Starting phenix.real_space_refine on Sun Sep 29 18:23:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/09_2024/6qsu_4629.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/09_2024/6qsu_4629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/09_2024/6qsu_4629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/09_2024/6qsu_4629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/09_2024/6qsu_4629.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qsu_4629/09_2024/6qsu_4629.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 46788 2.51 5 N 12972 2.21 5 O 15614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 336 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: 75758 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' NI': 2, 'BME': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "O" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "S" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "U" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "W" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "J" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 85 Classifications: {'water': 85} Link IDs: {None: 84} Chain: "H" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 90 Classifications: {'water': 90} Link IDs: {None: 89} Chain: "L" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "N" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "P" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Classifications: {'water': 79} Link IDs: {None: 78} Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 86 Classifications: {'water': 86} Link IDs: {None: 85} Chain: "T" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "V" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Time building chain proxies: 29.98, per 1000 atoms: 0.40 Number of scatterers: 75758 At special positions: 0 Unit cell: (171.243, 177.705, 172.32, 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 15614 8.00 N 12972 7.00 C 46788 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: 14.44 Conformation dependent library (CDL) restraints added in 6.8 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: 384 helices and 132 sheets defined 37.3% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.41 Creating SS restraints... Processing helix chain 'A' and resid 4 through 27 Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.584A pdb=" N VAL A 70 " --> pdb=" O PRO A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.612A pdb=" N MET A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.564A pdb=" N VAL A 150 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.658A pdb=" N PHE A 162 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 221 removed outlier: 3.540A pdb=" N LYS A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.828A 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: 3.721A pdb=" N SER B 113 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.528A pdb=" N THR B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 174 through 186 removed outlier: 4.258A 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 Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 227 through 242 Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 285 through 292 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 340 removed outlier: 4.022A pdb=" N ARG B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 353 removed outlier: 3.841A pdb=" N ASP B 348 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 3.934A 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: 3.695A pdb=" N LYS B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 417 removed outlier: 3.890A 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 490 removed outlier: 3.893A 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 27 Processing helix chain 'C' and resid 31 through 50 Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 66 through 70 removed outlier: 3.584A pdb=" N VAL C 70 " --> pdb=" O PRO C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.612A pdb=" N MET C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.564A pdb=" N VAL C 150 " --> pdb=" O PHE C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 162 removed outlier: 3.658A pdb=" N PHE C 162 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 221 removed outlier: 3.540A pdb=" N LYS C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 Processing helix chain 'E' and resid 31 through 50 Processing helix chain 'E' and resid 53 through 61 Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.584A pdb=" N VAL E 70 " --> pdb=" O PRO E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 78 removed outlier: 3.611A pdb=" N MET E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.563A pdb=" N VAL E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 162 removed outlier: 3.658A pdb=" N PHE E 162 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 221 removed outlier: 3.540A pdb=" N LYS E 212 " --> pdb=" O ASN E 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 27 Processing helix chain 'G' and resid 31 through 50 Processing helix chain 'G' and resid 53 through 61 Processing helix chain 'G' and resid 66 through 70 removed outlier: 3.583A pdb=" N VAL G 70 " --> pdb=" O PRO G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.612A pdb=" N MET G 77 " --> pdb=" O GLY G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 150 removed outlier: 3.564A pdb=" N VAL G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 162 removed outlier: 3.658A pdb=" N PHE G 162 " --> pdb=" O GLU G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 221 removed outlier: 3.540A pdb=" N LYS G 212 " --> pdb=" O ASN G 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 27 Processing helix chain 'I' and resid 31 through 50 Processing helix chain 'I' and resid 53 through 61 Processing helix chain 'I' and resid 66 through 70 removed outlier: 3.584A pdb=" N VAL I 70 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 78 removed outlier: 3.612A pdb=" N MET I 77 " --> pdb=" O GLY I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 150 removed outlier: 3.564A pdb=" N VAL I 150 " --> pdb=" O PHE I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 162 removed outlier: 3.657A pdb=" N PHE I 162 " --> pdb=" O GLU I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 221 removed outlier: 3.539A pdb=" N LYS I 212 " --> pdb=" O ASN I 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 27 Processing helix chain 'K' and resid 31 through 50 Processing helix chain 'K' and resid 53 through 61 Processing helix chain 'K' and resid 66 through 70 removed outlier: 3.584A pdb=" N VAL K 70 " --> pdb=" O PRO K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 78 removed outlier: 3.612A pdb=" N MET K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 150 removed outlier: 3.564A pdb=" N VAL K 150 " --> pdb=" O PHE K 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 162 removed outlier: 3.657A pdb=" N PHE K 162 " --> pdb=" O GLU K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 221 removed outlier: 3.540A pdb=" N LYS K 212 " --> pdb=" O ASN K 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE K 213 " --> pdb=" O GLU K 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 27 Processing helix chain 'M' and resid 31 through 50 Processing helix chain 'M' and resid 53 through 61 Processing helix chain 'M' and resid 66 through 70 removed outlier: 3.584A pdb=" N VAL M 70 " --> pdb=" O PRO M 67 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.611A pdb=" N MET M 77 " --> pdb=" O GLY M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 150 removed outlier: 3.564A pdb=" N VAL M 150 " --> pdb=" O PHE M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 162 removed outlier: 3.658A pdb=" N PHE M 162 " --> pdb=" O GLU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 221 removed outlier: 3.540A pdb=" N LYS M 212 " --> pdb=" O ASN M 208 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE M 213 " --> pdb=" O GLU M 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 27 Processing helix chain 'O' and resid 31 through 50 Processing helix chain 'O' and resid 53 through 61 Processing helix chain 'O' and resid 66 through 70 removed outlier: 3.584A pdb=" N VAL O 70 " --> pdb=" O PRO O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 78 removed outlier: 3.612A pdb=" N MET O 77 " --> pdb=" O GLY O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 150 removed outlier: 3.564A pdb=" N VAL O 150 " --> pdb=" O PHE O 147 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 162 removed outlier: 3.657A pdb=" N PHE O 162 " --> pdb=" O GLU O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 221 removed outlier: 3.540A pdb=" N LYS O 212 " --> pdb=" O ASN O 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE O 213 " --> pdb=" O GLU O 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 27 Processing helix chain 'Q' and resid 31 through 50 Processing helix chain 'Q' and resid 53 through 61 Processing helix chain 'Q' and resid 66 through 70 removed outlier: 3.584A pdb=" N VAL Q 70 " --> pdb=" O PRO Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 78 removed outlier: 3.611A pdb=" N MET Q 77 " --> pdb=" O GLY Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 146 through 150 removed outlier: 3.564A pdb=" N VAL Q 150 " --> pdb=" O PHE Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 162 removed outlier: 3.657A pdb=" N PHE Q 162 " --> pdb=" O GLU Q 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 207 through 221 removed outlier: 3.539A pdb=" N LYS Q 212 " --> pdb=" O ASN Q 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE Q 213 " --> pdb=" O GLU Q 209 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 27 Processing helix chain 'S' and resid 31 through 50 Processing helix chain 'S' and resid 53 through 61 Processing helix chain 'S' and resid 66 through 70 removed outlier: 3.584A pdb=" N VAL S 70 " --> pdb=" O PRO S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 78 removed outlier: 3.611A pdb=" N MET S 77 " --> pdb=" O GLY S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 150 removed outlier: 3.564A pdb=" N VAL S 150 " --> pdb=" O PHE S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 162 removed outlier: 3.658A pdb=" N PHE S 162 " --> pdb=" O GLU S 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 207 through 221 removed outlier: 3.540A pdb=" N LYS S 212 " --> pdb=" O ASN S 208 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE S 213 " --> pdb=" O GLU S 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 27 Processing helix chain 'U' and resid 31 through 50 Processing helix chain 'U' and resid 53 through 61 Processing helix chain 'U' and resid 66 through 70 removed outlier: 3.584A pdb=" N VAL U 70 " --> pdb=" O PRO U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 78 removed outlier: 3.611A pdb=" N MET U 77 " --> pdb=" O GLY U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 150 removed outlier: 3.563A pdb=" N VAL U 150 " --> pdb=" O PHE U 147 " (cutoff:3.500A) Processing helix chain 'U' and resid 157 through 162 removed outlier: 3.657A pdb=" N PHE U 162 " --> pdb=" O GLU U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 207 through 221 removed outlier: 3.540A pdb=" N LYS U 212 " --> pdb=" O ASN U 208 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE U 213 " --> pdb=" O GLU U 209 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 27 Processing helix chain 'W' and resid 31 through 50 Processing helix chain 'W' and resid 53 through 61 Processing helix chain 'W' and resid 66 through 70 removed outlier: 3.584A pdb=" N VAL W 70 " --> pdb=" O PRO W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 78 removed outlier: 3.611A pdb=" N MET W 77 " --> pdb=" O GLY W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 146 through 150 removed outlier: 3.563A pdb=" N VAL W 150 " --> pdb=" O PHE W 147 " (cutoff:3.500A) Processing helix chain 'W' and resid 157 through 162 removed outlier: 3.657A pdb=" N PHE W 162 " --> pdb=" O GLU W 159 " (cutoff:3.500A) Processing helix chain 'W' and resid 207 through 221 removed outlier: 3.540A pdb=" N LYS W 212 " --> pdb=" O ASN W 208 " (cutoff:3.500A) removed outlier: 3.828A 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: 3.720A pdb=" N SER J 113 " --> pdb=" O ASN J 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 151 removed outlier: 3.528A pdb=" N THR J 147 " --> pdb=" O GLN J 143 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER J 151 " --> pdb=" O THR J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 170 Processing helix chain 'J' and resid 174 through 186 removed outlier: 4.258A 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 Processing helix chain 'J' and resid 223 through 225 No H-bonds generated for 'chain 'J' and resid 223 through 225' Processing helix chain 'J' and resid 227 through 242 Processing helix chain 'J' and resid 257 through 266 Processing helix chain 'J' and resid 285 through 292 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 340 removed outlier: 4.022A pdb=" N ARG J 340 " --> pdb=" O ASP J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 353 removed outlier: 3.840A pdb=" N ASP J 348 " --> pdb=" O ILE J 344 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.695A pdb=" N LYS J 408 " --> pdb=" O ARG J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 417 removed outlier: 3.889A 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 490 removed outlier: 3.894A 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: 3.719A pdb=" N SER D 113 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 151 removed outlier: 3.527A pdb=" N THR D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 151 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 170 Processing helix chain 'D' and resid 174 through 186 removed outlier: 4.259A 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 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'D' and resid 257 through 266 Processing helix chain 'D' and resid 285 through 292 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 340 removed outlier: 4.022A pdb=" N ARG D 340 " --> pdb=" O ASP D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 353 removed outlier: 3.841A pdb=" N ASP D 348 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.695A pdb=" N LYS D 408 " --> pdb=" O ARG D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 417 removed outlier: 3.889A 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 490 removed outlier: 3.894A 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: 3.720A pdb=" N SER F 113 " --> pdb=" O ASN F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 151 removed outlier: 3.527A pdb=" N THR F 147 " --> pdb=" O GLN F 143 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER F 151 " --> pdb=" O THR F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 170 Processing helix chain 'F' and resid 174 through 186 removed outlier: 4.259A 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 Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'F' and resid 227 through 242 Processing helix chain 'F' and resid 257 through 266 Processing helix chain 'F' and resid 285 through 292 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 340 removed outlier: 4.022A pdb=" N ARG F 340 " --> pdb=" O ASP F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 353 removed outlier: 3.841A pdb=" N ASP F 348 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.695A pdb=" N LYS F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 417 removed outlier: 3.890A 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 490 removed outlier: 3.894A 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: 3.720A pdb=" N SER H 113 " --> pdb=" O ASN H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 151 removed outlier: 3.527A pdb=" N THR H 147 " --> pdb=" O GLN H 143 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 151 " --> pdb=" O THR H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 170 Processing helix chain 'H' and resid 174 through 186 removed outlier: 4.259A 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 Processing helix chain 'H' and resid 223 through 225 No H-bonds generated for 'chain 'H' and resid 223 through 225' Processing helix chain 'H' and resid 227 through 242 Processing helix chain 'H' and resid 257 through 266 Processing helix chain 'H' and resid 285 through 292 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 340 removed outlier: 4.022A pdb=" N ARG H 340 " --> pdb=" O ASP