHE C 133 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 267 through 271 removed outlier: 3.708A pdb=" N THR C 312 " --> pdb=" O ASN C 370 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 7 through 9 removed outlier: 6.880A pdb=" N VAL F 64 " --> pdb=" O GLN F 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 163 through 165 removed outlier: 3.589A pdb=" N ALA F 165 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 267 through 271 removed outlier: 3.708A pdb=" N THR F 312 " --> pdb=" O ASN F 370 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 7 through 9 removed outlier: 6.880A pdb=" N VAL L 64 " --> pdb=" O GLN L 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'L' and resid 163 through 165 removed outlier: 3.588A pdb=" N ALA L 165 " --> pdb=" O PHE L 133 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N GLU L 3 " --> pdb=" O GLN L 131 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE L 133 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL L 5 " --> pdb=" O PHE L 133 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 267 through 271 removed outlier: 3.708A pdb=" N THR L 312 " --> pdb=" O ASN L 370 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'R' and resid 7 through 9 removed outlier: 6.880A pdb=" N VAL R 64 " --> pdb=" O GLN R 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'R' and resid 163 through 165 removed outlier: 3.589A pdb=" N ALA R 165 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLU R 3 " --> pdb=" O GLN R 131 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE R 133 " --> pdb=" O GLU R 3 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL R 5 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'R' and resid 267 through 271 removed outlier: 3.709A pdb=" N THR R 312 " --> pdb=" O ASN R 370 " (cutoff:3.500A) 1422 hydrogen bonds defined for protein. 3690 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: 14.84 Time building geometry restraints manager: 19.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10928 1.32 - 1.44: 14451 1.44 - 1.57: 32019 1.57 - 1.69: 88 1.69 - 1.81: 570 Bond restraints: 58056 Sorted by residual: bond pdb=" C24 EPB L 502 " pdb=" S1 EPB L 502 " ideal model delta sigma weight residual 1.524 1.720 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C24 EPB R 502 " pdb=" S1 EPB R 502 " ideal model delta sigma weight residual 1.524 1.719 -0.195 2.00e-02 2.50e+03 9.55e+01 bond pdb=" C24 EPB C 502 " pdb=" S1 EPB C 502 " ideal model delta sigma weight residual 1.524 1.719 -0.195 2.00e-02 2.50e+03 9.55e+01 bond pdb=" C23 EPB I 502 " pdb=" N26 EPB I 502 " ideal model delta sigma weight residual 1.572 1.377 0.195 2.00e-02 2.50e+03 9.51e+01 bond pdb=" C23 EPB F 502 " pdb=" N26 EPB F 502 " ideal model delta sigma weight residual 1.572 1.377 0.195 2.00e-02 2.50e+03 9.51e+01 ... (remaining 58051 not shown) Histogram of bond angle deviations from ideal: 59.24 - 74.49: 18 74.49 - 89.73: 6 89.73 - 104.97: 1100 104.97 - 120.21: 54026 120.21 - 135.45: 23570 Bond angle restraints: 78720 Sorted by residual: angle pdb=" C6 EPB I 502 " pdb=" C5 EPB I 502 " pdb=" O41 EPB I 502 " ideal model delta sigma weight residual 141.31 113.79 27.52 3.00e+00 1.11e-01 8.42e+01 angle pdb=" C6 EPB L 502 " pdb=" C5 EPB L 502 " pdb=" O41 EPB L 502 " ideal model delta sigma weight residual 141.31 113.82 27.49 3.00e+00 1.11e-01 8.40e+01 angle pdb=" C6 EPB F 502 " pdb=" C5 EPB F 502 " pdb=" O41 EPB F 502 " ideal model delta sigma weight residual 141.31 113.84 27.47 3.00e+00 1.11e-01 8.39e+01 angle pdb=" C6 EPB R 502 " pdb=" C5 EPB R 502 " pdb=" O41 EPB R 502 " ideal model delta sigma weight residual 141.31 113.85 27.46 3.00e+00 1.11e-01 8.38e+01 angle pdb=" C6 EPB C 502 " pdb=" C5 EPB C 502 " pdb=" O41 EPB C 502 " ideal model delta sigma weight residual 141.31 113.90 27.41 3.00e+00 1.11e-01 8.35e+01 ... (remaining 78715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 34368 35.97 - 71.95: 321 71.95 - 107.92: 76 107.92 - 143.90: 41 143.90 - 179.87: 102 Dihedral angle restraints: 34908 sinusoidal: 14124 harmonic: 20784 Sorted by residual: dihedral pdb=" C5' GTP B 500 " pdb=" O5' GTP B 500 " pdb=" PA GTP B 500 " pdb=" O3A GTP B 500 " ideal model delta sinusoidal sigma weight residual 69.27 -111.26 -179.47 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP K 500 " pdb=" O5' GTP K 500 " pdb=" PA GTP K 500 " pdb=" O3A GTP K 500 " ideal model delta sinusoidal