Starting phenix.real_space_refine on Mon Mar 18 08:36:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izr_9757/03_2024/6izr_9757_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izr_9757/03_2024/6izr_9757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izr_9757/03_2024/6izr_9757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izr_9757/03_2024/6izr_9757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izr_9757/03_2024/6izr_9757_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6izr_9757/03_2024/6izr_9757_updated.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.016 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 60 5.49 5 Mg 30 5.21 5 S 300 5.16 5 C 53670 2.51 5 N 14100 2.21 5 O 16200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 245": "NH1" <-> "NH2" Residue "2 ARG 245": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "E ARG 245": "NH1" <-> "NH2" Residue "G ARG 245": "NH1" <-> "NH2" Residue "H ARG 245": "NH1" <-> "NH2" Residue "J ARG 245": "NH1" <-> "NH2" Residue "K ARG 245": "NH1" <-> "NH2" Residue "M ARG 245": "NH1" <-> "NH2" Residue "N ARG 245": "NH1" <-> "NH2" Residue "P ARG 245": "NH1" <-> "NH2" Residue "Q ARG 245": "NH1" <-> "NH2" Residue "b ARG 245": "NH1" <-> "NH2" Residue "c ARG 245": "NH1" <-> "NH2" Residue "e ARG 245": "NH1" <-> "NH2" Residue "f ARG 245": "NH1" <-> "NH2" Residue "h ARG 245": "NH1" <-> "NH2" Residue "i ARG 245": "NH1" <-> "NH2" Residue "k ARG 245": "NH1" <-> "NH2" Residue "l ARG 245": "NH1" <-> "NH2" Residue "n ARG 245": "NH1" <-> "NH2" Residue "o ARG 245": "NH1" <-> "NH2" Residue "q ARG 245": "NH1" <-> "NH2" Residue "r ARG 245": "NH1" <-> "NH2" Residue "t ARG 245": "NH1" <-> "NH2" Residue "u ARG 245": "NH1" <-> "NH2" Residue "w ARG 245": "NH1" <-> "NH2" Residue "x ARG 245": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 84360 Number of models: 1 Model: "" Number of chains: 60 Chain: "1" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "2" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "A" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "B" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "D" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "E" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "G" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "H" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "J" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "K" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "M" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "N" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "P" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "Q" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "b" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "c" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "e" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "f" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "h" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "i" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "k" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "l" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "n" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "o" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "q" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "r" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "t" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "u" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "w" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "x" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2784 Classifications: {'peptide': 349} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 339} Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 32.47, per 1000 atoms: 0.38 Number of scatterers: 84360 At special positions: 0 Unit cell: (254.221, 263.538, 155.727, 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 300 16.00 P 60 15.00 Mg 30 11.99 O 16200 8.00 N 14100 7.00 C 53670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.64 Conformation dependent library (CDL) restraints added in 12.1 seconds 20820 Ramachandran restraints generated. 10410 Oldfield, 0 Emsley, 10410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19500 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 414 helices and 150 sheets defined 32.6% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.56 Creating SS restraints... Processing helix chain '1' and resid 39 through 43 Processing helix chain '1' and resid 50 through 52 No H-bonds generated for 'chain '1' and resid 50 through 52' Processing helix chain '1' and resid 71 through 75 removed outlier: 3.552A pdb=" N ARG 1 75 " --> pdb=" O GLU 1 71 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 71 through 75' Processing helix chain '1' and resid 92 through 104 removed outlier: 3.782A pdb=" N LEU 1 97 " --> pdb=" O GLU 1 93 " (cutoff:3.500A) Processing helix chain '1' and resid 131 through 140 Processing helix chain '1' and resid 170 through 173 No H-bonds generated for 'chain '1' and resid 170 through 173' Processing helix chain '1' and resid 178 through 181 No H-bonds generated for 'chain '1' and resid 178 through 181' Processing helix chain '1' and resid 229 through 244 removed outlier: 3.765A pdb=" N TYR 1 233 " --> pdb=" O ILE 1 230 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN 1 234 " --> pdb=" O ASN 1 231 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR 1 235 " --> pdb=" O ILE 1 232 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET 1 236 " --> pdb=" O TYR 1 233 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP 1 237 " --> pdb=" O ASN 1 234 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE 1 240 " --> pdb=" O ASP 1 237 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP 1 242 " --> pdb=" O ALA 1 239 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER 1 244 " --> pdb=" O THR 1 241 " (cutoff:3.500A) Processing helix chain '1' and resid 252 through 261 removed outlier: 3.875A pdb=" N GLU 1 260 " --> pdb=" O MET 1 256 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU 1 261 " --> pdb=" O LEU 1 257 " (cutoff:3.500A) Processing helix chain '1' and resid 274 through 295 removed outlier: 4.581A pdb=" N LYS 1 291 " --> pdb=" O ASN 1 287 " (cutoff:3.500A) Processing helix chain '1' and resid 298 through 300 No H-bonds generated for 'chain '1' and resid 298 through 300' Processing helix chain '1' and resid 320 through 323 removed outlier: 3.552A pdb=" N ILE 1 323 " --> pdb=" O LEU 1 320 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 320 through 323' Processing helix chain '1' and resid 337 through 346 removed outlier: 3.537A pdb=" N PHE 1 345 " --> pdb=" O GLY 1 341 " (cutoff:3.500A) Processing helix chain '2' and resid 39 through 43 Processing helix chain '2' and resid 50 through 52 No H-bonds generated for 'chain '2' and resid 50 through 52' Processing helix chain '2' and resid 71 through 75 removed outlier: 3.552A pdb=" N ARG 2 75 " --> pdb=" O GLU 2 71 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 71 through 75' Processing helix chain '2' and resid 92 through 104 removed outlier: 3.782A pdb=" N LEU 2 97 " --> pdb=" O GLU 2 93 " (cutoff:3.500A) Processing helix chain '2' and resid 131 through 140 Processing helix chain '2' and resid 170 through 173 No H-bonds generated for 'chain '2' and resid 170 through 173' Processing helix chain '2' and resid 178 through 181 No H-bonds generated for 'chain '2' and resid 178 through 181' Processing helix chain '2' and resid 229 through 244 removed outlier: 3.765A pdb=" N TYR 2 233 " --> pdb=" O ILE 2 230 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN 2 234 " --> pdb=" O ASN 2 231 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR 2 235 " --> pdb=" O ILE 2 232 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET 2 236 " --> pdb=" O TYR 2 233 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP 2 237 " --> pdb=" O ASN 2 234 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE 2 240 " --> pdb=" O ASP 2 237 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP 2 242 " --> pdb=" O ALA 2 239 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER 2 244 " --> pdb=" O THR 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 252 through 261 removed outlier: 3.876A pdb=" N GLU 2 260 " --> pdb=" O MET 2 256 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU 2 261 " --> pdb=" O LEU 2 257 " (cutoff:3.500A) Processing helix chain '2' and resid 274 through 295 removed outlier: 4.581A pdb=" N LYS 2 291 " --> pdb=" O ASN 2 287 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 300 No H-bonds generated for 'chain '2' and resid 298 through 300' Processing helix chain '2' and resid 320 through 323 removed outlier: 3.552A pdb=" N ILE 2 323 " --> pdb=" O LEU 2 320 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 320 through 323' Processing helix chain '2' and resid 337 through 346 removed outlier: 3.537A pdb=" N PHE 2 345 " --> pdb=" O GLY 2 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.567A pdb=" N PHE A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 43' Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 71 through 74 No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.776A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.550A pdb=" N MET A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.681A pdb=" N TYR A 233 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 236 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP A 237 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 240 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 242 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A 244 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.676A pdb=" N GLU A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 294 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 310 through 315 Processing helix chain 'A' and resid 317 through 323 removed outlier: 4.278A pdb=" N LEU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE A 323 " --> pdb=" O HIS A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.501A pdb=" N PHE A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.671A pdb=" N PHE B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 39 through 43' Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 92 through 103 removed outlier: 3.755A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 127 No H-bonds generated for 'chain 'B' and resid 125 through 127' Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.528A pdb=" N PHE B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 170 through 174' Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.859A pdb=" N LYS B 238 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.568A pdb=" N MET B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 260 " --> pdb=" O MET B 256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 294 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 310 through 315 removed outlier: 3.896A pdb=" N LYS B 314 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL B 315 " --> pdb=" O GLY B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 315' Processing helix chain 'B' and resid 320 through 322 No H-bonds generated for 'chain 'B' and resid 320 through 322' Processing helix chain 'B' and resid 337 through 348 removed outlier: 3.609A pdb=" N PHE B 345 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 43 removed outlier: 3.670A pdb=" N PHE D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 39 through 43' Processing helix chain 'D' and resid 71 through 75 Processing helix chain 'D' and resid 92 through 103 removed outlier: 3.756A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 127 No H-bonds generated for 'chain 'D' and resid 125 through 127' Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 170 through 174 removed outlier: 3.528A pdb=" N PHE D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 170 through 174' Processing helix chain 'D' and resid 229 through 244 removed outlier: 3.859A pdb=" N LYS D 238 " --> pdb=" O ASN D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.568A pdb=" N MET D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 294 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 310 through 315 removed outlier: 3.897A pdb=" N LYS D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL D 315 " --> pdb=" O GLY D 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 310 through 315' Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 337 through 348 removed outlier: 3.610A pdb=" N PHE D 345 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 43 Processing helix chain 'E' and resid 71 through 75 Processing helix chain 'E' and resid 92 through 103 Processing helix chain 'E' and resid 124 through 127 No H-bonds generated for 'chain 'E' and resid 124 through 127' Processing helix chain 'E' and resid 131 through 140 removed outlier: 5.162A pdb=" N LYS E 139 " --> pdb=" O ASN E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 174 No H-bonds generated for 'chain 'E' and resid 171 through 174' Processing helix chain 'E' and resid 229 through 244 removed outlier: 4.193A pdb=" N MET E 236 " --> pdb=" O TYR E 233 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP E 237 " --> pdb=" O ASN E 234 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP E 242 " --> pdb=" O ALA E 239 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER E 244 " --> pdb=" O THR E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.673A pdb=" N CYS E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.534A pdb=" N ILE E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 279 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS E 291 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 311 through 315 removed outlier: 4.018A pdb=" N VAL E 315 " --> pdb=" O GLY E 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 311 through 315' Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'E' and resid 337 through 346 Processing helix chain 'G' and resid 39 through 43 Processing helix chain 'G' and resid 71 through 75 Processing helix chain 'G' and resid 92 through 103 Processing helix chain 'G' and resid 124 through 127 No H-bonds generated for 'chain 'G' and resid 124 through 127' Processing helix chain 'G' and resid 131 through 140 removed outlier: 5.163A pdb=" N LYS G 139 " --> pdb=" O ASN G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 174 No H-bonds generated for 'chain 'G' and resid 171 through 174' Processing helix chain 'G' and resid 229 through 244 removed outlier: 4.192A pdb=" N MET G 236 " --> pdb=" O TYR G 233 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP G 237 " --> pdb=" O ASN G 234 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP G 242 " --> pdb=" O ALA G 239 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER G 244 " --> pdb=" O THR G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 261 removed outlier: 3.672A pdb=" N CYS G 259 " --> pdb=" O LEU G 255 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU G 260 " --> pdb=" O MET G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 295 removed outlier: 3.534A pdb=" N ILE G 278 " --> pdb=" O LYS G 274 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS G 279 " --> pdb=" O LYS G 275 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS G 291 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU G 295 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 302 Processing helix chain 'G' and resid 311 through 315 removed outlier: 4.018A pdb=" N VAL G 315 " --> pdb=" O GLY G 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 311 through 315' Processing helix chain 'G' and resid 321 through 323 No H-bonds generated for 'chain 'G' and resid 321 through 323' Processing helix chain 'G' and resid 337 through 346 Processing helix chain 'H' and resid 39 through 43 removed outlier: 3.520A pdb=" N PHE H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 39 through 43' Processing helix chain 'H' and resid 50 through 52 No H-bonds generated for 'chain 'H' and resid 50 through 52' Processing helix chain 'H' and resid 71 through 75 removed outlier: 3.561A pdb=" N ARG H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 75' Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.658A pdb=" N ALA H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 127 No H-bonds generated for 'chain 'H' and resid 124 through 127' Processing helix chain 'H' and resid 131 through 140 Processing helix chain 'H' and resid 170 through 174 Processing helix chain 'H' and resid 181 through 183 No H-bonds generated for 'chain 'H' and resid 181 through 183' Processing helix chain 'H' and resid 218 through 220 No H-bonds generated for 'chain 'H' and resid 218 through 220' Processing helix chain 'H' and resid 229 through 243 removed outlier: 3.519A pdb=" N ASP H 237 " --> pdb=" O TYR H 233 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS H 238 " --> pdb=" O ASN H 234 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN H 243 " --> pdb=" O ALA H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 261 removed outlier: 3.521A pdb=" N MET H 256 " --> pdb=" O THR H 252 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU H 260 " --> pdb=" O MET H 256 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU H 261 " --> pdb=" O LEU