Starting phenix.real_space_refine on Mon Sep 30 01:44:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/09_2024/6zja_11233.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/09_2024/6zja_11233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/09_2024/6zja_11233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/09_2024/6zja_11233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/09_2024/6zja_11233.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/09_2024/6zja_11233.cif" } resolution = 2.0 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ni 24 6.56 5 S 360 5.16 5 C 46920 2.51 5 N 13008 2.21 5 O 17639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 276 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 77951 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "B" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "E" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "G" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "I" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "K" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "M" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "O" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "Q" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "S" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "U" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "W" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "J" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "B" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 206 Classifications: {'water': 206} Link IDs: {None: 205} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "K" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "M" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "O" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "S" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "U" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "W" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "J" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 223 Classifications: {'water': 223} Link IDs: {None: 222} Chain: "D" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 213 Classifications: {'water': 213} Link IDs: {None: 212} Chain: "F" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 206 Classifications: {'water': 206} Link IDs: {None: 205} Chain: "H" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 210 Classifications: {'water': 210} Link IDs: {None: 209} Chain: "L" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 201 Classifications: {'water': 201} Link IDs: {None: 200} Chain: "N" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Classifications: {'water': 204} Link IDs: {None: 203} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 213 Classifications: {'water': 213} Link IDs: {None: 212} Chain: "R" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 208 Classifications: {'water': 208} Link IDs: {None: 207} Chain: "T" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Classifications: {'water': 204} Link IDs: {None: 203} Chain: "V" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 199 Classifications: {'water': 199} Link IDs: {None: 198} Chain: "X" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 209 Classifications: {'water': 209} Link IDs: {None: 208} Time building chain proxies: 34.73, per 1000 atoms: 0.45 Number of scatterers: 77951 At special positions: 0 Unit cell: (172.733, 180.316, 171.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ni 24 28.00 S 360 16.00 O 17639 8.00 N 13008 7.00 C 46920 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.06 Conformation dependent library (CDL) restraints added in 7.8 seconds 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17544 Finding SS restraints... Secondary structure from input PDB file: 396 helices and 144 sheets defined 37.7% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.54 Creating SS restraints... Processing helix chain 'A' and resid 4 through 26 Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.565A pdb=" N GLY A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.577A pdb=" N GLN A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.941A pdb=" N VAL A 70 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.569A pdb=" N MET A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.555A pdb=" N VAL A 150 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.749A pdb=" N PHE A 162 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 221 removed outlier: 3.797A pdb=" N LYS A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 14 Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.553A pdb=" N SER B 113 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 174 through 186 removed outlier: 4.303A pdb=" N ASN B 178 " --> pdb=" O PRO B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 203 through 213 removed outlier: 3.621A pdb=" N GLN B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 227 through 242 removed outlier: 3.515A pdb=" N LYS B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.529A pdb=" N LYS B 288 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 291 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 328 through 339 Processing helix chain 'B' and resid 340 through 353 removed outlier: 4.136A pdb=" N ASP B 348 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 Processing helix chain 'B' and resid 398 through 408 removed outlier: 3.817A pdb=" N LYS B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 417 removed outlier: 3.806A pdb=" N ALA B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 479 through 482 Processing helix chain 'B' and resid 484 through 489 removed outlier: 3.885A pdb=" N ASP B 488 " --> pdb=" O LYS B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'B' and resid 502 through 508 Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'C' and resid 4 through 26 Processing helix chain 'C' and resid 31 through 50 removed outlier: 3.565A pdb=" N GLY C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 61 removed outlier: 3.577A pdb=" N GLN C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.941A pdb=" N VAL C 70 " --> pdb=" O PRO C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.568A pdb=" N MET C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.555A pdb=" N VAL C 150 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 162 removed outlier: 3.748A pdb=" N PHE C 162 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 221 removed outlier: 3.797A pdb=" N LYS C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 Processing helix chain 'E' and resid 31 through 50 removed outlier: 3.565A pdb=" N GLY E 50 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 61 removed outlier: 3.577A pdb=" N GLN E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.940A pdb=" N VAL E 70 " --> pdb=" O PRO E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 removed outlier: 3.567A pdb=" N MET E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.555A pdb=" N VAL E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 162 removed outlier: 3.749A pdb=" N PHE E 162 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 221 removed outlier: 3.797A pdb=" N LYS E 212 " --> pdb=" O ASN E 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 26 Processing helix chain 'G' and resid 31 through 50 removed outlier: 3.565A pdb=" N GLY G 50 " --> pdb=" O GLU G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 61 removed outlier: 3.578A pdb=" N GLN G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 66 through 70 removed outlier: 3.941A pdb=" N VAL G 70 " --> pdb=" O PRO G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.568A pdb=" N MET G 77 " --> pdb=" O GLY G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 150 removed outlier: 3.555A pdb=" N VAL G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 162 removed outlier: 3.748A pdb=" N PHE G 162 " --> pdb=" O GLU G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 221 removed outlier: 3.798A pdb=" N LYS G 212 " --> pdb=" O ASN G 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 26 Processing helix chain 'I' and resid 31 through 50 removed outlier: 3.566A pdb=" N GLY I 50 " --> pdb=" O GLU I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 61 removed outlier: 3.577A pdb=" N GLN I 59 " --> pdb=" O ALA I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 66 through 70 removed outlier: 3.941A pdb=" N VAL I 70 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 78 removed outlier: 3.567A pdb=" N MET I 77 " --> pdb=" O GLY I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 150 removed outlier: 3.555A pdb=" N VAL I 150 " --> pdb=" O PHE I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 162 removed outlier: 3.749A pdb=" N PHE I 162 " --> pdb=" O GLU I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 221 removed outlier: 3.797A pdb=" N LYS I 212 " --> pdb=" O ASN I 208 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 26 Processing helix chain 'K' and resid 31 through 50 removed outlier: 3.565A pdb=" N GLY K 50 " --> pdb=" O GLU K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 61 removed outlier: 3.578A pdb=" N GLN K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 66 through 70 removed outlier: 3.941A pdb=" N VAL K 70 " --> pdb=" O PRO K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 78 removed outlier: 3.568A pdb=" N MET K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 150 removed outlier: 3.556A pdb=" N VAL K 150 " --> pdb=" O PHE K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 162 removed outlier: 3.748A pdb=" N PHE K 162 " --> pdb=" O GLU K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 221 removed outlier: 3.798A pdb=" N LYS K 212 " --> pdb=" O ASN K 208 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE K 213 " --> pdb=" O GLU K 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 26 Processing helix chain 'M' and resid 31 through 50 removed outlier: 3.565A pdb=" N GLY M 50 " --> pdb=" O GLU M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 61 removed outlier: 3.578A pdb=" N GLN M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'M' and resid 66 through 70 removed outlier: 3.940A pdb=" N VAL M 70 " --> pdb=" O PRO M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.568A pdb=" N MET M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 150 removed outlier: 3.556A pdb=" N VAL M 150 " --> pdb=" O PHE M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 162 removed outlier: 3.749A pdb=" N PHE M 162 " --> pdb=" O GLU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 221 removed outlier: 3.797A pdb=" N LYS M 212 " --> pdb=" O ASN M 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE M 213 " --> pdb=" O GLU M 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 26 Processing helix chain 'O' and resid 31 through 50 removed outlier: 3.565A pdb=" N GLY O 50 " --> pdb=" O GLU O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 61 removed outlier: 3.578A pdb=" N GLN O 59 " --> pdb=" O ALA O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 64 No H-bonds generated for 'chain 'O' and resid 62 through 64' Processing helix chain 'O' and resid 66 through 70 removed outlier: 3.940A pdb=" N VAL O 70 " --> pdb=" O PRO O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 78 removed outlier: 3.568A pdb=" N MET O 77 " --> pdb=" O GLY O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 150 removed outlier: 3.556A pdb=" N VAL O 150 " --> pdb=" O PHE O 147 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 162 removed outlier: 3.749A pdb=" N PHE O 162 " --> pdb=" O GLU O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 221 removed outlier: 3.798A pdb=" N LYS O 212 " --> pdb=" O ASN O 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE O 213 " --> pdb=" O GLU O 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 26 Processing helix chain 'Q' and resid 31 through 50 removed outlier: 3.565A pdb=" N GLY Q 50 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 61 removed outlier: 3.578A pdb=" N GLN Q 59 " --> pdb=" O ALA Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 64 No H-bonds generated for 'chain 'Q' and resid 62 through 64' Processing helix chain 'Q' and resid 66 through 70 removed outlier: 3.940A pdb=" N VAL Q 70 " --> pdb=" O PRO Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 78 removed outlier: 3.567A pdb=" N MET Q 77 " --> pdb=" O GLY Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 150 removed outlier: 3.556A pdb=" N VAL Q 150 " --> pdb=" O PHE Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 162 removed outlier: 3.749A pdb=" N PHE Q 162 " --> pdb=" O GLU Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 207 through 221 removed outlier: 3.798A pdb=" N LYS Q 212 " --> pdb=" O ASN Q 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE Q 213 " --> pdb=" O GLU Q 209 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 26 Processing helix chain 'S' and resid 31 through 50 removed outlier: 3.566A pdb=" N GLY S 50 " --> pdb=" O GLU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 61 removed outlier: 3.577A pdb=" N GLN S 59 " --> pdb=" O ALA S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 66 through 70 removed outlier: 3.941A pdb=" N VAL S 70 " --> pdb=" O PRO S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 78 removed outlier: 3.568A pdb=" N MET S 77 " --> pdb=" O GLY S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 150 removed outlier: 3.555A pdb=" N VAL S 150 " --> pdb=" O PHE S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 162 removed outlier: 3.749A pdb=" N PHE S 162 " --> pdb=" O GLU S 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 207 through 221 removed outlier: 3.797A pdb=" N LYS S 212 " --> pdb=" O ASN S 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE S 213 " --> pdb=" O GLU S 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 26 Processing helix chain 'U' and resid 31 through 50 removed outlier: 3.566A pdb=" N GLY U 50 " --> pdb=" O GLU U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 61 removed outlier: 3.577A pdb=" N GLN U 59 " --> pdb=" O ALA U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 64 No H-bonds generated for 'chain 'U' and resid 62 through 64' Processing helix chain 'U' and resid 66 through 70 removed outlier: 3.941A pdb=" N VAL U 70 " --> pdb=" O PRO U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 78 removed outlier: 3.568A pdb=" N MET U 77 " --> pdb=" O GLY U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 