H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 353 removed outlier: 3.841A pdb=" N ASP H 348 " --> pdb=" O ILE H 344 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.695A pdb=" N LYS H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 417 removed outlier: 3.889A 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 490 removed outlier: 3.894A 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: 3.721A pdb=" N SER L 113 " --> pdb=" O ASN L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 151 removed outlier: 3.527A pdb=" N THR L 147 " --> pdb=" O GLN L 143 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER L 151 " --> pdb=" O THR L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 170 Processing helix chain 'L' and resid 174 through 186 removed outlier: 4.259A 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 Processing helix chain 'L' and resid 223 through 225 No H-bonds generated for 'chain 'L' and resid 223 through 225' Processing helix chain 'L' and resid 227 through 242 Processing helix chain 'L' and resid 257 through 266 Processing helix chain 'L' and resid 285 through 292 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 340 removed outlier: 4.023A pdb=" N ARG L 340 " --> pdb=" O ASP L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 353 removed outlier: 3.841A pdb=" N ASP L 348 " --> pdb=" O ILE L 344 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.695A pdb=" N LYS L 408 " --> pdb=" O ARG L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 417 removed outlier: 3.890A 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 490 removed outlier: 3.893A 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: 3.720A pdb=" N SER N 113 " --> pdb=" O ASN N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 151 removed outlier: 3.527A pdb=" N THR N 147 " --> pdb=" O GLN N 143 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER N 151 " --> pdb=" O THR N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 170 Processing helix chain 'N' and resid 174 through 186 removed outlier: 4.259A 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 Processing helix chain 'N' and resid 223 through 225 No H-bonds generated for 'chain 'N' and resid 223 through 225' Processing helix chain 'N' and resid 227 through 242 Processing helix chain 'N' and resid 257 through 266 Processing helix chain 'N' and resid 285 through 292 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 340 removed outlier: 4.022A pdb=" N ARG N 340 " --> pdb=" O ASP N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 340 through 353 removed outlier: 3.841A pdb=" N ASP N 348 " --> pdb=" O ILE N 344 " (cutoff:3.500A) removed outlier: 3.934A 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: 3.695A pdb=" N LYS N 408 " --> pdb=" O ARG N 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 410 through 417 removed outlier: 3.890A 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 490 removed outlier: 3.893A 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: 3.720A pdb=" N SER P 113 " --> pdb=" O ASN P 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 151 removed outlier: 3.527A pdb=" N THR P 147 " --> pdb=" O GLN P 143 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER P 151 " --> pdb=" O THR P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 170 Processing helix chain 'P' and resid 174 through 186 removed outlier: 4.259A 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 Processing helix chain 'P' and resid 223 through 225 No H-bonds generated for 'chain 'P' and resid 223 through 225' Processing helix chain 'P' and resid 227 through 242 Processing helix chain 'P' and resid 257 through 266 Processing helix chain 'P' and resid 285 through 292 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 340 removed outlier: 4.022A pdb=" N ARG P 340 " --> pdb=" O ASP P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 340 through 353 removed outlier: 3.841A pdb=" N ASP P 348 " --> pdb=" O ILE P 344 " (cutoff:3.500A) removed outlier: 3.934A 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: 3.695A pdb=" N LYS P 408 " --> pdb=" O ARG P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 410 through 417 removed outlier: 3.889A 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 490 removed outlier: 3.893A 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: 3.720A pdb=" N SER R 113 " --> pdb=" O ASN R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 151 removed outlier: 3.528A pdb=" N THR R 147 " --> pdb=" O GLN R 143 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER R 151 " --> pdb=" O THR R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 170 Processing helix chain 'R' and resid 174 through 186 removed outlier: 4.259A 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 Processing helix chain 'R' and resid 223 through 225 No H-bonds generated for 'chain 'R' and resid 223 through 225' Processing helix chain 'R' and resid 227 through 242 Processing helix chain 'R' and resid 257 through 266 Processing helix chain 'R' and resid 285 through 292 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 340 removed outlier: 4.022A pdb=" N ARG R 340 " --> pdb=" O ASP R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 353 removed outlier: 3.841A pdb=" N ASP R 348 " --> pdb=" O ILE R 344 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.696A pdb=" N LYS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 410 through 417 removed outlier: 3.889A 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 490 removed outlier: 3.893A 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: 3.721A pdb=" N SER T 113 " --> pdb=" O ASN T 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 143 through 151 removed outlier: 3.527A pdb=" N THR T 147 " --> pdb=" O GLN T 143 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER T 151 " --> pdb=" O THR T 147 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 170 Processing helix chain 'T' and resid 174 through 186 removed outlier: 4.259A 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 Processing helix chain 'T' and resid 223 through 225 No H-bonds generated for 'chain 'T' and resid 223 through 225' Processing helix chain 'T' and resid 227 through 242 Processing helix chain 'T' and resid 257 through 266 Processing helix chain 'T' and resid 285 through 292 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 340 removed outlier: 4.022A pdb=" N ARG T 340 " --> pdb=" O ASP T 336 " (cutoff:3.500A) Processing helix chain 'T' and resid 340 through 353 removed outlier: 3.841A pdb=" N ASP T 348 " --> pdb=" O ILE T 344 " (cutoff:3.500A) removed outlier: 3.932A 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: 3.695A pdb=" N LYS T 408 " --> pdb=" O ARG T 404 " (cutoff:3.500A) Processing helix chain 'T' and resid 410 through 417 removed outlier: 3.889A 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 490 removed outlier: 3.895A 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: 3.720A pdb=" N SER V 113 " --> pdb=" O ASN V 110 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 151 removed outlier: 3.527A pdb=" N THR V 147 " --> pdb=" O GLN V 143 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER V 151 " --> pdb=" O THR V 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 164 through 170 Processing helix chain 'V' and resid 174 through 186 removed outlier: 4.259A 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 Processing helix chain 'V' and resid 223 through 225 No H-bonds generated for 'chain 'V' and resid 223 through 225' Processing helix chain 'V' and resid 227 through 242 Processing helix chain 'V' and resid 257 through 266 Processing helix chain 'V' and resid 285 through 292 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 340 removed outlier: 4.022A pdb=" N ARG V 340 " --> pdb=" O ASP V 336 " (cutoff:3.500A) Processing helix chain 'V' and resid 340 through 353 removed outlier: 3.841A pdb=" N ASP V 348 " --> pdb=" O ILE V 344 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.696A pdb=" N LYS V 408 " --> pdb=" O ARG V 404 " (cutoff:3.500A) Processing helix chain 'V' and resid 410 through 417 removed outlier: 3.890A 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 490 removed outlier: 3.893A 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: 3.720A pdb=" N SER X 113 " --> pdb=" O ASN X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 151 removed outlier: 3.527A pdb=" N THR X 147 " --> pdb=" O GLN X 143 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER X 151 " --> pdb=" O THR X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 170 Processing helix chain 'X' and resid 174 through 186 removed outlier: 4.259A 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 Processing helix chain 'X' and resid 223 through 225 No H-bonds generated for 'chain 'X' and resid 223 through 225' Processing helix chain 'X' and resid 227 through 242 Processing helix chain 'X' and resid 257 through 266 Processing helix chain 'X' and resid 285 through 292 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 340 removed outlier: 4.022A pdb=" N ARG X 340 " --> pdb=" O ASP X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 340 through 353 removed outlier: 3.841A pdb=" N ASP X 348 " --> pdb=" O ILE X 344 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.695A pdb=" N LYS X 408 " --> pdb=" O ARG X 404 " (cutoff:3.500A) Processing helix chain 'X' and resid 410 through 417 removed outlier: 3.890A 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 490 removed outlier: 3.894A 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: 5.193A pdb=" N ILE B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS B 89 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 80 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 76 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR B 82 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU B 74 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA B 84 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN B 72 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE B 69 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS B 89 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY B 80 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL B 76 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR B 82 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU B 74 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA B 84 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN B 72 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL B 128 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 74 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ALA B 130 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N VAL B 76 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET B 448 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 6.624A 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: 6.577A pdb=" N GLY B 132 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE B 157 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP B 134 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLY B 159 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N HIS B 136 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY B 217 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE B 218 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS B 248 " --> pdb=" O PHE B 218 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE B 220 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL B 245 " --> pdb=" O HIS B 271 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET B 270 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA B 298 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR B 272 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR B 300 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 491 through 494 Processing sheet with id=AB2, first strand: chain 'B' and resid 536 through 538 Processing sheet with id=AB3, first strand: chain 'C' and resid 80 through 87 Processing sheet with id=AB4, first strand: chain 'C' and resid 111 through 112 Processing sheet with id=AB5, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'C' and resid 139 through 142 Processing sheet with id=AB8, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AB9, first strand: chain 'E' and resid 80 through 87 Processing sheet with id=AC1, first strand: chain 'E' and resid 111 through 112 Processing sheet with id=AC2, first strand: chain 'E' and resid 118 through 120 Processing sheet with id=AC3, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AC4, first strand: chain 'E' and resid 139 through 142 Processing sheet with id=AC5, first strand: chain 'E' and resid 194 through 195 Processing sheet with id=AC6, first strand: chain 'G' and resid 80 through 87 Processing sheet with id=AC7, first strand: chain 'G' and resid 111 through 112 Processing sheet with id=AC8, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AC9, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AD1, first strand: chain 'G' and resid 139 through 142 Processing sheet with id=AD2, first strand: chain 'G' and resid 194 through 195 Processing sheet with id=AD3, first strand: chain 'I' and resid 80 through 87 Processing sheet with id=AD4, first strand: chain 'I' and resid 111 through 112 Processing sheet with id=AD5, first strand: chain 'I' and resid 118 through 120 Processing sheet with id=AD6, first strand: chain 'I' and resid 154 through 155 Processing sheet with id=AD7, first strand: chain 'I' and resid 139 through 142 Processing sheet with id=AD8, first strand: chain 'I' and resid 194 through 195 Processing sheet with id=AD9, first strand: chain 'K' and resid 80 through 87 Processing sheet with id=AE1, first strand: chain 'K' and resid 111 through 112 Processing sheet with id=AE2, first strand: chain 'K' and resid 118 through 120 Processing sheet with id=AE3, first strand: chain 'K' and resid 154 through 155 Processing sheet with id=AE4, first strand: chain 'K' and resid 139 through 142 Processing sheet with id=AE5, first strand: chain 'K' and resid 194 through 195 Processing sheet with id=AE6, first strand: chain 'M' and resid 80 through 87 Processing sheet with id=AE7, first strand: chain 'M' and resid 111 through 112 Processing sheet with id=AE8, first strand: chain 'M' and resid 118 through 120 Processing sheet with id=AE9, first strand: chain 'M' and resid 154 through 155 Processing sheet with id=AF1, first strand: chain 'M' and resid 139 through 142 Processing sheet with id=AF2, first strand: chain 'M' and resid 194 through 195 Processing sheet with id=AF3, first strand: chain 'O' and resid 80 through 87 Processing sheet with id=AF4, first strand: chain 'O' and resid 111 through 112 Processing sheet with id=AF5, first strand: chain 'O' and resid 118 through 120 Processing sheet with id=AF6, first strand: chain 'O' and resid 154 through 155 Processing sheet with id=AF7, first strand: chain 'O' and resid 139 through 142 Processing sheet with id=AF8, first strand: chain 'O' and resid 194 through 195 Processing sheet with id=AF9, first strand: chain 'Q' and resid 80 through 87 Processing sheet with id=AG1, first strand: chain 'Q' and resid 111 through 112 Processing sheet with id=AG2, first strand: chain 'Q' and resid 118 through 120 Processing sheet with id=AG3, first strand: chain 'Q' and resid 154 through 155 Processing sheet with id=AG4, first strand: chain 'Q' and resid 139 through 142 Processing sheet with id=AG5, first strand: chain 'Q' and resid 194 through 195 Processing sheet with id=AG6, first strand: chain 'S' and resid 80 through 87 Processing sheet with id=AG7, first strand: chain 'S' and resid 111 through 112 Processing sheet with id=AG8, first strand: chain 'S' and resid 118 through 120 Processing sheet with id=AG9, first strand: chain 'S' and resid 154 through 155 Processing sheet with id=AH1, first strand: chain 'S' and resid 139 through 142 Processing sheet with id=AH2, first strand: chain 'S' and resid 194 through 195 Processing sheet with id=AH3, first strand: chain 'U' and resid 80 through 87 Processing sheet with id=AH4, first strand: chain 'U' and resid 111 through 112 Processing sheet with id=AH5, first strand: chain 'U' and resid 118 through 120 removed outlier: 3.560A pdb=" N LYS V 2 " --> pdb=" O ILE U 120 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'U' and resid 154 through 155 Processing sheet with id=AH7, first strand: chain 'U' and resid 139 through 142 Processing sheet with id=AH8, first