H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 293 removed outlier: 4.034A pdb=" N LYS H 291 " --> pdb=" O ASN H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 302 Processing helix chain 'H' and resid 311 through 316 removed outlier: 4.167A pdb=" N VAL H 315 " --> pdb=" O GLY H 311 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU H 316 " --> pdb=" O GLY H 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 311 through 316' Processing helix chain 'H' and resid 320 through 323 removed outlier: 3.621A pdb=" N ILE H 323 " --> pdb=" O LEU H 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 320 through 323' Processing helix chain 'H' and resid 335 through 348 removed outlier: 4.107A pdb=" N ASN H 338 " --> pdb=" O GLU H 335 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE H 340 " --> pdb=" O ALA H 337 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU H 344 " --> pdb=" O GLY H 341 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE H 345 " --> pdb=" O TYR H 342 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN H 348 " --> pdb=" O PHE H 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 43 removed outlier: 3.520A pdb=" N PHE J 43 " --> pdb=" O LEU J 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 39 through 43' Processing helix chain 'J' and resid 50 through 52 No H-bonds generated for 'chain 'J' and resid 50 through 52' Processing helix chain 'J' and resid 71 through 75 removed outlier: 3.561A pdb=" N ARG J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 71 through 75' Processing helix chain 'J' and resid 92 through 105 removed outlier: 3.658A pdb=" N ALA J 101 " --> pdb=" O LEU J 97 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU J 102 " --> pdb=" O LEU J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 127 No H-bonds generated for 'chain 'J' and resid 124 through 127' Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 170 through 174 Processing helix chain 'J' and resid 181 through 183 No H-bonds generated for 'chain 'J' and resid 181 through 183' Processing helix chain 'J' and resid 218 through 220 No H-bonds generated for 'chain 'J' and resid 218 through 220' Processing helix chain 'J' and resid 229 through 243 removed outlier: 3.519A pdb=" N ASP J 237 " --> pdb=" O TYR J 233 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS J 238 " --> pdb=" O ASN J 234 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP J 242 " --> pdb=" O LYS J 238 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN J 243 " --> pdb=" O ALA J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 261 removed outlier: 3.521A pdb=" N MET J 256 " --> pdb=" O THR J 252 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU J 260 " --> pdb=" O MET J 256 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU J 261 " --> pdb=" O LEU J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 293 removed outlier: 4.034A pdb=" N LYS J 291 " --> pdb=" O ASN J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 302 Processing helix chain 'J' and resid 311 through 316 removed outlier: 4.167A pdb=" N VAL J 315 " --> pdb=" O GLY J 311 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU J 316 " --> pdb=" O GLY J 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 311 through 316' Processing helix chain 'J' and resid 320 through 323 removed outlier: 3.621A pdb=" N ILE J 323 " --> pdb=" O LEU J 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 320 through 323' Processing helix chain 'J' and resid 335 through 348 removed outlier: 4.107A pdb=" N ASN J 338 " --> pdb=" O GLU J 335 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE J 340 " --> pdb=" O ALA J 337 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU J 344 " --> pdb=" O GLY J 341 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE J 345 " --> pdb=" O TYR J 342 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN J 348 " --> pdb=" O PHE J 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 43 removed outlier: 3.515A pdb=" N PHE K 43 " --> pdb=" O LEU K 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 43' Processing helix chain 'K' and resid 71 through 74 No H-bonds generated for 'chain 'K' and resid 71 through 74' Processing helix chain 'K' and resid 92 through 105 Processing helix chain 'K' and resid 126 through 129 No H-bonds generated for 'chain 'K' and resid 126 through 129' Processing helix chain 'K' and resid 131 through 140 removed outlier: 3.635A pdb=" N LYS K 139 " --> pdb=" O ASN K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 174 Processing helix chain 'K' and resid 229 through 244 removed outlier: 3.552A pdb=" N TYR K 233 " --> pdb=" O ILE K 230 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR K 235 " --> pdb=" O ILE K 232 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET K 236 " --> pdb=" O TYR K 233 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP K 237 " --> pdb=" O ASN K 234 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 238 " --> pdb=" O THR K 235 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER K 244 " --> pdb=" O THR K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 261 removed outlier: 3.763A pdb=" N GLU K 260 " --> pdb=" O MET K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 295 removed outlier: 3.690A pdb=" N ILE K 278 " --> pdb=" O LYS K 274 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS K 279 " --> pdb=" O LYS K 275 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS K 291 " --> pdb=" O ASN K 287 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP K 293 " --> pdb=" O ILE K 289 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU K 295 " --> pdb=" O LYS K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 302 Processing helix chain 'K' and resid 311 through 314 No H-bonds generated for 'chain 'K' and resid 311 through 314' Processing helix chain 'K' and resid 320 through 323 removed outlier: 3.758A pdb=" N ILE K 323 " --> pdb=" O LEU K 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 320 through 323' Processing helix chain 'K' and resid 337 through 348 removed outlier: 3.520A pdb=" N PHE K 345 " --> pdb=" O GLY K 341 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN K 348 " --> pdb=" O GLU K 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 39 through 43 removed outlier: 3.514A pdb=" N PHE M 43 " --> pdb=" O LEU M 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 39 through 43' Processing helix chain 'M' and resid 71 through 74 No H-bonds generated for 'chain 'M' and resid 71 through 74' Processing helix chain 'M' and resid 92 through 105 Processing helix chain 'M' and resid 126 through 129 No H-bonds generated for 'chain 'M' and resid 126 through 129' Processing helix chain 'M' and resid 131 through 140 removed outlier: 3.635A pdb=" N LYS M 139 " --> pdb=" O ASN M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 229 through 244 removed outlier: 3.552A pdb=" N TYR M 233 " --> pdb=" O ILE M 230 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR M 235 " --> pdb=" O ILE M 232 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET M 236 " --> pdb=" O TYR M 233 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP M 237 " --> pdb=" O ASN M 234 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS M 238 " --> pdb=" O THR M 235 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER M 244 " --> pdb=" O THR M 241 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 261 removed outlier: 3.763A pdb=" N GLU M 260 " --> pdb=" O MET M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 295 removed outlier: 3.690A pdb=" N ILE M 278 " --> pdb=" O LYS M 274 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS M 279 " --> pdb=" O LYS M 275 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS M 291 " --> pdb=" O ASN M 287 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP M 293 " --> pdb=" O ILE M 289 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU M 295 " --> pdb=" O LYS M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 298 through 302 Processing helix chain 'M' and resid 311 through 314 No H-bonds generated for 'chain 'M' and resid 311 through 314' Processing helix chain 'M' and resid 320 through 323 removed outlier: 3.757A pdb=" N ILE M 323 " --> pdb=" O LEU M 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 320 through 323' Processing helix chain 'M' and resid 337 through 348 removed outlier: 3.520A pdb=" N PHE M 345 " --> pdb=" O GLY M 341 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN M 348 " --> pdb=" O GLU M 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 43 removed outlier: 3.731A pdb=" N PHE N 43 " --> pdb=" O LEU N 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 39 through 43' Processing helix chain 'N' and resid 71 through 75 Processing helix chain 'N' and resid 92 through 103 Processing helix chain 'N' and resid 126 through 129 No H-bonds generated for 'chain 'N' and resid 126 through 129' Processing helix chain 'N' and resid 131 through 137 Processing helix chain 'N' and resid 171 through 174 No H-bonds generated for 'chain 'N' and resid 171 through 174' Processing helix chain 'N' and resid 229 through 244 removed outlier: 3.560A pdb=" N TYR N 233 " --> pdb=" O ILE N 230 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET N 236 " --> pdb=" O TYR N 233 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS N 238 " --> pdb=" O THR N 235 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA N 239 " --> pdb=" O MET N 236 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP N 242 " --> pdb=" O ALA N 239 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER N 244 " --> pdb=" O THR N 241 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 261 removed outlier: 3.732A pdb=" N CYS N 259 " --> pdb=" O LEU N 255 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU N 260 " --> pdb=" O MET N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 295 removed outlier: 3.860A pdb=" N LYS N 291 " --> pdb=" O ASN N 287 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU N 295 " --> pdb=" O LYS N 291 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 302 Processing helix chain 'N' and resid 313 through 315 No H-bonds generated for 'chain 'N' and resid 313 through 315' Processing helix chain 'N' and resid 337 through 348 removed outlier: 3.545A pdb=" N GLY N 341 " --> pdb=" O ALA N 337 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS N 347 " --> pdb=" O LEU N 343 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLN N 348 " --> pdb=" O GLU N 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 43 removed outlier: 3.730A pdb=" N PHE P 43 " --> pdb=" O LEU P 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 39 through 43' Processing helix chain 'P' and resid 71 through 75 Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 126 through 129 No H-bonds generated for 'chain 'P' and resid 126 through 129' Processing helix chain 'P' and resid 131 through 137 Processing helix chain 'P' and resid 171 through 174 No H-bonds generated for 'chain 'P' and resid 171 through 174' Processing helix chain 'P' and resid 229 through 244 removed outlier: 3.561A pdb=" N TYR P 233 " --> pdb=" O ILE P 230 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET P 236 " --> pdb=" O TYR P 233 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS P 238 " --> pdb=" O THR P 235 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA P 239 " --> pdb=" O MET P 236 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP P 242 " --> pdb=" O ALA P 239 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER P 244 " --> pdb=" O THR P 241 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 261 removed outlier: 3.733A pdb=" N CYS P 259 " --> pdb=" O LEU P 255 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU P 260 " --> pdb=" O MET P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 274 through 295 removed outlier: 3.860A pdb=" N LYS P 291 " --> pdb=" O ASN P 287 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU P 295 " --> pdb=" O LYS P 291 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 302 Processing helix chain 'P' and resid 313 through 315 No H-bonds generated for 'chain 'P' and resid 313 through 315' Processing helix chain 'P' and resid 337 through 348 removed outlier: 3.545A pdb=" N GLY P 341 " --> pdb=" O ALA P 337 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS P 347 " --> pdb=" O LEU P 343 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLN P 348 " --> pdb=" O GLU P 344 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 43 removed outlier: 3.568A pdb=" N PHE Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 39 through 43' Processing helix chain 'Q' and resid 50 through 52 No H-bonds generated for 'chain 'Q' and resid 50 through 52' Processing helix chain 'Q' and resid 71 through 74 No H-bonds generated for 'chain 'Q' and resid 71 through 74' Processing helix chain 'Q' and resid 92 through 105 removed outlier: 3.775A pdb=" N ALA Q 101 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU Q 102 " --> pdb=" O LEU Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 140 removed outlier: 3.548A pdb=" N MET Q 137 " --> pdb=" O ALA Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 174 Processing helix chain 'Q' and resid 181 through 183 No H-bonds generated for 'chain 'Q' and resid 181 through 183' Processing helix chain 'Q' and resid 229 through 244 removed outlier: 3.680A pdb=" N TYR Q 233 " --> pdb=" O ILE Q 230 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET Q 236 " --> pdb=" O TYR Q 233 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP Q 237 " --> pdb=" O ASN Q 234 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE Q 240 " --> pdb=" O ASP Q 237 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP Q 242 " --> pdb=" O ALA Q 239 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER Q 244 " --> pdb=" O THR Q 241 " (cutoff:3.500A) Processing helix chain 'Q' and resid 252 through 261 removed outlier: 3.676A pdb=" N GLU Q 260 " --> pdb=" O MET Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 274 through 294 Processing helix chain 'Q' and resid 298 through 300 No H-bonds generated for 'chain 'Q' and resid 298 through 300' Processing helix chain 'Q' and resid 310 through 315 Processing helix chain 'Q' and resid 317 through 323 removed outlier: 4.278A pdb=" N LEU Q 322 " --> pdb=" O ASN Q 318 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE Q 323 " --> pdb=" O HIS Q 319 " (cutoff:3.500A) Processing helix chain 'Q' and resid 337 through 348 removed outlier: 3.501A pdb=" N PHE Q 345 " --> pdb=" O GLY Q 341 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN Q 348 " --> pdb=" O GLU Q 344 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 43 Processing helix chain 'b' and resid 71 through 74 No H-bonds generated for 'chain 'b' and resid 71 through 74' Processing helix chain 'b' and resid 92 through 104 Processing helix chain 'b' and resid 131 through 140 Processing helix chain 'b' and resid 170 through 173 No H-bonds generated for 'chain 'b' and resid 170 through 173' Processing helix chain 'b' and resid 229 through 244 removed outlier: 3.555A pdb=" N TYR b 233 " --> pdb=" O ILE b 230 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN b 234 " --> pdb=" O ASN b 231 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET b 236 " --> pdb=" O TYR b 233 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP b 237 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS b 238 " --> pdb=" O THR b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 252 through 261 removed outlier: 3.785A pdb=" N GLU b 260 " --> pdb=" O MET b 256 " (cutoff:3.500A) Processing helix chain 'b' and resid 274 through 295 removed outlier: 3.619A pdb=" N ILE b 288 " --> pdb=" O LEU b 284 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE b 289 " --> pdb=" O SER b 285 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 302 Processing helix chain 'b' and resid 310 through 315 removed outlier: 3.512A pdb=" N LYS b 314 " --> pdb=" O GLY b 310 " (cutoff:3.500A) Processing helix chain 'b' and resid 337 through 347 removed outlier: 3.953A pdb=" N PHE b 345 " --> pdb=" O GLY b 341 " (cutoff:3.500A) Processing helix chain 'c' and resid 39 through 43 removed outlier: 3.528A pdb=" N PHE c 43 " --> pdb=" O LEU c 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 39 through 43' Processing helix chain 'c' and resid 71 through 74 No H-bonds generated for 'chain 'c' and resid 71 through 74' Processing helix chain 'c' and resid 92 through 103 removed outlier: 3.653A pdb=" N ALA c 101 " --> pdb=" O LEU c 97 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU c 102 " --> pdb=" O LEU c 98 " (cutoff:3.500A) Processing helix chain 'c' and resid 131 through 139 Processing helix chain 'c' and resid 171 through 174 No H-bonds generated for 'chain 'c' and resid 171 through 174' Processing helix chain 'c' and resid 181 through 183 No H-bonds generated for 'chain 'c' and resid 181 through 183' Processing helix chain 'c' and resid 218 through 220 No H-bonds generated for 'chain 'c' and resid 218 through 220' Processing helix chain 'c' and resid 229 through 244 removed outlier: 3.666A pdb=" N LYS c 238 " --> pdb=" O ASN c 234 " (cutoff:3.500A) Processing helix chain 'c' and resid 252 through 261 removed outlier: 3.560A pdb=" N MET c 256 " --> pdb=" O THR c 252 