150 removed outlier: 3.556A pdb=" N VAL U 150 " --> pdb=" O PHE U 147 " (cutoff:3.500A) Processing helix chain 'U' and resid 157 through 162 removed outlier: 3.748A pdb=" N PHE U 162 " --> pdb=" O GLU U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 207 through 221 removed outlier: 3.798A pdb=" N LYS U 212 " --> pdb=" O ASN U 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE U 213 " --> pdb=" O GLU U 209 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 26 Processing helix chain 'W' and resid 31 through 50 removed outlier: 3.565A pdb=" N GLY W 50 " --> pdb=" O GLU W 46 " (cutoff:3.500A) Processing helix chain 'W' and resid 53 through 61 removed outlier: 3.578A pdb=" N GLN W 59 " --> pdb=" O ALA W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 64 No H-bonds generated for 'chain 'W' and resid 62 through 64' Processing helix chain 'W' and resid 66 through 70 removed outlier: 3.941A pdb=" N VAL W 70 " --> pdb=" O PRO W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 78 removed outlier: 3.568A pdb=" N MET W 77 " --> pdb=" O GLY W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 146 through 150 removed outlier: 3.555A pdb=" N VAL W 150 " --> pdb=" O PHE W 147 " (cutoff:3.500A) Processing helix chain 'W' and resid 157 through 162 removed outlier: 3.748A pdb=" N PHE W 162 " --> pdb=" O GLU W 159 " (cutoff:3.500A) Processing helix chain 'W' and resid 207 through 221 removed outlier: 3.798A pdb=" N LYS W 212 " --> pdb=" O ASN W 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE W 213 " --> pdb=" O GLU W 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 14 Processing helix chain 'J' and resid 109 through 113 removed outlier: 3.553A pdb=" N SER J 113 " --> pdb=" O ASN J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR J 147 " --> pdb=" O GLN J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 170 Processing helix chain 'J' and resid 174 through 186 removed outlier: 4.303A pdb=" N ASN J 178 " --> pdb=" O PRO J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 189 No H-bonds generated for 'chain 'J' and resid 187 through 189' Processing helix chain 'J' and resid 203 through 213 removed outlier: 3.622A pdb=" N GLN J 210 " --> pdb=" O SER J 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE J 211 " --> pdb=" O LEU J 207 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 225 Processing helix chain 'J' and resid 227 through 242 removed outlier: 3.514A pdb=" N LYS J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 266 Processing helix chain 'J' and resid 285 through 292 removed outlier: 3.528A pdb=" N LYS J 288 " --> pdb=" O ASP J 285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY J 291 " --> pdb=" O LYS J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 304 No H-bonds generated for 'chain 'J' and resid 302 through 304' Processing helix chain 'J' and resid 309 through 322 Processing helix chain 'J' and resid 328 through 339 Processing helix chain 'J' and resid 340 through 353 removed outlier: 4.136A pdb=" N ASP J 348 " --> pdb=" O ILE J 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR J 349 " --> pdb=" O ALA J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 371 through 388 Processing helix chain 'J' and resid 398 through 408 removed outlier: 3.818A pdb=" N LYS J 408 " --> pdb=" O ARG J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 417 removed outlier: 3.806A pdb=" N ALA J 414 " --> pdb=" O THR J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 438 through 442 Processing helix chain 'J' and resid 479 through 482 Processing helix chain 'J' and resid 484 through 489 removed outlier: 3.884A pdb=" N ASP J 488 " --> pdb=" O LYS J 484 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 501 Processing helix chain 'J' and resid 502 through 508 Processing helix chain 'J' and resid 523 through 527 Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.553A pdb=" N SER D 113 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 170 Processing helix chain 'D' and resid 174 through 186 removed outlier: 4.304A pdb=" N ASN D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 189 No H-bonds generated for 'chain 'D' and resid 187 through 189' Processing helix chain 'D' and resid 203 through 213 removed outlier: 3.621A pdb=" N GLN D 210 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.514A pdb=" N LYS D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 266 Processing helix chain 'D' and resid 285 through 292 removed outlier: 3.528A pdb=" N LYS D 288 " --> pdb=" O ASP D 285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY D 291 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 309 through 322 Processing helix chain 'D' and resid 328 through 339 Processing helix chain 'D' and resid 340 through 353 removed outlier: 4.136A pdb=" N ASP D 348 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 388 Processing helix chain 'D' and resid 398 through 408 removed outlier: 3.818A pdb=" N LYS D 408 " --> pdb=" O ARG D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 417 removed outlier: 3.806A pdb=" N ALA D 414 " --> pdb=" O THR D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 442 Processing helix chain 'D' and resid 479 through 482 Processing helix chain 'D' and resid 484 through 489 removed outlier: 3.884A pdb=" N ASP D 488 " --> pdb=" O LYS D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'D' and resid 502 through 508 Processing helix chain 'D' and resid 523 through 527 Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.554A pdb=" N SER F 113 " --> pdb=" O ASN F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR F 147 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 170 Processing helix chain 'F' and resid 174 through 186 removed outlier: 4.304A pdb=" N ASN F 178 " --> pdb=" O PRO F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 189 No H-bonds generated for 'chain 'F' and resid 187 through 189' Processing helix chain 'F' and resid 203 through 213 removed outlier: 3.622A pdb=" N GLN F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE F 211 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 227 through 242 removed outlier: 3.515A pdb=" N LYS F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 266 Processing helix chain 'F' and resid 285 through 292 removed outlier: 3.529A pdb=" N LYS F 288 " --> pdb=" O ASP F 285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY F 291 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 322 Processing helix chain 'F' and resid 328 through 339 Processing helix chain 'F' and resid 340 through 353 removed outlier: 4.136A pdb=" N ASP F 348 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR F 349 " --> pdb=" O ALA F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 388 Processing helix chain 'F' and resid 398 through 408 removed outlier: 3.817A pdb=" N LYS F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 417 removed outlier: 3.806A pdb=" N ALA F 414 " --> pdb=" O THR F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 442 Processing helix chain 'F' and resid 479 through 482 Processing helix chain 'F' and resid 484 through 489 removed outlier: 3.885A pdb=" N ASP F 488 " --> pdb=" O LYS F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'F' and resid 502 through 508 Processing helix chain 'F' and resid 523 through 527 Processing helix chain 'H' and resid 5 through 14 Processing helix chain 'H' and resid 109 through 113 removed outlier: 3.553A pdb=" N SER H 113 " --> pdb=" O ASN H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR H 147 " --> pdb=" O GLN H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 170 Processing helix chain 'H' and resid 174 through 186 removed outlier: 4.304A pdb=" N ASN H 178 " --> pdb=" O PRO H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'H' and resid 203 through 213 removed outlier: 3.621A pdb=" N GLN H 210 " --> pdb=" O SER H 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE H 211 " --> pdb=" O LEU H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 225 Processing helix chain 'H' and resid 227 through 242 removed outlier: 3.515A pdb=" N LYS H 240 " --> pdb=" O ASP H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 266 Processing helix chain 'H' and resid 285 through 292 removed outlier: 3.528A pdb=" N LYS H 288 " --> pdb=" O ASP H 285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY H 291 " --> pdb=" O LYS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 304 No H-bonds generated for 'chain 'H' and resid 302 through 304' Processing helix chain 'H' and resid 309 through 322 Processing helix chain 'H' and resid 328 through 339 Processing helix chain 'H' and resid 340 through 353 removed outlier: 4.136A pdb=" N ASP H 348 " --> pdb=" O ILE H 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR H 349 " --> pdb=" O ALA H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 388 Processing helix chain 'H' and resid 398 through 408 removed outlier: 3.818A pdb=" N LYS H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 417 removed outlier: 3.806A pdb=" N ALA H 414 " --> pdb=" O THR H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 442 Processing helix chain 'H' and resid 479 through 482 Processing helix chain 'H' and resid 484 through 489 removed outlier: 3.884A pdb=" N ASP H 488 " --> pdb=" O LYS H 484 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 501 Processing helix chain 'H' and resid 502 through 508 Processing helix chain 'H' and resid 523 through 527 Processing helix chain 'L' and resid 5 through 14 Processing helix chain 'L' and resid 109 through 113 removed outlier: 3.552A pdb=" N SER L 113 " --> pdb=" O ASN L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR L 147 " --> pdb=" O GLN L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 170 Processing helix chain 'L' and resid 174 through 186 removed outlier: 4.304A pdb=" N ASN L 178 " --> pdb=" O PRO L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 189 No H-bonds generated for 'chain 'L' and resid 187 through 189' Processing helix chain 'L' and resid 203 through 213 removed outlier: 3.621A pdb=" N GLN L 210 " --> pdb=" O SER L 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE L 211 " --> pdb=" O LEU L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 225 Processing helix chain 'L' and resid 227 through 242 removed outlier: 3.515A pdb=" N LYS L 240 " --> pdb=" O ASP L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 266 Processing helix chain 'L' and resid 285 through 292 removed outlier: 3.528A pdb=" N LYS L 288 " --> pdb=" O ASP L 285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY L 291 " --> pdb=" O LYS L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 304 No H-bonds generated for 'chain 'L' and resid 302 through 304' Processing helix chain 'L' and resid 309 through 322 Processing helix chain 'L' and resid 328 through 339 Processing helix chain 'L' and resid 340 through 353 removed outlier: 4.136A pdb=" N ASP L 348 " --> pdb=" O ILE L 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR L 349 " --> pdb=" O ALA L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 388 Processing helix chain 'L' and resid 398 through 408 removed outlier: 3.817A pdb=" N LYS L 408 " --> pdb=" O ARG L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 417 removed outlier: 3.806A pdb=" N ALA L 414 " --> pdb=" O THR L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 438 through 442 Processing helix chain 'L' and resid 479 through 482 Processing helix chain 'L' and resid 484 through 489 removed outlier: 3.884A pdb=" N ASP L 488 " --> pdb=" O LYS L 484 " (cutoff:3.500A) Processing helix chain 'L' and resid 495 through 501 Processing helix chain 'L' and resid 502 through 508 Processing helix chain 'L' and resid 523 through 527 Processing helix chain 'N' and resid 5 through 14 Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.553A pdb=" N SER N 113 " --> pdb=" O ASN N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR N 147 " --> pdb=" O GLN N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 170 Processing helix chain 'N' and resid 174 through 186 removed outlier: 4.304A pdb=" N ASN N 178 " --> pdb=" O PRO N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 189 No H-bonds generated for 'chain 'N' and resid 187 through 189' Processing helix chain 'N' and resid 203 through 213 removed outlier: 3.621A pdb=" N GLN N 210 " --> pdb=" O SER N 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE N 211 " --> pdb=" O LEU N 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 225 Processing helix chain 'N' and resid 227 through 242 removed outlier: 3.514A pdb=" N LYS N 240 " --> pdb=" O ASP N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 257 through 266 Processing helix chain 'N' and resid 285 through 292 removed outlier: 3.528A pdb=" N LYS N 288 " --> pdb=" O ASP N 285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY N 291 " --> pdb=" O LYS N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 304 No H-bonds generated for 'chain 'N' and resid 302 through 304' Processing helix chain 'N' and resid 309 through 322 Processing helix chain 'N' and resid 328 through 339 Processing helix chain 'N' and resid 340 through 353 removed outlier: 4.136A pdb=" N ASP N 348 " --> pdb=" O ILE N 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR N 349 " --> pdb=" O ALA N 345 " (cutoff:3.500A) Processing helix chain 'N' and resid 371 through 388 Processing helix chain 'N' and resid 398 through 408 removed outlier: 3.817A pdb=" N LYS N 408 " --> pdb=" O ARG N 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 410 through 417 removed outlier: 3.806A pdb=" N ALA N 414 " --> pdb=" O THR N 410 " (cutoff:3.500A) Processing helix chain 'N' and resid 438 through 442 Processing helix chain 'N' and resid 479 through 482 Processing helix chain 'N' and resid 484 through 489 removed outlier: 3.885A pdb=" N ASP N 488 " --> pdb=" O LYS N 484 " (cutoff:3.500A) Processing helix chain 'N' and resid 495 through 501 Processing helix chain 'N' and resid 502 through 508 Processing helix chain 'N' and resid 523 through 527 Processing helix chain 'P' and resid 5 through 14 Processing helix chain 'P' and resid 109 through 113 removed outlier: 3.553A pdb=" N SER P 113 " --> pdb=" O ASN P 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR P 147 " --> pdb=" O GLN P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 170 Processing helix chain 'P' and resid 174 through 186 removed outlier: 4.304A pdb=" N ASN P 178 " --> pdb=" O