sigma weight residual 69.27 -112.13 -178.60 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' GTP M 500 " pdb=" O5' GTP M 500 " pdb=" PA GTP M 500 " pdb=" O3A GTP M 500 " ideal model delta sinusoidal sigma weight residual 69.27 -108.36 177.62 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 34905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 8254 0.123 - 0.246: 339 0.246 - 0.369: 29 0.369 - 0.492: 0 0.492 - 0.615: 6 Chirality restraints: 8628 Sorted by residual: chirality pdb=" C5 EPB L 502 " pdb=" C4 EPB L 502 " pdb=" C6 EPB L 502 " pdb=" O41 EPB L 502 " both_signs ideal model delta sigma weight residual True 1.77 -2.38 -0.61 2.00e-01 2.50e+01 9.44e+00 chirality pdb=" C5 EPB C 502 " pdb=" C4 EPB C 502 " pdb=" C6 EPB C 502 " pdb=" O41 EPB C 502 " both_signs ideal model delta sigma weight residual True 1.77 -2.38 -0.61 2.00e-01 2.50e+01 9.41e+00 chirality pdb=" C5 EPB I 502 " pdb=" C4 EPB I 502 " pdb=" C6 EPB I 502 " pdb=" O41 EPB I 502 " both_signs ideal model delta sigma weight residual True 1.77 -2.38 -0.61 2.00e-01 2.50e+01 9.40e+00 ... (remaining 8625 not shown) Planarity restraints: 10260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GDP N 501 " -0.044 2.00e-02 2.50e+03 4.51e-02 6.11e+01 pdb=" N9 GDP N 501 " 0.018 2.00e-02 2.50e+03 pdb=" C8 GDP N 501 " 0.062 2.00e-02 2.50e+03 pdb=" N7 GDP N 501 " 0.043 2.00e-02 2.50e+03 pdb=" C5 GDP N 501 " -0.009 2.00e-02 2.50e+03 pdb=" C6 GDP N 501 " -0.019 2.00e-02 2.50e+03 pdb=" O6 GDP N 501 " -0.025 2.00e-02 2.50e+03 pdb=" N1 GDP N 501 " -0.022 2.00e-02 2.50e+03 pdb=" C2 GDP N 501 " -0.024 2.00e-02 2.50e+03 pdb=" N2 GDP N 501 " 0.103 2.00e-02 2.50e+03 pdb=" N3 GDP N 501 " -0.056 2.00e-02 2.50e+03 pdb=" C4 GDP N 501 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP C 501 " -0.042 2.00e-02 2.50e+03 4.28e-02 5.50e+01 pdb=" N9 GDP C 501 " 0.017 2.00e-02 2.50e+03 pdb=" C8 GDP C 501 " 0.059 2.00e-02 2.50e+03 pdb=" N7 GDP C 501 " 0.040 2.00e-02 2.50e+03 pdb=" C5 GDP C 501 " -0.008 2.00e-02 2.50e+03 pdb=" C6 GDP C 501 " -0.019 2.00e-02 2.50e+03 pdb=" O6 GDP C 501 " -0.021 2.00e-02 2.50e+03 pdb=" N1 GDP C 501 " -0.024 2.00e-02 2.50e+03 pdb=" C2 GDP C 501 " -0.024 2.00e-02 2.50e+03 pdb=" N2 GDP C 501 " 0.098 2.00e-02 2.50e+03 pdb=" N3 GDP C 501 " -0.051 2.00e-02 2.50e+03 pdb=" C4 GDP C 501 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP L 501 " 0.050 2.00e-02 2.50e+03 4.17e-02 5.21e+01 pdb=" N9 GDP L 501 " -0.020 2.00e-02 2.50e+03 pdb=" C8 GDP L 501 " -0.059 2.00e-02 2.50e+03 pdb=" N7 GDP L 501 " -0.040 2.00e-02 2.50e+03 pdb=" C5 GDP L 501 " 0.006 2.00e-02 2.50e+03 pdb=" C6 GDP L 501 " 0.018 2.00e-02 2.50e+03 pdb=" O6 GDP L 501 " 0.029 2.00e-02 2.50e+03 pdb=" N1 GDP L 501 " 0.020 2.00e-02 2.50e+03 pdb=" C2 GDP L 501 " 0.020 2.00e-02 2.50e+03 pdb=" N2 GDP L 501 " -0.091 2.00e-02 2.50e+03 pdb=" N3 GDP L 501 " 0.047 2.00e-02 2.50e+03 pdb=" C4 GDP L 501 " 0.020 2.00e-02 2.50e+03 ... (remaining 10257 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 859 2.63 - 3.20: 50849 3.20 - 3.76: 89555 3.76 - 4.33: 122391 4.33 - 4.90: 191938 Nonbonded interactions: 455592 Sorted by model distance: nonbonded pdb="MG MG O 501 " pdb=" O2B ANP O 502 " model vdw 2.060 2.170 nonbonded pdb="MG MG J 501 " pdb=" O2B ANP J 502 " model vdw 2.067 2.170 nonbonded pdb="MG MG P 501 " pdb=" O2B ANP P 502 " model vdw 2.073 2.170 nonbonded pdb="MG MG G 501 " pdb=" O2B ANP G 502 " model vdw 2.073 2.170 nonbonded pdb="MG MG A 501 " pdb=" O2B ANP A 502 " model vdw 2.075 2.170 ... (remaining 455587 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 'D' selection = chain 'G' selection = chain 'J' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'N' selection = chain 'R' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'O' selection = chain 'P' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'M' selection = chain 'Q' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'N' selection = chain 'R' } Set refine NCS operators NCS operators will be refined. 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 5.180 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 101.810 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.010 0.196 58056 Z= 0.633 Angle : 1.207 27.522 78720 Z= 0.586 Chirality : 0.063 0.615 8628 Planarity : 0.007 0.064 10260 Dihedral : 17.429 179.875 21576 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % 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: -4.85 (0.07), residues: 7158 helix: -3.82 (0.05), residues: 2580 sheet: -1.84 (0.15), residues: 1032 loop : -3.17 (0.08), residues: 3546 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14316 Ramachandran restraints generated. 