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU c 261 " --> pdb=" O LEU c 257 " (cutoff:3.500A) Processing helix chain 'c' and resid 274 through 295 removed outlier: 3.597A pdb=" N ILE c 278 " --> pdb=" O LYS c 274 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS c 291 " --> pdb=" O ASN c 287 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU c 295 " --> pdb=" O LYS c 291 " (cutoff:3.500A) Processing helix chain 'c' and resid 298 through 302 Processing helix chain 'c' and resid 311 through 315 removed outlier: 3.915A pdb=" N VAL c 315 " --> pdb=" O GLY c 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 311 through 315' Processing helix chain 'c' and resid 321 through 323 No H-bonds generated for 'chain 'c' and resid 321 through 323' Processing helix chain 'c' and resid 337 through 348 removed outlier: 3.697A pdb=" N PHE c 345 " --> pdb=" O GLY c 341 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN c 348 " --> pdb=" O GLU c 344 " (cutoff:3.500A) Processing helix chain 'e' and resid 39 through 43 removed outlier: 3.578A pdb=" N PHE e 43 " --> pdb=" O LEU e 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 39 through 43' Processing helix chain 'e' and resid 50 through 52 No H-bonds generated for 'chain 'e' and resid 50 through 52' Processing helix chain 'e' and resid 71 through 74 No H-bonds generated for 'chain 'e' and resid 71 through 74' Processing helix chain 'e' and resid 92 through 105 removed outlier: 3.709A pdb=" N LEU e 104 " --> pdb=" O THR e 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 140 removed outlier: 4.685A pdb=" N GLN e 132 " --> pdb=" O ILE e 128 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA e 133 " --> pdb=" O LYS e 129 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET e 137 " --> pdb=" O ALA e 133 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS e 139 " --> pdb=" O ASN e 135 " (cutoff:3.500A) Processing helix chain 'e' and resid 171 through 174 No H-bonds generated for 'chain 'e' and resid 171 through 174' Processing helix chain 'e' and resid 178 through 181 No H-bonds generated for 'chain 'e' and resid 178 through 181' Processing helix chain 'e' and resid 230 through 244 removed outlier: 3.695A pdb=" N MET e 236 " --> pdb=" O ILE e 232 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP e 237 " --> pdb=" O TYR e 233 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS e 238 " --> pdb=" O ASN e 234 " (cutoff:3.500A) Processing helix chain 'e' and resid 254 through 261 removed outlier: 3.961A pdb=" N CYS e 259 " --> pdb=" O LEU e 255 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU e 260 " --> pdb=" O MET e 256 " (cutoff:3.500A) Processing helix chain 'e' and resid 274 through 292 removed outlier: 4.315A pdb=" N LYS e 291 " --> pdb=" O ASN e 287 " (cutoff:3.500A) Processing helix chain 'e' and resid 298 through 302 Processing helix chain 'e' and resid 311 through 314 No H-bonds generated for 'chain 'e' and resid 311 through 314' Processing helix chain 'e' and resid 320 through 323 removed outlier: 3.612A pdb=" N ILE e 323 " --> pdb=" O LEU e 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 320 through 323' Processing helix chain 'e' and resid 335 through 344 removed outlier: 4.124A pdb=" N ASN e 338 " --> pdb=" O GLU e 335 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA e 339 " --> pdb=" O PHE e 336 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE e 340 " --> pdb=" O ALA e 337 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY e 341 " --> pdb=" O ASN e 338 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU e 344 " --> pdb=" O GLY e 341 " (cutoff:3.500A) Processing helix chain 'f' and resid 39 through 43 Processing helix chain 'f' and resid 71 through 74 No H-bonds generated for 'chain 'f' and resid 71 through 74' Processing helix chain 'f' and resid 92 through 104 Processing helix chain 'f' and resid 131 through 140 Processing helix chain 'f' and resid 170 through 173 No H-bonds generated for 'chain 'f' and resid 170 through 173' Processing helix chain 'f' and resid 229 through 244 removed outlier: 3.555A pdb=" N TYR f 233 " --> pdb=" O ILE f 230 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN f 234 " --> pdb=" O ASN f 231 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET f 236 " --> pdb=" O TYR f 233 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP f 237 " --> pdb=" O ASN f 234 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS f 238 " --> pdb=" O THR f 235 " (cutoff:3.500A) Processing helix chain 'f' and resid 252 through 261 removed outlier: 3.786A pdb=" N GLU f 260 " --> pdb=" O MET f 256 " (cutoff:3.500A) Processing helix chain 'f' and resid 274 through 295 removed outlier: 3.619A pdb=" N ILE f 288 " --> pdb=" O LEU f 284 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE f 289 " --> pdb=" O SER f 285 " (cutoff:3.500A) Processing helix chain 'f' and resid 298 through 302 Processing helix chain 'f' and resid 310 through 315 removed outlier: 3.512A pdb=" N LYS f 314 " --> pdb=" O GLY f 310 " (cutoff:3.500A) Processing helix chain 'f' and resid 337 through 347 removed outlier: 3.953A pdb=" N PHE f 345 " --> pdb=" O GLY f 341 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 43 Processing helix chain 'h' and resid 50 through 52 No H-bonds generated for 'chain 'h' and resid 50 through 52' Processing helix chain 'h' and resid 71 through 74 No H-bonds generated for 'chain 'h' and resid 71 through 74' Processing helix chain 'h' and resid 92 through 103 Processing helix chain 'h' and resid 126 through 129 No H-bonds generated for 'chain 'h' and resid 126 through 129' Processing helix chain 'h' and resid 131 through 140 Processing helix chain 'h' and resid 170 through 173 No H-bonds generated for 'chain 'h' and resid 170 through 173' Processing helix chain 'h' and resid 181 through 183 No H-bonds generated for 'chain 'h' and resid 181 through 183' Processing helix chain 'h' and resid 229 through 244 removed outlier: 3.732A pdb=" N ASP h 237 " --> pdb=" O TYR h 233 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS h 238 " --> pdb=" O ASN h 234 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA h 239 " --> pdb=" O THR h 235 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE h 240 " --> pdb=" O MET h 236 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR h 241 " --> pdb=" O ASP h 237 " (cutoff:3.500A) Processing helix chain 'h' and resid 252 through 261 removed outlier: 4.073A pdb=" N MET h 256 " --> pdb=" O THR h 252 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU h 257 " --> pdb=" O GLU h 253 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS h 259 " --> pdb=" O LEU h 255 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU h 260 " --> pdb=" O MET h 256 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU h 261 " --> pdb=" O LEU h 257 " (cutoff:3.500A) Processing helix chain 'h' and resid 274 through 295 removed outlier: 3.789A pdb=" N LYS h 291 " --> pdb=" O ASN h 287 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP h 293 " --> pdb=" O ILE h 289 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY h 294 " --> pdb=" O ASN h 290 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU h 295 " --> pdb=" O LYS h 291 " (cutoff:3.500A) Processing helix chain 'h' and resid 310 through 315 Processing helix chain 'h' and resid 319 through 323 removed outlier: 4.577A pdb=" N LEU h 322 " --> pdb=" O HIS h 319 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE h 323 " --> pdb=" O LEU h 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 319 through 323' Processing helix chain 'h' and resid 335 through 345 removed outlier: 3.878A pdb=" N ASN h 338 " --> pdb=" O GLU h 335 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA h 339 " --> pdb=" O PHE h 336 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE h 340 " --> pdb=" O ALA h 337 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU h 344 " --> pdb=" O GLY h 341 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE h 345 " --> pdb=" O TYR h 342 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 43 removed outlier: 3.579A pdb=" N PHE i 43 " --> pdb=" O LEU i 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 39 through 43' Processing helix chain 'i' and resid 50 through 52 No H-bonds generated for 'chain 'i' and resid 50 through 52' Processing helix chain 'i' and resid 71 through 74 No H-bonds generated for 'chain 'i' and resid 71 through 74' Processing helix chain 'i' and resid 92 through 105 removed outlier: 3.709A pdb=" N LEU i 104 " --> pdb=" O THR i 100 " (cutoff:3.500A) Processing helix chain 'i' and resid 127 through 140 removed outlier: 4.685A pdb=" N GLN i 132 " --> pdb=" O ILE i 128 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA i 133 " --> pdb=" O LYS i 129 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET i 137 " --> pdb=" O ALA i 133 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS i 139 " --> pdb=" O ASN i 135 " (cutoff:3.500A) Processing helix chain 'i' and resid 171 through 174 No H-bonds generated for 'chain 'i' and resid 171 through 174' Processing helix chain 'i' and resid 178 through 181 No H-bonds generated for 'chain 'i' and resid 178 through 181' Processing helix chain 'i' and resid 230 through 244 removed outlier: 3.696A pdb=" N MET i 236 " --> pdb=" O ILE i 232 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP i 237 " --> pdb=" O TYR i 233 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS i 238 " --> pdb=" O ASN i 234 " (cutoff:3.500A) Processing helix chain 'i' and resid 254 through 261 removed outlier: 3.962A pdb=" N CYS i 259 " --> pdb=" O LEU i 255 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU i 260 " --> pdb=" O MET i 256 " (cutoff:3.500A) Processing helix chain 'i' and resid 274 through 292 removed outlier: 4.315A pdb=" N LYS i 291 " --> pdb=" O ASN i 287 " (cutoff:3.500A) Processing helix chain 'i' and resid 298 through 302 Processing helix chain 'i' and resid 311 through 314 No H-bonds generated for 'chain 'i' and resid 311 through 314' Processing helix chain 'i' and resid 320 through 323 removed outlier: 3.611A pdb=" N ILE i 323 " --> pdb=" O LEU i 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 320 through 323' Processing helix chain 'i' and resid 335 through 344 removed outlier: 4.124A pdb=" N ASN i 338 " --> pdb=" O GLU i 335 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA i 339 " --> pdb=" O PHE i 336 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE i 340 " --> pdb=" O ALA i 337 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY i 341 " --> pdb=" O ASN i 338 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU i 344 " --> pdb=" O GLY i 341 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 43 No H-bonds generated for 'chain 'k' and resid 40 through 43' Processing helix chain 'k' and resid 71 through 74 No H-bonds generated for 'chain 'k' and resid 71 through 74' Processing helix chain 'k' and resid 92 through 105 removed outlier: 3.504A pdb=" N LEU k 102 " --> pdb=" O LEU k 98 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU k 105 " --> pdb=" O ALA k 101 " (cutoff:3.500A) Processing helix chain 'k' and resid 131 through 140 removed outlier: 3.545A pdb=" N ASP k 136 " --> pdb=" O GLN k 132 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS k 139 " --> pdb=" O ASN k 135 " (cutoff:3.500A) Processing helix chain 'k' and resid 171 through 174 No H-bonds generated for 'chain 'k' and resid 171 through 174' Processing helix chain 'k' and resid 178 through 183 removed outlier: 3.589A pdb=" N SER k 182 " --> pdb=" O ASN k 178 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER k 183 " --> pdb=" O ASN k 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 178 through 183' Processing helix chain 'k' and resid 218 through 220 No H-bonds generated for 'chain 'k' and resid 218 through 220' Processing helix chain 'k' and resid 229 through 244 removed outlier: 3.714A pdb=" N ASP k 237 " --> pdb=" O TYR k 233 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS k 238 " --> pdb=" O ASN k 234 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR k 241 " --> pdb=" O ASP k 237 " (cutoff:3.500A) Processing helix chain 'k' and resid 254 through 258 removed outlier: 3.645A pdb=" N LEU k 258 " --> pdb=" O GLN k 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 254 through 258' Processing helix chain 'k' and resid 274 through 293 removed outlier: 3.530A pdb=" N THR k 283 " --> pdb=" O LYS k 279 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU k 284 " --> pdb=" O ALA k 280 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS k 291 " --> pdb=" O ASN k 287 " (cutoff:3.500A) Processing helix chain 'k' and resid 298 through 302 Processing helix chain 'k' and resid 310 through 316 Processing helix chain 'k' and resid 320 through 323 removed outlier: 4.098A pdb=" N ILE k 323 " --> pdb=" O LEU k 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 320 through 323' Processing helix chain 'k' and resid 337 through 341 Processing helix chain 'k' and resid 345 through 348 removed outlier: 3.659A pdb=" N GLN k 348 " --> pdb=" O PHE k 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 345 through 348' Processing helix chain 'l' and resid 39 through 43 Processing helix chain 'l' and resid 50 through 52 No H-bonds generated for 'chain 'l' and resid 50 through 52' Processing helix chain 'l' and resid 71 through 74 No H-bonds generated for 'chain 'l' and resid 71 through 74' Processing helix chain 'l' and resid 92 through 103 Processing helix chain 'l' and resid 126 through 129 No H-bonds generated for 'chain 'l' and resid 126 through 129' Processing helix chain 'l' and resid 131 through 140 Processing helix chain 'l' and resid 170 through 173 No H-bonds generated for 'chain 'l' and resid 170 through 173' Processing helix chain 'l' and resid 181 through 183 No H-bonds generated for 'chain 'l' and resid 181 through 183' Processing helix chain 'l' and resid 229 through 244 removed outlier: 3.732A pdb=" N ASP l 237 " --> pdb=" O TYR l 233 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS l 238 " --> pdb=" O ASN l 234 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA l 239 " --> pdb=" O THR l 235 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE l 240 " --> pdb=" O MET l 236 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR l 241 " --> pdb=" O ASP l 237 " (cutoff:3.500A) Processing helix chain 'l' and resid 252 through 261 removed outlier: 4.073A pdb=" N MET l 256 " --> pdb=" O THR l 252 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU l 257 " --> pdb=" O GLU l 253 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS l 259 " --> pdb=" O LEU l 255 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU l 260 " --> pdb=" O MET l 256 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU l 261 " --> pdb=" O LEU l 257 " (cutoff:3.500A) Processing helix chain 'l' and resid 274 through 295 removed outlier: 3.789A pdb=" N LYS l 291 " --> pdb=" O ASN l 287 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP l 293 " --> pdb=" O ILE l 289 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY l 294 " --> pdb=" O ASN l 290 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU l 295 " --> pdb=" O LYS l 291 " (cutoff:3.500A) Processing helix chain 'l' and resid 310 through 315 Processing helix chain 'l' and resid 319 through 323 removed outlier: 4.577A pdb=" N LEU l 322 " --> pdb=" O HIS l 319 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE l 323 " --> pdb=" O LEU l 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 319 through 323' Processing helix chain 'l' and resid 335 through 345 removed outlier: 3.878A pdb=" N ASN l 338 " --> pdb=" O GLU l 335 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA l 339 " --> pdb=" O PHE l 336 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE l 340 " --> pdb=" O ALA l 337 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU l 344 " --> pdb=" O GLY l 341 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE l 345 " --> pdb=" O TYR l 342 " (cutoff:3.500A) Processing helix chain 'n' and resid 39 through 43 removed outlier: 3.602A pdb=" N PHE n 43 " --> pdb=" O LEU n 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 39 through 43' Processing helix chain 'n' and resid 50 through 52 No H-bonds generated for 'chain 'n' and resid 50 through 52' Processing helix chain 'n' and resid 71 through 74 No H-bonds generated for 'chain 'n' and resid 71 through 74' Processing helix chain 'n' and resid 92 through 105 removed outlier: 3.586A pdb=" N VAL n 96 " --> pdb=" O GLU n 92 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU n 97 " --> pdb=" O GLU n 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU n 105 " --> pdb=" O ALA n 101 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 129 No H-bonds generated for 'chain 'n' and resid 126 through 129' Processing helix chain 'n' and resid 131 through 140 Processing helix chain 'n' and resid 170 through 174 Processing helix chain 'n' and resid 181 through 183 No H-bonds generated for 'chain 'n' and resid 181 through 183' Processing helix chain 'n' and resid 230 through 244 removed outlier: 4.019A pdb=" N ASP n 237 " --> pdb=" O TYR n 233 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS n 238 " --> pdb=" O ASN n 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA n 239 " --> pdb=" O THR n 235 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP n 242 " --> pdb=" O LYS n 238 " (cutoff:3.500A) Processing helix chain 'n' and resid 254 through 261 removed outlier: 3.565A pdb=" N CYS n 259 " --> pdb=" O LEU n 255 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU n 260 " --> pdb=" O MET n 256 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU n 261 " --> pdb=" O LEU n 257 " (cutoff:3.500A) Processing helix chain 'n' and resid 274 through 295 removed outlier: 3.585A pdb=" N ILE n 278 " --> pdb=" O LYS n 274 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER n 285 " --> pdb=" O ARG n 281 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS n 291 " --> pdb=" O ASN n 287 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU n 295 " --> pdb=" O LYS n 291 " (cutoff:3.500A) Processing helix chain 'n' and resid 298 through 302 removed outlier: 3.558A pdb=" N ASN n 301 " --> pdb=" O SER n 298 " (cutoff:3.500A) Processing helix chain 'n' and resid 311 through 315 Processing helix chain 'n' and resid 320 through 323 removed outlier: 3.652A pdb=" N ILE n 323 " --> pdb=" O LEU n 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 320 through 323' Processing helix chain 'n' and resid 337 through 346 removed outlier: 3.628A pdb=" N PHE n 345 " --> pdb=" O GLY n 341 " (cutoff:3.500A) Processing helix chain 'o' and resid 40 through 43 No H-bonds generated for 'chain 'o' and resid 40 through 43' Processing helix chain 'o' and resid 71 through 74 No H-bonds generated for 'chain 'o' and resid 71 through 74' Processing helix chain 'o' and resid 92 through 105 removed outlier: 3.504A pdb=" N LEU o 102 " --> pdb=" O LEU o 98 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU o 105 " --> pdb=" O ALA o 101 " (cutoff:3.500A) Processing helix chain 'o' and resid 131 through 140 removed outlier: 3.545A pdb=" N ASP o 136 " --> pdb=" O GLN o 132 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS o 139 " --> pdb=" O ASN o 135 " (cutoff:3.500A) Processing helix chain 'o' and resid 171 through 174 No H-bonds generated for 'chain 'o' and resid 171 through 174' Processing helix chain 'o' and resid 178 through 183 removed outlier: 3.589A pdb=" N SER o 182 " --> pdb=" O ASN o 178 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SER o 183 " --> pdb=" O ASN o 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 178 through 183' Processing helix chain 'o' and resid 218 through 220 No H-bonds generated for 'chain 'o' and resid 218 through 220' Processing helix chain 'o' and resid 229 through 244 removed outlier: 3.715A pdb=" N ASP o 237 " --> pdb=" O TYR o 233 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS o 238 " --> pdb=" O ASN o 234 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR o 241 " --> pdb=" O ASP o 237 " (cutoff:3.500A) Processing helix chain 'o' and resid 254 through 258 removed outlier: 3.646A pdb=" N LEU o 258 " --> pdb=" O GLN o 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 254 through 258' Processing helix chain 'o' and resid 274 through 293 removed outlier: 3.529A pdb=" N THR o 283 " --> pdb=" O LYS o 279 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU o 284 " --> pdb=" O ALA o 280 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS o 291 " --> pdb=" O ASN o 287 " (cutoff:3.500A) Processing helix chain 'o' and resid 298 through 302 Processing helix chain 'o' and resid 310 through 316 Processing helix chain 'o' and resid 320 through 323 removed outlier: 4.098A pdb=" N ILE o 323 " --> pdb=" O LEU o 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 320 through 323' Processing helix chain 'o' and resid 337 through 341 Processing helix chain 'o' and resid 345 through 348 removed outlier: 3.659A pdb=" N GLN o 348 " --> pdb=" O PHE o 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 345 through 348' Processing helix chain 'q' and resid 39 through 43 removed outlier: 3.629A pdb=" N PHE q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 39 through 43' Processing helix chain 'q' and resid 71 through 75 Processing helix chain 'q' and resid 92 through 105 removed outlier: 3.537A pdb=" N LEU q 97 " --> pdb=" O GLU q 93 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA q 101 " --> pdb=" O LEU q 97 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY q 103 " --> pdb=" O ALA q 99 " (cutoff:3.500A) Processing helix chain 'q' and resid 125 through 129 removed outlier: 4.033A pdb=" N ILE q 128 " --> pdb=" O GLU q 125 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS q 129 " --> pdb=" O HIS q 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 125 through 129' Processing helix chain 'q' and resid 131 through 140 removed outlier: 3.609A pdb=" N MET q 137 " --> pdb=" O ALA q 133 " (cutoff:3.500A) Processing helix chain 'q' and resid 171 through 174 No H-bonds generated for 'chain 'q' and resid 171 through 174' Processing helix chain 'q' and resid 181 through 184 No H-bonds generated for 'chain 'q' and resid 181 through 184' Processing helix chain 'q' and resid 229 through 243 removed outlier: 3.860A pdb=" N TYR q 233 " --> pdb=" O ILE q 230 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET q 236 " --> pdb=" O TYR q 233 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA q 239 " --> pdb=" O MET q 236 " (cutoff:3.500A) Processing helix chain 'q' and resid 252 through 261 removed outlier: 3.597A pdb=" N MET q 256 " --> pdb=" O THR q 252 " (cutoff:3.500A) Processing helix chain 'q' and resid 275 through 295 removed outlier: 3.647A pdb=" N LYS q 279 " --> pdb=" O LYS q 275 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY q 294 " --> pdb=" O ASN q 290 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU q 295 " --> pdb=" O LYS q 291 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 302 Processing helix chain 'q' and resid 311 through 315 removed outlier: 4.033A pdb=" N VAL q 315 " --> pdb=" O GLY q 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 311 through 315' Processing helix chain 'q' and resid 320 through 323 removed outlier: 3.725A pdb=" N ILE q 323 " --> pdb=" O LEU q 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 320 through 323' Processing helix chain 'q' and resid 337 through 343 Processing helix chain 'r' and resid 39 through 43 removed outlier: 3.603A pdb=" N PHE r 43 " --> pdb=" O LEU r 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 39 through 43' Processing helix chain 'r' and resid 50 through 52 No H-bonds generated for 'chain 'r' and resid 50 through 52' Processing helix chain 'r' and resid 71 through 74 No H-bonds generated for 'chain 'r' and resid 71 through 74' Processing helix chain 'r' and resid 92 through 105 removed outlier: 3.587A pdb=" N VAL r 96 " --> pdb=" O GLU r 92 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU r 97 " --> pdb=" O GLU r 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU r 105 " --> pdb=" O ALA r 101 " (cutoff:3.500A) Processing helix chain 'r' and resid 126 through 129 No H-bonds generated for 'chain 'r' and resid 126 through 129' Processing helix chain 'r' and resid 131 through 140 Processing helix chain 'r' and resid 170 through 174 Processing helix chain 'r' and resid 181 through 183 No H-bonds generated for 'chain 'r' and resid 181 through 183' Processing helix chain 'r' and resid 230 through 244 removed outlier: 4.019A pdb=" N ASP r 237 " --> pdb=" O TYR r 233 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS r 238 " --> pdb=" O ASN r 234 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA r 239 " --> pdb=" O THR r 235 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP r 242 " --> pdb=" O LYS r 238 " (cutoff:3.500A) Processing helix chain 'r' and resid 254 through 261 removed outlier: 3.565A pdb=" N CYS r 259 " --> pdb=" O LEU r 255 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU r 260 " --> pdb=" O MET r 256 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU r 261 " --> pdb=" O LEU r 257 " (cutoff:3.500A) Processing helix chain 'r' and resid 274 through 295 removed outlier: 3.585A pdb=" N ILE r 278 " --> pdb=" O LYS r 274 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER r 285 " --> pdb=" O ARG r 281 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS r 291 " --> pdb=" O ASN r 287 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU r 295 " --> pdb=" O LYS r 291 " (cutoff:3.500A) Processing helix chain 'r' and resid 298 through 302 removed outlier: 3.558A pdb=" N ASN r 301 " --> pdb=" O SER r 298 " (cutoff:3.500A) Processing helix chain 'r' and resid 311 through 315 Processing helix chain 'r' and resid 320 through 323 removed outlier: 3.652A pdb=" N ILE r 323 " --> pdb=" O LEU r 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 320 through 323' Processing helix chain 'r' and resid 337 through 346 removed outlier: 3.627A pdb=" N PHE r 345 " --> pdb=" O GLY r 341 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 43 Processing helix chain 't' and resid 50 through 52 No H-bonds generated for 'chain 't' and resid 50 through 52' Processing helix chain 't' and resid 71 through 74 No H-bonds generated for 'chain 't' and resid 71 through 74' Processing helix chain 't' and resid 92 through 105 removed outlier: 3.854A pdb=" N ALA t 101 " --> pdb=" O LEU t 97 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU t 102 " --> pdb=" O LEU t 98 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY t 103 " --> pdb=" O ALA t 99 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU t 104 " --> pdb=" O THR t 100 " (cutoff:3.500A) Processing helix chain 't' and resid 125 through 129 removed outlier: 3.827A pdb=" N LYS t 129 " --> pdb=" O GLU t 125 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 125 through 129' Processing helix chain 't' and resid 131 through 140 Processing helix chain 't' and resid 170 through 174 Processing helix chain 't' and resid 181 through 183 No H-bonds generated for 'chain 't' and resid 181 through 183' Processing helix chain 't' and resid 229 through 244 removed outlier: 3.507A pdb=" N ASN t 234 " --> pdb=" O ASN t 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET t 236 " --> pdb=" O TYR t 233 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP t 237 " --> pdb=" O ASN t 234 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA t 239 " --> pdb=" O MET t 236 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR t 241 " --> pdb=" O LYS t 238 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER t 244 " --> pdb=" O THR t 241 " (cutoff:3.500A) Processing helix chain 't' and resid 252 through 261 removed outlier: 3.653A pdb=" N MET t 256 " --> pdb=" O THR t 252 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS t 259 " --> pdb=" O LEU t 255 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU t 260 " --> pdb=" O MET t 256 " (cutoff:3.500A) Processing helix chain 't' and resid 274 through 294 removed outlier: 3.526A pdb=" N SER t 285 " --> pdb=" O ARG t 281 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR t 286 " --> pdb=" O LYS t 282 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS t 291 " --> pdb=" O ASN t 287 " (cutoff:3.500A) Processing helix chain 't' and resid 298 through 302 Processing helix chain 't' and resid 311 through 314 No H-bonds generated for 'chain 't' and resid 311 through 314' Processing helix chain 't' and resid 321 through 323 No H-bonds generated for 'chain 't' and resid 321 through 323' Processing helix chain 't' and resid 337 through 344 Processing helix chain 't' and resid 346 through 348 No H-bonds generated for 'chain 't' and resid 346 through 348' Processing helix chain 'u' and resid 39 through 43 removed outlier: 3.630A pdb=" N PHE u 43 " --> pdb=" O LEU u 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 39 through 43' Processing helix chain 'u' and resid 71 through 75 Processing helix chain 'u' and resid 92 through 105 removed outlier: 3.538A pdb=" N LEU u 97 " --> pdb=" O GLU u 93 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA u 101 " --> pdb=" O LEU u 97 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY u 103 " --> pdb=" O ALA u 99 " (cutoff:3.500A) Processing helix chain 'u' and resid 125 through 129 removed outlier: 4.033A pdb=" N ILE u 128 " --> pdb=" O GLU u 125 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS u 129 " --> pdb=" O HIS u 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 125 through 129' Processing helix chain 'u' and resid 131 through 140 removed outlier: 3.609A pdb=" N MET u 137 " --> pdb=" O ALA u 133 " (cutoff:3.500A) Processing helix chain 'u' and resid 171 through 174 No H-bonds generated for 'chain 'u' and resid 171 through 174' Processing helix chain 'u' and resid 181 through 184 No H-bonds generated for 'chain 'u' and resid 181 through 184' Processing helix chain 'u' and resid 229 through 243 removed outlier: 3.861A pdb=" N TYR u 233 " --> pdb=" O ILE u 230 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET u 236 " --> pdb=" O TYR u 233 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA u 239 " --> pdb=" O MET u 236 " (cutoff:3.500A) Processing helix chain 'u' and resid 252 through 261 removed outlier: 3.597A pdb=" N MET u 256 " --> pdb=" O THR u 252 " (cutoff:3.500A) Processing helix chain 'u' and resid 275 through 295 removed outlier: 3.646A pdb=" N LYS u 279 " --> pdb=" O LYS u 275 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY u 294 " --> pdb=" O ASN u 290 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU u 295 " --> pdb=" O LYS u 291 " (cutoff:3.500A) Processing helix chain 'u' and resid 298 through 302 Processing helix chain 'u' and resid 311 through 315 removed outlier: 4.034A pdb=" N VAL u 315 " --> pdb=" O GLY u 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 311 through 315' Processing helix chain 'u' and resid 320 through 323 removed outlier: 3.724A pdb=" N ILE u 323 " --> pdb=" O LEU u 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 320 through 323' Processing helix chain 'u' and resid 337 through 343 Processing helix chain 'w' and resid 39 through 43 removed outlier: 3.528A pdb=" N PHE w 43 " --> pdb=" O LEU w 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 39 through 43' Processing helix chain 'w' and resid 71 through 74 No H-bonds generated for 'chain 'w' and resid 71 through 74' Processing helix chain 'w' and resid 92 through 103 removed outlier: 3.653A pdb=" N ALA w 101 " --> pdb=" O LEU w 97 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU w 102 " --> pdb=" O LEU w 98 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 Processing helix chain 'w' and resid 171 through 174 No H-bonds generated for 'chain 'w' and resid 171 through 174' Processing helix chain 'w' and resid 181 through 183 No H-bonds generated for 'chain 'w' and resid 181 through 183' Processing helix chain 'w' and resid 218 through 220 No H-bonds generated for 'chain 'w' and resid 218 through 220' Processing helix chain 'w' and resid 229 through 244 removed outlier: 3.666A pdb=" N LYS w 238 " --> pdb=" O ASN w 234 " (cutoff:3.500A) Processing helix chain 'w' and resid 252 through 261 removed outlier: 3.561A pdb=" N MET w 256 " --> pdb=" O THR w 252 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU w 261 " --> pdb=" O LEU w 257 " (cutoff:3.500A) Processing helix chain 'w' and resid 274 through 295 removed outlier: 3.597A pdb=" N ILE w 278 " --> pdb=" O LYS w 274 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS w 291 " --> pdb=" O ASN w 287 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU w 295 " --> pdb=" O LYS w 291 " (cutoff:3.500A) Processing helix chain 'w' and resid 298 through 302 Processing helix chain 'w' and resid 311 through 315 removed outlier: 3.916A pdb=" N VAL w 315 " --> pdb=" O GLY w 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 311 through 315' Processing helix chain 'w' and resid 321 through 323 No H-bonds generated for 'chain 'w' and resid 321 through 323' Processing helix chain 'w' and resid 337 through 348 removed outlier: 3.698A pdb=" N PHE w 345 " --> pdb=" O GLY w 341 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN w 348 " --> pdb=" O GLU w 344 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 43 Processing helix chain 'x' and resid 50 through 52 No H-bonds generated for 'chain 'x' and resid 50 through 52' Processing helix chain 'x' and resid 71 through 74 No H-bonds generated for 'chain 'x' and resid 71 through 74' Processing helix chain 'x' and resid 92 through 105 removed outlier: 3.855A pdb=" N ALA x 101 " --> pdb=" O LEU x 97 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU x 102 " --> pdb=" O LEU x 98 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY x 103 " --> pdb=" O ALA x 99 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU x 104 " --> pdb=" O THR x 100 " (cutoff:3.500A) Processing helix chain 'x' and resid 125 through 129 removed outlier: 3.826A pdb=" N LYS x 129 " --> pdb=" O GLU x 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 125 through 129' Processing helix chain 'x' and resid 131 through 140 Processing helix chain 'x' and resid 170 through 174 Processing helix chain 'x' and resid 181 through 183 No H-bonds generated for 'chain 'x' and resid 181 through 183' Processing helix chain 'x' and resid 229 through 244 removed outlier: 3.507A pdb=" N ASN x 234 " --> pdb=" O ASN x 231 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET x 236 " --> pdb=" O TYR x 233 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP x 237 " --> pdb=" O ASN x 234 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA x 239 " --> pdb=" O MET x 236 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR x 241 " --> pdb=" O LYS x 238 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER x 244 " --> pdb=" O THR x 241 " (cutoff:3.500A) Processing helix chain 'x' and resid 252 through 261 removed outlier: 3.653A pdb=" N MET x 256 " --> pdb=" O THR x 252 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS x 259 " --> pdb=" O LEU x 255 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU x 260 " --> pdb=" O MET x 256 " (cutoff:3.500A) Processing helix chain 'x' and resid 274 through 294 removed outlier: 3.526A pdb=" N SER x 285 " --> pdb=" O ARG x 281 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR x 286 " --> pdb=" O LYS x 282 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS x 291 " --> pdb=" O ASN x 287 " (cutoff:3.500A) Processing helix chain 'x' and resid 298 through 302 Processing helix chain 'x' and resid 311 through 314 No H-bonds generated for 'chain 'x' and resid 311 through 314' Processing helix chain 'x' and resid 321 through 323 No H-bonds generated for 'chain 'x' and resid 321 through 323' Processing helix chain 'x' and resid 337 through 344 Processing helix chain 'x' and resid 346 through 348 No H-bonds generated for 'chain 'x' and resid 346 through 348' Processing sheet with id= A, first strand: chain '1' and resid 4 through 7 removed outlier: 3.703A pdb=" N PHE 1 166 " --> pdb=" O THR 1 120 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '1' and resid 14 through 18 removed outlier: 3.530A pdb=" N PHE 1 27 " --> pdb=" O ILE 1 15 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '1' and resid 31 through 33 removed outlier: 4.251A pdb=" N ILE 1 53 " --> pdb=" O VAL 1 69 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '1' and resid 214 through 217 removed outlier: 3.977A pdb=" N GLU 1 217 " --> pdb=" O VAL 1 205 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL 1 205 " --> pdb=" O GLU 1 217 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLY 1 192 " --> pdb=" O ASN 1 304 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE 1 306 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE 1 194 " --> pdb=" O ILE 1 306 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE 1 308 " --> pdb=" O ILE 1 194 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL 1 196 " --> pdb=" O ILE 1 308 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 263 through 265 removed outlier: 3.843A pdb=" N ILE 1 264 " --> pdb=" O ILE 1 271 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 4 through 7 removed outlier: 3.703A pdb=" N PHE 2 166 " --> pdb=" O THR 2 120 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '2' and resid 14 through 18 removed outlier: 3.530A pdb=" N PHE 2 27 " --> pdb=" O ILE 2 15 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '2' and resid 31 through 33 removed outlier: 4.250A pdb=" N ILE 2 53 " --> pdb=" O VAL 2 69 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '2' and resid 214 through 217 removed outlier: 3.977A pdb=" N GLU 2 217 " --> pdb=" O VAL 2 205 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL 2 205 " --> pdb=" O GLU 2 217 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLY 2 192 " --> pdb=" O ASN 2 304 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE 2 306 " --> pdb=" O GLY 2 192 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE 2 194 " --> pdb=" O ILE 2 306 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE 2 308 " --> pdb=" O ILE 2 194 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL 2 196 " --> pdb=" O ILE 2 308 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '2' and resid 263 through 265 removed outlier: 3.843A pdb=" N ILE 2 264 " --> pdb=" O ILE 2 271 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 4 through 7 Processing sheet with id= L, first strand: chain 'A' and resid 14 through 18 Processing sheet with id= M, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.281A pdb=" N LYS A 65 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A 57 " --> pdb=" O LYS A 65 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 53 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 144 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 154 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 222 through 224 removed outlier: 3.533A pdb=" N PHE A 206 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLY A 192 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE A 306 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE A 194 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE A 308 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 205 through 208 removed outlier: 4.827A pdb=" N VAL A 205 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 217 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 263 through 265 removed outlier: 4.027A pdb=" N ILE A 264 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 116 through 119 removed outlier: 6.324A pdb=" N TYR B 4 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL B 119 " --> pdb=" O TYR B 4 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 6 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.960A pdb=" N THR B 144 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 156 " --> pdb=" O HIS B 143 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE B 152 " --> pdb=" O PHE B 147 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 214 through 216 removed outlier: 3.634A pdb=" N PHE B 206 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N GLY B 192 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE B 306 " --> pdb=" O GLY B 192 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE B 194 " --> pdb=" O ILE B 306 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE B 308 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 196 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 263 through 265 Processing sheet with id= U, first strand: chain 'D' and resid 116 through 119 removed outlier: 6.324A pdb=" N TYR D 4 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL D 119 " --> pdb=" O TYR D 4 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE D 6 " --> pdb=" O VAL D 119 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 65 through 68 removed outlier: 3.960A pdb=" N THR D 144 " --> pdb=" O LEU D 58 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 156 " --> pdb=" O HIS D 143 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE D 152 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 214 through 216 removed outlier: 3.634A pdb=" N PHE D 206 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLY D 192 " --> pdb=" O ASN D 304 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE D 306 " --> pdb=" O GLY D 192 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE D 194 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE D 308 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL D 196 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 263 through 265 Processing sheet with id= Y, first strand: chain 'E' and resid 116 through 119 removed outlier: 6.714A pdb=" N TYR E 4 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL E 119 " --> pdb=" O TYR E 4 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE E 6 " --> pdb=" O VAL E 119 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 31 through 33 removed outlier: 4.176A pdb=" N ILE E 53 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE E 152 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 222 through 224 removed outlier: 3.631A pdb=" N PHE E 206 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE E 191 " --> pdb=" O PHE E 206 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN E 304 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY E 192 " --> pdb=" O ASN E 304 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE E 306 " --> pdb=" O GLY E 192 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE E 194 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE E 308 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 206 through 208 Processing sheet with id= AC, first strand: chain 'E' and resid 263 through 266 removed outlier: 3.530A pdb=" N ILE E 264 " --> pdb=" O ILE E 271 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 116 through 119 removed outlier: 6.713A pdb=" N TYR G 4 " --> pdb=" O HIS G 117 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL G 119 " --> pdb=" O TYR G 4 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE G 6 " --> pdb=" O VAL G 119 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 31 through 33 removed outlier: 4.177A pdb=" N ILE G 53 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE G 152 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 222 through 224 removed outlier: 3.631A pdb=" N PHE G 206 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE G 191 " --> pdb=" O PHE G 206 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN G 304 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLY G 192 " --> pdb=" O ASN G 304 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE G 306 " --> pdb=" O GLY G 192 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE G 194 " --> pdb=" O ILE G 306 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE G 308 " --> pdb=" O ILE G 194 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 206 through 208 Processing sheet with id= AH, first strand: chain 'G' and resid 263 through 266 removed outlier: 3.531A pdb=" N ILE G 264 " --> pdb=" O ILE G 271 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 14 through 18 Processing sheet with id= AJ, first strand: chain 'H' and resid 64 through 68 removed outlier: 3.537A pdb=" N THR H 144 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 119 through 122 removed outlier: 7.545A pdb=" N THR H 164 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU H 122 " --> pdb=" O THR H 164 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE H 166 " --> pdb=" O LEU H 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'H' and resid 222 through 224 removed outlier: 7.746A pdb=" N GLY H 192 " --> pdb=" O ASN H 304 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE H 306 " --> pdb=" O GLY H 192 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE H 194 " --> pdb=" O ILE H 306 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE H 308 " --> pdb=" O ILE H 194 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 206 through 208 Processing sheet with id= AN, first strand: chain 'H' and resid 263 through 265 Processing sheet with id= AO, first strand: chain 'J' and resid 14 through 18 Processing sheet with id= AP, first strand: chain 'J' and resid 64 through 68 removed outlier: 3.537A pdb=" N THR J 144 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'J' and resid 119 through 122 removed outlier: 7.544A pdb=" N THR J 164 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU J 122 " --> pdb=" O THR J 164 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N PHE J 166 " --> pdb=" O LEU J 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'J' and resid 222 through 224 removed outlier: 7.745A pdb=" N GLY J 192 " --> pdb=" O ASN J 304 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE J 306 " --> pdb=" O GLY J 192 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE J 194 " --> pdb=" O ILE J 306 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE J 308 " --> pdb=" O ILE J 194 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'J' and resid 206 through 208 Processing sheet with id= AT, first strand: chain 'J' and resid 263 through 265 Processing sheet with id= AU, first strand: chain 'K' and resid 24 through 28 removed outlier: 3.583A pdb=" N LYS K 16 " --> pdb=" O ASP K 9 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'K' and resid 31 through 33 removed outlier: 3.518A pdb=" N LYS K 65 " --> pdb=" O ILE K 57 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR K 144 " --> pdb=" O LEU K 58 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'K' and resid 328 through 330 removed outlier: 6.337A pdb=" N ILE K 306 " --> pdb=" O GLN K 329 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N MET K 307 " --> pdb=" O PHE K 190 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLY K 192 " --> pdb=" O MET K 307 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA K 309 " --> pdb=" O GLY K 192 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE K 194 " --> pdb=" O ALA K 309 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'K' and resid 206 through 208 Processing sheet with id= AY, first strand: chain 'K' and resid 263 through 265 Processing sheet with id= AZ, first strand: chain 'M' and resid 24 through 28 removed outlier: 3.582A pdb=" N LYS M 16 " --> pdb=" O ASP M 9 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'M' and resid 31 through 33 removed outlier: 3.518A pdb=" N LYS M 65 " --> pdb=" O ILE M 57 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR M 144 " --> pdb=" O LEU M 58 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'M' and resid 328 through 330 removed outlier: 6.337A pdb=" N ILE M 306 " --> pdb=" O GLN M 329 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N MET M 307 " --> pdb=" O PHE M 190 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLY M 192 " --> pdb=" O MET M 307 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA M 309 " --> pdb=" O GLY M 192 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE M 194 " --> pdb=" O ALA M 309 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'M' and resid 206 through 208 Processing sheet with id= BD, first strand: chain 'M' and resid 263 through 265 Processing sheet with id= BE, first strand: chain 'N' and resid 24 through 28 removed outlier: 3.662A pdb=" N LYS N 16 " --> pdb=" O ASP N 9 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS N 115 " --> pdb=" O TYR N 4 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE N 6 " --> pdb=" O LYS N 115 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N HIS N 117 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE N 8 " --> pdb=" O HIS N 117 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL N 119 " --> pdb=" O ILE N 8 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'N' and resid 31 through 33 removed outlier: 3.529A pdb=" N PHE N 147 " --> pdb=" O PHE N 152 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE N 152 " --> pdb=" O PHE N 147 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'N' and resid 222 through 224 removed outlier: 3.524A pdb=" N PHE N 206 " --> pdb=" O ILE N 191 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY N 192 " --> pdb=" O ASN N 304 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE N 306 " --> pdb=" O GLY N 192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE N 194 " --> pdb=" O ILE N 306 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE N 308 " --> pdb=" O ILE N 194 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL N 196 " --> pdb=" O ILE N 308 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'N' and resid 206 through 208 Processing sheet with id= BI, first strand: chain 'N' and resid 263 through 265 Processing sheet with id= BJ, first strand: chain 'P' and resid 24 through 28 removed outlier: 3.662A pdb=" N LYS P 16 " --> pdb=" O ASP P 9 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS P 115 " --> pdb=" O TYR P 4 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE P 6 " --> pdb=" O LYS P 115 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N HIS P 117 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE P 8 " --> pdb=" O HIS P 117 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL P 119 " --> pdb=" O ILE P 8 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'P' and resid 31 through 33 removed outlier: 3.529A pdb=" N PHE P 147 " --> pdb=" O PHE P 152 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE P 152 " --> pdb=" O PHE P 147 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'P' and resid 222 through 224 removed outlier: 3.523A pdb=" N PHE P 206 " --> pdb=" O ILE P 191 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLY P 192 " --> pdb=" O ASN P 304 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE P 306 " --> pdb=" O GLY P 192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE P 194 " --> pdb=" O ILE P 306 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE P 308 " --> pdb=" O ILE P 194 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL P 196 " --> pdb=" O ILE P 308 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'P' and resid 206 through 208 Processing sheet with id= BN, first strand: chain 'P' and resid 263 through 265 Processing sheet with id= BO, first strand: chain 'Q' and resid 4 through 7 Processing sheet with id= BP, first strand: chain 'Q' and resid 14 through 18 Processing sheet with id= BQ, first strand: chain 'Q' and resid 31 through 33 removed outlier: 4.281A pdb=" N LYS Q 65 " --> pdb=" O ILE Q 57 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE Q 57 " --> pdb=" O LYS Q 65 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE Q 53 " --> pdb=" O VAL Q 69 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR Q 144 