PRO P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 187 through 189 No H-bonds generated for 'chain 'P' and resid 187 through 189' Processing helix chain 'P' and resid 203 through 213 removed outlier: 3.621A pdb=" N GLN P 210 " --> pdb=" O SER P 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE P 211 " --> pdb=" O LEU P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 225 Processing helix chain 'P' and resid 227 through 242 removed outlier: 3.515A pdb=" N LYS P 240 " --> pdb=" O ASP P 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 266 Processing helix chain 'P' and resid 285 through 292 removed outlier: 3.528A pdb=" N LYS P 288 " --> pdb=" O ASP P 285 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY P 291 " --> pdb=" O LYS P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 302 through 304 No H-bonds generated for 'chain 'P' and resid 302 through 304' Processing helix chain 'P' and resid 309 through 322 Processing helix chain 'P' and resid 328 through 339 Processing helix chain 'P' and resid 340 through 353 removed outlier: 4.136A pdb=" N ASP P 348 " --> pdb=" O ILE P 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR P 349 " --> pdb=" O ALA P 345 " (cutoff:3.500A) Processing helix chain 'P' and resid 371 through 388 Processing helix chain 'P' and resid 398 through 408 removed outlier: 3.818A pdb=" N LYS P 408 " --> pdb=" O ARG P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 410 through 417 removed outlier: 3.805A pdb=" N ALA P 414 " --> pdb=" O THR P 410 " (cutoff:3.500A) Processing helix chain 'P' and resid 438 through 442 Processing helix chain 'P' and resid 479 through 482 Processing helix chain 'P' and resid 484 through 489 removed outlier: 3.884A pdb=" N ASP P 488 " --> pdb=" O LYS P 484 " (cutoff:3.500A) Processing helix chain 'P' and resid 495 through 501 Processing helix chain 'P' and resid 502 through 508 Processing helix chain 'P' and resid 523 through 527 Processing helix chain 'R' and resid 5 through 14 Processing helix chain 'R' and resid 109 through 113 removed outlier: 3.553A pdb=" N SER R 113 " --> pdb=" O ASN R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR R 147 " --> pdb=" O GLN R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 170 Processing helix chain 'R' and resid 174 through 186 removed outlier: 4.304A pdb=" N ASN R 178 " --> pdb=" O PRO R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 189 No H-bonds generated for 'chain 'R' and resid 187 through 189' Processing helix chain 'R' and resid 203 through 213 removed outlier: 3.621A pdb=" N GLN R 210 " --> pdb=" O SER R 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 225 Processing helix chain 'R' and resid 227 through 242 removed outlier: 3.514A pdb=" N LYS R 240 " --> pdb=" O ASP R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 266 Processing helix chain 'R' and resid 285 through 292 removed outlier: 3.528A pdb=" N LYS R 288 " --> pdb=" O ASP R 285 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY R 291 " --> pdb=" O LYS R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 304 No H-bonds generated for 'chain 'R' and resid 302 through 304' Processing helix chain 'R' and resid 309 through 322 Processing helix chain 'R' and resid 328 through 339 Processing helix chain 'R' and resid 340 through 353 removed outlier: 4.136A pdb=" N ASP R 348 " --> pdb=" O ILE R 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR R 349 " --> pdb=" O ALA R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 371 through 388 Processing helix chain 'R' and resid 398 through 408 removed outlier: 3.817A pdb=" N LYS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 410 through 417 removed outlier: 3.806A pdb=" N ALA R 414 " --> pdb=" O THR R 410 " (cutoff:3.500A) Processing helix chain 'R' and resid 438 through 442 Processing helix chain 'R' and resid 479 through 482 Processing helix chain 'R' and resid 484 through 489 removed outlier: 3.884A pdb=" N ASP R 488 " --> pdb=" O LYS R 484 " (cutoff:3.500A) Processing helix chain 'R' and resid 495 through 501 Processing helix chain 'R' and resid 502 through 508 Processing helix chain 'R' and resid 523 through 527 Processing helix chain 'T' and resid 5 through 14 Processing helix chain 'T' and resid 109 through 113 removed outlier: 3.554A pdb=" N SER T 113 " --> pdb=" O ASN T 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR T 147 " --> pdb=" O GLN T 143 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 170 Processing helix chain 'T' and resid 174 through 186 removed outlier: 4.304A pdb=" N ASN T 178 " --> pdb=" O PRO T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 187 through 189 No H-bonds generated for 'chain 'T' and resid 187 through 189' Processing helix chain 'T' and resid 203 through 213 removed outlier: 3.621A pdb=" N GLN T 210 " --> pdb=" O SER T 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE T 211 " --> pdb=" O LEU T 207 " (cutoff:3.500A) Processing helix chain 'T' and resid 221 through 225 Processing helix chain 'T' and resid 227 through 242 removed outlier: 3.515A pdb=" N LYS T 240 " --> pdb=" O ASP T 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 257 through 266 Processing helix chain 'T' and resid 285 through 292 removed outlier: 3.528A pdb=" N LYS T 288 " --> pdb=" O ASP T 285 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY T 291 " --> pdb=" O LYS T 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 302 through 304 No H-bonds generated for 'chain 'T' and resid 302 through 304' Processing helix chain 'T' and resid 309 through 322 Processing helix chain 'T' and resid 328 through 339 Processing helix chain 'T' and resid 340 through 353 removed outlier: 4.135A pdb=" N ASP T 348 " --> pdb=" O ILE T 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR T 349 " --> pdb=" O ALA T 345 " (cutoff:3.500A) Processing helix chain 'T' and resid 371 through 388 Processing helix chain 'T' and resid 398 through 408 removed outlier: 3.818A pdb=" N LYS T 408 " --> pdb=" O ARG T 404 " (cutoff:3.500A) Processing helix chain 'T' and resid 410 through 417 removed outlier: 3.806A pdb=" N ALA T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) Processing helix chain 'T' and resid 438 through 442 Processing helix chain 'T' and resid 479 through 482 Processing helix chain 'T' and resid 484 through 489 removed outlier: 3.884A pdb=" N ASP T 488 " --> pdb=" O LYS T 484 " (cutoff:3.500A) Processing helix chain 'T' and resid 495 through 501 Processing helix chain 'T' and resid 502 through 508 Processing helix chain 'T' and resid 523 through 527 Processing helix chain 'V' and resid 5 through 14 Processing helix chain 'V' and resid 109 through 113 removed outlier: 3.553A pdb=" N SER V 113 " --> pdb=" O ASN V 110 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR V 147 " --> pdb=" O GLN V 143 " (cutoff:3.500A) Processing helix chain 'V' and resid 164 through 170 Processing helix chain 'V' and resid 174 through 186 removed outlier: 4.304A pdb=" N ASN V 178 " --> pdb=" O PRO V 174 " (cutoff:3.500A) Processing helix chain 'V' and resid 187 through 189 No H-bonds generated for 'chain 'V' and resid 187 through 189' Processing helix chain 'V' and resid 203 through 213 removed outlier: 3.621A pdb=" N GLN V 210 " --> pdb=" O SER V 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE V 211 " --> pdb=" O LEU V 207 " (cutoff:3.500A) Processing helix chain 'V' and resid 221 through 225 Processing helix chain 'V' and resid 227 through 242 removed outlier: 3.515A pdb=" N LYS V 240 " --> pdb=" O ASP V 236 " (cutoff:3.500A) Processing helix chain 'V' and resid 257 through 266 Processing helix chain 'V' and resid 285 through 292 removed outlier: 3.529A pdb=" N LYS V 288 " --> pdb=" O ASP V 285 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY V 291 " --> pdb=" O LYS V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 302 through 304 No H-bonds generated for 'chain 'V' and resid 302 through 304' Processing helix chain 'V' and resid 309 through 322 Processing helix chain 'V' and resid 328 through 339 Processing helix chain 'V' and resid 340 through 353 removed outlier: 4.136A pdb=" N ASP V 348 " --> pdb=" O ILE V 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR V 349 " --> pdb=" O ALA V 345 " (cutoff:3.500A) Processing helix chain 'V' and resid 371 through 388 Processing helix chain 'V' and resid 398 through 408 removed outlier: 3.818A pdb=" N LYS V 408 " --> pdb=" O ARG V 404 " (cutoff:3.500A) Processing helix chain 'V' and resid 410 through 417 removed outlier: 3.806A pdb=" N ALA V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 442 Processing helix chain 'V' and resid 479 through 482 Processing helix chain 'V' and resid 484 through 489 removed outlier: 3.884A pdb=" N ASP V 488 " --> pdb=" O LYS V 484 " (cutoff:3.500A) Processing helix chain 'V' and resid 495 through 501 Processing helix chain 'V' and resid 502 through 508 Processing helix chain 'V' and resid 523 through 527 Processing helix chain 'X' and resid 5 through 14 Processing helix chain 'X' and resid 109 through 113 removed outlier: 3.553A pdb=" N SER X 113 " --> pdb=" O ASN X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 152 removed outlier: 3.743A pdb=" N THR X 147 " --> pdb=" O GLN X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 170 Processing helix chain 'X' and resid 174 through 186 removed outlier: 4.304A pdb=" N ASN X 178 " --> pdb=" O PRO X 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 189 No H-bonds generated for 'chain 'X' and resid 187 through 189' Processing helix chain 'X' and resid 203 through 213 removed outlier: 3.621A pdb=" N GLN X 210 " --> pdb=" O SER X 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE X 211 " --> pdb=" O LEU X 207 " (cutoff:3.500A) Processing helix chain 'X' and resid 221 through 225 Processing helix chain 'X' and resid 227 through 242 removed outlier: 3.515A pdb=" N LYS X 240 " --> pdb=" O ASP X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 257 through 266 Processing helix chain 'X' and resid 285 through 292 removed outlier: 3.529A pdb=" N LYS X 288 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY X 291 " --> pdb=" O LYS X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 302 through 304 No H-bonds generated for 'chain 'X' and resid 302 through 304' Processing helix chain 'X' and resid 309 through 322 Processing helix chain 'X' and resid 328 through 339 Processing helix chain 'X' and resid 340 through 353 removed outlier: 4.136A pdb=" N ASP X 348 " --> pdb=" O ILE X 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR X 349 " --> pdb=" O ALA X 345 " (cutoff:3.500A) Processing helix chain 'X' and resid 371 through 388 Processing helix chain 'X' and resid 398 through 408 removed outlier: 3.817A pdb=" N LYS X 408 " --> pdb=" O ARG X 404 " (cutoff:3.500A) Processing helix chain 'X' and resid 410 through 417 removed outlier: 3.806A pdb=" N ALA X 414 " --> pdb=" O THR X 410 " (cutoff:3.500A) Processing helix chain 'X' and resid 438 through 442 Processing helix chain 'X' and resid 479 through 482 Processing helix chain 'X' and resid 484 through 489 removed outlier: 3.884A pdb=" N ASP X 488 " --> pdb=" O LYS X 484 " (cutoff:3.500A) Processing helix chain 'X' and resid 495 through 501 Processing helix chain 'X' and resid 502 through 508 Processing helix chain 'X' and resid 523 through 527 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 87 Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 120 Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 142 Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS B 89 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE B 86 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR B 71 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE B 88 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE B 69 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS B 89 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE B 86 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR B 71 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE B 88 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE B 69 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA B 130 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET B 448 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE B 449 " --> pdb=" O ALA B 456 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 132 through 138 removed outlier: 6.665A pdb=" N GLY B 132 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE B 157 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 134 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY B 159 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N HIS B 136 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 197 through 198 removed outlier: 6.471A pdb=" N VAL B 245 " --> pdb=" O HIS B 271 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET B 270 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA B 298 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR B 272 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR B 300 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 491 through 494 Processing sheet with id=AB3, first strand: chain 'B' and resid 536 through 538 Processing sheet with id=AB4, first strand: chain 'C' and resid 80 through 87 Processing sheet with id=AB5, first strand: chain 'C' and resid 111 through 112 Processing sheet with id=AB6, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'C' and resid 139 through 142 Processing sheet with id=AB9, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AC1, first strand: chain 'E' and resid 80 through 87 Processing sheet with id=AC2, first strand: chain 'E' and resid 111 through 112 Processing sheet with id=AC3, first strand: chain 'E' and resid 118 through 120 Processing sheet with id=AC4, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AC5, first strand: chain 'E' and resid 139 through 142 Processing sheet with id=AC6, first strand: chain 'E' and resid 194 through 195 Processing sheet with id=AC7, first strand: chain 'G' and resid 80 through 87 Processing sheet with id=AC8, first strand: chain 'G' and resid 111 through 112 Processing sheet with id=AC9, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AD1, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AD2, first strand: chain 'G' and resid 139 through 142 Processing sheet with id=AD3, first strand: chain 'G' and resid 194 through 195 Processing sheet with id=AD4, first strand: chain 'I' and resid 80 through 87 Processing