strand: chain 'U' and resid 194 through 195 Processing sheet with id=AH9, first strand: chain 'W' and resid 80 through 87 Processing sheet with id=AI1, first strand: chain 'W' and resid 111 through 112 Processing sheet with id=AI2, first strand: chain 'W' and resid 118 through 120 Processing sheet with id=AI3, first strand: chain 'W' and resid 154 through 155 Processing sheet with id=AI4, first strand: chain 'W' and resid 139 through 142 Processing sheet with id=AI5, first strand: chain 'W' and resid 194 through 195 Processing sheet with id=AI6, first strand: chain 'J' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS J 89 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY J 80 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL J 76 " --> pdb=" O GLY J 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR J 82 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU J 74 " --> pdb=" O TYR J 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA J 84 " --> pdb=" O ASN J 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN J 72 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE J 69 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS J 89 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY J 80 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL J 76 " --> pdb=" O GLY J 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR J 82 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU J 74 " --> pdb=" O TYR J 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA J 84 " --> pdb=" O ASN J 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN J 72 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL J 128 " --> pdb=" O ASN J 72 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU J 74 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA J 130 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL J 76 " --> pdb=" O ALA J 130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET J 448 " --> pdb=" O LEU J 436 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE J 449 " --> pdb=" O ALA J 456 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 132 through 138 removed outlier: 6.576A pdb=" N GLY J 132 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE J 157 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP J 134 " --> pdb=" O ILE J 157 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLY J 159 " --> pdb=" O ASP J 134 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N HIS J 136 " --> pdb=" O GLY J 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY J 217 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE J 218 " --> pdb=" O ALA J 246 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS J 248 " --> pdb=" O PHE J 218 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE J 220 " --> pdb=" O HIS J 248 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL J 245 " --> pdb=" O HIS J 271 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET J 270 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA J 298 " --> pdb=" O MET J 270 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR J 272 " --> pdb=" O ALA J 298 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR J 300 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 491 through 494 Processing sheet with id=AJ1, first strand: chain 'J' and resid 536 through 538 Processing sheet with id=AJ2, first strand: chain 'D' and resid 92 through 97 removed outlier: 5.194A pdb=" N ILE D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS D 89 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL D 76 " --> pdb=" O GLY D 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR D 82 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU D 74 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA D 84 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN D 72 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE D 69 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'D' and resid 92 through 97 removed outlier: 5.194A pdb=" N ILE D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS D 89 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY D 80 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL D 76 " --> pdb=" O GLY D 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR D 82 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU D 74 " --> pdb=" O TYR D 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA D 84 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN D 72 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL D 128 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU D 74 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ALA D 130 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL D 76 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET D 448 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE D 449 " --> pdb=" O ALA D 456 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 132 through 138 removed outlier: 6.575A pdb=" N GLY D 132 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE D 157 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP D 134 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLY D 159 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N HIS D 136 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY D 217 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE D 218 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS D 248 " --> pdb=" O PHE D 218 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE D 220 " --> pdb=" O HIS D 248 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL D 245 " --> pdb=" O HIS D 271 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET D 270 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA D 298 " --> pdb=" O MET D 270 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR D 272 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR D 300 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 491 through 494 Processing sheet with id=AJ6, first strand: chain 'D' and resid 536 through 538 Processing sheet with id=AJ7, first strand: chain 'F' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS F 89 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY F 80 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL F 76 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR F 82 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU F 74 " --> pdb=" O TYR F 82 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ALA F 84 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN F 72 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE F 69 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'F' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS F 89 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY F 80 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL F 76 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR F 82 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU F 74 " --> pdb=" O TYR F 82 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ALA F 84 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN F 72 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL F 128 " --> pdb=" O ASN F 72 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 74 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ALA F 130 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL F 76 " --> pdb=" O ALA F 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET F 448 " --> pdb=" O LEU F 436 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE F 449 " --> pdb=" O ALA F 456 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'F' and resid 132 through 138 removed outlier: 6.576A pdb=" N GLY F 132 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE F 157 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP F 134 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLY F 159 " --> pdb=" O ASP F 134 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N HIS F 136 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY F 217 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE F 218 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS F 248 " --> pdb=" O PHE F 218 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE F 220 " --> pdb=" O HIS F 248 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL F 245 " --> pdb=" O HIS F 271 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET F 270 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA F 298 " --> pdb=" O MET F 270 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N THR F 272 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR F 300 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'F' and resid 491 through 494 Processing sheet with id=AK2, first strand: chain 'F' and resid 536 through 538 Processing sheet with id=AK3, first strand: chain 'H' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS H 89 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL H 76 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR H 82 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU H 74 " --> pdb=" O TYR H 82 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ALA H 84 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN H 72 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE H 69 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'H' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS H 89 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL H 76 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR H 82 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU H 74 " --> pdb=" O TYR H 82 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ALA H 84 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN H 72 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL H 128 " --> pdb=" O ASN H 72 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU H 74 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA H 130 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL H 76 " --> pdb=" O ALA H 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET H 448 " --> pdb=" O LEU H 436 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE H 449 " --> pdb=" O ALA H 456 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'H' and resid 132 through 138 removed outlier: 6.577A pdb=" N GLY H 132 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE H 157 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP H 134 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLY H 159 " --> pdb=" O ASP H 134 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N HIS H 136 " --> pdb=" O GLY H 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY H 217 " --> pdb=" O PHE H 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE H 218 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS H 248 " --> pdb=" O PHE H 218 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE H 220 " --> pdb=" O HIS H 248 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL H 245 " --> pdb=" O HIS H 271 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET H 270 " --> pdb=" O LEU H 296 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA H 298 " --> pdb=" O MET H 270 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR H 272 " --> pdb=" O ALA H 298 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR H 300 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'H' and resid 491 through 494 Processing sheet with id=AK7, first strand: chain 'H' and resid 536 through 538 Processing sheet with id=AK8, first strand: chain 'L' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LYS L 89 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY L 80 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL L 76 " --> pdb=" O GLY L 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR L 82 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU L 74 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA L 84 " --> pdb=" O ASN L 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN L 72 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE L 69 " --> pdb=" O LEU L 121 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'L' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LYS L 89 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY L 80 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL L 76 " --> pdb=" O GLY L 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR L 82 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LEU L 74 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA L 84 " --> pdb=" O ASN L 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN L 72 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL L 128 " --> pdb=" O ASN L 72 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU L 74 " --> pdb=" O VAL L 128 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ALA L 130 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL L 76 " --> pdb=" O ALA L 130 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET L 448 " --> pdb=" O LEU L 436 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE L 449 " --> pdb=" O ALA L 456 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'L' and resid 132 through 138 removed outlier: 6.576A pdb=" N GLY L 132 " --> pdb=" O THR L 155 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE L 157 " --> pdb=" O GLY L 132 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP L 134 " --> pdb=" O ILE L 157 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLY L 159 " --> pdb=" O ASP L 134 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N HIS L 136 " --> pdb=" O GLY L 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY L 217 " --> pdb=" O PHE L 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE L 218 " --> pdb=" O ALA L 246 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS L 248 " --> pdb=" O PHE L 218 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE L 220 " --> pdb=" O HIS L 248 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL L 245 " --> pdb=" O HIS L 271 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET L 270 " --> pdb=" O LEU L 296 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA L 298 " --> pdb=" O MET L 270 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR L 272 " --> pdb=" O ALA L 298 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR L 300 " --> pdb=" O THR L 272 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'L' and resid 491 through 494 Processing sheet with id=AL3, first strand: chain 'L' and resid 536 through 538 Processing sheet with id=AL4, first strand: chain 'N' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE N 93 " --> pdb=" O LYS N 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS N 89 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL N 76 " --> pdb=" O GLY N 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR N 82 " --> pdb=" O LEU N 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU N 74 " --> pdb=" O TYR N 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA N 84 " --> pdb=" O ASN N 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN N 72 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE N 69 " --> pdb=" O LEU N 121 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'N' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE N 93 " --> pdb=" O LYS N 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS N 89 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL N 76 " --> pdb=" O GLY N 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR N 82 " --> pdb=" O LEU N 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU N 74 " --> pdb=" O TYR N 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA N 84 " --> pdb=" O ASN N 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN N 72 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL N 128 " --> pdb=" O ASN N 72 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU N 74 " --> pdb=" O VAL N 128 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA N 130 " --> pdb=" O LEU N 74 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N VAL N 76 " --> pdb=" O ALA N 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET N 448 " --> pdb=" O LEU N 436 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE N 449 " --> pdb=" O ALA N 456 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'N' and resid 132 through 138 removed outlier: 6.576A pdb=" N GLY N 132 " --> pdb=" O THR N 155 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE N 157 " --> pdb=" O GLY N 132 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP N 134 " --> pdb=" O ILE N 157 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLY N 159 " --> pdb=" O ASP N 134 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N HIS N 136 " --> pdb=" O GLY N 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY N 217 " --> pdb=" O PHE N 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE N 218 " --> pdb=" O ALA N 246 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS N 248 " --> pdb=" O PHE N 218 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE N 220 " --> pdb=" O HIS N 248 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL N 245 " --> pdb=" O HIS N 271 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET N 270 " --> pdb=" O LEU N 296 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA N 298 " --> pdb=" O MET N 270 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR N 272 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR N 300 " --> pdb=" O THR N 272 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'N' and resid 491 through 494 Processing sheet with id=AL8, first strand: chain 'N' and resid 536 through 538 Processing sheet with id=AL9, first strand: chain 'P' and resid 92 through 97 removed outlier: 5.194A pdb=" N ILE P 93 " --> pdb=" O LYS P 89 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LYS P 89 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY P 80 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL P 76 " --> pdb=" O GLY P 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR P 82 " --> pdb=" O LEU P 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU P 74 " --> pdb=" O TYR P 82 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ALA P 84 " --> pdb=" O ASN P 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN P 72 " --> pdb=" O ALA P 84 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE P 69 " --> pdb=" O LEU P 121 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'P' and resid 92 through 97 removed outlier: 5.194A pdb=" N ILE P 93 " --> pdb=" O LYS P 89 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LYS P 89 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY P 80 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL P 76 " --> pdb=" O GLY P 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR P 82 " --> pdb=" O LEU P 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU P 74 " --> pdb=" O TYR P 82 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ALA P 84 " --> pdb=" O ASN P 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN P 72 " --> pdb=" O ALA P 84 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL P 128 " --> pdb=" O ASN P 72 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU P 74 " --> pdb=" O VAL P 128 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA P 130 " --> pdb=" O LEU P 74 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL P 76 " --> pdb=" O ALA P 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET P 448 " --> pdb=" O LEU P 436 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE P 449 " --> pdb=" O ALA P 456 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'P' and resid 132 through 138 removed outlier: 6.577A pdb=" N GLY P 132 " --> pdb=" O THR P 155 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE P 157 " --> pdb=" O GLY P 132 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP P 134 " --> pdb=" O ILE P 157 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLY P 159 " --> pdb=" O ASP P 134 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N HIS P 136 " --> pdb=" O GLY P 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY P 217 " --> pdb=" O PHE P 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE P 218 " --> pdb=" O ALA P 246 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS P 248 " --> pdb=" O PHE P 218 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE P 220 " --> pdb=" O HIS P 248 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL P 245 " --> pdb=" O HIS P 271 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET P 270 " --> pdb=" O LEU P 296 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA P 298 " --> pdb=" O MET P 270 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR P 272 " --> pdb=" O ALA P 298 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR P 300 " --> pdb=" O THR P 272 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'P' and resid 491 through 494 Processing sheet with id=AM4, first strand: chain 'P' and resid 536 through 538 Processing sheet with id=AM5, first strand: chain 'R' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE R 93 " --> pdb=" O LYS R 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS R 89 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL R 76 " --> pdb=" O GLY R 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR R 82 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU R 74 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA R 84 " --> pdb=" O ASN R 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN R 72 " --> pdb=" O ALA R 84 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE R 69 " --> pdb=" O LEU R 121 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'R' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE R 93 " --> pdb=" O LYS R 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS R 89 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL R 76 " --> pdb=" O GLY R 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR R 82 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU R 74 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA R 84 " --> pdb=" O ASN R 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN R 72 " --> pdb=" O ALA R 84 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL R 128 " --> pdb=" O ASN R 72 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU R 74 " --> pdb=" O VAL R 128 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA R 130 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL R 76 " --> pdb=" O ALA R 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET R 448 " --> pdb=" O LEU R 436 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE R 449 " --> pdb=" O ALA R 456 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'R' and resid 132 through 138 removed outlier: 6.577A pdb=" N GLY R 132 " --> pdb=" O THR R 155 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE R 157 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP R 134 " --> pdb=" O ILE R 157 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLY R 159 " --> pdb=" O ASP R 134 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N HIS R 136 " --> pdb=" O GLY R 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY R 217 " --> pdb=" O PHE R 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE R 218 " --> pdb=" O ALA R 246 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS R 248 " --> pdb=" O PHE R 218 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE R 220 " --> pdb=" O HIS R 248 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL R 245 " --> pdb=" O HIS R 271 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET R 270 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA R 298 " --> pdb=" O MET R 270 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR R 272 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR R 300 " --> pdb=" O THR R 272 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'R' and resid 491 through 494 Processing sheet with id=AM9, first strand: chain 'R' and resid 536 through 538 Processing sheet with id=AN1, first strand: chain 'T' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE T 93 " --> pdb=" O LYS T 89 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LYS T 89 " --> pdb=" O ILE T 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY T 80 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL T 76 " --> pdb=" O GLY T 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR T 82 " --> pdb=" O LEU T 74 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU T 74 " --> pdb=" O TYR T 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA T 84 " --> pdb=" O ASN T 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN T 72 " --> pdb=" O ALA T 84 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE T 69 " --> pdb=" O LEU T 121 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'T' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE T 93 " --> pdb=" O LYS T 89 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LYS T 89 " --> pdb=" O ILE T 93 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY T 80 " --> pdb=" O VAL T 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL T 76 " --> pdb=" O GLY T 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR T 82 " --> pdb=" O LEU T 74 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU T 74 " --> pdb=" O TYR T 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA T 84 " --> pdb=" O ASN T 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN T 72 " --> pdb=" O ALA T 84 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL T 128 " --> pdb=" O ASN T 72 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU T 74 " --> pdb=" O VAL T 128 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA T 130 " --> pdb=" O LEU T 74 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL T 76 " --> pdb=" O ALA T 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET T 448 " --> pdb=" O LEU T 436 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE T 449 " --> pdb=" O ALA T 456 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'T' and resid 132 through 138 removed outlier: 6.577A pdb=" N GLY T 132 " --> pdb=" O THR T 155 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE T 157 " --> pdb=" O GLY T 132 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP T 134 " --> pdb=" O ILE T 157 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLY T 159 " --> pdb=" O ASP T 134 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N HIS T 136 " --> pdb=" O GLY T 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY T 217 " --> pdb=" O PHE T 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE T 218 " --> pdb=" O ALA T 246 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS T 248 " --> pdb=" O PHE T 218 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE T 220 " --> pdb=" O HIS T 248 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL T 245 " --> pdb=" O HIS T 271 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET T 270 " --> pdb=" O LEU T 296 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA T 298 " --> pdb=" O MET T 270 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR T 272 " --> pdb=" O ALA T 298 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR T 300 " --> pdb=" O THR T 272 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'T' and resid 491 through 494 Processing sheet with id=AN5, first strand: chain 'T' and resid 536 through 538 Processing sheet with id=AN6, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.194A pdb=" N ILE V 93 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS V 89 " --> pdb=" O ILE V 93 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY V 80 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL V 76 " --> pdb=" O GLY V 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR V 82 " --> pdb=" O LEU V 74 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU V 74 " --> pdb=" O TYR V 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA V 84 " --> pdb=" O ASN V 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN V 72 " --> pdb=" O ALA V 84 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE V 69 " --> pdb=" O LEU V 121 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'V' and resid 92 through 97 removed outlier: 5.194A pdb=" N ILE V 93 " --> pdb=" O LYS V 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS V 89 " --> pdb=" O ILE V 93 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY V 80 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL V 76 " --> pdb=" O GLY V 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR V 82 " --> pdb=" O LEU V 74 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU V 74 " --> pdb=" O TYR V 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA V 84 " --> pdb=" O ASN V 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN V 72 " --> pdb=" O ALA V 84 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL V 128 " --> pdb=" O ASN V 72 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU V 74 " --> pdb=" O VAL V 128 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ALA V 130 " --> pdb=" O LEU V 74 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL V 76 " --> pdb=" O ALA V 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET V 448 " --> pdb=" O LEU V 436 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE V 449 " --> pdb=" O ALA V 456 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'V' and resid 132 through 138 removed outlier: 6.576A pdb=" N GLY V 132 " --> pdb=" O THR V 155 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE V 157 " --> pdb=" O GLY V 132 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP V 134 " --> pdb=" O ILE V 157 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLY V 159 " --> pdb=" O ASP V 134 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N HIS V 136 " --> pdb=" O GLY V 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY V 217 " --> pdb=" O PHE V 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE V 218 " --> pdb=" O ALA V 246 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS V 248 " --> pdb=" O PHE V 218 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE V 220 " --> pdb=" O HIS V 248 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL V 245 " --> pdb=" O HIS V 271 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N MET V 270 " --> pdb=" O LEU V 296 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA V 298 " --> pdb=" O MET V 270 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR V 272 " --> pdb=" O ALA V 298 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR V 300 " --> pdb=" O THR V 272 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'V' and resid 491 through 494 Processing sheet with id=AO1, first strand: chain 'V' and resid 536 through 538 Processing sheet with id=AO2, first strand: chain 'X' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE X 93 " --> pdb=" O LYS X 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS X 89 " --> pdb=" O ILE X 93 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY X 80 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL X 76 " --> pdb=" O GLY X 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR X 82 " --> pdb=" O LEU X 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU X 74 " --> pdb=" O TYR X 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA X 84 " --> pdb=" O ASN X 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN X 72 " --> pdb=" O ALA X 84 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE X 69 " --> pdb=" O LEU X 121 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'X' and resid 92 through 97 removed outlier: 5.193A pdb=" N ILE X 93 " --> pdb=" O LYS X 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS X 89 " --> pdb=" O ILE X 93 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY X 80 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL X 76 " --> pdb=" O GLY X 80 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR X 82 " --> pdb=" O LEU X 74 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU X 74 " --> pdb=" O TYR X 82 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ALA X 84 " --> pdb=" O ASN X 72 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN X 72 " --> pdb=" O ALA X 84 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL X 128 " --> pdb=" O ASN X 72 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU X 74 " --> pdb=" O VAL X 128 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA X 130 " --> pdb=" O LEU X 74 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL X 76 " --> pdb=" O ALA X 130 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET X 448 " --> pdb=" O LEU X 436 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE X 449 " --> pdb=" O ALA X 456 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'X' and resid 132 through 138 removed outlier: 6.577A pdb=" N GLY X 132 " --> pdb=" O THR X 155 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE X 157 " --> pdb=" O GLY X 132 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASP X 134 " --> pdb=" O ILE X 157 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLY X 159 " --> pdb=" O ASP X 134 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N HIS X 136 " --> pdb=" O GLY X 159 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY X 217 " --> pdb=" O PHE X 195 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE X 218 " --> pdb=" O ALA X 246 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N HIS X 248 " --> pdb=" O PHE X 218 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE X 220 " --> pdb=" O HIS X 248 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL X 245 " --> pdb=" O HIS X 271 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET X 270 " --> pdb=" O LEU X 296 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA X 298 " --> pdb=" O MET X 270 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR X 272 " --> pdb=" O ALA X 298 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR X 300 " --> pdb=" O THR X 272 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'X' and resid 491 through 494 Processing sheet with id=AO6, first strand: chain 'X' and resid 536 through 538 2963 hydrogen bonds defined for protein. 