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG Q 154 " --> pdb=" O ILE Q 145 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'Q' and resid 222 through 224 removed outlier: 3.533A pdb=" N PHE Q 206 " --> pdb=" O ILE Q 191 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLY Q 192 " --> pdb=" O ASN Q 304 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE Q 306 " --> pdb=" O GLY Q 192 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE Q 194 " --> pdb=" O ILE Q 306 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE Q 308 " --> pdb=" O ILE Q 194 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'Q' and resid 205 through 208 removed outlier: 4.827A pdb=" N VAL Q 205 " --> pdb=" O GLU Q 217 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU Q 217 " --> pdb=" O VAL Q 205 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'Q' and resid 263 through 265 removed outlier: 4.026A pdb=" N ILE Q 264 " --> pdb=" O ILE Q 271 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'b' and resid 116 through 119 removed outlier: 6.502A pdb=" N TYR b 4 " --> pdb=" O HIS b 117 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL b 119 " --> pdb=" O TYR b 4 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE b 6 " --> pdb=" O VAL b 119 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS b 16 " --> pdb=" O ASP b 9 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY b 17 " --> pdb=" O VAL b 25 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'b' and resid 31 through 33 removed outlier: 3.847A pdb=" N LYS b 65 " --> pdb=" O ILE b 57 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU b 58 " --> pdb=" O THR b 144 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR b 144 " --> pdb=" O LEU b 58 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'b' and resid 328 through 330 removed outlier: 6.307A pdb=" N ILE b 306 " --> pdb=" O GLN b 329 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLY b 192 " --> pdb=" O MET b 307 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA b 309 " --> pdb=" O GLY b 192 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE b 194 " --> pdb=" O ALA b 309 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'b' and resid 205 through 208 removed outlier: 4.813A pdb=" N VAL b 205 " --> pdb=" O GLU b 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU b 217 " --> pdb=" O VAL b 205 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'b' and resid 263 through 265 Processing sheet with id= BZ, first strand: chain 'c' and resid 24 through 28 removed outlier: 4.572A pdb=" N GLY c 121 " --> pdb=" O ILE c 8 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE c 166 " --> pdb=" O THR c 120 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'c' and resid 31 through 33 Processing sheet with id= CB, first strand: chain 'c' and resid 214 through 216 removed outlier: 4.164A pdb=" N PHE c 206 " --> pdb=" O ILE c 191 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLY c 192 " --> pdb=" O ASN c 304 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE c 306 " --> pdb=" O GLY c 192 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE c 194 " --> pdb=" O ILE c 306 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE c 308 " --> pdb=" O ILE c 194 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'c' and resid 263 through 265 Processing sheet with id= CD, first strand: chain 'e' and resid 24 through 28 removed outlier: 4.285A pdb=" N GLY e 121 " --> pdb=" O ILE e 8 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE e 166 " --> pdb=" O THR e 120 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU e 122 " --> pdb=" O PHE e 166 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'e' and resid 31 through 33 removed outlier: 3.834A pdb=" N ILE e 53 " --> pdb=" O VAL e 69 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE e 156 " --> pdb=" O HIS e 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE e 145 " --> pdb=" O ARG e 154 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG e 154 " --> pdb=" O ILE e 145 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'e' and resid 192 through 196 Processing sheet with id= CG, first strand: chain 'e' and resid 205 through 208 removed outlier: 4.841A pdb=" N VAL e 205 " --> pdb=" O GLU e 217 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU e 217 " --> pdb=" O VAL e 205 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'e' and resid 263 through 265 removed outlier: 3.559A pdb=" N ILE e 264 " --> pdb=" O ILE e 271 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'e' and resid 306 through 308 Processing sheet with id= CJ, first strand: chain 'f' and resid 116 through 119 removed outlier: 6.501A pdb=" N TYR f 4 " --> pdb=" O HIS f 117 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL f 119 " --> pdb=" O TYR f 4 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE f 6 " --> pdb=" O VAL f 119 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS f 16 " --> pdb=" O ASP f 9 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY f 17 " --> pdb=" O VAL f 25 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'f' and resid 31 through 33 removed outlier: 3.846A pdb=" N LYS f 65 " --> pdb=" O ILE f 57 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU f 58 " --> pdb=" O THR f 144 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR f 144 " --> pdb=" O LEU f 58 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'f' and resid 328 through 330 removed outlier: 6.307A pdb=" N ILE f 306 " --> pdb=" O GLN f 329 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N GLY f 192 " --> pdb=" O MET f 307 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA f 309 " --> pdb=" O GLY f 192 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE f 194 " --> pdb=" O ALA f 309 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'f' and resid 205 through 208 removed outlier: 4.813A pdb=" N VAL f 205 " --> pdb=" O GLU f 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU f 217 " --> pdb=" O VAL f 205 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'f' and resid 263 through 265 Processing sheet with id= CO, first strand: chain 'h' and resid 6 through 9 removed outlier: 3.552A pdb=" N GLY h 17 " --> pdb=" O VAL h 25 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'h' and resid 31 through 33 Processing sheet with id= CQ, first strand: chain 'h' and resid 222 through 225 removed outlier: 4.014A pdb=" N ASN h 304 " --> pdb=" O PHE h 190 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY h 192 " --> pdb=" O ASN h 304 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE h 306 " --> pdb=" O GLY h 192 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE h 194 " --> pdb=" O ILE h 306 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE h 308 " --> pdb=" O ILE h 194 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL h 196 " --> pdb=" O ILE h 308 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'h' and resid 206 through 208 Processing sheet with id= CS, first strand: chain 'h' and resid 263 through 265 removed outlier: 3.676A pdb=" N ILE h 264 " --> pdb=" O ILE h 271 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'i' and resid 24 through 28 removed outlier: 4.285A pdb=" N GLY i 121 " --> pdb=" O ILE i 8 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE i 166 " --> pdb=" O THR i 120 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU i 122 " --> pdb=" O PHE i 166 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'i' and resid 31 through 33 removed outlier: 3.833A pdb=" N ILE i 53 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE i 156 " --> pdb=" O HIS i 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE i 145 " --> pdb=" O ARG i 154 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG i 154 " --> pdb=" O ILE i 145 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'i' and resid 192 through 196 Processing sheet with id= CW, first strand: chain 'i' and resid 205 through 208 removed outlier: 4.841A pdb=" N VAL i 205 " --> pdb=" O GLU i 217 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU i 217 " --> pdb=" O VAL i 205 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'i' and resid 263 through 265 removed outlier: 3.558A pdb=" N ILE i 264 " --> pdb=" O ILE i 271 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'i' and resid 306 through 308 Processing sheet with id= CZ, first strand: chain 'k' and resid 24 through 28 removed outlier: 3.629A pdb=" N GLY k 17 " --> pdb=" O VAL k 25 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE k 27 " --> pdb=" O ILE k 15 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE k 8 " --> pdb=" O VAL k 119 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY k 121 " --> pdb=" O ILE k 8 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'k' and resid 31 through 34 removed outlier: 4.406A pdb=" N GLU k 66 " --> pdb=" O GLY k 34 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS k 65 " --> pdb=" O ILE k 57 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE k 53 " --> pdb=" O VAL k 69 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS k 54 " --> pdb=" O VAL k 148 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'k' and resid 328 through 330 removed outlier: 6.355A pdb=" N ILE k 306 " --> pdb=" O GLN k 329 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N MET k 307 " --> pdb=" O PHE k 190 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY k 192 " --> pdb=" O MET k 307 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA k 309 " --> pdb=" O GLY k 192 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE k 194 " --> pdb=" O ALA k 309 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'k' and resid 263 through 266 Processing sheet with id= DD, first strand: chain 'l' and resid 6 through 9 removed outlier: 3.553A pdb=" N GLY l 17 " --> pdb=" O VAL l 25 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'l' and resid 31 through 33 Processing sheet with id= DF, first strand: chain 'l' and resid 222 through 225 removed outlier: 4.014A pdb=" N ASN l 304 " --> pdb=" O PHE l 190 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLY l 192 " --> pdb=" O ASN l 304 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE l 306 " --> pdb=" O GLY l 192 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE l 194 " --> pdb=" O ILE l 306 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE l 308 " --> pdb=" O ILE l 194 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL l 196 " --> pdb=" O ILE l 308 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'l' and resid 206 through 208 Processing sheet with id= DH, first strand: chain 'l' and resid 263 through 265 removed outlier: 3.676A pdb=" N ILE l 264 " --> pdb=" O ILE l 271 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'n' and resid 24 through 28 removed outlier: 3.643A pdb=" N LYS n 16 " --> pdb=" O ASP n 9 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS n 117 " --> pdb=" O ILE n 6 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE n 8 " --> pdb=" O HIS n 117 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL n 119 " --> pdb=" O ILE n 8 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR n 164 " --> pdb=" O THR n 120 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU n 122 " --> pdb=" O THR n 164 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE n 166 " --> pdb=" O LEU n 122 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain 'n' and resid 65 through 69 removed outlier: 4.115A pdb=" N ILE n 53 " --> pdb=" O VAL n 69 " (cutoff:3.500A) Processing sheet with id= DK, first strand: chain 'n' and resid 222 through 224 removed outlier: 3.614A pdb=" N ASN n 304 " --> pdb=" O PHE n 190 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N GLY n 192 " --> pdb=" O ASN n 304 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE n 306 " --> pdb=" O GLY n 192 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE n 194 " --> pdb=" O ILE n 306 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE n 308 " --> pdb=" O ILE n 194 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL n 196 " --> pdb=" O ILE n 308 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'n' and resid 206 through 208 Processing sheet with id= DM, first strand: chain 'n' and resid 263 through 265 Processing sheet with id= DN, first strand: chain 'o' and resid 24 through 28 removed outlier: 3.628A pdb=" N GLY o 17 " --> pdb=" O VAL o 25 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE o 27 " --> pdb=" O ILE o 15 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE o 8 " --> pdb=" O VAL o 119 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY o 121 " --> pdb=" O ILE o 8 " (cutoff:3.500A) Processing sheet with id= DO, first strand: chain 'o' and resid 31 through 34 removed outlier: 4.406A pdb=" N GLU o 66 " --> pdb=" O GLY o 34 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS o 65 " --> pdb=" O ILE o 57 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE o 53 " --> pdb=" O VAL o 69 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS o 54 " --> pdb=" O VAL o 148 " (cutoff:3.500A) Processing sheet with id= DP, first strand: chain 'o' and resid 328 through 330 removed outlier: 6.355A pdb=" N ILE o 306 " --> pdb=" O GLN o 329 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N MET o 307 " --> pdb=" O PHE o 190 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY o 192 " --> pdb=" O MET o 307 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA o 309 " --> pdb=" O GLY o 192 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE o 194 " --> pdb=" O ALA o 309 " (cutoff:3.500A) Processing sheet with id= DQ, first strand: chain 'o' and resid 263 through 266 Processing sheet with id= DR, first strand: chain 'q' and resid 24 through 28 removed outlier: 4.197A pdb=" N GLY q 121 " --> pdb=" O ILE q 8 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR q 164 " --> pdb=" O THR q 120 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU q 122 " --> pdb=" O THR q 164 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE q 166 " --> pdb=" O LEU q 122 " (cutoff:3.500A) Processing sheet with id= DS, first strand: chain 'q' and resid 31 through 33 removed outlier: 3.541A pdb=" N VAL q 69 " --> pdb=" O ILE q 53 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE q 53 " --> pdb=" O VAL q 69 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR q 144 " --> pdb=" O LEU q 58 " (cutoff:3.500A) Processing sheet with id= DT, first strand: chain 'q' and resid 306 through 309 removed outlier: 7.454A pdb=" N MET q 307 " --> pdb=" O PHE q 190 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLY q 192 " --> pdb=" O MET q 307 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ALA q 309 " --> pdb=" O GLY q 192 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE q 194 " --> pdb=" O ALA q 309 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE q 191 " --> pdb=" O PHE q 206 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE q 206 " --> pdb=" O ILE q 191 " (cutoff:3.500A) Processing sheet with id= DU, first strand: chain 'q' and resid 206 through 208 Processing sheet with id= DV, first strand: chain 'q' and resid 263 through 266 removed outlier: 3.568A pdb=" N ILE q 264 " --> pdb=" O ILE q 271 " (cutoff:3.500A) Processing sheet with id= DW, first strand: chain 'r' and resid 24 through 28 removed outlier: 3.643A pdb=" N LYS r 16 " --> pdb=" O ASP r 9 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N HIS r 117 " --> pdb=" O ILE r 6 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE r 8 " --> pdb=" O HIS r 117 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL r 119 " --> pdb=" O ILE r 8 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR r 164 " --> pdb=" O THR r 120 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU r 122 " --> pdb=" O THR r 164 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE r 166 " --> pdb=" O LEU r 122 " (cutoff:3.500A) Processing sheet with id= DX, first strand: chain 'r' and resid 65 through 69 removed outlier: 4.115A pdb=" N ILE r 53 " --> pdb=" O VAL r 69 " (cutoff:3.500A) Processing sheet with id= DY, first strand: chain 'r' and resid 222 through 224 removed outlier: 3.613A pdb=" N ASN r 304 " --> pdb=" O PHE r 190 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N GLY r 192 " --> pdb=" O ASN r 304 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE r 306 " --> pdb=" O GLY r 192 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE r 194 " --> pdb=" O ILE r 306 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE r 308 " --> pdb=" O ILE r 194 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL r 196 " --> pdb=" O ILE r 308 " (cutoff:3.500A) Processing sheet with id= DZ, first strand: chain 'r' and resid 206 through 208 Processing sheet with id= EA, first strand: chain 'r' and resid 263 through 265 Processing sheet with id= ,, first strand: chain 't' and resid 24 through 28 removed outlier: 5.988A pdb=" N HIS t 117 " --> pdb=" O ILE t 6 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE t 8 " --> pdb=" O HIS t 117 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL t 119 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU t 122 " --> pdb=" O PHE t 166 " (cutoff:3.500A) Processing sheet with id= -, first strand: chain 't' and resid 31 through 33 removed