7158 Oldfield, 0 Emsley, 7158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.262 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1874 time to fit residues: 22.9987 Evaluate side-chains 59 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.243 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3517 Evaluate side-chains 147 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 147 average time/residue: 0.1364 time to fit residues: 23.8397 Evaluate side-chains 74 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.308 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0293 time to fit residues: 0.4886 Evaluate side-chains 116 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.291 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1411 time to fit residues: 19.2064 Evaluate side-chains 60 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.291 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 602 optimal weight: 4.9990 chunk 541 optimal weight: 20.0000 chunk 300 optimal weight: 10.0000 chunk 184 optimal weight: 0.0870 chunk 365 optimal weight: 40.0000 chunk 289 optimal weight: 20.0000 chunk 559 optimal weight: 0.1980 chunk 216 optimal weight: 1.9990 chunk 340 optimal weight: 9.9990 chunk 416 optimal weight: 20.0000 chunk 648 optimal weight: 5.9990 overall best weight: 2.6564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 403 HIS Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 GLN E 201 ASN E 237 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 GLN C 337 ASN C 370 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 58056 Z= 0.226 Angle : 0.712 8.319 78720 Z= 0.364 Chirality : 0.046 0.280 8628 Planarity : 0.006 0.088 10260 Dihedral : 21.943 171.661 8370 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.08), residues: 7158 helix: -2.78 (0.08), residues: 2574 sheet: -1.13 (0.16), residues: 1014 loop : -2.79 (0.08), residues: 3570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14308 Ramachandran restraints generated. 7154 Oldfield, 0 Emsley, 7154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14308 Ramachandran restraints generated. 7154 Oldfield, 0 Emsley, 7154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.277 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 77 average time/residue: 0.1567 time to fit residues: 13.8894 Evaluate side-chains 47 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.242 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3409 Evaluate side-chains 111 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 0.307 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.1164 time to fit residues: 15.9343 Evaluate side-chains 69 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.312 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4276 Evaluate side-chains 96 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.301 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1166 time to fit residues: 13.8137 Evaluate side-chains 57 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 360 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 539 optimal weight: 2.9990 chunk 441 optimal weight: 0.0270 chunk 178 optimal weight: 8.9990 chunk 649 optimal weight: 0.0970 chunk 701 optimal weight: 0.0170 chunk 578 optimal weight: 7.9990 chunk 644 optimal weight: 30.0000 chunk 221 optimal weight: 30.0000 chunk 521 optimal weight: 6.9990 overall best weight: 2.0278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN E 172 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 ASN I 131 GLN I 264 HIS I 334 GLN I 370 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 58056 Z= 0.240 Angle : 0.808 15.327 78720 Z= 0.409 Chirality : 0.049 0.335 8628 Planarity : 0.013 0.324 10260 Dihedral : 21.654 170.101 8370 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.08), residues: 7158 helix: -2.50 (0.09), residues: 2490 sheet: -0.96 (0.16), residues: 1014 loop : -2.56 (0.09), residues: 3654 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13452 Ramachandran restraints generated. 6726 Oldfield, 0 Emsley, 6726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13452 Ramachandran restraints generated. 