7776 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: 36.22 Time building geometry restraints manager: 17.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 22441 1.33 - 1.45: 10750 1.45 - 1.57: 42037 1.57 - 1.69: 0 1.69 - 1.81: 660 Bond restraints: 75888 Sorted by residual: bond pdb=" NZ KCX D 219 " pdb=" CX KCX D 219 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" NZ KCX J 219 " pdb=" CX KCX J 219 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" NZ KCX X 219 " pdb=" CX KCX X 219 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" NZ KCX F 219 " pdb=" CX KCX F 219 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" NZ KCX V 219 " pdb=" CX KCX V 219 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.84e+01 ... (remaining 75883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 100081 1.70 - 3.41: 1868 3.41 - 5.11: 267 5.11 - 6.81: 76 6.81 - 8.52: 56 Bond angle restraints: 102348 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 121.54 130.06 -8.52 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C GLY G 197 " pdb=" N PHE G 198 " pdb=" CA PHE G 198 " ideal model delta sigma weight residual 121.54 130.06 -8.52 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C GLY C 197 " pdb=" N PHE C 198 " pdb=" CA PHE C 198 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C GLY O 197 " pdb=" N PHE O 198 " pdb=" CA PHE O 198 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C GLY I 197 " pdb=" N PHE I 198 " pdb=" CA PHE I 198 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.97e+01 ... (remaining 102343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 42263 16.84 - 33.69: 2701 33.69 - 50.53: 456 50.53 - 67.37: 252 67.37 - 84.22: 144 Dihedral angle restraints: 45816 sinusoidal: 18384 harmonic: 27432 Sorted by residual: dihedral pdb=" CA GLU D 188 " pdb=" C GLU D 188 " pdb=" N TYR D 189 " pdb=" CA TYR D 189 " ideal model delta harmonic sigma weight residual -180.00 -152.89 -27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA GLU R 188 " pdb=" C GLU R 188 " pdb=" N TYR R 189 " pdb=" CA TYR R 189 " ideal model delta harmonic sigma weight residual -180.00 -152.91 -27.09 0 5.00e+00 4.00e-02 2.94e+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 -152.91 -27.09 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 45813 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 6100 0.035 - 0.070: 3521 0.070 - 0.105: 1295 0.105 - 0.140: 436 0.140 - 0.174: 48 Chirality restraints: 11400 Sorted by residual: chirality pdb=" CA ASN L 301 " pdb=" N ASN L 301 " pdb=" C ASN L 301 " pdb=" CB ASN L 301 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA THR D 469 " pdb=" N THR D 469 " pdb=" C THR D 469 " pdb=" CB THR D 469 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA ASN T 301 " pdb=" N ASN T 301 " pdb=" C ASN T 301 " pdb=" CB ASN T 301 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 11397 not shown) Planarity restraints: 13404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 283 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO L 284 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO L 284 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 284 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA P 283 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO P 284 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO P 284 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO P 284 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA X 283 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO X 284 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO X 284 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO X 284 " -0.025 5.00e-02 4.00e+02 ... (remaining 13401 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 496 2.51 - 3.11: 57853 3.11 - 3.71: 130046 3.71 - 4.30: 203849 4.30 - 4.90: 314666 Nonbonded interactions: 706910 Sorted by model distance: nonbonded pdb=" NE2 HIS J 274 " pdb="NI NI J 601 " model vdw 1.918 2.260 nonbonded pdb=" NE2 HIS T 274 " pdb="NI NI T 601 " model vdw 1.919 2.260 nonbonded pdb=" NE2 HIS V 274 " pdb="NI NI V 601 " model vdw 1.919 2.260 nonbonded pdb=" NE2 HIS R 274 " pdb="NI NI R 601 " model vdw 1.919 2.260 nonbonded pdb=" NE2 HIS L 274 " pdb="NI NI L 601 " model vdw 1.919 2.260 ... (remaining 706905 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: 1.390 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: 0.050 Extract box with map and model: 2.040 Check model and map are aligned: 0.420 Set scattering table: 0.510 Process input model: 135.140 Find NCS groups from input model: 2.400 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:8.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 0.086 75888 Z= 0.378 Angle : 0.652 8.517 102348 Z= 0.362 Chirality : 0.050 0.174 11400 Planarity : 0.005 0.048 13404 Dihedral : 13.440 84.218 28272 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.61 % Allowed : 4.84 % Favored : 94.55 % 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: 0.27 (0.08), residues: 9600 helix: 0.88 (0.09), residues: 2856 sheet: 1.18 (0.15), residues: 1020 loop : -0.34 (0.08), residues: 5724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 377 HIS 0.008 0.002 HIS V 248 PHE 0.019 0.002 PHE A 198 TYR 0.025 0.002 TYR K 15 ARG 0.005 0.001 ARG V 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 1483 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1435 time to evaluate : 6.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7810 (mtt) cc_final: 0.7429 (mtm) REVERT: A 220 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7630 (mt-10) REVERT: B 104 MET cc_start: 0.8355 (mmm) cc_final: 0.8078 (mmm) REVERT: B 353 MET cc_start: 0.8528 (mtp) cc_final: 0.8148 (mtp) REVERT: E 44 MET cc_start: 0.8622 (mtm) cc_final: 0.8402 (mtm) REVERT: E 125 LYS cc_start: 0.7670 (mmmt) cc_final: 0.7428 (mmtm) REVERT: G 12 MET cc_start: 0.8397 (tmm) cc_final: 0.8154 (tmm) REVERT: G 60 GLU cc_start: 0.8133 (tt0) cc_final: 0.7917 (tt0) REVERT: K 77 MET cc_start: 0.8627 (mtp) cc_final: 0.8383 (mtp) REVERT: K 125 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7651 (mmtm) REVERT: M 71 MET cc_start: 0.8882 (mtp) cc_final: 0.8298 (mtp) REVERT: Q 71 MET cc_start: 0.8819 (mtp) cc_final: 0.8438 (mtp) REVERT: Q 203 ASP cc_start: 0.8057 (m-30) cc_final: 0.7761 (m-30) REVERT: S 71 MET cc_start: 0.8828 (mtp) cc_final: 0.8574 (mtp) REVERT: U 58 MET cc_start: 0.7988 (mtt) cc_final: 0.7746 (mtm) REVERT: U 97 HIS cc_start: 0.8241 (m90) cc_final: 0.7816 (m90) REVERT: J 12 MET cc_start: 0.8506 (mtm) cc_final: 0.8250 (mtp) REVERT: J 60 ASN cc_start: 0.8147 (m110) cc_final: 0.7933 (m110) REVERT: J 92 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8545 (mptt) REVERT: J 319 MET cc_start: 0.6688 (mmm) cc_final: 0.6235 (tpp) REVERT: J 540 PRO cc_start: 0.8470 (Cg_exo) cc_final: 0.8250 (Cg_endo) REVERT: D 92 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8332 (mmtp) REVERT: D 333 GLN cc_start: 0.7984 (mt0) cc_final: 0.7782 (mt0) REVERT: D 478 MET cc_start: 0.8542 (mmt) cc_final: 0.7841 (mmp) REVERT: D 548 ASP cc_start: 0.8236 (m-30) cc_final: 0.8025 (m-30) REVERT: F 65 GLU cc_start: 0.7825 (tt0) cc_final: 0.7572 (tt0) REVERT: H 65 GLU cc_start: 0.7672 (tt0) cc_final: 0.7435 (tt0) REVERT: H 182 MET cc_start: 0.8760 (mmm) cc_final: 0.8472 (mmm) REVERT: H 317 MET cc_start: 0.7844 (ttm) cc_final: 0.7529 (ttp) REVERT: H 353 MET cc_start: 0.8457 (mtp) cc_final: 0.8235 (mtp) REVERT: H 478 MET cc_start: 0.8699 (mmt) cc_final: 0.8496 (mmt) REVERT: L 262 MET cc_start: 0.8548 (mmm) cc_final: 0.8236 (mmm) REVERT: L 478 MET cc_start: 0.8714 (mmt) cc_final: 0.7620 (mmt) REVERT: N 110 ASN cc_start: 0.8543 (m-40) cc_final: 0.8250 (m-40) REVERT: N 182 MET cc_start: 0.8799 (mmm) cc_final: 0.8509 (mmm) REVERT: N 191 MET cc_start: 0.8717 (tpp) cc_final: 0.8458 (tpp) REVERT: N 276 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: N 319 MET cc_start: 0.6773 (mmm) cc_final: 0.6239 (tpp) REVERT: N 460 MET cc_start: 0.8691 (tpp) cc_final: 0.8462 (tpp) REVERT: P 105 GLN cc_start: 0.8675 (mt0) cc_final: 0.8414 (mt0) REVERT: P 182 MET cc_start: 0.8879 (mmm) cc_final: 0.8641 (mmm) REVERT: P 276 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: P 543 TYR cc_start: 0.8845 (m-10) cc_final: 0.8642 (m-10) REVERT: R 478 MET cc_start: 0.8767 (mmt) cc_final: 0.8475 (mmp) REVERT: R 533 THR cc_start: 0.8756 (p) cc_final: 0.8550 (p) REVERT: X 182 MET cc_start: 0.8581 (mmm) cc_final: 0.8191 (mmm) REVERT: X 319 MET cc_start: 0.6742 (mmm) cc_final: 0.6461 (tpp) outliers start: 48 outliers final: 2 residues processed: 1468 average time/residue: 1.7978 time to fit residues: 3403.4360 Evaluate side-chains 1035 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1031 time to evaluate : 6.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain O residue 236 ILE Chi-restraints excluded: chain N residue 276 GLU Chi-restraints excluded: chain P residue 276 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 800 optimal weight: 0.9990 chunk 718 optimal weight: 0.9980 chunk 398 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 484 optimal weight: 0.6980 chunk 383 optimal weight: 4.9990 chunk 743 optimal weight: 1.9990 chunk 287 optimal weight: 0.8980 chunk 451 optimal weight: 0.9980 chunk 553 optimal weight: 5.9990 chunk 860 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 309 ASN B 539 ASN C 97 HIS E 97 HIS G 97 HIS I 31 ASN I 97 HIS I 133 ASN I 208 ASN K 151 ASN O 97 HIS Q 97 HIS S 97 HIS W 208 ASN D 34 HIS D 309 ASN F 34 HIS F 60 ASN F 333 GLN H 34 HIS H 309 ASN H 333 GLN L 34 HIS L 309 ASN N 34 HIS N 314 HIS N 333 GLN N 544 HIS P 60 ASN P 333 GLN R 60 ASN R 309 ASN R 333 GLN T 34 HIS T 60 ASN T 309 ASN T 314 HIS T 535 HIS V 34 HIS ** V 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 309 ASN V 333 GLN V 512 GLN X 309 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 75888 Z= 0.169 Angle : 0.545 7.994 102348 Z= 0.300 Chirality : 0.046 0.200 11400 Planarity : 0.004 0.053 13404 Dihedral : 5.084 42.506 10366 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.96 % Allowed : 9.75 % Favored : 88.29 % 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: 0.63 (0.09), residues: 9600 helix: 1.53 (0.10), residues: 2844 sheet: 1.08 (0.15), residues: 1068 loop : -0.26 (0.08), residues: 5688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 377 HIS 0.010 0.001 HIS J 535 PHE 0.013 0.001 PHE U 198 TYR 0.023 0.001 TYR G 15 ARG 0.007 0.000 ARG W 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 1260 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1105 time to evaluate : 6.474 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7766 (mtt) cc_final: 0.7483 (mtm) REVERT: A 80 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: A 130 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7931 (tptm) REVERT: B 550 LYS cc_start: 0.8291 (mtpp) cc_final: 0.7921 (mtmt) REVERT: B 565 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8428 (tt) REVERT: C 80 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7615 (pt0) REVERT: E 125 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7444 (mmtm) REVERT: E 203 ASP cc_start: 0.7781 (m-30) cc_final: 0.7439 (m-30) REVERT: G 12 MET cc_start: 0.8268 (tmm) cc_final: 0.8037 (tmm) REVERT: G 60 GLU cc_start: 0.8104 (tt0) cc_final: 0.7866 (tt0) REVERT: G 80 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: M 58 MET cc_start: 0.7824 (mtt) cc_final: 0.7624 (mtm) REVERT: M 71 MET cc_start: 0.8940 (mtp) cc_final: 0.8447 (mtp) REVERT: M 130 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7523 (ttmm) REVERT: O 125 LYS cc_start: 0.7876 (mmpt) cc_final: 0.7630 (mmtm) REVERT: Q 71 MET cc_start: 0.8772 (mtp) cc_final: 0.8365 (mtp) REVERT: U 77 MET cc_start: 0.8426 (mtp) cc_final: 0.8218 (mtm) REVERT: U 97 HIS cc_start: 0.8267 (m90) cc_final: 0.7778 (m90) REVERT: U 209 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: W 60 GLU cc_start: 0.8045 (tt0) cc_final: 0.7827 (tt0) REVERT: J 1 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6268 (tmt) REVERT: J 12 MET cc_start: 0.8524 (mtm) cc_final: 0.8274 (mtp) REVERT: J 60 ASN cc_start: 0.8228 (m110) cc_final: 0.7998 (m110) REVERT: J 103 ASP cc_start: 0.7986 (m-30) cc_final: 0.7758 (m-30) REVERT: D 396 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7110 (t70) REVERT: D 548 ASP cc_start: 0.8191 (m-30) cc_final: 0.7946 (m-30) REVERT: D 565 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (tt) REVERT: F 27 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: F 154 THR cc_start: 0.8268 (p) cc_final: 0.8068 (p) REVERT: F 550 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7921 (mtpt) REVERT: H 65 GLU cc_start: 0.7714 (tt0) cc_final: 0.7497 (tt0) REVERT: H 182 MET cc_start: 0.8853 (mmm) cc_final: 0.8602 (mmm) REVERT: H 340 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.7888 (mtm-85) REVERT: H 353 MET cc_start: 0.8484 (mtp) cc_final: 0.8163 (mtp) REVERT: L 262 MET cc_start: 0.8551 (mmm) cc_final: 0.8154 (mmm) REVERT: L 478 MET cc_start: 0.8713 (mmt) cc_final: 0.8243 (mmt) REVERT: N 110 ASN cc_start: 0.8484 (m-40) cc_final: 0.8250 (m-40) REVERT: N 182 MET cc_start: 0.8877 (mmm) cc_final: 0.8573 (mmm) REVERT: N 191 MET cc_start: 0.8689 (tpp) cc_final: 0.8198 (tpp) REVERT: N 276 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7632 (tm-30) REVERT: N 319 MET cc_start: 0.6655 (mmm) cc_final: 0.6173 (tpp) REVERT: N 396 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7194 (t70) REVERT: N 537 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7246 (mm-30) REVERT: P 53 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: P 182 MET cc_start: 0.8892 (mmm) cc_final: 0.8548 (mmm) REVERT: P 276 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: P 319 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6589 (mpp) REVERT: P 396 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7112 (t70) REVERT: P 550 LYS cc_start: 0.8278 (mtpp) cc_final: 0.8022 (mtmt) REVERT: R 182 MET cc_start: 0.8913 (mmm) cc_final: 0.8613 (mmm) REVERT: R 478 MET cc_start: 0.8743 (mmt) cc_final: 0.8471 (mmp) REVERT: R 535 HIS cc_start: 0.8430 (t70) cc_final: 0.8075 (t-90) REVERT: R 550 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7887 (mtpt) REVERT: R 555 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7902 (ptpt) REVERT: T 550 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7692 (mtmt) REVERT: V 104 MET cc_start: 0.8401 (mmm) cc_final: 0.8046 (mmm) REVERT: V 239 ASP cc_start: 0.7994 (m-30) cc_final: 0.7764 (m-30) REVERT: V 288 LYS cc_start: 0.8480 (ptpp) cc_final: 0.8264 (ptmt) REVERT: X 182 MET cc_start: 0.8821 (mmm) cc_final: 0.8340 (mmm) REVERT: X 385 LYS cc_start: 0.8124 (mttp) cc_final: 0.7799 (mmtp) REVERT: X 478 MET cc_start: 0.8666 (mmt) cc_final: 0.7664 (mmt) REVERT: X 555 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7834 (ptpt) outliers start: 155 outliers final: 37 residues processed: 1170 average time/residue: 1.8090 time to fit residues: 2725.2552 Evaluate side-chains 1061 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1004 time to evaluate : 6.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain M residue 44 MET Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 55 MET Chi-restraints excluded: chain H residue 240 LYS Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 276 GLU Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 555 LYS Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 478 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 716 optimal weight: 4.9990 chunk 586 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 chunk 862 optimal weight: 8.9990 chunk 931 optimal weight: 0.0370 chunk 768 optimal weight: 6.9990 chunk 855 optimal weight: 3.9990 chunk 294 optimal weight: 0.8980 chunk 691 optimal weight: 8.