sheet with id=AD5, first strand: chain 'I' and resid 111 through 112 Processing sheet with id=AD6, first strand: chain 'I' and resid 118 through 120 Processing sheet with id=AD7, first strand: chain 'I' and resid 154 through 155 Processing sheet with id=AD8, first strand: chain 'I' and resid 139 through 142 Processing sheet with id=AD9, first strand: chain 'I' and resid 194 through 195 Processing sheet with id=AE1, first strand: chain 'K' and resid 80 through 87 Processing sheet with id=AE2, first strand: chain 'K' and resid 111 through 112 Processing sheet with id=AE3, first strand: chain 'K' and resid 118 through 120 Processing sheet with id=AE4, first strand: chain 'K' and resid 154 through 155 Processing sheet with id=AE5, first strand: chain 'K' and resid 139 through 142 Processing sheet with id=AE6, first strand: chain 'K' and resid 194 through 195 Processing sheet with id=AE7, first strand: chain 'M' and resid 80 through 87 Processing sheet with id=AE8, first strand: chain 'M' and resid 111 through 112 Processing sheet with id=AE9, first strand: chain 'M' and resid 118 through 120 Processing sheet with id=AF1, first strand: chain 'M' and resid 154 through 155 Processing sheet with id=AF2, first strand: chain 'M' and resid 139 through 142 Processing sheet with id=AF3, first strand: chain 'M' and resid 194 through 195 Processing sheet with id=AF4, first strand: chain 'O' and resid 80 through 87 Processing sheet with id=AF5, first strand: chain 'O' and resid 111 through 112 Processing sheet with id=AF6, first strand: chain 'O' and resid 118 through 120 removed outlier: 3.504A pdb=" N LYS P 2 " --> pdb=" O ILE O 120 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 154 through 155 Processing sheet with id=AF8, first strand: chain 'O' and resid 139 through 142 Processing sheet with id=AF9, first strand: chain 'O' and resid 194 through 195 Processing sheet with id=AG1, first strand: chain 'Q' and resid 80 through 87 Processing sheet with id=AG2, first strand: chain 'Q' and resid 111 through 112 Processing sheet with id=AG3, first strand: chain 'Q' and resid 118 through 120 Processing sheet with id=AG4, first strand: chain 'Q' and resid 154 through 155 Processing sheet with id=AG5, first strand: chain 'Q' and resid 139 through 142 Processing sheet with id=AG6, first strand: chain 'Q' and resid 194 through 195 Processing sheet with id=AG7, first strand: chain 'S' and resid 80 through 87 Processing sheet with id=AG8, first strand: chain 'S' and resid 111 through 112 Processing sheet with id=AG9, first strand: chain 'S' and resid 118 through 120 Processing sheet with id=AH1, first strand: chain 'S' and resid 154 through 155 Processing sheet with id=AH2, first strand: chain 'S' and resid 139 through 142 Processing sheet with id=AH3, first strand: chain 'S' and resid 194 through 195 Processing sheet with id=AH4, first strand: chain 'U' and resid 80 through 87 Processing sheet with id=AH5, first strand: chain 'U' and resid 111 through 112 Processing sheet with id=AH6, first strand: chain 'U' and resid 118 through 120 Processing sheet with id=AH7, first strand: chain 'U' and resid 154 through 155 Processing sheet with id=AH8, first strand: chain 'U' and resid 139 through 142 Processing sheet with id=AH9, first strand: chain 'U' and resid 194 through 195 Processing sheet with id=AI1, first strand: chain 'W' and resid 80 through 87 Processing sheet with id=AI2, first strand: chain 'W' and resid 111 through 112 Processing sheet with id=AI3, first strand: chain 'W' and resid 118 through 120 Processing sheet with id=AI4, first strand: chain 'W' and resid 154 through 155 Processing sheet with id=AI5, first strand: chain 'W' and resid 139 through 142 Processing sheet with id=AI6, first strand: chain 'W' and resid 194 through 195 Processing sheet with id=AI7, first strand: chain 'J' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS J 89 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY J 80 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL J 76 " --> pdb=" O GLY J 80 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR J 82 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU J 74 " --> pdb=" O TYR J 82 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA J 84 " --> pdb=" O ASN J 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN J 72 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS J 89 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY J 80 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL J 76 " --> pdb=" O GLY J 80 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR J 82 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU J 74 " --> pdb=" O TYR J 82 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA J 84 " --> pdb=" O ASN J 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN J 72 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA J 130 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET J 448 " --> pdb=" O LEU J 436 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE J 449 " --> pdb=" O ALA J 456 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 132 through 138 removed outlier: 6.665A pdb=" N GLY J 132 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE J 157 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP J 134 " --> pdb=" O ILE J 157 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLY J 159 " --> pdb=" O ASP J 134 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N HIS J 136 " --> pdb=" O GLY J 159 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'J' and resid 197 through 198 removed outlier: 6.472A pdb=" N VAL J 245 " --> pdb=" O HIS J 271 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET J 270 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA J 298 " --> pdb=" O MET J 270 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR J 272 " --> pdb=" O ALA J 298 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR J 300 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'J' and resid 491 through 494 Processing sheet with id=AJ3, first strand: chain 'J' and resid 536 through 538 Processing sheet with id=AJ4, first strand: chain 'D' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS D 89 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL D 76 " --> pdb=" O GLY D 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR D 82 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU D 74 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA D 84 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN D 72 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS D 89 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL D 76 " --> pdb=" O GLY D 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR D 82 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU D 74 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA D 84 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN D 72 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA D 130 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET D 448 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE D 449 " --> pdb=" O ALA D 456 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'D' and resid 132 through 138 removed outlier: 6.666A pdb=" N GLY D 132 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE D 157 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP D 134 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY D 159 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N HIS D 136 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 197 through 198 removed outlier: 6.471A pdb=" N VAL D 245 " --> pdb=" O HIS D 271 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET D 270 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA D 298 " --> pdb=" O MET D 270 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR D 272 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR D 300 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 491 through 494 Processing sheet with id=AJ9, first strand: chain 'D' and resid 536 through 538 Processing sheet with id=AK1, first strand: chain 'F' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS F 89 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY F 80 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL F 76 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR F 82 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU F 74 " --> pdb=" O TYR F 82 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA F 84 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN F 72 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'F' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS F 89 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY F 80 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL F 76 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR F 82 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU F 74 " --> pdb=" O TYR F 82 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA F 84 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN F 72 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA F 130 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET F 448 " --> pdb=" O LEU F 436 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE F 449 " --> pdb=" O ALA F 456 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'F' and resid 132 through 138 removed outlier: 6.666A pdb=" N GLY F 132 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE F 157 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP F 134 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY F 159 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N HIS F 136 " --> pdb=" O GLY F 159 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'F' and resid 197 through 198 removed outlier: 6.471A pdb=" N VAL F 245 " --> pdb=" O HIS F 271 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET F 270 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA F 298 " --> pdb=" O MET F 270 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR F 272 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR F 300 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'F' and resid 491 through 494 Processing sheet with id=AK6, first strand: chain 'F' and resid 536 through 538 Processing sheet with id=AK7, first strand: chain 'H' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS H 89 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL H 76 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR H 82 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU H 74 " --> pdb=" O TYR H 82 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA H 84 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN H 72 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'H' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS H 89 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL H 76 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR H 82 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU H 74 " --> pdb=" O TYR H 82 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA H 84 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN H 72 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA H 130 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET H 448 " --> pdb=" O LEU H 436 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE H 449 " --> pdb=" O ALA H 456 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'H' and resid 132 through 138 removed outlier: 6.665A pdb=" N GLY H 132 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE H 157 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP H 134 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY H 159 " --> pdb=" O ASP H 134 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N HIS H 136 " --> pdb=" O GLY H 159 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'H' and resid 197 through 198 removed outlier: 6.470A pdb=" N VAL H 245 " --> pdb=" O HIS H 271 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET H 270 " --> pdb=" O LEU H 296 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA H 298 " --> pdb=" O MET H 270 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR H 272 " --> pdb=" O ALA H 298 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR H 300 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'H' and resid 491 through 494 Processing sheet with id=AL3, first strand: chain 'H' and resid 536 through 538 Processing sheet with id=AL4, first strand: chain 'L' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS L 89 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY L 80 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL L 76 " --> pdb=" O GLY L 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR L 82 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU L 74 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA L 84 " --> pdb=" O ASN L 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN L 72 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'L' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS L 89 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY L 80 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL L 76 " --> pdb=" O GLY L 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR L 82 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU L 74 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA L 84 " --> pdb=" O ASN L 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN L 72 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA L 130 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET L 448 " --> pdb=" O LEU L 436 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE L 449 " --> pdb=" O ALA L 456 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'L' and resid 132 through 138 removed outlier: 6.666A pdb=" N GLY L 132 " --> pdb=" O THR L 155 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE L 157 " --> pdb=" O GLY L 132 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP L 134 " --> pdb=" O ILE L 157 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY L 159 " --> pdb=" O ASP L 134 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N HIS L 136 " --> pdb=" O GLY L 159 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'L' and resid 197 through 198 removed outlier: 6.471A pdb=" N VAL L 245 " --> pdb=" O HIS L 271 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET L 270 " --> pdb=" O LEU L 296 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA L 298 " --> pdb=" O MET L 270 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR L 272 " --> pdb=" O ALA L 298 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR L 300 " --> pdb=" O THR L 272 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'L' and resid 491 through 494 Processing sheet with id=AL9, first strand: chain 'L' and resid 536 through 538 Processing sheet with id=AM1, first strand: chain 'N' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE N 93 " --> pdb=" O LYS N 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS N 89 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL N 76 " --> pdb=" O GLY N 80 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR N 82 " --> pdb=" O LEU N 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU N 74 " --> pdb=" O TYR N 82 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA N 84 " --> pdb=" O ASN N 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN N 72 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'N' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE N 93 " --> pdb=" O LYS N 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS N 89 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL N 76 " --> pdb=" O GLY N 80 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR N 82 " --> pdb=" O LEU N 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU N 74 " --> pdb=" O TYR N 82 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA N 84 " --> pdb=" O ASN N 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN N 72 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA N 130 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET N 448 " --> pdb=" O LEU N 436 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE N 449 " --> pdb=" O ALA N 456 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'N' and resid 132 through 138 removed outlier: 6.665A pdb=" N GLY N 132 " --> pdb=" O THR N 155 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE N 157 " --> pdb=" O GLY N 132 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP N 134 " --> pdb=" O ILE N 157 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY N 159 " --> pdb=" O ASP N 134 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N HIS N 136 " --> pdb=" O GLY N 159 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'N' and resid 197 through 198 removed outlier: 6.471A pdb=" N VAL N 245 " --> pdb=" O HIS N 271 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET N 270 " --> pdb=" O LEU N 296 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA N 298 " --> pdb=" O MET N 270 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR N 272 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR N 300 " --> pdb=" O THR N 272 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'N' and resid 491 through 494 Processing sheet with id=AM6, first strand: chain 'N' and resid 536 through 538 Processing sheet with id=AM7, first strand: chain 'P' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE P 93 " --> pdb=" O LYS P 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS P 89 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE P 86 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N THR P 71 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE P 88 " --> pdb=" O ILE P 69 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE P 69 " --> pdb=" O ILE P 88 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'P' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE P 93 " --> pdb=" O LYS P 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS P 89 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE P 86 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N THR P 71 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE P 88 " --> pdb=" O ILE P 69 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE P 69 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA P 130 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET P 448 " --> pdb=" O LEU P 436 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE P 449 " --> pdb=" O ALA P 456 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'P' and resid 132 through 138 removed outlier: 6.666A pdb=" N GLY P 132 " --> pdb=" O THR P 155 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE P 157 " --> pdb=" O GLY P 132 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP P 134 " --> pdb=" O ILE P 157 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY P 159 " --> pdb=" O ASP P 134 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N HIS P 136 " --> pdb=" O GLY P 159 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'P' and resid 197 through 198 removed outlier: 6.471A pdb=" N VAL P 245 " --> pdb=" O HIS P 271 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET P 270 " --> pdb=" O LEU P 296 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA P 298 " --> pdb=" O MET P 270 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR P 272 " --> pdb=" O ALA P 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR P 300 " --> pdb=" O THR P 272 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'P' and resid 491 through 494 Processing sheet with id=AN3, first strand: chain 'P' and resid 536 through 538 Processing sheet with id=AN4, first strand: chain 'R' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE R 93 " --> pdb=" O LYS R 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS R 89 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL R 76 " --> pdb=" O GLY R 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR R 82 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU R 74 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA R 84 " --> pdb=" O ASN R 72 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN R 72 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'R' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE R 93 " --> pdb=" O LYS R 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS R 89 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLY R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL R 76 " --> pdb=" O GLY R 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR R 82 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU R 74 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA R 84 " --> pdb=" O ASN R 72 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN R 72 " --> pdb=" O ALA R 84 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA R 130 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET R 448 " --> pdb=" O LEU R 436 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE R 449 " --> pdb=" O ALA R 456 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'R' and resid 132 through 138 removed outlier: 6.666A pdb=" N GLY R 132 " --> pdb=" O THR R 155 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE R 157 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP R 134 " --> pdb=" O ILE R 157 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY R 159 " --> pdb=" O ASP R 134 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N HIS R 136 " --> pdb=" O GLY R 159 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'R' and resid 197 through 198 removed outlier: 6.471A pdb=" N VAL R 245 " --> pdb=" O HIS R 271 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET R 270 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA R 298 " --> pdb=" O MET R 270 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR R 272 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR R 300 " --> pdb=" O THR R 272 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'R' and resid 491 through 494 Processing sheet with id=AN9, first strand: chain 'R' and resid 536 through 538 Processing sheet with id=AO1, first strand: chain 'T' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE T 93 " --> pdb=" O LYS T 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS T 89 " --> pdb=" O ILE T 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY T 80 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL T 76 " --> pdb=" O GLY T 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR T 82 " --> pdb=" O LEU T 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU T 74 " --> pdb=" O TYR T 82 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA T 84 " --> pdb=" O ASN T 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN T 72 " --> pdb=" O ALA T 84 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'T' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE T 93 " --> pdb=" O LYS T 89 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS T 89 " --> pdb=" O ILE T 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY T 80 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL T 76 " --> pdb=" O GLY T 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR T 82 " --> pdb=" O LEU T 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU T 74 " --> pdb=" O TYR T 82 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA T 84 " --> pdb=" O ASN T 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN T 72 " --> pdb=" O ALA T 84 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA T 130 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET T 448 " --> pdb=" O LEU T 436 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE T 449 " --> pdb=" O ALA T 456 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'T' and resid 132 through 138 removed outlier: 6.666A pdb=" N GLY T 132 " --> pdb=" O THR T 155 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE T 157 " --> pdb=" O GLY T 132 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASP T 134 " --> pdb=" O ILE T 157 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLY T 159 " --> pdb=" O ASP T 134 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N HIS T 136 " --> pdb=" O GLY T 159 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'T' and resid 197 through 198 removed outlier: 6.471A pdb=" N VAL T 245 " --> pdb=" O HIS T 271 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET T 270 " --> pdb=" O LEU T 296 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA T 298 " --> pdb=" O MET T 270 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR T 272 " --> pdb=" O ALA T 298 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR T 300 " --> pdb=" O THR T 272 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'T' and resid 491 through 494 Processing sheet with id=AO6, first strand: chain 'T' and resid 536 through 538 Processing sheet with id=AO7, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.123A pdb=" N ILE V 93 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS V 89 " --> pdb=" O ILE V 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY V 80 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL V 76 " --> pdb=" O GLY V 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR V 82 " --> pdb=" O LEU V 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU V 74 " --> pdb=" O TYR V 82 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA V 84 " --> pdb=" O ASN V 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN V 72 " --> pdb=" O ALA V 84 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.123A pdb=" N ILE V 93 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS V 89 " --> pdb=" O ILE V 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY V 80 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL V 76 " --> pdb=" O GLY V 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR V 82 " --> pdb=" O LEU V 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU V 74 " --> pdb=" O TYR V 82 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA V 84 " --> pdb=" O ASN V 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN V 72 " --> pdb=" O ALA V 84 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA V 130 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET V 448 " --> pdb=" O LEU V 436 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE V 449 " --> pdb=" O ALA V 456 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'V' and resid 132 through 138 removed outlier: 6.666A pdb=" N GLY V 132 " --> pdb=" O THR V 155 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE V 157 " --> pdb=" O GLY V 132 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP V 134 " --> pdb=" O ILE V 157 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY V 159 " --> pdb=" O ASP V 134 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N HIS V 136 " --> pdb=" O GLY V 159 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'V' and resid 197 through 198 removed outlier: 6.471A pdb=" N VAL V 245 " --> pdb=" O HIS V 271 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET V 270 " --> pdb=" O LEU V 296 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ALA V 298 " --> pdb=" O MET V 270 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR V 272 " --> pdb=" O ALA V 298 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR V 300 " --> pdb=" O THR V 272 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'V' and resid 491 through 494 Processing sheet with id=AP3, first strand: chain 'V' and resid 536 through 538 Processing sheet with id=AP4, first strand: chain 'X' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE X 93 " --> pdb=" O LYS X 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS X 89 " --> pdb=" O ILE X 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY X 80 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL X 76 " --> pdb=" O GLY X 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR X 82 " --> pdb=" O LEU X 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU X 74 " --> pdb=" O TYR X 82 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA X 84 " --> pdb=" O ASN X 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN X 72 " --> pdb=" O ALA X 84 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'X' and resid 92 through 97 removed outlier: 5.122A pdb=" N ILE X 93 " --> pdb=" O LYS X 89 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS X 89 " --> pdb=" O ILE X 93 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY X 80 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL X 76 " --> pdb=" O GLY X 80 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N TYR X 82 " --> pdb=" O LEU X 74 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU X 74 " --> pdb=" O TYR X 82 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA X 84 " --> pdb=" O ASN X 72 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN X 72 " --> pdb=" O ALA X 84 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA X 130 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET X 448 " --> pdb=" O LEU X 436 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE X 449 " --> pdb=" O ALA X 456 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'X' and resid 132 through 138 removed outlier: 6.665A pdb=" N GLY X 132 " --> pdb=" O THR X 155 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE X 157 " --> pdb=" O GLY X 132 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP X 134 " --> pdb=" O ILE X 157 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY X 159 " --> pdb=" O ASP X 134 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N HIS X 136 " --> pdb=" O GLY X 159 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'X' and resid 197 through 198 removed outlier: 6.471A pdb=" N VAL X 245 " --> pdb=" O HIS X 271 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET X 270 " --> pdb=" O LEU X 296 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA X 298 " --> pdb=" O MET X 270 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR X 272 " --> pdb=" O ALA X 298 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR X 300 " --> pdb=" O THR X 272 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'X' and resid 491 through 494 Processing sheet with id=AP9, first strand: chain 'X' and resid 536 through 538 2995 hydrogen bonds defined for protein. 