6726 Oldfield, 0 Emsley, 6726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.1626 time to fit residues: 12.8041 Evaluate side-chains 51 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.286 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3510 Evaluate side-chains 99 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 95 average time/residue: 0.1109 time to fit residues: 13.1613 Evaluate side-chains 67 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.305 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3654 time to fit residues: 0.7985 Evaluate side-chains 86 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1350 time to fit residues: 14.0384 Evaluate side-chains 59 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 641 optimal weight: 0.3980 chunk 488 optimal weight: 10.0000 chunk 337 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 309 optimal weight: 8.9990 chunk 436 optimal weight: 0.0020 chunk 651 optimal weight: 8.9990 chunk 690 optimal weight: 0.3980 chunk 340 optimal weight: 30.0000 chunk 617 optimal weight: 30.0000 chunk 185 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 105 ASN ** Q 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 ASN ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 180 GLN Q 237 GLN ** Q 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 GLN L 334 GLN L 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 58056 Z= 0.237 Angle : 0.808 13.044 78720 Z= 0.404 Chirality : 0.050 0.331 8628 Planarity : 0.010 0.241 10260 Dihedral : 21.445 169.207 8370 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.08), residues: 7158 helix: -2.51 (0.09), residues: 2484 sheet: -1.28 (0.16), residues: 1104 loop : -2.61 (0.09), residues: 3570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11746 Ramachandran restraints generated. 5873 Oldfield, 0 Emsley, 5873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1667 time to fit residues: 12.8378 Evaluate side-chains 50 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.246 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3419 Evaluate side-chains 108 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.1197 time to fit residues: 15.6208 Evaluate side-chains 74 residues out of total 369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4199 Evaluate side-chains 93 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 92 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.1220 time to fit residues: 13.9032 Evaluate side-chains 64 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.292 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/iotbx/cli_parser.py", line 870, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 771, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.1307 > 50: distance: 0 - 1: 3.900 distance: 1 - 2: 3.285 distance: 2 - 3: 5.461 distance: 2 - 6: 13.247 distance: 6 - 7: 15.229 distance: 7 - 8: 5.291 distance: 7 - 10: 14.476 distance: 8 - 9: 8.432 distance: 8 - 18: 6.221 distance: 9 - 40: 8.353 distance: 10 - 11: 6.783 distance: 11 - 12: 3.928 distance: 12 - 14: 5.792 distance: 13 - 15: 5.577 distance: 14 - 16: 11.450 distance: 15 - 16: 11.786 distance: 16 - 17: 8.647 distance: 18 - 19: 8.138 distance: 19 - 20: 7.273 distance: 19 - 22: 10.107 distance: 20 - 21: 12.961 distance: 20 - 26: 10.270 distance: 23 - 25: 3.227 distance: 26 - 27: 7.482 distance: 27 - 28: 8.222 distance: 27 - 30: 3.850 distance: 28 - 29: 8.378 distance: 28 - 34: 31.538 distance: 30 - 31: 4.729 distance: 30 - 32: 3.357 distance: 31 - 33: 8.635 distance: 34 - 35: 61.131 distance: 35 - 36: 39.044 distance: 35 - 38: 29.174 distance: 36 - 37: 11.889 distance: 36 - 40: 7.335 distance: 38 - 39: 19.296 distance: 40 - 41: 10.221 distance: 41 - 42: 6.123 distance: 42 - 43: 7.086 distance: 48 - 49: 4.124 distance: 51 - 52: 4.679 distance: 52 - 53: 3.906 distance: 52 - 55: 10.606 distance: 53 - 54: 4.303 distance: 53 - 62: 18.918 distance: 55 - 56: 6.775 distance: 56 - 57: 3.732 distance: 59 - 60: 7.416 distance: 59 - 61: 4.266 distance: 62 - 63: 11.507 distance: 63 - 64: 31.639 distance: 63 - 66: 18.076 distance: 64 - 65: 22.974 distance: 64 - 70: 6.364 distance: 66 - 67: 8.626 distance: 67 - 68: 3.615 distance: 67 - 69: 3.821 distance: 70 - 71: 12.520 distance: 71 - 72: 9.789 distance: 71 - 74: 11.757 distance: 72 - 73: 8.273 distance: 72 - 78: 5.287 distance: 74 - 75: 4.449 distance: 75 - 76: 10.111 distance: 75 - 77: 6.975 distance: 78 - 79: 5.756