outlier: 4.003A pdb=" N LYS t 65 " --> pdb=" O ILE t 57 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE t 57 " --> pdb=" O LYS t 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG t 154 " --> pdb=" O ILE t 145 " (cutoff:3.500A) Processing sheet with id= ., first strand: chain 't' and resid 222 through 224 removed outlier: 3.569A pdb=" N ALA t 222 " --> pdb=" O ILE t 203 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE t 203 " --> pdb=" O ALA t 222 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLY t 192 " --> pdb=" O ASN t 304 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE t 306 " --> pdb=" O GLY t 192 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE t 194 " --> pdb=" O ILE t 306 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE t 308 " --> pdb=" O ILE t 194 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL t 196 " --> pdb=" O ILE t 308 " (cutoff:3.500A) Processing sheet with id= /, first strand: chain 't' and resid 206 through 208 Processing sheet with id= 0, first strand: chain 't' and resid 263 through 266 removed outlier: 3.516A pdb=" N ILE t 264 " --> pdb=" O ILE t 271 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'u' and resid 24 through 28 removed outlier: 4.197A pdb=" N GLY u 121 " --> pdb=" O ILE u 8 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR u 164 " --> pdb=" O THR u 120 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LEU u 122 " --> pdb=" O THR u 164 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE u 166 " --> pdb=" O LEU u 122 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'u' and resid 31 through 33 removed outlier: 3.541A pdb=" N VAL u 69 " --> pdb=" O ILE u 53 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE u 53 " --> pdb=" O VAL u 69 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR u 144 " --> pdb=" O LEU u 58 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'u' and resid 306 through 309 removed outlier: 7.453A pdb=" N MET u 307 " --> pdb=" O PHE u 190 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLY u 192 " --> pdb=" O MET u 307 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ALA u 309 " --> pdb=" O GLY u 192 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE u 194 " --> pdb=" O ALA u 309 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE u 191 " --> pdb=" O PHE u 206 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE u 206 " --> pdb=" O ILE u 191 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'u' and resid 206 through 208 Processing sheet with id= 5, first strand: chain 'u' and resid 263 through 266 removed outlier: 3.568A pdb=" N ILE u 264 " --> pdb=" O ILE u 271 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'w' and resid 24 through 28 removed outlier: 4.572A pdb=" N GLY w 121 " --> pdb=" O ILE w 8 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE w 166 " --> pdb=" O THR w 120 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'w' and resid 31 through 33 Processing sheet with id= 8, first strand: chain 'w' and resid 214 through 216 removed outlier: 4.163A pdb=" N PHE w 206 " --> pdb=" O ILE w 191 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLY w 192 " --> pdb=" O ASN w 304 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE w 306 " --> pdb=" O GLY w 192 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ILE w 194 " --> pdb=" O ILE w 306 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE w 308 " --> pdb=" O ILE w 194 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'w' and resid 263 through 265 Processing sheet with id= :, first strand: chain 'x' and resid 24 through 28 removed outlier: 5.989A pdb=" N HIS x 117 " --> pdb=" O ILE x 6 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE x 8 " --> pdb=" O HIS x 117 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL x 119 " --> pdb=" O ILE x 8 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU x 122 " --> pdb=" O PHE x 166 " (cutoff:3.500A) Processing sheet with id= ;, first strand: chain 'x' and resid 31 through 33 removed outlier: 4.004A pdb=" N LYS x 65 " --> pdb=" O ILE x 57 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE x 57 " --> pdb=" O LYS x 65 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG x 154 " --> pdb=" O ILE x 145 " (cutoff:3.500A) Processing sheet with id= <, first strand: chain 'x' and resid 222 through 224 removed outlier: 3.569A pdb=" N ALA x 222 " --> pdb=" O ILE x 203 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE x 203 " --> pdb=" O ALA x 222 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLY x 192 " --> pdb=" O ASN x 304 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE x 306 " --> pdb=" O GLY x 192 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE x 194 " --> pdb=" O ILE x 306 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE x 308 " --> pdb=" O ILE x 194 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL x 196 " --> pdb=" O ILE x 308 " (cutoff:3.500A) Processing sheet with id= =, first strand: chain 'x' and resid 206 through 208 Processing sheet with id= >, first strand: chain 'x' and resid 263 through 266 removed outlier: 3.516A pdb=" N ILE x 264 " --> pdb=" O ILE x 271 " (cutoff:3.500A) 2458 hydrogen bonds defined for protein. 6630 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: 44.39 Time building geometry restraints manager: 29.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 27133 1.34 - 1.46: 15862 1.46 - 1.58: 42205 1.58 - 1.69: 90 1.69 - 1.81: 540 Bond restraints: 85830 Sorted by residual: bond pdb=" C LEU G 110 " pdb=" N PRO G 111 " ideal model delta sigma weight residual 1.330 1.350 -0.020 1.22e-02 6.72e+03 2.70e+00 bond pdb=" C LEU E 110 " pdb=" N PRO E 111 " ideal model delta sigma weight residual 1.330 1.350 -0.020 1.22e-02 6.72e+03 2.66e+00 bond pdb=" C ARG Q 75 " pdb=" N GLN Q 76 " ideal model delta sigma weight residual 1.331 1.364 -0.033 2.07e-02 2.33e+03 2.59e+00 bond pdb=" C ARG q 37 " pdb=" N SER q 38 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.40e-02 5.10e+03 2.50e+00 bond pdb=" C ARG u 37 " pdb=" N SER u 38 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.40e-02 5.10e+03 2.45e+00 ... (remaining 85825 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.70: 1334 105.70 - 113.34: 47562 113.34 - 120.98: 41718 120.98 - 128.62: 24731 128.62 - 136.26: 335 Bond angle restraints: 115680 Sorted by residual: angle pdb=" N ILE K 288 " pdb=" CA ILE K 288 " pdb=" C ILE K 288 " ideal model delta sigma weight residual 112.96 107.42 5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" N ILE M 288 " pdb=" CA ILE M 288 " pdb=" C ILE M 288 " ideal model delta sigma weight residual 112.96 107.44 5.52 1.00e+00 1.00e+00 3.04e+01 angle pdb=" N ILE K 128 " pdb=" CA ILE K 128 " pdb=" C ILE K 128 " ideal model delta sigma weight residual 112.96 107.46 5.50 1.00e+00 1.00e+00 3.03e+01 angle pdb=" N ILE M 128 " pdb=" CA ILE M 128 " pdb=" C ILE M 128 " ideal model delta sigma weight residual 112.96 107.46 5.50 1.00e+00 1.00e+00 3.03e+01 angle pdb=" N SER 1 38 " pdb=" CA SER 1 38 " pdb=" C SER 1 38 " ideal model delta sigma weight residual 114.64 106.98 7.66 1.52e+00 4.33e-01 2.54e+01 ... (remaining 115675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 51417 33.26 - 66.52: 335 66.52 - 99.79: 78 99.79 - 133.05: 0 133.05 - 166.31: 40 Dihedral angle restraints: 51870 sinusoidal: 21690 harmonic: 30180 Sorted by residual: dihedral pdb=" O2A ADP c 401 " pdb=" O3A ADP c 401 " pdb=" PA ADP c 401 " pdb=" PB ADP c 401 " ideal model delta sinusoidal sigma weight residual 300.00 133.69 166.31 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O2A ADP w 401 " pdb=" O3A ADP w 401 " pdb=" PA ADP w 401 " pdb=" PB ADP w 401 " ideal model delta sinusoidal sigma weight residual 300.00 133.70 166.30 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O2A ADP x 401 " pdb=" O3A ADP x 401 " pdb=" PA ADP x 401 " pdb=" PB ADP x 401 " ideal model delta sinusoidal sigma weight residual 300.00 133.70 166.30 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 51867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 8978 0.050 - 0.099: 2994 0.099 - 0.149: 788 0.149 - 0.198: 114 0.198 - 0.248: 26 Chirality restraints: 12900 Sorted by residual: chirality pdb=" CB ILE e 26 " pdb=" CA ILE e 26 " pdb=" CG1 ILE e 26 " pdb=" CG2 ILE e 26 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE i 26 " pdb=" CA ILE i 26 " pdb=" CG1 ILE i 26 " pdb=" CG2 ILE i 26 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE i 264 " pdb=" CA ILE i 264 " pdb=" CG1 ILE i 264 " pdb=" CG2 ILE i 264 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 12897 not shown) Planarity restraints: 14880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 166 " 0.050 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO E 167 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO E 167 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 167 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 166 " 0.050 5.00e-02 4.00e+02 7.64e-02 9.35e+00 pdb=" N PRO G 167 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO G 167 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 167 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE i 345 " -0.014 2.00e-02 2.50e+03 1.62e-02 4.59e+00 pdb=" CG PHE i 345 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE i 345 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE i 345 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE i 345 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE i 345 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE i 345 " 0.001 2.00e-02 2.50e+03 ... (remaining 14877 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1316 2.65 - 3.21: 75316 3.21 - 3.77: 130435 3.77 - 4.34: 185799 4.34 - 4.90: 292090 Nonbonded interactions: 684956 Sorted by model distance: nonbonded pdb=" NE2 GLN 1 168 " pdb="MG MG 1 402 " model vdw 2.086 2.250 nonbonded pdb=" NE2 GLN 2 168 " pdb="MG MG 2 402 " model vdw 2.086 2.250 nonbonded pdb=" NE2 GLN B 168 " pdb="MG MG B 402 " model vdw 2.090 2.250 nonbonded pdb=" NE2 GLN D 168 " pdb="MG MG D 402 " model vdw 2.090 2.250 nonbonded pdb=" NE2 GLN G 168 " pdb="MG MG G 402 " model vdw 2.101 2.250 ... (remaining 684951 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 '1' selection = chain '2' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain '1' selection = chain '2' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'n' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' } 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 5.890 Check model and map are aligned: 0.900 Set scattering table: 0.570 Process input model: 190.320 Find NCS groups from input model: 5.250 Set up NCS constraints: 1.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.030 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 : 0.004 0.035 85830 Z= 0.249 Angle : 0.901 10.296 115680 Z= 0.500 Chirality : 0.053 0.248 12900 Planarity : 0.005 0.076 14880 Dihedral : 11.504 166.310 32370 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.26 % Allowed : 2.51 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.07), residues: 10410 helix: -3.76 (0.05), residues: 3090 sheet: -2.71 (0.09), residues: 2550 loop : -1.71 (0.08), residues: 4770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP h 296 HIS 0.010 0.002 HIS c 117 PHE 0.035 0.003 PHE i 345 TYR 0.025 0.002 TYR w 233 ARG 0.014 0.001 ARG H 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20820 Ramachandran restraints generated. 10410 Oldfield, 0 Emsley, 10410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20820 Ramachandran restraints generated. 10410 Oldfield, 0 Emsley, 10410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 5 THR cc_start: 0.5686 (m) cc_final: 0.5466 (p) REVERT: 1 57 ILE cc_start: 0.8123 (mt) cc_final: 0.7733 (tp) REVERT: 1 60 GLU cc_start: 0.6208 (pt0) cc_final: 0.5994 (tt0) REVERT: 1 95 LYS cc_start: 0.9233 (mttt) cc_final: 0.8484 (mmtp) REVERT: 1 122 LEU cc_start: 0.9087 (mm) cc_final: 0.8784 (mt) REVERT: 1 124 LEU cc_start: 0.8932 (tp) cc_final: 0.8614 (tt) REVERT: 1 130 GLN cc_start: 0.8639 (mt0) cc_final: 0.8418 (mt0) REVERT: 1 207 ARG cc_start: 0.6696 (ttm-80) cc_final: 0.6457 (ttp-170) REVERT: 1 227 LEU cc_start: 0.8840 (mt) cc_final: 0.8570 (mm) REVERT: 1 230 ILE cc_start: 0.8923 (tt) cc_final: 0.8545 (pt) REVERT: 1 233 TYR cc_start: 0.7248 (m-10) cc_final: 0.6775 (m-80) REVERT: 1 250 LEU cc_start: 0.8281 (mt) cc_final: 0.7986 (mt) REVERT: 1 254 GLN cc_start: 0.8650 (mt0) cc_final: 0.8370 (mt0) REVERT: 1 256 MET cc_start: 0.8737 (mtp) cc_final: 0.8234 (tpp) REVERT: 1 257 LEU cc_start: 0.9344 (tp) cc_final: 0.8830 (mt) REVERT: 1 260 GLU cc_start: 0.8057 (tt0) cc_final: 0.7486 (mm-30) REVERT: 1 269 ASP cc_start: 0.8649 (t0) cc_final: 0.8205 (t70) REVERT: 1 276 ASP cc_start: 0.9017 (m-30) cc_final: 0.8755 (m-30) REVERT: 1 287 ASN cc_start: 0.9228 (m-40) cc_final: 0.8903 (p0) REVERT: 1 333 ASN cc_start: 0.7802 (m-40) cc_final: 0.7550 (t0) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1541 time to fit residues: 20.2806 Evaluate side-chains 63 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 861 optimal weight: 0.9990 chunk 773 optimal weight: 0.0570 chunk 428 optimal weight: 0.0040 chunk 264 optimal weight: 8.9990 chunk 521 optimal weight: 0.0870 chunk 413 optimal weight: 0.0870 chunk 799 optimal weight: 50.0000 chunk 309 optimal weight: 0.0770 chunk 486 optimal weight: 9.9990 chunk 595 optimal weight: 20.0000 chunk 926 optimal weight: 0.0040 overall best weight: 0.0458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 14 GLN J 52 ASN J 54 HIS J 155 ASN ** J 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.9203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 85830 Z= 0.172 Angle : 0.714 6.239 115680 Z= 0.391 Chirality : 0.045 0.138 12900 Planarity : 0.004 0.029 14880 Dihedral : 11.088 120.000 11310 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.08), residues: 10410 helix: -1.30 (0.07), residues: 3630 sheet: -1.32 (0.11), residues: 2070 loop : -1.21 (0.08), residues: 4710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 296 HIS 0.004 0.001 HIS x 126 PHE 0.018 0.002 PHE P 147 TYR 0.008 0.001 TYR B 233 ARG 0.003 0.001 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASP cc_start: 0.7510 (t70) cc_final: 0.7148 (t0) REVERT: J 40 ASP cc_start: 0.6990 (m-30) cc_final: 0.5564 (m-30) REVERT: J 49 ILE cc_start: 0.8847 (tt) cc_final: 0.8530 (tt) REVERT: J 100 THR cc_start: 0.9237 (m) cc_final: 0.9022 (p) REVERT: J 123 PRO cc_start: 0.8766 (Cg_exo) cc_final: 0.8483 (Cg_endo) REVERT: J 137 MET cc_start: 0.8908 (tpt) cc_final: 0.8696 (tpt) REVERT: J 138 LEU cc_start: 0.8662 (mt) cc_final: 0.8377 (mt) REVERT: J 151 ASN cc_start: 0.8934 (m-40) cc_final: 0.8702 (p0) REVERT: J 158 PHE cc_start: 0.7399 (m-80) cc_final: 0.6713 (m-80) REVERT: J 182 SER cc_start: 0.7653 (p) cc_final: 0.7405 (m) REVERT: J 198 PHE cc_start: 0.8172 (t80) cc_final: 0.7618 (t80) REVERT: J 256 MET cc_start: 0.8826 (mtp) cc_final: 0.8615 (ttt) REVERT: J 330 LEU cc_start: 0.8669 (tp) cc_final: 0.7931 (pp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1447 time to fit residues: 24.3775 Evaluate side-chains 71 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 514 optimal weight: 30.0000 chunk 287 optimal weight: 30.0000 chunk 770 optimal weight: 3.9990 chunk 630 optimal weight: 0.6980 chunk 255 optimal weight: 3.9990 chunk 927 optimal weight: 0.3980 chunk 1002 optimal weight: 0.0060 chunk 826 optimal weight: 20.0000 chunk 920 optimal weight: 40.0000 chunk 316 optimal weight: 8.9990 chunk 744 optimal weight: 40.0000 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 ASN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 231 ASN J 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 1.0425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 85830 Z= 0.220 Angle : 0.774 6.577 115680 Z= 0.409 Chirality : 0.045 0.151 12900 Planarity : 0.004 0.021 14880 Dihedral : 9.781 120.755 11310 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.32 % Allowed : 3.86 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.08), residues: 10410 helix: -0.40 (0.08), residues: 3600 sheet: -0.91 (0.11), residues: 2130 loop : -1.34 (0.08), residues: 4680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 296 HIS 0.004 0.001 HIS 1 54 PHE 0.015 0.002 PHE 2 303 TYR 0.047 0.003 TYR P 61 ARG 0.004 0.001 ARG f 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 123 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8047 (Cg_endo) REVERT: J 134 LEU cc_start: 0.9703 (tp) cc_final: 0.9481 (tt) REVERT: J 137 MET cc_start: 0.9046 (tpt) cc_final: 0.8593 (tpt) REVERT: J 151 ASN cc_start: 0.8829 (m-40) cc_final: 0.8529 (m-40) REVERT: J 182 SER cc_start: 0.8177 (p) cc_final: 0.7749 (m) REVERT: J 198 PHE cc_start: 0.8510 (t80) cc_final: 0.7676 (t80) REVERT: J 293 ASP cc_start: 0.8468 (m-30) cc_final: 0.8075 (m-30) REVERT: J 306 ILE cc_start: 0.6751 (mt) cc_final: 0.6392 (mm) REVERT: J 307 MET cc_start: 0.8419 (mpp) cc_final: 0.8090 (mmm) REVERT: J 317 TYR cc_start: 0.8896 (t80) cc_final: 0.8680 (t80) REVERT: J 327 MET cc_start: 0.7651 (tmm) cc_final: 0.7199 (tmm) REVERT: J 330 LEU cc_start: 0.8498 (tp) cc_final: 0.7850 (pp) REVERT: J 343 LEU cc_start: 0.9477 (mt) cc_final: 0.9178 (mt) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.1234 time to fit residues: 15.3712 Evaluate side-chains 70 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 916 optimal weight: 30.0000 chunk 697 optimal weight: 40.0000 chunk 481 optimal weight: 40.0000 chunk 102 optimal weight: 30.0000 chunk 442 optimal weight: 20.0000 chunk 623 optimal weight: 5.9990 chunk 931 optimal weight: 40.0000 chunk 985 optimal weight: 0.0050 chunk 486 optimal weight: 0.0040 chunk 882 optimal weight: 20.0000 chunk 265 optimal weight: 0.0470 overall best weight: 5.2110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 52 ASN ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 1.