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 168 ASN B 309 ASN B 539 ASN I 208 ASN K 151 ASN W 208 ASN J 168 ASN D 168 ASN D 203 ASN F 34 HIS F 333 GLN H 34 HIS H 168 ASN H 309 ASN H 539 ASN L 34 HIS L 309 ASN L 314 HIS L 333 GLN N 34 HIS N 168 ASN N 314 HIS P 314 HIS P 333 GLN R 34 HIS R 60 ASN T 34 HIS T 168 ASN T 309 ASN T 314 HIS V 34 HIS V 168 ASN V 333 GLN X 309 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 75888 Z= 0.212 Angle : 0.556 8.635 102348 Z= 0.302 Chirality : 0.047 0.200 11400 Planarity : 0.004 0.055 13404 Dihedral : 5.032 50.356 10362 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.05 % Allowed : 11.00 % Favored : 86.95 % 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: 0.61 (0.09), residues: 9600 helix: 1.51 (0.10), residues: 2844 sheet: 0.27 (0.13), residues: 1380 loop : -0.10 (0.09), residues: 5376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 377 HIS 0.008 0.001 HIS B 248 PHE 0.020 0.002 PHE W 198 TYR 0.023 0.002 TYR A 15 ARG 0.008 0.000 ARG K 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 1200 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1038 time to evaluate : 6.477 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7763 (mtt) cc_final: 0.7386 (mtm) REVERT: A 77 MET cc_start: 0.8306 (mtm) cc_final: 0.8089 (mtp) REVERT: A 80 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7604 (pt0) REVERT: A 130 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7889 (tptm) REVERT: B 550 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7902 (mtmt) REVERT: C 80 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7669 (pt0) REVERT: E 125 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7601 (mmtm) REVERT: G 12 MET cc_start: 0.8197 (tmm) cc_final: 0.7982 (tmm) REVERT: G 60 GLU cc_start: 0.8096 (tt0) cc_final: 0.7865 (tt0) REVERT: I 25 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6815 (mt-10) REVERT: K 80 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: K 125 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7712 (mmmt) REVERT: M 58 MET cc_start: 0.7917 (mtt) cc_final: 0.7659 (mtm) REVERT: M 71 MET cc_start: 0.8895 (mtp) cc_final: 0.8374 (mtp) REVERT: M 130 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7676 (ttmm) REVERT: O 122 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6448 (pm20) REVERT: Q 71 MET cc_start: 0.8787 (mtp) cc_final: 0.8471 (mtp) REVERT: Q 134 VAL cc_start: 0.8070 (OUTLIER) cc_final: 0.7861 (t) REVERT: U 209 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7775 (mp0) REVERT: J 60 ASN cc_start: 0.8281 (m110) cc_final: 0.8027 (m110) REVERT: J 103 ASP cc_start: 0.7979 (m-30) cc_final: 0.7731 (m-30) REVERT: D 396 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7131 (t70) REVERT: H 65 GLU cc_start: 0.7682 (tt0) cc_final: 0.7436 (tt0) REVERT: H 182 MET cc_start: 0.8900 (mmm) cc_final: 0.8581 (mmm) REVERT: H 212 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: H 311 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6775 (tt0) REVERT: H 353 MET cc_start: 0.8491 (mtp) cc_final: 0.8127 (mtp) REVERT: L 53 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: L 262 MET cc_start: 0.8514 (mmm) cc_final: 0.8176 (mmm) REVERT: L 550 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7993 (mtmt) REVERT: N 182 MET cc_start: 0.8870 (mmm) cc_final: 0.8546 (mmm) REVERT: N 191 MET cc_start: 0.8739 (tpp) cc_final: 0.8294 (tpp) REVERT: N 319 MET cc_start: 0.6656 (mmm) cc_final: 0.6106 (tpp) REVERT: N 396 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7247 (t70) REVERT: N 537 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7211 (mm-30) REVERT: P 27 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: P 276 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7445 (pm20) REVERT: P 288 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8294 (ptmt) REVERT: P 319 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6630 (mpp) REVERT: P 396 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7097 (t70) REVERT: P 421 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7230 (pt0) REVERT: P 537 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7482 (mm-30) REVERT: P 550 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7970 (mtmt) REVERT: R 182 MET cc_start: 0.8890 (mmm) cc_final: 0.8596 (mmm) REVERT: R 478 MET cc_start: 0.8760 (mmt) cc_final: 0.8496 (mmp) REVERT: R 555 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7947 (ptpt) REVERT: T 396 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7305 (t70) REVERT: T 559 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8076 (tttm) REVERT: V 288 LYS cc_start: 0.8454 (ptpp) cc_final: 0.8248 (ptmt) REVERT: V 319 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6222 (mpt) REVERT: V 385 LYS cc_start: 0.8279 (mttp) cc_final: 0.7981 (mttp) REVERT: V 537 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: X 182 MET cc_start: 0.8828 (mmm) cc_final: 0.8365 (mmm) REVERT: X 385 LYS cc_start: 0.8122 (mttp) cc_final: 0.7796 (mmtp) REVERT: X 478 MET cc_start: 0.8685 (mmt) cc_final: 0.7680 (mmt) REVERT: X 555 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7854 (ptpt) outliers start: 162 outliers final: 55 residues processed: 1113 average time/residue: 1.8593 time to fit residues: 2668.0401 Evaluate side-chains 1059 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 977 time to evaluate : 6.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 122 GLU Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain S residue 183 SER Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain J residue 319 MET Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 555 LYS Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain H residue 212 GLU Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 252 LEU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 316 ASP Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain P residue 537 GLU Chi-restraints excluded: chain P residue 567 SER Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 240 LYS Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 555 LYS Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 559 LYS Chi-restraints excluded: chain V residue 319 MET Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain V residue 537 GLU Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 852 optimal weight: 0.7980 chunk 648 optimal weight: 8.9990 chunk 447 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 411 optimal weight: 2.9990 chunk 579 optimal weight: 4.9990 chunk 865 optimal weight: 4.9990 chunk 916 optimal weight: 0.7980 chunk 452 optimal weight: 1.9990 chunk 820 optimal weight: 7.9990 chunk 246 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS B 539 ASN S 31 ASN W 208 ASN J 535 HIS D 309 ASN F 34 HIS F 314 HIS F 333 GLN H 34 HIS H 301 ASN H 309 ASN H 539 ASN L 34 HIS L 168 ASN L 309 ASN L 333 GLN N 34 HIS N 301 ASN N 314 HIS P 333 GLN R 34 HIS R 60 ASN T 34 HIS T 309 ASN T 314 HIS V 34 HIS ** V 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 HIS V 333 GLN X 309 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 75888 Z= 0.243 Angle : 0.564 10.070 102348 Z= 0.307 Chirality : 0.047 0.218 11400 Planarity : 0.004 0.053 13404 Dihedral : 5.073 47.107 10359 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.34 % Allowed : 11.46 % Favored : 86.20 % 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: 0.56 (0.08), residues: 9600 helix: 1.46 (0.10), residues: 2844 sheet: 0.56 (0.14), residues: 1260 loop : -0.21 (0.08), residues: 5496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 377 HIS 0.008 0.001 HIS B 248 PHE 0.020 0.002 PHE O 198 TYR 0.025 0.002 TYR E 15 ARG 0.008 0.000 ARG O 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 1211 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1026 time to evaluate : 6.488 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7778 (mtt) cc_final: 0.7404 (mtm) REVERT: A 77 MET cc_start: 0.8331 (mtm) cc_final: 0.8034 (mtp) REVERT: A 80 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7669 (pt0) REVERT: A 130 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7877 (tptm) REVERT: B 550 LYS cc_start: 0.8306 (mtpp) cc_final: 0.8056 (mtmt) REVERT: C 80 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7691 (pt0) REVERT: C 130 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7628 (tttp) REVERT: E 125 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7643 (mmtm) REVERT: G 12 MET cc_start: 0.8202 (tmm) cc_final: 0.7976 (tmm) REVERT: G 60 GLU cc_start: 0.8090 (tt0) cc_final: 0.7855 (tt0) REVERT: I 58 MET cc_start: 0.8076 (mtm) cc_final: 0.7790 (mtt) REVERT: K 80 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7616 (pt0) REVERT: K 125 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7762 (mmmt) REVERT: M 58 MET cc_start: 0.7863 (mtt) cc_final: 0.7589 (mtm) REVERT: M 71 MET cc_start: 0.8851 (mtp) cc_final: 0.8298 (mtp) REVERT: M 130 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7779 (ttmm) REVERT: O 72 ASP cc_start: 0.8120 (t0) cc_final: 0.7762 (t0) REVERT: Q 60 GLU cc_start: 0.7861 (tt0) cc_final: 0.7613 (tt0) REVERT: Q 71 MET cc_start: 0.8794 (mtp) cc_final: 0.8523 (mtp) REVERT: Q 80 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7641 (pt0) REVERT: U 116 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: U 209 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7731 (tp30) REVERT: J 60 ASN cc_start: 0.8298 (m110) cc_final: 0.8062 (m110) REVERT: J 103 ASP cc_start: 0.7959 (m-30) cc_final: 0.7748 (m-30) REVERT: D 2 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8154 (ttpp) REVERT: F 27 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7529 (m-30) REVERT: F 550 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7903 (mtpt) REVERT: H 65 GLU cc_start: 0.7690 (tt0) cc_final: 0.7438 (tt0) REVERT: H 182 MET cc_start: 0.8912 (mmm) cc_final: 0.8571 (mmm) REVERT: H 311 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6814 (tt0) REVERT: H 353 MET cc_start: 0.8488 (mtp) cc_final: 0.8159 (mtp) REVERT: H 537 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7270 (mm-30) REVERT: L 262 MET cc_start: 0.8526 (mmm) cc_final: 0.8205 (mmm) REVERT: L 366 MET cc_start: 0.7051 (ptp) cc_final: 0.6578 (ptp) REVERT: N 53 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: N 182 MET cc_start: 0.8857 (mmm) cc_final: 0.8539 (mmm) REVERT: N 191 MET cc_start: 0.8754 (tpp) cc_final: 0.8289 (tpp) REVERT: N 319 MET cc_start: 0.6671 (mmm) cc_final: 0.6083 (tpp) REVERT: N 396 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7233 (t70) REVERT: N 537 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7158 (mm-30) REVERT: P 27 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: P 53 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: P 276 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7386 (pm20) REVERT: P 319 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6590 (mpp) REVERT: P 396 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7127 (t70) REVERT: P 421 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7238 (pt0) REVERT: P 537 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7463 (mm-30) REVERT: P 550 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7953 (mtmt) REVERT: R 27 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7770 (m-30) REVERT: R 182 MET cc_start: 0.8891 (mmm) cc_final: 0.8611 (mmm) REVERT: R 319 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6075 (tpp) REVERT: R 478 MET cc_start: 0.8770 (mmt) cc_final: 0.8489 (mmp) REVERT: R 537 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: R 555 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7942 (ptpt) REVERT: T 1 MET cc_start: 0.7018 (tmm) cc_final: 0.6786 (tmm) REVERT: T 53 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: T 396 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7280 (t70) REVERT: T 551 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: T 555 LYS cc_start: 0.8131 (ptpp) cc_final: 0.7846 (mmtp) REVERT: V 204 ASP cc_start: 0.7971 (m-30) cc_final: 0.7758 (m-30) REVERT: V 288 LYS cc_start: 0.8451 (ptpp) cc_final: 0.8244 (ptmt) REVERT: V 319 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6372 (mpt) REVERT: X 182 MET cc_start: 0.8805 (mmm) cc_final: 0.8548 (mmm) REVERT: X 385 LYS cc_start: 0.8135 (mttp) cc_final: 0.7811 (mmtp) REVERT: X 478 MET cc_start: 0.8724 (mmt) cc_final: 0.7745 (mmt) REVERT: X 555 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7865 (ptpt) REVERT: X 559 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8008 (tttp) outliers start: 185 outliers final: 79 residues processed: 1112 average time/residue: 1.7748 time to fit residues: 2544.9615 Evaluate side-chains 1098 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 985 time to evaluate : 6.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 2 LYS Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 555 LYS Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain H residue 240 LYS Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 537 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 316 ASP Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 252 LEU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain P residue 537 GLU Chi-restraints excluded: chain P residue 559 LYS Chi-restraints excluded: chain P residue 567 SER Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 537 GLU Chi-restraints excluded: chain R residue 555 LYS Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 421 GLU Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 319 MET Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 559 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 763 optimal weight: 5.9990 chunk 520 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 682 optimal weight: 0.5980 chunk 378 optimal weight: 1.9990 chunk 781 optimal weight: 10.0000 chunk 633 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 467 optimal weight: 8.9990 chunk 822 optimal weight: 0.8980 chunk 231 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 HIS ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN S 31 ASN W 208 ASN ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN F 34 HIS F 314 HIS F 333 GLN H 34 HIS H 309 ASN H 539 ASN L 34 HIS ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS N 314 HIS P 333 GLN R 34 HIS R 60 ASN R 535 HIS T 34 HIS T 309 ASN V 34 HIS V 314 HIS V 333 GLN X 309 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 75888 Z= 0.213 Angle : 0.544 10.078 102348 Z= 0.296 Chirality : 0.046 0.207 11400 Planarity : 0.004 0.053 13404 Dihedral : 5.004 48.847 10359 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.33 % Allowed : 11.99 % Favored : 85.69 % 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: 0.58 (0.08), residues: 9600 helix: 1.51 (0.10), residues: 2844 sheet: 0.56 (0.14), residues: 1260 loop : -0.21 (0.08), residues: 5496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 181 HIS 0.007 0.001 HIS X 248 PHE 0.020 0.001 PHE O 198 TYR 0.024 0.002 TYR G 15 ARG 0.009 0.000 ARG O 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 1227 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1043 time to evaluate : 6.497 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7748 (mtt) cc_final: 0.7372 (mtm) REVERT: A 66 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7870 (mttm) REVERT: A 77 MET cc_start: 0.8276 (mtm) cc_final: 0.7952 (mtp) REVERT: A 80 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: A 130 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7854 (tptm) REVERT: B 394 LYS cc_start: 0.7543 (mtpt) cc_final: 0.7285 (ptpp) REVERT: B 550 LYS cc_start: 0.8275 (mtpp) cc_final: 0.8051 (mtmt) REVERT: C 80 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: C 130 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7603 (tttp) REVERT: E 125 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7579 (mmtm) REVERT: G 12 MET cc_start: 0.8155 (tmm) cc_final: 0.7945 (tmm) REVERT: G 60 GLU cc_start: 0.8068 (tt0) cc_final: 0.7833 (tt0) REVERT: I 25 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6874 (mt-10) REVERT: K 80 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7607 (pt0) REVERT: K 125 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7798 (mmmt) REVERT: K 219 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8287 (tppt) REVERT: M 58 