7836 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: 46.45 Time building geometry restraints manager: 16.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 13139 1.32 - 1.45: 19023 1.45 - 1.58: 43234 1.58 - 1.71: 24 1.71 - 1.84: 672 Bond restraints: 76092 Sorted by residual: bond pdb=" C16 DJM L 603 " pdb=" N18 DJM L 603 " ideal model delta sigma weight residual 1.347 1.489 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C16 DJM D 603 " pdb=" N18 DJM D 603 " ideal model delta sigma weight residual 1.347 1.489 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C16 DJM B 603 " pdb=" N18 DJM B 603 " ideal model delta sigma weight residual 1.347 1.489 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C16 DJM F 603 " pdb=" N18 DJM F 603 " ideal model delta sigma weight residual 1.347 1.489 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C16 DJM H 603 " pdb=" N18 DJM H 603 " ideal model delta sigma weight residual 1.347 1.489 -0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 76087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 100438 2.36 - 4.73: 1904 4.73 - 7.09: 234 7.09 - 9.45: 36 9.45 - 11.81: 36 Bond angle restraints: 102648 Sorted by residual: angle pdb=" C GLY U 197 " pdb=" N PHE U 198 " pdb=" CA PHE U 198 " ideal model delta sigma weight residual 121.54 131.81 -10.27 1.91e+00 2.74e-01 2.89e+01 angle pdb=" C GLY E 197 " pdb=" N PHE E 198 " pdb=" CA PHE E 198 " ideal model delta sigma weight residual 121.54 131.79 -10.25 1.91e+00 2.74e-01 2.88e+01 angle pdb=" C GLY O 197 " pdb=" N PHE O 198 " pdb=" CA PHE O 198 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" C GLY W 197 " pdb=" N PHE W 198 " pdb=" CA PHE W 198 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" C GLY Q 197 " pdb=" N PHE Q 198 " pdb=" CA PHE Q 198 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 ... (remaining 102643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 42413 17.43 - 34.85: 2431 34.85 - 52.28: 564 52.28 - 69.70: 264 69.70 - 87.13: 216 Dihedral angle restraints: 45888 sinusoidal: 18456 harmonic: 27432 Sorted by residual: dihedral pdb=" CA GLU X 188 " pdb=" C GLU X 188 " pdb=" N TYR X 189 " pdb=" CA TYR X 189 " ideal model delta harmonic sigma weight residual -180.00 -151.12 -28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLU J 188 " pdb=" C GLU J 188 " pdb=" N TYR J 189 " pdb=" CA TYR J 189 " ideal model delta harmonic sigma weight residual -180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLU H 188 " pdb=" C GLU H 188 " pdb=" N TYR H 189 " pdb=" CA TYR H 189 " ideal model delta harmonic sigma weight residual -180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 45885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 9483 0.074 - 0.148: 1777 0.148 - 0.222: 116 0.222 - 0.296: 12 0.296 - 0.370: 12 Chirality restraints: 11400 Sorted by residual: chirality pdb=" CA ASN B 301 " pdb=" N ASN B 301 " pdb=" C ASN B 301 " pdb=" CB ASN B 301 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA ASN P 301 " pdb=" N ASN P 301 " pdb=" C ASN P 301 " pdb=" CB ASN P 301 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA ASN N 301 " pdb=" N ASN N 301 " pdb=" C ASN N 301 " pdb=" CB ASN N 301 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 11397 not shown) Planarity restraints: 13440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE O 87 " -0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO O 88 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO O 88 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 88 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 87 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO G 88 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO G 88 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 88 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 87 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO C 88 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 88 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 88 " -0.031 5.00e-02 4.00e+02 ... (remaining 13437 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 574 2.56 - 3.14: 60782 3.14 - 3.73: 126948 3.73 - 4.31: 195960 4.31 - 4.90: 304530 Nonbonded interactions: 688794 Sorted by model distance: nonbonded pdb="NI NI H 601 " pdb=" O19 DJM H 603 " model vdw 1.974 2.180 nonbonded pdb="NI NI P 601 " pdb=" O19 DJM P 603 " model vdw 1.974 2.180 nonbonded pdb="NI NI D 601 " pdb=" O19 DJM D 603 " model vdw 1.974 2.180 nonbonded pdb="NI NI N 601 " pdb=" O19 DJM N 603 " model vdw 1.974 2.180 nonbonded pdb="NI NI F 601 " pdb=" O19 DJM F 603 " model vdw 1.975 2.180 ... (remaining 688789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.390 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: 0.060 Extract box with map and model: 2.260 Check model and map are aligned: 0.440 Set scattering table: 0.540 Process input model: 155.470 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 183.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 0.006 0.142 76092 Z= 0.406 Angle : 0.863 11.815 102648 Z= 0.494 Chirality : 0.057 0.370 11400 Planarity : 0.006 0.056 13440 Dihedral : 14.309 87.130 28344 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.37 % Allowed : 4.70 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: -0.40 (0.08), residues: 9600 helix: -0.14 (0.09), residues: 2868 sheet: 0.82 (0.15), residues: 996 loop : -0.48 (0.08), residues: 5736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP J 437 HIS 0.015 0.002 HIS R 248 PHE 0.023 0.003 PHE C 198 TYR 0.020 0.002 TYR S 15 ARG 0.006 0.001 ARG J 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1189 time to evaluate : 6.720 Fit side-chains REVERT: A 1 MET cc_start: 0.8499 (mtm) cc_final: 0.8059 (mtm) REVERT: A 208 ASN cc_start: 0.8721 (m-40) cc_final: 0.8515 (m110) REVERT: B 262 MET cc_start: 0.8608 (mmm) cc_final: 0.8293 (mmm) REVERT: B 366 MET cc_start: 0.6843 (ttt) cc_final: 0.6585 (ttt) REVERT: B 527 MET cc_start: 0.9026 (mmp) cc_final: 0.8689 (mmp) REVERT: C 1 MET cc_start: 0.8516 (mtm) cc_final: 0.8294 (mtm) REVERT: C 58 MET cc_start: 0.7805 (mtt) cc_final: 0.7573 (mtp) REVERT: C 71 MET cc_start: 0.8747 (mtp) cc_final: 0.8481 (mtp) REVERT: G 1 MET cc_start: 0.8501 (mtm) cc_final: 0.8060 (mtm) REVERT: I 12 MET cc_start: 0.8431 (tmm) cc_final: 0.8221 (tmm) REVERT: I 86 MET cc_start: 0.8177 (ttm) cc_final: 0.7975 (ttp) REVERT: O 26 LYS cc_start: 0.6752 (mtmp) cc_final: 0.6488 (mmtt) REVERT: O 152 ARG cc_start: 0.8162 (ptm-80) cc_final: 0.7926 (ptt180) REVERT: Q 1 MET cc_start: 0.8570 (mtm) cc_final: 0.8297 (mtm) REVERT: U 1 MET cc_start: 0.8372 (mtm) cc_final: 0.8074 (mtm) REVERT: U 58 MET cc_start: 0.7858 (mtt) cc_final: 0.7550 (mtt) REVERT: W 77 MET cc_start: 0.9030 (mtp) cc_final: 0.8713 (mtp) REVERT: J 353 MET cc_start: 0.8613 (mtp) cc_final: 0.8390 (mtm) REVERT: J 366 MET cc_start: 0.6975 (ttt) cc_final: 0.6700 (ttt) REVERT: D 55 MET cc_start: 0.8424 (mtm) cc_final: 0.8120 (mtp) REVERT: D 191 MET cc_start: 0.9096 (tpp) cc_final: 0.8822 (tpp) REVERT: F 338 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7989 (mmm160) REVERT: H 262 MET cc_start: 0.8656 (mmm) cc_final: 0.8397 (mmm) REVERT: H 270 MET cc_start: 0.8726 (tpp) cc_final: 0.8399 (tpp) REVERT: H 391 LYS cc_start: 0.8003 (pttm) cc_final: 0.7764 (pttm) REVERT: H 527 MET cc_start: 0.9099 (mmp) cc_final: 0.8803 (mmp) REVERT: N 182 MET cc_start: 0.9167 (mmm) cc_final: 0.8754 (mmm) REVERT: N 366 MET cc_start: 0.6960 (ttt) cc_final: 0.6578 (ttt) REVERT: N 467 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8605 (pt) REVERT: P 317 MET cc_start: 0.7977 (mtp) cc_final: 0.7642 (mtm) REVERT: R 55 MET cc_start: 0.8445 (mtm) cc_final: 0.8046 (mtp) REVERT: R 191 MET cc_start: 0.9124 (tpp) cc_final: 0.8642 (tpp) REVERT: T 27 ASP cc_start: 0.7379 (t0) cc_final: 0.7137 (t70) REVERT: T 55 MET cc_start: 0.8480 (mtm) cc_final: 0.7992 (mtp) REVERT: V 270 MET cc_start: 0.8723 (tpp) cc_final: 0.8245 (tpp) REVERT: V 478 MET cc_start: 0.9171 (mmp) cc_final: 0.8925 (mmp) outliers start: 108 outliers final: 10 residues processed: 1216 average time/residue: 1.9459 time to fit residues: 3008.9324 Evaluate side-chains 898 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 887 time to evaluate : 6.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain V residue 201 THR Chi-restraints excluded: chain X residue 201 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 800 optimal weight: 0.8980 chunk 718 optimal weight: 0.7980 chunk 398 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 484 optimal weight: 6.9990 chunk 383 optimal weight: 20.0000 chunk 743 optimal weight: 1.9990 chunk 287 optimal weight: 7.9990 chunk 451 optimal weight: 5.9990 chunk 553 optimal weight: 9.9990 chunk 860 optimal weight: 4.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 558 ASN C 97 HIS E 97 HIS G 97 HIS G 208 ASN I 97 HIS K 42 HIS K 97 HIS M 42 HIS M 97 HIS O 42 HIS O 208 ASN Q 208 ASN S 97 HIS U 97 HIS W 42 HIS W 97 HIS J 544 HIS D 34 HIS D 233 HIS D 314 HIS H 544 HIS H 558 ASN L 314 HIS N 544 HIS P 544 HIS R 233 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS X 544 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 76092 Z= 0.218 Angle : 0.678 8.868 102648 Z= 0.381 Chirality : 0.050 0.273 11400 Planarity : 0.005 0.050 13440 Dihedral : 7.092 66.428 10442 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.68 % Allowed : 7.69 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.08 (0.08), residues: 9600 helix: 0.72 (0.09), residues: 3024 sheet: 0.76 (0.15), residues: 1044 loop : -0.42 (0.08), residues: 5532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 437 HIS 0.012 0.002 HIS D 34 PHE 0.025 0.002 PHE I 198 TYR 0.024 0.002 TYR S 15 ARG 0.005 0.001 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 917 time to evaluate : 6.758 Fit side-chains REVERT: B 262 MET cc_start: 0.8609 (mmm) cc_final: 0.8240 (mmm) REVERT: B 366 MET cc_start: 0.6938 (ttt) cc_final: 0.6583 (ttt) REVERT: B 501 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7568 (mptt) REVERT: I 86 MET cc_start: 0.8218 (ttm) cc_final: 0.8009 (ttp) REVERT: O 26 LYS cc_start: 0.7080 (mtmp) cc_final: 0.6842 (mmtt) REVERT: U 152 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8003 (ptt180) REVERT: J 317 MET cc_start: 0.7955 (mtp) cc_final: 0.7672 (mtp) REVERT: J 366 MET cc_start: 0.7025 (ttt) cc_final: 0.6697 (ttt) REVERT: J 537 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: D 55 MET cc_start: 0.8303 (mtm) cc_final: 0.7992 (mtp) REVERT: D 191 MET cc_start: 0.9043 (tpp) cc_final: 0.8754 (tpp) REVERT: F 501 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7585 (mptt) REVERT: F 541 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: F 551 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: H 270 MET cc_start: 0.8779 (tpp) cc_final: 0.8517 (tpp) REVERT: H 391 LYS cc_start: 0.8046 (pttm) cc_final: 0.7693 (pttm) REVERT: N 182 MET cc_start: 0.9085 (mmm) cc_final: 0.8773 (mmm) REVERT: N 191 MET cc_start: 0.9122 (tpp) cc_final: 0.8825 (tpp) REVERT: N 366 MET cc_start: 0.6990 (ttt) cc_final: 0.6738 (ttt) REVERT: N 467 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8377 (pt) REVERT: N 551 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: R 191 MET cc_start: 0.9048 (tpp) cc_final: 0.8644 (tpp) REVERT: T 55 MET cc_start: 0.8287 (mtm) cc_final: 0.7817 (mtp) REVERT: T 501 LYS cc_start: 0.7958 (mttp) cc_final: 0.7736 (mptt) REVERT: T 551 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: V 270 MET cc_start: 0.8755 (tpp) cc_final: 0.8258 (tpp) REVERT: V 551 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: X 551 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7232 (tt0) outliers start: 54 outliers final: 18 residues processed: 947 average time/residue: 1.9657 time to fit residues: 2367.9015 Evaluate side-chains 909 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 880 time to evaluate : 6.