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 85830 Z= 0.225 Angle : 0.754 6.369 115680 Z= 0.398 Chirality : 0.044 0.156 12900 Planarity : 0.003 0.019 14880 Dihedral : 8.901 104.395 11310 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.08), residues: 10410 helix: 0.16 (0.09), residues: 3600 sheet: -0.60 (0.10), residues: 2520 loop : -1.05 (0.09), residues: 4290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP i 296 HIS 0.005 0.001 HIS h 54 PHE 0.024 0.002 PHE 1 345 TYR 0.029 0.002 TYR H 61 ARG 0.005 0.001 ARG h 299 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASP cc_start: 0.6951 (t0) cc_final: 0.6522 (t0) REVERT: J 23 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8233 (ttpt) REVERT: J 24 ARG cc_start: 0.8030 (ptp-170) cc_final: 0.7731 (ptp90) REVERT: J 49 ILE cc_start: 0.8770 (tt) cc_final: 0.8526 (tt) REVERT: J 123 PRO cc_start: 0.8795 (Cg_exo) cc_final: 0.7477 (Cg_endo) REVERT: J 137 MET cc_start: 0.9117 (tpt) cc_final: 0.8266 (tpt) REVERT: J 138 LEU cc_start: 0.8964 (mm) cc_final: 0.8746 (mm) REVERT: J 151 ASN cc_start: 0.8858 (m-40) cc_final: 0.8544 (m-40) REVERT: J 182 SER cc_start: 0.8147 (p) cc_final: 0.7817 (m) REVERT: J 198 PHE cc_start: 0.8768 (t80) cc_final: 0.8053 (t80) REVERT: J 233 TYR cc_start: 0.8883 (m-80) cc_final: 0.8134 (m-80) REVERT: J 258 LEU cc_start: 0.9170 (tp) cc_final: 0.8931 (tp) REVERT: J 293 ASP cc_start: 0.8448 (m-30) cc_final: 0.7981 (m-30) REVERT: J 307 MET cc_start: 0.8178 (mpp) cc_final: 0.7808 (mmm) REVERT: J 317 TYR cc_start: 0.8975 (t80) cc_final: 0.8577 (t80) REVERT: J 330 LEU cc_start: 0.8522 (tp) cc_final: 0.7860 (pp) REVERT: J 345 PHE cc_start: 0.8466 (t80) cc_final: 0.8154 (t80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.1277 time to fit residues: 15.2226 Evaluate side-chains 64 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 821 optimal weight: 30.0000 chunk 559 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 734 optimal weight: 0.0970 chunk 406 optimal weight: 8.9990 chunk 841 optimal weight: 40.0000 chunk 681 optimal weight: 40.0000 chunk 1 optimal weight: 30.0000 chunk 503 optimal weight: 9.9990 chunk 884 optimal weight: 30.0000 chunk 248 optimal weight: 30.0000 overall best weight: 4.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 ASN ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 1.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 85830 Z= 0.217 Angle : 0.755 9.000 115680 Z= 0.395 Chirality : 0.045 0.159 12900 Planarity : 0.003 0.021 14880 Dihedral : 8.552 99.620 11310 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.32 % Allowed : 1.29 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.08), residues: 10410 helix: 0.54 (0.09), residues: 3540 sheet: -0.44 (0.11), residues: 2460 loop : -1.08 (0.09), residues: 4410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP b 296 HIS 0.004 0.001 HIS w 54 PHE 0.017 0.002 PHE i 152 TYR 0.021 0.002 TYR k 61 ARG 0.003 0.000 ARG e 299 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 5 THR cc_start: 0.8892 (p) cc_final: 0.7876 (p) REVERT: J 9 ASP cc_start: 0.7178 (t0) cc_final: 0.6809 (t0) REVERT: J 24 ARG cc_start: 0.8069 (ptp-170) cc_final: 0.7546 (ptp90) REVERT: J 49 ILE cc_start: 0.8665 (tt) cc_final: 0.8425 (tt) REVERT: J 75 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7565 (mtt-85) REVERT: J 134 LEU cc_start: 0.9748 (tt) cc_final: 0.9528 (tt) REVERT: J 137 MET cc_start: 0.9036 (tpt) cc_final: 0.8373 (tpt) REVERT: J 138 LEU cc_start: 0.9002 (mm) cc_final: 0.8726 (mm) REVERT: J 151 ASN cc_start: 0.8861 (m-40) cc_final: 0.8558 (m-40) REVERT: J 173 ILE cc_start: 0.8534 (mp) cc_final: 0.8191 (mt) REVERT: J 185 LEU cc_start: 0.7828 (pp) cc_final: 0.7413 (pp) REVERT: J 198 PHE cc_start: 0.8859 (t80) cc_final: 0.8283 (t80) REVERT: J 223 THR cc_start: 0.8856 (m) cc_final: 0.8534 (m) REVERT: J 233 TYR cc_start: 0.8559 (m-80) cc_final: 0.8169 (m-80) REVERT: J 237 ASP cc_start: 0.7923 (m-30) cc_final: 0.7553 (m-30) REVERT: J 258 LEU cc_start: 0.9085 (tp) cc_final: 0.8827 (tp) REVERT: J 293 ASP cc_start: 0.8436 (m-30) cc_final: 0.7917 (m-30) REVERT: J 307 MET cc_start: 0.8265 (mpp) cc_final: 0.7913 (mmm) REVERT: J 317 TYR cc_start: 0.9004 (t80) cc_final: 0.8726 (t80) REVERT: J 330 LEU cc_start: 0.8617 (tp) cc_final: 0.7735 (pp) REVERT: J 343 LEU cc_start: 0.9650 (mt) cc_final: 0.9433 (mt) REVERT: J 345 PHE cc_start: 0.8462 (t80) cc_final: 0.8215 (t80) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1351 time to fit residues: 15.5405 Evaluate side-chains 65 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 331 optimal weight: 0.8980 chunk 887 optimal weight: 0.0050 chunk 194 optimal weight: 30.0000 chunk 578 optimal weight: 50.0000 chunk 243 optimal weight: 20.0000 chunk 986 optimal weight: 40.0000 chunk 819 optimal weight: 50.0000 chunk 456 optimal weight: 0.6980 chunk 82 optimal weight: 0.0570 chunk 326 optimal weight: 3.9990 chunk 518 optimal weight: 40.0000 overall best weight: 1.1314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 ASN ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 1.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 85830 Z= 0.205 Angle : 0.745 7.154 115680 Z= 0.393 Chirality : 0.045 0.150 12900 Planarity : 0.003 0.031 14880 Dihedral : 7.988 91.255 11310 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.32 % Allowed : 1.61 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.08), residues: 10410 helix: 0.48 (0.09), residues: 3540 sheet: -0.68 (0.10), residues: 2460 loop : -0.95 (0.10), residues: 4410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP b 296 HIS 0.004 0.001 HIS t 54 PHE 0.015 0.001 PHE M 152 TYR 0.014 0.001 TYR i 61 ARG 0.004 0.000 ARG b 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 9 ASP cc_start: 0.7338 (t0) cc_final: 0.6799 (t0) REVERT: J 23 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8222 (ttpt) REVERT: J 49 ILE cc_start: 0.8776 (tt) cc_final: 0.8551 (tt) REVERT: J 134 LEU cc_start: 0.9751 (tt) cc_final: 0.9542 (tt) REVERT: J 137 MET cc_start: 0.9007 (tpt) cc_final: 0.8376 (tpt) REVERT: J 151 ASN cc_start: 0.8755 (m-40) cc_final: 0.8530 (m-40) REVERT: J 182 SER cc_start: 0.8208 (p) cc_final: 0.7530 (m) REVERT: J 198 PHE cc_start: 0.8965 (t80) cc_final: 0.8162 (t80) REVERT: J 258 LEU cc_start: 0.9045 (tp) cc_final: 0.8775 (tp) REVERT: J 293 ASP cc_start: 0.8472 (m-30) cc_final: 0.8009 (m-30) REVERT: J 307 MET cc_start: 0.8242 (mpp) cc_final: 0.7817 (mmm) REVERT: J 330 LEU cc_start: 0.8641 (tp) cc_final: 0.7806 (pp) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 0.1505 time to fit residues: 17.7753 Evaluate side-chains 60 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 951 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 562 optimal weight: 0.0010 chunk 720 optimal weight: 0.2980 chunk 558 optimal weight: 0.0770 chunk 830 optimal weight: 5.9990 chunk 551 optimal weight: 7.9990 chunk 983 optimal weight: 30.0000 chunk 615 optimal weight: 40.0000 chunk 599 optimal weight: 1.9990 chunk 453 optimal weight: 0.2980 overall best weight: 0.5346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 ASN J 76 GLN ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 1.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 85830 Z= 0.203 Angle : 0.772 7.582 115680 Z= 0.404 Chirality : 0.046 0.176 12900 Planarity : 0.004 0.035 14880 Dihedral : 7.668 85.302 11310 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.64 % Allowed : 0.32 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.08), residues: 10410 helix: 0.47 (0.09), residues: 3630 sheet: -0.35 (0.11), residues: 2460 loop : -1.04 (0.10), residues: 4320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP b 296 HIS 0.003 0.001 HIS t 54 PHE 0.016 0.002 PHE l 345 TYR 0.012 0.001 TYR t 61 ARG 0.008 0.001 ARG q 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 5 THR cc_start: 0.8875 (p) cc_final: 0.7936 (p) REVERT: J 49 ILE cc_start: 0.8790 (tt) cc_final: 0.8573 (tt) REVERT: J 89 ILE cc_start: 0.8804 (pt) cc_final: 0.8603 (pt) REVERT: J 90 ASN cc_start: 0.9057 (p0) cc_final: 0.7962 (t0) REVERT: J 137 MET cc_start: 0.8903 (tpt) cc_final: 0.8216 (tpt) REVERT: J 151 ASN cc_start: 0.8676 (m-40) cc_final: 0.8426 (m-40) REVERT: J 182 SER cc_start: 0.7975 (p) cc_final: 0.7291 (p) REVERT: J 198 PHE cc_start: 0.8674 (t80) cc_final: 0.7941 (t80) REVERT: J 233 TYR cc_start: 0.8545 (m-80) cc_final: 0.8185 (m-80) REVERT: J 258 LEU cc_start: 0.9032 (tp) cc_final: 0.8706 (tp) REVERT: J 293 ASP cc_start: 0.8336 (m-30) cc_final: 0.7888 (m-30) REVERT: J 307 MET cc_start: 0.7994 (mpp) cc_final: 0.7767 (mmm) REVERT: J 317 TYR cc_start: 0.9104 (t80) cc_final: 0.8131 (t80) REVERT: J 330 LEU cc_start: 0.8743 (tp) cc_final: 0.8347 (tp) outliers start: 2 outliers final: 0 residues processed: 92 average time/residue: 0.1249 time to fit residues: 13.7289 Evaluate side-chains 67 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 608 optimal weight: 40.0000 chunk 392 optimal weight: 3.9990 chunk 587 optimal weight: 2.9990 chunk 296 optimal weight: 0.0040 chunk 193 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 chunk 625 optimal weight: 20.0000 chunk 669 optimal weight: 20.0000 chunk 486 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 772 optimal weight: 0.0170 overall best weight: 3.0036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 HIS ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 1.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 85830 Z= 0.215 Angle : 0.797 7.306 115680 Z= 0.421 Chirality : 0.048 0.177 12900 Planarity : 0.004 0.036 14880 Dihedral : 7.353 80.211 11310 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.08), residues: 10410 helix: 0.33 (0.09), residues: 3690 sheet: -0.71 (0.11), residues: 2430 loop : -1.20 (0.09), residues: 4290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP r 296 HIS 0.003 0.001 HIS t 54 PHE 0.027 0.002 PHE l 216 TYR 0.010 0.001 TYR t 61 ARG 0.005 0.001 ARG t 207 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 5 THR cc_start: 0.8914 (p) cc_final: 0.7990 (p) REVERT: J 36 ASP cc_start: 0.7852 (p0) cc_final: 0.7601 (p0) REVERT: J 49 ILE cc_start: 0.8691 (tt) cc_final: 0.8482 (tt) REVERT: J 151 ASN cc_start: 0.8696 (m-40) cc_final: 0.8460 (m-40) REVERT: J 182 SER cc_start: 0.7478 (p) cc_final: 0.7246 (p) REVERT: J 198 PHE cc_start: 0.8604 (t80) cc_final: 0.7979 (t80) REVERT: J 220 MET cc_start: 0.8472 (pmm) cc_final: 0.7679 (pmm) REVERT: J 258 LEU cc_start: 0.9110 (tp) cc_final: 0.8883 (tp) REVERT: J 317 TYR cc_start: 0.9129 (t80) cc_final: 0.8201 (t80) REVERT: J 330 LEU cc_start: 0.8782 (tp) cc_final: 0.8221 (tp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1352 time to fit residues: 13.2258 Evaluate side-chains 60 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 894 optimal weight: 20.0000 chunk 941 optimal weight: 4.9990 chunk 859 optimal weight: 2.9990 chunk 916 optimal weight: 0.3980 chunk 551 optimal weight: 8.9990 chunk 399 optimal weight: 20.0000 chunk 719 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 827 optimal weight: 4.9990 chunk 866 optimal weight: 10.0000 chunk 912 optimal weight: 7.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 ASN ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 1.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 85830 Z= 0.231 Angle : 0.844 8.274 115680 Z= 0.449 Chirality : 0.049 0.250 12900 Planarity : 0.004 0.031 14880 Dihedral : 7.479 79.636 11310 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.32 % Allowed : 0.00 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.08), residues: 10410 helix: 0.15 (0.09), residues: 3450 sheet: -0.53 (0.11), residues: 2370 loop : -0.89 (0.09), residues: 4590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.010 TRP D 296 HIS 0.003 0.001 HIS t 54 PHE 0.024 0.002 PHE P 158 TYR 0.006 0.001 TYR o 61 ARG 0.006 0.001 ARG 1 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.254 Fit side-chains REVERT: J 5 THR cc_start: 0.8885 (p) cc_final: 0.7829 (p) REVERT: J 9 ASP cc_start: 0.6957 (t0) cc_final: 0.6512 (t0) REVERT: J 22 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8462 (t0) REVERT: J 49 ILE cc_start: 0.8709 (tt) cc_final: 0.8499 (tt) REVERT: J 112 ASN cc_start: 0.7424 (p0) cc_final: 0.6791 (p0) REVERT: J 115 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8370 (mmmt) REVERT: J 151 ASN cc_start: 0.8650 (m-40) cc_final: 0.8419 (m-40) REVERT: J 173 ILE cc_start: 0.8686 (mp) cc_final: 0.8484 (mt) REVERT: J 198 PHE cc_start: 0.8482 (t80) cc_final: 0.7926 (t80) REVERT: J 220 MET cc_start: 0.8045 (pmm) cc_final: 0.7586 (pmm) REVERT: J 233 TYR cc_start: 0.8811 (m-10) cc_final: 0.8262 (m-80) REVERT: J 258 LEU cc_start: 0.9239 (tp) cc_final: 0.8942 (tp) REVERT: J 279 LYS cc_start: 0.9244 (mmtm) cc_final: 0.8990 (mtmm) REVERT: J 317 TYR cc_start: 0.9102 (t80) cc_final: 0.8255 (t80) REVERT: J 330 LEU cc_start: 0.8800 (tp) cc_final: 0.8274 (tp) REVERT: J 340 ILE cc_start: 0.8675 (pt) cc_final: 0.8284 (pt) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.1169 time to fit residues: 12.2960 Evaluate side-chains 57 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 601 optimal weight: 2.9990 chunk 968 optimal weight: 7.9990 chunk 591 optimal weight: 30.0000 chunk 459 optimal weight: 20.0000 chunk 673 optimal weight: 0.9980 chunk 1016 optimal weight: 40.0000 chunk 935 optimal weight: 20.0000 chunk 809 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 625 optimal weight: 50.0000 chunk 496 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 1.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 85830 Z= 0.227 Angle : 0.841 7.563 115680 Z= 0.445 Chirality : 0.049 0.196 12900 Planarity : 0.004 0.036 14880 Dihedral : 7.682 78.135 11310 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.08), residues: 10410 helix: 0.23 (0.09), residues: 3450 sheet: -0.70 (0.11), residues: 2190 loop : -0.96 (0.09), residues: 4770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.010 TRP A 296 HIS 0.002 0.001 HIS h 54 PHE 0.019 0.002 PHE u 345 TYR 0.009 0.001 TYR q 61 ARG 0.002 0.000 ARG A 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20126 Ramachandran restraints generated. 10063 Oldfield, 0 Emsley, 10063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.256 Fit side-chains REVERT: J 5 THR cc_start: 0.8924 (p) cc_final: 0.7930 (p) REVERT: J 36 ASP cc_start: 0.7832 (p0) cc_final: 0.7554 (p0) REVERT: J 76 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8223 (tp40) REVERT: J 88 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8141 (mmtm) REVERT: J 104 LEU cc_start: 0.9432 (mm) cc_final: 0.9213 (mm) REVERT: J 115 LYS cc_start: 0.8459 (mmtm) cc_final: 0.7993 (tppt) REVERT: J 137 MET cc_start: 0.9299 (ttm) cc_final: 0.8954 (mtp) REVERT: J 151 ASN cc_start: 0.8693 (m-40) cc_final: 0.8481 (m-40) REVERT: J 198 PHE cc_start: 0.8540 (t80) cc_final: 0.7994 (t80) REVERT: J 258 LEU cc_start: 0.9141 (tp) cc_final: 0.8841 (tp) REVERT: J 279 LYS cc_start: 0.9356 (mmtm) cc_final: 0.9116 (mtmm) REVERT: J 330 LEU cc_start: 0.8811 (tp) cc_final: 0.8584 (tp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1380 time to fit residues: 12.5502 Evaluate side-chains 54 residues out of total 311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 642 optimal weight: 30.0000 chunk 861 optimal weight: 30.0000 chunk 247 optimal weight: 10.0000 chunk 746 optimal weight: 8.9990 chunk 119 optimal weight: 30.0000 chunk 224 optimal weight: 0.0970 chunk 810 optimal weight: 7.9990 chunk 339 optimal weight: 20.0000 chunk 832 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 7.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 22 ASN J 90 ASN J 126 HIS J 162 ASN J 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.089707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.073634 restraints weight = 11535.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.075911 restraints weight = 8107.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.077607 restraints weight = 6188.104| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 1.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 85830 Z= 0.237 Angle : 0.823 7.123 115680 Z= 0.442 Chirality : 0.048 0.180 12900 Planarity : 0.005 0.039 14880 Dihedral : 7.627 75.436 11310 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 0.64 % Allowed : 0.32 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.08), residues: 10410 helix: 0.28 (0.09), residues: 3450 sheet: -0.79 (0.10), residues: 2340 loop : -1.08 (0.09), residues: 4620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.009 TRP e 296 HIS 0.004 0.001 HIS t 54 PHE 0.018 0.002 PHE K 345 TYR 0.012 0.002 TYR J 61 ARG 0.004 0.001 ARG k 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8192.05 seconds wall clock time: 152 minutes 14.99 seconds (9134.99 seconds total)