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 501 LYS Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain O residue 86 MET Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain J residue 537 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 501 LYS Chi-restraints excluded: chain F residue 541 GLU Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 201 THR Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 201 THR Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 478 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 716 optimal weight: 0.6980 chunk 586 optimal weight: 0.6980 chunk 237 optimal weight: 4.9990 chunk 862 optimal weight: 0.9990 chunk 931 optimal weight: 9.9990 chunk 768 optimal weight: 9.9990 chunk 855 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 chunk 691 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 34 HIS B 558 ASN C 97 HIS E 97 HIS G 97 HIS I 97 HIS M 97 HIS O 208 ASN U 97 HIS J 544 HIS D 34 HIS D 314 HIS F 528 GLN H 333 GLN H 535 HIS H 544 HIS L 314 HIS N 544 HIS P 544 HIS R 314 HIS T 34 HIS T 333 GLN V 34 HIS X 544 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 76092 Z= 0.196 Angle : 0.637 8.771 102648 Z= 0.357 Chirality : 0.049 0.265 11400 Planarity : 0.005 0.051 13440 Dihedral : 6.941 68.115 10440 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.83 % Allowed : 8.32 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.24 (0.08), residues: 9600 helix: 1.03 (0.09), residues: 3036 sheet: 0.74 (0.15), residues: 1044 loop : -0.41 (0.08), residues: 5520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP F 437 HIS 0.011 0.001 HIS D 34 PHE 0.024 0.002 PHE I 198 TYR 0.022 0.002 TYR C 15 ARG 0.007 0.001 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 890 time to evaluate : 6.801 Fit side-chains REVERT: A 71 MET cc_start: 0.8818 (mtp) cc_final: 0.8532 (mtp) REVERT: B 262 MET cc_start: 0.8586 (mmm) cc_final: 0.8256 (mmm) REVERT: B 366 MET cc_start: 0.6957 (ttt) cc_final: 0.6620 (ttt) REVERT: E 86 MET cc_start: 0.8170 (ttm) cc_final: 0.7961 (ttp) REVERT: G 1 MET cc_start: 0.8529 (mtm) cc_final: 0.8039 (mtm) REVERT: O 26 LYS cc_start: 0.7026 (mtmp) cc_final: 0.6726 (mmtm) REVERT: O 152 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.8002 (ptt-90) REVERT: Q 152 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7959 (ptt-90) REVERT: U 152 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7944 (ptt180) REVERT: J 317 MET cc_start: 0.7919 (mtp) cc_final: 0.7698 (mtp) REVERT: J 366 MET cc_start: 0.7071 (ttt) cc_final: 0.6743 (ttt) REVERT: D 55 MET cc_start: 0.8268 (mtm) cc_final: 0.7957 (mtp) REVERT: F 551 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: H 270 MET cc_start: 0.8783 (tpp) cc_final: 0.8524 (tpp) REVERT: H 391 LYS cc_start: 0.8079 (pttm) cc_final: 0.7778 (pttm) REVERT: N 182 MET cc_start: 0.9065 (mmm) cc_final: 0.8771 (mmm) REVERT: N 191 MET cc_start: 0.9097 (tpp) cc_final: 0.8758 (tpp) REVERT: N 366 MET cc_start: 0.6984 (ttt) cc_final: 0.6669 (ttt) REVERT: N 467 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8314 (pt) REVERT: N 551 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: P 317 MET cc_start: 0.7979 (mtp) cc_final: 0.7737 (mtm) REVERT: P 555 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.8029 (mtmm) REVERT: T 55 MET cc_start: 0.8229 (mtm) cc_final: 0.7782 (mtp) REVERT: T 501 LYS cc_start: 0.7937 (mttp) cc_final: 0.7706 (mptt) REVERT: T 551 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: V 270 MET cc_start: 0.8744 (tpp) cc_final: 0.8218 (tpp) REVERT: V 551 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: X 248 HIS cc_start: 0.9167 (OUTLIER) cc_final: 0.8008 (t-170) REVERT: X 501 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7580 (mttt) REVERT: X 551 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7224 (tt0) outliers start: 66 outliers final: 28 residues processed: 930 average time/residue: 1.9759 time to fit residues: 2340.8689 Evaluate side-chains 922 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 882 time to evaluate : 6.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain O residue 152 ARG Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 501 LYS Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain P residue 555 LYS Chi-restraints excluded: chain R residue 2 LYS Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 201 THR Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 201 THR Chi-restraints excluded: chain X residue 248 HIS Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 852 optimal weight: 0.9990 chunk 648 optimal weight: 0.7980 chunk 447 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 411 optimal weight: 0.9980 chunk 579 optimal weight: 0.7980 chunk 865 optimal weight: 6.9990 chunk 916 optimal weight: 0.9990 chunk 452 optimal weight: 9.9990 chunk 820 optimal weight: 0.7980 chunk 246 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 208 ASN B 34 HIS B 558 ASN C 97 HIS E 79 HIS E 97 HIS G 97 HIS I 97 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS D 496 GLN H 233 HIS H 333 GLN H 535 HIS H 544 HIS L 314 HIS N 544 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS V 333 GLN X 34 HIS X 544 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 76092 Z= 0.131 Angle : 0.526 8.416 102648 Z= 0.292 Chirality : 0.046 0.243 11400 Planarity : 0.004 0.053 13440 Dihedral : 6.501 67.275 10439 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.56 % Allowed : 9.02 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.65 (0.09), residues: 9600 helix: 1.61 (0.10), residues: 2940 sheet: 0.91 (0.15), residues: 1044 loop : -0.28 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 437 HIS 0.011 0.001 HIS D 34 PHE 0.017 0.001 PHE E 198 TYR 0.018 0.001 TYR U 15 ARG 0.008 0.000 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 903 time to evaluate : 6.789 Fit side-chains REVERT: B 262 MET cc_start: 0.8593 (mmm) cc_final: 0.8276 (mmm) REVERT: B 316 ASP cc_start: 0.7892 (t70) cc_final: 0.7660 (t70) REVERT: B 366 MET cc_start: 0.6875 (ttt) cc_final: 0.6611 (ttt) REVERT: G 1 MET cc_start: 0.8508 (mtm) cc_final: 0.8044 (mtm) REVERT: Q 152 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7942 (ptt-90) REVERT: J 366 MET cc_start: 0.7038 (ttt) cc_final: 0.6678 (ttt) REVERT: D 55 MET cc_start: 0.8019 (mtm) cc_final: 0.7728 (mtp) REVERT: F 315 MET cc_start: 0.8276 (tpp) cc_final: 0.7892 (tpp) REVERT: F 551 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: H 27 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7127 (t0) REVERT: H 270 MET cc_start: 0.8769 (tpp) cc_final: 0.8455 (tpp) REVERT: H 391 LYS cc_start: 0.8082 (pttm) cc_final: 0.7762 (pttm) REVERT: L 348 ASP cc_start: 0.7812 (m-30) cc_final: 0.7605 (m-30) REVERT: N 182 MET cc_start: 0.9012 (mmm) cc_final: 0.8804 (mmm) REVERT: N 366 MET cc_start: 0.6964 (ttt) cc_final: 0.6658 (ttt) REVERT: N 551 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: R 501 LYS cc_start: 0.7804 (mttp) cc_final: 0.7578 (mppt) REVERT: T 27 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7116 (t70) REVERT: T 55 MET cc_start: 0.8012 (mtm) cc_final: 0.7552 (mtp) REVERT: T 551 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: X 317 MET cc_start: 0.7969 (mtm) cc_final: 0.7543 (mtm) REVERT: X 501 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7502 (mttt) outliers start: 44 outliers final: 19 residues processed: 933 average time/residue: 1.9294 time to fit residues: 2297.3607 Evaluate side-chains 902 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 876 time to evaluate : 6.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 467 ILE Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 501 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 763 optimal weight: 8.9990 chunk 520 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 682 optimal weight: 0.8980 chunk 378 optimal weight: 8.9990 chunk 781 optimal weight: 0.6980 chunk 633 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 467 optimal weight: 0.7980 chunk 822 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 208 ASN B 34 HIS B 558 ASN C 97 HIS E 79 HIS E 97 HIS G 97 HIS I 97 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS F 314 HIS H 333 GLN H 535 HIS L 314 HIS L 544 HIS N 333 GLN N 544 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS V 333 GLN X 34 HIS X 544 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 76092 Z= 0.125 Angle : 0.506 8.395 102648 Z= 0.280 Chirality : 0.045 0.236 11400 Planarity : 0.004 0.052 13440 Dihedral : 6.306 65.901 10434 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.59 % Allowed : 9.42 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.80 (0.09), residues: 9600 helix: 1.79 (0.10), residues: 2940 sheet: 0.97 (0.15), residues: 1044 loop : -0.22 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 437 HIS 0.009 0.001 HIS X 34 PHE 0.017 0.001 PHE E 198 TYR 0.017 0.001 TYR M 15 ARG 0.007 0.000 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 903 time to evaluate : 6.803 Fit side-chains revert: symmetry clash REVERT: B 316 ASP cc_start: 0.7828 (t70) cc_final: 0.7616 (t70) REVERT: B 366 MET cc_start: 0.6824 (ttt) cc_final: 0.6616 (ttt) REVERT: B 551 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: Q 152 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7929 (ptt-90) REVERT: U 44 MET cc_start: 0.8439 (mtm) cc_final: 0.8188 (mtm) REVERT: J 366 MET cc_start: 0.7016 (ttt) cc_final: 0.6738 (ttt) REVERT: J 551 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7082 (tt0) REVERT: F 315 MET cc_start: 0.8213 (tpp) cc_final: 0.7871 (tpp) REVERT: F 322 HIS cc_start: 0.7785 (m-70) cc_final: 0.7514 (m-70) REVERT: F 551 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: H 27 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7134 (t0) REVERT: H 391 LYS cc_start: 0.8067 (pttm) cc_final: 0.7738 (pttm) REVERT: N 191 MET cc_start: 0.8982 (tpp) cc_final: 0.8568 (tpp) REVERT: N 366 MET cc_start: 0.6978 (ttt) cc_final: 0.6657 (ttt) REVERT: N 551 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: R 501 LYS cc_start: 0.7770 (mttp) cc_final: 0.7517 (mppt) REVERT: T 27 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7121 (t70) REVERT: T 551 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7180 (tt0) REVERT: V 315 MET cc_start: 0.8183 (tpp) cc_final: 0.7827 (tpt) REVERT: V 551 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: X 191 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.7983 (tpp) REVERT: X 501 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7503 (mttt) REVERT: X 551 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7175 (tp30) outliers start: 47 outliers final: 25 residues processed: 936 average time/residue: 1.9442 time to fit residues: 2317.6230 Evaluate side-chains 917 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 880 time to evaluate : 6.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain J residue 551 GLU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain F residue 467 ILE Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 501 LYS Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 191 MET Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 469 THR Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 308 optimal weight: 0.0020 chunk 825 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 538 optimal weight: 7.9990 chunk 226 optimal weight: 20.0000 chunk 917 optimal weight: 1.9990 chunk 761 optimal weight: 0.9990 chunk 424 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 303 optimal weight: 3.9990 chunk 481 optimal weight: 20.0000 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 208 ASN B 34 HIS B 558 ASN C 79 HIS C 97 HIS E 79 HIS E 97 HIS G 97 HIS I 97 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS H 333 GLN H 535 HIS L 34 HIS L 314 HIS N 333 GLN N 544 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS V 333 GLN X 34 HIS X 314 HIS X 544 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 76092 Z= 0.155 Angle : 0.562 8.428 102648 Z= 0.313 Chirality : 0.047 0.241 11400 Planarity : 0.004 0.051 13440 Dihedral : 6.525 66.096 10434 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.68 % Allowed : 9.41 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.71 (0.09), residues: 9600 helix: 1.70 (0.10), residues: 2940 sheet: 0.89 (0.15), residues: 1044 loop : -0.26 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 437 HIS 0.010 0.001 HIS X 34 PHE 0.021 0.001 PHE G 198 TYR 0.022 0.002 TYR S 15 ARG 0.009 0.000 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 894 time to evaluate : 6.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 316 ASP cc_start: 0.7924 (t70) cc_final: 0.7663 (t70) REVERT: B 366 MET cc_start: 0.6807 (ttt) cc_final: 0.6557 (ttt) REVERT: B 551 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: G 116 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: Q 152 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7947 (ptt-90) REVERT: J 366 MET cc_start: 0.7012 (ttt) cc_final: 0.6677 (ttt) REVERT: J 551 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7104 (tt0) REVERT: D 55 MET cc_start: 0.8184 (mtm) cc_final: 0.7912 (mtp) REVERT: F 551 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: H 27 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7125 (t0) REVERT: H 391 LYS cc_start: 0.8085 (pttm) cc_final: 0.7750 (pttm) REVERT: N 366 MET cc_start: 0.7015 (ttt) cc_final: 0.6696 (ttt) REVERT: N 467 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8164 (pt) REVERT: N 551 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7253 (tt0) REVERT: R 501 LYS cc_start: 0.7822 (mttp) cc_final: 0.7551 (mppt) REVERT: T 27 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7114 (t70) REVERT: T 55 MET cc_start: 0.8115 (mtm) cc_final: 0.7784 (mtp) REVERT: T 551 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: V 551 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: X 191 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8087 (tpp) REVERT: X 501 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7520 (mttt) REVERT: X 551 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7179 (tp30) outliers start: 54 outliers final: 25 residues processed: 930 average time/residue: 2.0027 time to fit residues: 2366.5090 Evaluate side-chains 922 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 883 time to evaluate : 6.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain J residue 551 GLU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain F residue 501 LYS Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 501 LYS Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 191 MET Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 469 THR Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 884 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 522 optimal weight: 4.9990 chunk 669 optimal weight: 7.9990 chunk 518 optimal weight: 5.9990 chunk 772 optimal weight: 6.9990 chunk 512 optimal weight: 9.9990 chunk 913 optimal weight: 4.9990 chunk 571 optimal weight: 0.6980 chunk 557 optimal weight: 6.9990 chunk 421 optimal weight: 8.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 34 HIS B 558 ASN C 79 HIS C 97 HIS C 224 HIS E 79 HIS E 97 HIS G 97 HIS I 97 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS H 333 GLN H 535 HIS L 34 HIS L 314 HIS N 333 GLN P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS V 333 GLN X 34 HIS X 544 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 76092 Z= 0.284 Angle : 0.746 9.508 102648 Z= 0.418 Chirality : 0.053 0.269 11400 Planarity : 0.006 0.047 13440 Dihedral : 7.040 72.355 10434 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.76 % Allowed : 9.41 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.24 (0.08), residues: 9600 helix: 1.10 (0.09), residues: 3024 sheet: 0.27 (0.13), residues: 1284 loop : -0.37 (0.08), residues: 5292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP F 437 HIS 0.014 0.002 HIS B 417 PHE 0.031 0.003 PHE I 198 TYR 0.026 0.002 TYR I 15 ARG 0.012 0.001 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 904 time to evaluate : 6.718 Fit side-chains REVERT: B 366 MET cc_start: 0.6956 (ttt) cc_final: 0.6602 (ttt) REVERT: G 116 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: Q 152 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8006 (ptt-90) REVERT: U 152 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8001 (ptt180) REVERT: J 366 MET cc_start: 0.7048 (ttt) cc_final: 0.6647 (ttt) REVERT: D 55 MET cc_start: 0.8439 (mtm) cc_final: 0.8156 (mtp) REVERT: F 501 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7416 (mptt) REVERT: F 551 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: H 27 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7112 (t0) REVERT: H 501 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7540 (mptt) REVERT: N 366 MET cc_start: 0.7028 (ttt) cc_final: 0.6695 (ttt) REVERT: N 467 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8481 (pt) REVERT: N 551 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: P 330 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5730 (pm20) REVERT: R 338 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7861 (mmm160) REVERT: T 27 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7154 (t70) REVERT: T 55 MET cc_start: 0.8395 (mtm) cc_final: 0.7966 (mtp) REVERT: T 551 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: V 322 HIS cc_start: 0.7948 (m-70) cc_final: 0.7748 (m90) REVERT: V 551 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7305 (tt0) REVERT: X 501 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7610 (mttt) REVERT: X 551 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7227 (tt0) outliers start: 60 outliers final: 29 residues processed: 942 average time/residue: 2.0170 time to fit residues: 2408.0068 Evaluate side-chains 933 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 889 time to evaluate : 7.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain M residue 22 LYS Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain J residue 501 LYS Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 501 LYS Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 501 LYS Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain L residue 501 LYS Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 501 LYS Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 330 GLU Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 469 THR Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 565 optimal weight: 0.7980 chunk 364 optimal weight: 8.9990 chunk 545 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 580 optimal weight: 5.9990 chunk 622 optimal weight: 0.0060 chunk 451 optimal weight: 4.9990 chunk 85 optimal weight: 0.0970 chunk 718 optimal weight: 1.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 208 ASN B 34 HIS B 558 ASN C 79 HIS C 97 HIS E 79 HIS E 97 HIS G 97 HIS I 97 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS H 333 GLN H 535 HIS L 34 HIS L 314 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS V 333 GLN X 34 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 76092 Z= 0.154 Angle : 0.570 8.548 102648 Z= 0.318 Chirality : 0.047 0.251 11400 Planarity : 0.004 0.051 13440 Dihedral : 6.644 71.455 10432 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.70 % Allowed : 9.66 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.59 (0.08), residues: 9600 helix: 1.60 (0.10), residues: 2940 sheet: 0.77 (0.15), residues: 1044 loop : -0.31 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 437 HIS 0.012 0.001 HIS X 34 PHE 0.022 0.001 PHE E 198 TYR 0.021 0.002 TYR U 15 ARG 0.009 0.000 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 896 time to evaluate : 7.012 Fit side-chains revert: symmetry clash REVERT: B 316 ASP cc_start: 0.7939 (t70) cc_final: 0.7673 (t70) REVERT: B 366 MET cc_start: 0.6926 (ttt) cc_final: 0.6631 (ttt) REVERT: G 116 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: Q 152 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7952 (ptt-90) REVERT: J 366 MET cc_start: 0.7018 (ttt) cc_final: 0.6740 (ttt) REVERT: D 55 MET cc_start: 0.8206 (mtm) cc_final: 0.7905 (mtp) REVERT: F 315 MET cc_start: 0.8098 (mmm) cc_final: 0.7735 (tpp) REVERT: F 551 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: H 27 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7137 (t0) REVERT: N 366 MET cc_start: 0.6955 (ttt) cc_final: 0.6645 (ttt) REVERT: N 501 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7377 (mmtm) REVERT: N 551 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: R 501 LYS cc_start: 0.7838 (mttp) cc_final: 0.7597 (mppt) REVERT: T 27 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7103 (t70) REVERT: T 55 MET cc_start: 0.8153 (mtm) cc_final: 0.7698 (mtp) REVERT: T 551 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: V 551 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: X 501 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7523 (mttt) REVERT: X 551 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7189 (tp30) outliers start: 55 outliers final: 30 residues processed: 937 average time/residue: 1.9376 time to fit residues: 2317.6786 Evaluate side-chains 923 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 882 time to evaluate : 6.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain J residue 501 LYS Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain H residue 501 LYS Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 501 LYS Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 469 THR Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 831 optimal weight: 7.9990 chunk 875 optimal weight: 3.9990 chunk 798 optimal weight: 0.7980 chunk 851 optimal weight: 10.0000 chunk 512 optimal weight: 9.9990 chunk 370 optimal weight: 5.9990 chunk 668 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 769 optimal weight: 5.9990 chunk 805 optimal weight: 7.9990 chunk 848 optimal weight: 9.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 34 HIS B 558 ASN C 79 HIS C 97 HIS C 224 HIS E 79 HIS E 97 HIS G 97 HIS I 97 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS H 333 GLN H 535 HIS L 34 HIS L 314 HIS N 333 GLN P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS V 333 GLN X 34 HIS X 544 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 76092 Z= 0.292 Angle : 0.759 9.737 102648 Z= 0.425 Chirality : 0.053 0.264 11400 Planarity : 0.006 0.047 13440 Dihedral : 7.072 73.106 10432 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.70 % Allowed : 9.64 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.19 (0.08), residues: 9600 helix: 1.11 (0.09), residues: 2940 sheet: 0.21 (0.13), residues: 1284 loop : -0.41 (0.08), residues: 5376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP F 437 HIS 0.013 0.002 HIS H 417 PHE 0.031 0.003 PHE G 198 TYR 0.028 0.002 TYR I 15 ARG 0.012 0.001 ARG Q 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 893 time to evaluate : 6.828 Fit side-chains REVERT: B 366 MET cc_start: 0.6958 (ttt) cc_final: 0.6587 (ttt) REVERT: G 116 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: Q 152 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8007 (ptt-90) REVERT: U 152 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7998 (ptt180) REVERT: J 366 MET cc_start: 0.7054 (ttt) cc_final: 0.6656 (ttt) REVERT: D 8 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6767 (pt0) REVERT: D 55 MET cc_start: 0.8502 (mtm) cc_final: 0.8221 (mtp) REVERT: F 551 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: H 27 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7118 (t0) REVERT: H 501 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7545 (mptt) REVERT: N 366 MET cc_start: 0.7027 (ttt) cc_final: 0.6688 (ttt) REVERT: N 467 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8515 (pt) REVERT: N 551 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: T 27 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7161 (t70) REVERT: T 551 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: V 248 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.8338 (t-170) REVERT: V 322 HIS cc_start: 0.7970 (m-70) cc_final: 0.7747 (m90) REVERT: V 551 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: X 248 HIS cc_start: 0.9059 (OUTLIER) cc_final: 0.8119 (t-170) REVERT: X 501 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7609 (mttt) REVERT: X 551 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7223 (tt0) outliers start: 55 outliers final: 27 residues processed: 931 average time/residue: 1.9897 time to fit residues: 2352.1449 Evaluate side-chains 928 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 885 time to evaluate : 6.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain M residue 22 LYS Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain J residue 501 LYS Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 501 LYS Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 501 LYS Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 248 HIS Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 248 HIS Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 559 optimal weight: 8.9990 chunk 900 optimal weight: 2.9990 chunk 549 optimal weight: 5.9990 chunk 427 optimal weight: 5.9990 chunk 625 optimal weight: 9.9990 chunk 944 optimal weight: 7.9990 chunk 869 optimal weight: 5.9990 chunk 752 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 580 optimal weight: 4.9990 chunk 461 optimal weight: 0.0470 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 208 ASN B 34 HIS B 558 ASN C 79 HIS C 97 HIS E 79 HIS G 97 HIS I 97 HIS M 97 HIS J 544 HIS D 34 HIS D 314 HIS H 333 GLN H 535 HIS L 34 HIS L 314 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS V 333 GLN X 34 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 76092 Z= 0.253 Angle : 0.712 9.044 102648 Z= 0.399 Chirality : 0.052 0.267 11400 Planarity : 0.005 0.048 13440 Dihedral : 7.047 73.963 10432 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.63 % Allowed : 9.66 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.14 (0.08), residues: 9600 helix: 1.11 (0.09), residues: 2952 sheet: 0.26 (0.14), residues: 1104 loop : -0.47 (0.08), residues: 5544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP F 437 HIS 0.013 0.002 HIS X 34 PHE 0.028 0.002 PHE G 198 TYR 0.025 0.002 TYR O 15 ARG 0.012 0.001 ARG Q 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 895 time to evaluate : 6.883 Fit side-chains REVERT: A 116 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: B 366 MET cc_start: 0.6961 (ttt) cc_final: 0.6596 (ttt) REVERT: G 116 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: Q 152 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7994 (ptt-90) REVERT: U 152 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7976 (ptt180) REVERT: J 366 MET cc_start: 0.7042 (ttt) cc_final: 0.6646 (ttt) REVERT: D 55 MET cc_start: 0.8371 (mtm) cc_final: 0.8091 (mtp) REVERT: D 248 HIS cc_start: 0.9171 (OUTLIER) cc_final: 0.8654 (t-170) REVERT: F 551 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: H 27 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7160 (t0) REVERT: H 501 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7429 (mptt) REVERT: N 366 MET cc_start: 0.6992 (ttt) cc_final: 0.6682 (ttt) REVERT: N 467 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8454 (pt) REVERT: N 551 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: P 330 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5801 (pm20) REVERT: T 27 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7147 (t70) REVERT: T 55 MET cc_start: 0.8340 (mtm) cc_final: 0.7932 (mtp) REVERT: T 551 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: V 322 HIS cc_start: 0.7932 (m-70) cc_final: 0.7713 (m90) REVERT: V 551 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: X 501 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7603 (mttt) REVERT: X 551 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7273 (tp30) outliers start: 50 outliers final: 33 residues processed: 932 average time/residue: 2.0173 time to fit residues: 2384.3320 Evaluate side-chains 936 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 887 time to evaluate : 6.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain M residue 22 LYS Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain J residue 501 LYS Chi-restraints excluded: chain D residue 248 HIS Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 501 LYS Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain L residue 501 LYS Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 501 LYS Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 330 GLU Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain T residue 501 LYS Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain V residue 503 ILE Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 597 optimal weight: 3.9990 chunk 801 optimal weight: 0.5980 chunk 230 optimal weight: 8.9990 chunk 693 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 753 optimal weight: 8.9990 chunk 315 optimal weight: 0.8980 chunk 773 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 208 ASN B 34 HIS B 558 ASN C 79 HIS C 97 HIS C 224 HIS E 79 HIS G 97 HIS I 97 HIS K 97 HIS M 97 HIS J 544 HIS D 34 HIS D 314 HIS H 333 GLN H 535 HIS L 34 HIS L 314 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS V 333 GLN X 34 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.105495 restraints weight = 58022.045| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 0.80 r_work: 0.3040 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.2736 rms_B_bonded: 4.96 restraints_weight: 0.1250 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 76092 Z= 0.207 Angle : 0.654 8.744 102648 Z= 0.365 Chirality : 0.050 0.257 11400 Planarity : 0.005 0.049 13440 Dihedral : 6.922 74.682 10432 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.64 % Allowed : 9.72 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.08), residues: 9600 helix: 1.21 (0.09), residues: 2964 sheet: 0.34 (0.14), residues: 1104 loop : -0.44 (0.08), residues: 5532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP F 437 HIS 0.012 0.002 HIS X 34 PHE 0.027 0.002 PHE G 198 TYR 0.024 0.002 TYR C 15 ARG 0.010 0.001 ARG Q 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34640.04 seconds wall clock time: 591 minutes 30.90 seconds (35490.90 seconds total)