MET cc_start: 0.7887 (mtt) cc_final: 0.7633 (mtm) REVERT: M 71 MET cc_start: 0.8815 (mtp) cc_final: 0.8216 (mtp) REVERT: M 130 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7785 (ttmm) REVERT: O 72 ASP cc_start: 0.8093 (t0) cc_final: 0.7742 (t0) REVERT: Q 51 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8190 (mptp) REVERT: Q 60 GLU cc_start: 0.7868 (tt0) cc_final: 0.7617 (tt0) REVERT: Q 71 MET cc_start: 0.8791 (mtp) cc_final: 0.8504 (mtp) REVERT: Q 80 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: Q 134 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7917 (t) REVERT: U 116 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7064 (mm-30) REVERT: U 209 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: J 1 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6134 (tmt) REVERT: J 51 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8139 (tt) REVERT: J 60 ASN cc_start: 0.8321 (m110) cc_final: 0.8081 (m110) REVERT: J 103 ASP cc_start: 0.7924 (m-30) cc_final: 0.7706 (m-30) REVERT: F 27 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: F 550 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7912 (mtpt) REVERT: H 65 GLU cc_start: 0.7672 (tt0) cc_final: 0.7422 (tt0) REVERT: H 182 MET cc_start: 0.8914 (mmm) cc_final: 0.8588 (mmm) REVERT: H 311 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6827 (tt0) REVERT: H 537 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7280 (mm-30) REVERT: L 53 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: L 262 MET cc_start: 0.8508 (mmm) cc_final: 0.8200 (mmm) REVERT: L 550 LYS cc_start: 0.8328 (mtpp) cc_final: 0.7934 (mtmt) REVERT: N 182 MET cc_start: 0.8858 (mmm) cc_final: 0.8539 (mmm) REVERT: N 191 MET cc_start: 0.8738 (tpp) cc_final: 0.8286 (tpp) REVERT: N 319 MET cc_start: 0.6658 (mmm) cc_final: 0.6075 (tpp) REVERT: N 396 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7228 (t70) REVERT: N 537 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: P 27 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7641 (m-30) REVERT: P 53 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: P 276 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: P 319 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6584 (mpp) REVERT: P 385 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8130 (mttm) REVERT: P 396 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7134 (t70) REVERT: P 421 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7232 (pt0) REVERT: P 537 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7434 (mm-30) REVERT: R 27 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: R 182 MET cc_start: 0.8885 (mmm) cc_final: 0.8617 (mmm) REVERT: R 319 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.6088 (tpp) REVERT: R 340 ARG cc_start: 0.8308 (mtm-85) cc_final: 0.8068 (mtm-85) REVERT: R 444 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8721 (p) REVERT: R 478 MET cc_start: 0.8727 (mmt) cc_final: 0.8432 (mmp) REVERT: R 537 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: T 1 MET cc_start: 0.7043 (tmm) cc_final: 0.6792 (tmm) REVERT: T 53 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: T 396 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.7303 (t70) REVERT: T 551 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: T 555 LYS cc_start: 0.8109 (ptpp) cc_final: 0.7836 (mmtp) REVERT: T 559 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8055 (tttm) REVERT: V 204 ASP cc_start: 0.7952 (m-30) cc_final: 0.7737 (m-30) REVERT: V 288 LYS cc_start: 0.8427 (ptpp) cc_final: 0.8225 (ptmt) REVERT: V 385 LYS cc_start: 0.8267 (mttp) cc_final: 0.8009 (mmtp) REVERT: V 537 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7315 (mt-10) REVERT: X 182 MET cc_start: 0.8808 (mmm) cc_final: 0.8589 (mmm) REVERT: X 385 LYS cc_start: 0.8130 (mttp) cc_final: 0.7810 (mmtp) REVERT: X 478 MET cc_start: 0.8717 (mmt) cc_final: 0.7976 (mmt) REVERT: X 555 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7863 (ptpt) outliers start: 184 outliers final: 84 residues processed: 1133 average time/residue: 1.7956 time to fit residues: 2618.9114 Evaluate side-chains 1127 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1003 time to evaluate : 6.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 51 LYS Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain S residue 183 SER Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 319 MET Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 240 LYS Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 537 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 316 ASP Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain L residue 503 ILE Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 252 LEU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 385 LYS Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 477 GLU Chi-restraints excluded: chain P residue 537 GLU Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 444 VAL Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 537 GLU Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain T residue 559 LYS Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain V residue 261 THR Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 319 MET Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain V residue 537 GLU Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 308 optimal weight: 9.9990 chunk 825 optimal weight: 4.9990 chunk 181 optimal weight: 0.4980 chunk 538 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 917 optimal weight: 10.0000 chunk 761 optimal weight: 5.9990 chunk 424 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 303 optimal weight: 8.9990 chunk 481 optimal weight: 0.9980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 34 HIS ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN S 31 ASN W 208 ASN J 535 HIS D 309 ASN F 34 HIS F 314 HIS F 333 GLN H 34 HIS H 309 ASN H 539 ASN L 34 HIS ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 333 GLN N 34 HIS N 314 HIS P 333 GLN R 34 HIS R 60 ASN R 535 HIS T 34 HIS T 314 HIS V 34 HIS ** V 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 HIS V 333 GLN X 309 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 75888 Z= 0.289 Angle : 0.588 10.267 102348 Z= 0.320 Chirality : 0.048 0.220 11400 Planarity : 0.005 0.052 13404 Dihedral : 5.155 47.148 10359 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.43 % Allowed : 12.34 % Favored : 85.23 % 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: 0.43 (0.08), residues: 9600 helix: 1.23 (0.10), residues: 2916 sheet: 0.71 (0.15), residues: 1140 loop : -0.28 (0.08), residues: 5544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP F 437 HIS 0.008 0.001 HIS X 248 PHE 0.020 0.002 PHE S 198 TYR 0.027 0.002 TYR O 15 ARG 0.009 0.001 ARG O 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 1207 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1015 time to evaluate : 6.529 Fit side-chains REVERT: A 58 MET cc_start: 0.7766 (mtt) cc_final: 0.7326 (mtm) REVERT: A 66 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7876 (mttm) REVERT: A 77 MET cc_start: 0.8339 (mtm) cc_final: 0.8087 (mtp) REVERT: A 80 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: A 130 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7880 (tptm) REVERT: A 219 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8173 (tppt) REVERT: B 2 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7891 (ttpp) REVERT: B 537 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7364 (mt-10) REVERT: B 550 LYS cc_start: 0.8287 (mtpp) cc_final: 0.8077 (mtmt) REVERT: C 80 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7686 (pt0) REVERT: C 130 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7653 (tttp) REVERT: E 125 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7615 (mmtm) REVERT: G 12 MET cc_start: 0.8200 (tmm) cc_final: 0.7988 (tmm) REVERT: G 71 MET cc_start: 0.8696 (mtp) cc_final: 0.8455 (mtm) REVERT: I 25 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6916 (mt-10) REVERT: K 80 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7644 (pt0) REVERT: K 125 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7793 (mmmt) REVERT: K 219 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8310 (tppt) REVERT: M 58 MET cc_start: 0.7835 (mtt) cc_final: 0.7569 (mtm) REVERT: M 71 MET cc_start: 0.8798 (mtp) cc_final: 0.8315 (mtp) REVERT: M 80 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7642 (pt0) REVERT: M 130 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7825 (ttmm) REVERT: O 72 ASP cc_start: 0.8176 (t0) cc_final: 0.7820 (t0) REVERT: Q 51 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8253 (mptp) REVERT: Q 60 GLU cc_start: 0.7885 (tt0) cc_final: 0.7648 (tt0) REVERT: Q 71 MET cc_start: 0.8829 (mtp) cc_final: 0.8557 (mtp) REVERT: Q 80 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: Q 134 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7938 (t) REVERT: U 116 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7085 (mm-30) REVERT: U 209 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: J 1 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6164 (tmt) REVERT: J 60 ASN cc_start: 0.8338 (m110) cc_final: 0.8104 (m110) REVERT: J 103 ASP cc_start: 0.7907 (m-30) cc_final: 0.7682 (m-30) REVERT: D 537 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: F 154 THR cc_start: 0.8322 (p) cc_final: 0.8118 (p) REVERT: H 27 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7764 (m-30) REVERT: H 65 GLU cc_start: 0.7765 (tt0) cc_final: 0.7511 (tt0) REVERT: H 182 MET cc_start: 0.8910 (mmm) cc_final: 0.8547 (mmm) REVERT: H 311 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6791 (tt0) REVERT: H 537 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: L 340 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.8031 (mtm180) REVERT: L 550 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7935 (mtmt) REVERT: L 555 LYS cc_start: 0.8316 (ptpt) cc_final: 0.8095 (mttt) REVERT: N 182 MET cc_start: 0.8816 (mmm) cc_final: 0.8571 (mmm) REVERT: N 191 MET cc_start: 0.8761 (tpp) cc_final: 0.8291 (tpp) REVERT: N 319 MET cc_start: 0.6685 (mmm) cc_final: 0.6097 (tpp) REVERT: N 396 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7237 (t70) REVERT: N 537 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: P 27 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: P 276 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: P 319 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6624 (mpp) REVERT: P 385 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8140 (mttm) REVERT: P 396 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7145 (t70) REVERT: P 421 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7243 (pt0) REVERT: R 27 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: R 98 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7517 (tptp) REVERT: R 182 MET cc_start: 0.8873 (mmm) cc_final: 0.8560 (mmm) REVERT: R 319 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6115 (tpp) REVERT: R 340 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8064 (mtm-85) REVERT: R 478 MET cc_start: 0.8789 (mmt) cc_final: 0.8515 (mmp) REVERT: R 537 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: T 1 MET cc_start: 0.7082 (tmm) cc_final: 0.6824 (tmm) REVERT: T 53 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: T 396 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7290 (t70) REVERT: T 551 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: T 555 LYS cc_start: 0.8149 (ptpp) cc_final: 0.7869 (mmtp) REVERT: T 559 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8048 (tttm) REVERT: V 288 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8224 (ptmt) REVERT: V 537 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: X 182 MET cc_start: 0.8771 (mmm) cc_final: 0.8508 (mmm) REVERT: X 385 LYS cc_start: 0.8133 (mttp) cc_final: 0.7817 (mmtp) REVERT: X 478 MET cc_start: 0.8786 (mmt) cc_final: 0.7762 (mmt) REVERT: X 555 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7879 (ptpt) outliers start: 192 outliers final: 96 residues processed: 1107 average time/residue: 1.8276 time to fit residues: 2602.5844 Evaluate side-chains 1145 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1008 time to evaluate : 6.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain B residue 2 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 51 LYS Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain S residue 183 SER Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 366 MET Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 537 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 565 LEU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 537 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 252 LEU Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 316 ASP Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain L residue 503 ILE Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 252 LEU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 385 LYS Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 477 GLU Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 98 LYS Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 537 GLU Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 421 GLU Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain T residue 559 LYS Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain V residue 261 THR Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain V residue 537 GLU Chi-restraints excluded: chain V residue 565 LEU Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 884 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 chunk 522 optimal weight: 5.9990 chunk 669 optimal weight: 10.0000 chunk 518 optimal weight: 0.6980 chunk 772 optimal weight: 0.6980 chunk 512 optimal weight: 8.9990 chunk 913 optimal weight: 0.6980 chunk 571 optimal weight: 5.9990 chunk 557 optimal weight: 10.0000 chunk 421 optimal weight: 10.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 34 HIS ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN S 31 ASN W 208 ASN ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN F 34 HIS F 168 ASN F 314 HIS F 333 GLN H 34 HIS H 309 ASN H 539 ASN L 34 HIS ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 333 GLN N 34 HIS N 314 HIS P 333 GLN R 34 HIS T 34 HIS ** T 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 309 ASN T 314 HIS V 34 HIS V 314 HIS V 333 GLN V 544 HIS X 309 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 75888 Z= 0.171 Angle : 0.520 9.512 102348 Z= 0.282 Chirality : 0.045 0.213 11400 Planarity : 0.004 0.054 13404 Dihedral : 4.923 50.644 10359 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.07 % Allowed : 13.00 % Favored : 84.93 % 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: 0.61 (0.08), residues: 9600 helix: 1.59 (0.10), residues: 2844 sheet: 0.55 (0.14), residues: 1260 loop : -0.22 (0.08), residues: 5496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 181 HIS 0.006 0.001 HIS X 248 PHE 0.020 0.001 PHE O 198 TYR 0.022 0.001 TYR C 15 ARG 0.010 0.000 ARG O 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 1212 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1048 time to evaluate : 6.489 Fit side-chains REVERT: A 58 MET cc_start: 0.7772 (mtt) cc_final: 0.7412 (mtm) REVERT: A 66 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7876 (mttm) REVERT: A 77 MET cc_start: 0.8206 (mtm) cc_final: 0.7965 (mtp) REVERT: A 80 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: A 130 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7811 (tptm) REVERT: B 53 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7837 (tm-30) REVERT: B 394 LYS cc_start: 0.7580 (mtpt) cc_final: 0.7254 (ptpp) REVERT: C 80 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: C 130 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7594 (tttp) REVERT: E 125 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7632 (mmtm) REVERT: G 80 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7425 (pt0) REVERT: I 25 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6804 (mt-10) REVERT: I 58 MET cc_start: 0.7994 (mtm) cc_final: 0.7727 (mtm) REVERT: K 77 MET cc_start: 0.8433 (mtm) cc_final: 0.8106 (mtp) REVERT: K 80 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: K 125 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7806 (mmmt) REVERT: M 58 MET cc_start: 0.7821 (mtt) cc_final: 0.7592 (mtm) REVERT: M 71 MET cc_start: 0.8759 (mtp) cc_final: 0.8338 (mtp) REVERT: M 80 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7592 (pt0) REVERT: M 130 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7796 (ttmm) REVERT: O 72 ASP cc_start: 0.8062 (t0) cc_final: 0.7694 (t0) REVERT: Q 60 GLU cc_start: 0.7884 (tt0) cc_final: 0.7648 (tt0) REVERT: Q 71 MET cc_start: 0.8790 (mtp) cc_final: 0.8480 (mtp) REVERT: Q 80 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: Q 134 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7851 (t) REVERT: U 116 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: U 209 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7766 (tp30) REVERT: J 1 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6166 (tmt) REVERT: J 60 ASN cc_start: 0.8301 (m110) cc_final: 0.8060 (m110) REVERT: J 103 ASP cc_start: 0.7888 (m-30) cc_final: 0.7679 (m-30) REVERT: F 550 LYS cc_start: 0.8257 (mtpp) cc_final: 0.7896 (mtpt) REVERT: H 27 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7702 (m-30) REVERT: H 65 GLU cc_start: 0.7649 (tt0) cc_final: 0.7393 (tt0) REVERT: H 182 MET cc_start: 0.8916 (mmm) cc_final: 0.8598 (mmm) REVERT: H 311 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6790 (tt0) REVERT: L 53 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: L 366 MET cc_start: 0.7059 (ptp) cc_final: 0.6629 (ptp) REVERT: L 550 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7954 (mtmt) REVERT: N 53 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7879 (tm-30) REVERT: N 182 MET cc_start: 0.8858 (mmm) cc_final: 0.8518 (mmm) REVERT: N 191 MET cc_start: 0.8702 (tpp) cc_final: 0.8167 (tpp) REVERT: N 319 MET cc_start: 0.6649 (mmm) cc_final: 0.6067 (tpp) REVERT: N 396 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7215 (t70) REVERT: N 537 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7133 (mm-30) REVERT: P 27 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: P 53 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: P 276 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7388 (pm20) REVERT: P 319 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6621 (mpp) REVERT: P 385 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.8084 (mttm) REVERT: P 396 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7133 (t70) REVERT: P 421 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7218 (pt0) REVERT: R 27 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: R 182 MET cc_start: 0.8877 (mmm) cc_final: 0.8602 (mmm) REVERT: R 319 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6141 (tpp) REVERT: R 340 ARG cc_start: 0.8330 (mtm-85) cc_final: 0.7981 (mtm-85) REVERT: R 385 LYS cc_start: 0.8044 (mttp) cc_final: 0.7799 (mttm) REVERT: R 444 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8718 (p) REVERT: R 478 MET cc_start: 0.8678 (mmt) cc_final: 0.8389 (mmp) REVERT: T 1 MET cc_start: 0.7016 (tmm) cc_final: 0.6714 (tmm) REVERT: T 53 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: T 396 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7288 (t70) REVERT: T 555 LYS cc_start: 0.8053 (ptpp) cc_final: 0.7805 (mmtp) REVERT: V 204 ASP cc_start: 0.7959 (m-30) cc_final: 0.7750 (m-30) REVERT: X 385 LYS cc_start: 0.8116 (mttp) cc_final: 0.7800 (mmtp) REVERT: X 478 MET cc_start: 0.8708 (mmt) cc_final: 0.7929 (mmt) REVERT: X 555 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7872 (ptpt) outliers start: 164 outliers final: 75 residues processed: 1130 average time/residue: 1.8069 time to fit residues: 2629.6236 Evaluate side-chains 1121 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1011 time to evaluate : 6.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 80 GLU Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 316 ASP Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 316 ASP Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 252 LEU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 316 ASP Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 385 LYS Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 444 VAL Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 565 optimal weight: 1.9990 chunk 364 optimal weight: 10.0000 chunk 545 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 580 optimal weight: 9.9990 chunk 622 optimal weight: 10.0000 chunk 451 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 718 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 34 HIS ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN S 31 ASN W 208 ASN W 224 HIS J 535 HIS D 309 ASN F 34 HIS F 168 ASN F 314 HIS F 333 GLN H 34 HIS H 309 ASN H 539 ASN L 34 HIS ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS N 314 HIS P 333 GLN R 34 HIS R 60 ASN ** R 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 314 HIS T 496 GLN V 34 HIS V 314 HIS V 333 GLN V 544 HIS X 309 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 75888 Z= 0.293 Angle : 0.590 10.898 102348 Z= 0.320 Chirality : 0.048 0.214 11400 Planarity : 0.005 0.051 13404 Dihedral : 5.131 48.343 10359 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.87 % Allowed : 13.62 % Favored : 84.51 % 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: 0.43 (0.08), residues: 9600 helix: 1.25 (0.10), residues: 2916 sheet: 0.77 (0.15), residues: 1068 loop : -0.30 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP F 437 HIS 0.008 0.001 HIS X 248 PHE 0.020 0.002 PHE S 198 TYR 0.028 0.002 TYR O 15 ARG 0.010 0.001 ARG W 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 1161 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1013 time to evaluate : 6.673 Fit side-chains REVERT: A 58 MET cc_start: 0.7728 (mtt) cc_final: 0.7295 (mtm) REVERT: A 66 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7885 (mttm) REVERT: A 77 MET cc_start: 0.8296 (mtm) cc_final: 0.8044 (mtp) REVERT: A 80 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7657 (pt0) REVERT: A 130 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7860 (tptm) REVERT: A 219 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8152 (tppt) REVERT: B 394 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7329 (ptpp) REVERT: C 80 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7730 (pt0) REVERT: C 130 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7646 (tttp) REVERT: E 125 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7657 (mmtm) REVERT: I 25 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6863 (mt-10) REVERT: I 58 MET cc_start: 0.8038 (mtm) cc_final: 0.7762 (mtm) REVERT: K 18 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7666 (mm-30) REVERT: K 80 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: K 125 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7806 (mmmt) REVERT: K 219 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8309 (tppt) REVERT: M 58 MET cc_start: 0.7857 (mtt) cc_final: 0.7616 (mtm) REVERT: M 71 MET cc_start: 0.8763 (mtp) cc_final: 0.8259 (mtp) REVERT: M 80 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: M 130 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7859 (ttmm) REVERT: O 72 ASP cc_start: 0.8166 (t0) cc_final: 0.7826 (t0) REVERT: Q 60 GLU cc_start: 0.7888 (tt0) cc_final: 0.7650 (tt0) REVERT: Q 71 MET cc_start: 0.8832 (mtp) cc_final: 0.8544 (mtp) REVERT: Q 80 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: Q 134 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7892 (t) REVERT: U 116 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7083 (mm-30) REVERT: U 209 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7905 (tp30) REVERT: J 1 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6218 (tmt) REVERT: J 103 ASP cc_start: 0.7882 (m-30) cc_final: 0.7652 (m-30) REVERT: F 550 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7874 (mtpt) REVERT: H 27 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: H 65 GLU cc_start: 0.7756 (tt0) cc_final: 0.7501 (tt0) REVERT: H 182 MET cc_start: 0.8907 (mmm) cc_final: 0.8540 (mmm) REVERT: H 311 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: H 537 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7253 (mm-30) REVERT: L 366 MET cc_start: 0.7237 (ptp) cc_final: 0.6801 (ptp) REVERT: L 550 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7950 (mtmt) REVERT: L 555 LYS cc_start: 0.8303 (ptpt) cc_final: 0.8095 (mttt) REVERT: N 182 MET cc_start: 0.8815 (mmm) cc_final: 0.8581 (mmm) REVERT: N 191 MET cc_start: 0.8743 (tpp) cc_final: 0.8270 (tpp) REVERT: N 319 MET cc_start: 0.6693 (mmm) cc_final: 0.6094 (tpp) REVERT: N 396 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7238 (t70) REVERT: N 537 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: P 27 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: P 276 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: P 319 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6651 (mpp) REVERT: P 396 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7150 (t70) REVERT: P 421 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7243 (pt0) REVERT: P 551 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: R 27 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7798 (m-30) REVERT: R 182 MET cc_start: 0.8867 (mmm) cc_final: 0.8564 (mmm) REVERT: R 319 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6135 (tpp) REVERT: R 340 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8036 (mtm-85) REVERT: R 444 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8717 (p) REVERT: R 478 MET cc_start: 0.8789 (mmt) cc_final: 0.8524 (mmp) REVERT: R 537 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: T 1 MET cc_start: 0.7092 (tmm) cc_final: 0.6829 (tmm) REVERT: T 53 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: T 396 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7302 (t70) REVERT: T 551 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: T 555 LYS cc_start: 0.8079 (ptpp) cc_final: 0.7808 (mmtp) REVERT: X 385 LYS cc_start: 0.8127 (mttp) cc_final: 0.7808 (mmtp) REVERT: X 478 MET cc_start: 0.8757 (mmt) cc_final: 0.7744 (mmt) REVERT: X 555 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7875 (ptpt) outliers start: 148 outliers final: 88 residues processed: 1080 average time/residue: 1.8132 time to fit residues: 2518.7145 Evaluate side-chains 1126 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1003 time to evaluate : 6.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 555 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 421 GLU Chi-restraints excluded: chain H residue 537 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 252 LEU Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain L residue 503 ILE Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 252 LEU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 316 ASP Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 559 LYS Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 444 VAL Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 537 GLU Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 53 GLU Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 421 GLU Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 261 THR Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 831 optimal weight: 3.9990 chunk 875 optimal weight: 0.6980 chunk 798 optimal weight: 0.9990 chunk 851 optimal weight: 8.9990 chunk 512 optimal weight: 7.9990 chunk 370 optimal weight: 3.9990 chunk 668 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 769 optimal weight: 1.9990 chunk 805 optimal weight: 4.9990 chunk 848 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 34 HIS ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN S 31 ASN W 208 ASN ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 535 HIS D 309 ASN F 34 HIS F 314 HIS F 333 GLN H 34 HIS H 309 ASN H 539 ASN L 34 HIS ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 333 GLN N 34 HIS N 314 HIS R 34 HIS ** R 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS ** T 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 309 ASN T 314 HIS V 34 HIS V 314 HIS V 333 GLN V 544 HIS X 309 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 75888 Z= 0.218 Angle : 0.551 10.421 102348 Z= 0.299 Chirality : 0.047 0.215 11400 Planarity : 0.004 0.054 13404 Dihedral : 5.047 49.341 10359 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.87 % Allowed : 13.58 % Favored : 84.55 % 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: 0.52 (0.08), residues: 9600 helix: 1.48 (0.10), residues: 2844 sheet: 0.52 (0.14), residues: 1260 loop : -0.26 (0.08), residues: 5496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 181 HIS 0.007 0.001 HIS X 248 PHE 0.020 0.001 PHE O 198 TYR 0.025 0.002 TYR G 15 ARG 0.010 0.000 ARG O 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 1169 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1021 time to evaluate : 6.610 Fit side-chains REVERT: A 58 MET cc_start: 0.7729 (mtt) cc_final: 0.7371 (mtm) REVERT: A 66 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7886 (mttm) REVERT: A 77 MET cc_start: 0.8283 (mtm) cc_final: 0.8004 (mtp) REVERT: A 80 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: A 130 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7832 (tptm) REVERT: B 53 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: B 394 LYS cc_start: 0.7661 (mtpt) cc_final: 0.7325 (ptpp) REVERT: C 80 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7712 (pt0) REVERT: C 130 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7631 (tttp) REVERT: E 125 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7671 (mmtm) REVERT: G 51 LYS cc_start: 0.8481 (mptp) cc_final: 0.8213 (mmmt) REVERT: G 80 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: I 25 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6862 (mt-10) REVERT: I 58 MET cc_start: 0.8040 (mtm) cc_final: 0.7761 (mtm) REVERT: K 80 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7638 (pt0) REVERT: K 125 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7794 (mmmt) REVERT: K 219 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8275 (tppt) REVERT: M 58 MET cc_start: 0.7827 (mtt) cc_final: 0.7585 (mtm) REVERT: M 71 MET cc_start: 0.8762 (mtp) cc_final: 0.8319 (mtp) REVERT: M 80 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: M 130 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7855 (ttmm) REVERT: O 72 ASP cc_start: 0.8150 (t0) cc_final: 0.7801 (t0) REVERT: Q 51 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8244 (mptp) REVERT: Q 60 GLU cc_start: 0.7869 (tt0) cc_final: 0.7633 (tt0) REVERT: Q 71 MET cc_start: 0.8801 (mtp) cc_final: 0.8493 (mtp) REVERT: Q 80 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7604 (pt0) REVERT: Q 134 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7879 (t) REVERT: U 116 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: U 209 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7904 (tp30) REVERT: W 21 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7514 (tmm-80) REVERT: J 1 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6152 (tmt) REVERT: J 60 ASN cc_start: 0.8340 (m110) cc_final: 0.8115 (m110) REVERT: J 103 ASP cc_start: 0.7837 (m-30) cc_final: 0.7636 (m-30) REVERT: F 550 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7883 (mtpt) REVERT: H 27 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7749 (m-30) REVERT: H 65 GLU cc_start: 0.7708 (tt0) cc_final: 0.7449 (tt0) REVERT: H 182 MET cc_start: 0.8912 (mmm) cc_final: 0.8578 (mmm) REVERT: H 311 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: L 366 MET cc_start: 0.7092 (ptp) cc_final: 0.6641 (ptp) REVERT: L 550 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7952 (mtmt) REVERT: L 555 LYS cc_start: 0.8290 (ptpt) cc_final: 0.8089 (mttt) REVERT: N 53 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: N 182 MET cc_start: 0.8831 (mmm) cc_final: 0.8520 (mmm) REVERT: N 191 MET cc_start: 0.8728 (tpp) cc_final: 0.8272 (tpp) REVERT: N 319 MET cc_start: 0.6674 (mmm) cc_final: 0.6082 (tpp) REVERT: N 396 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7232 (t70) REVERT: N 537 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7116 (mm-30) REVERT: P 27 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: P 276 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: P 319 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6638 (mpp) REVERT: P 396 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7179 (t70) REVERT: P 421 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7227 (pt0) REVERT: P 551 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: R 27 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7798 (m-30) REVERT: R 98 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7509 (tptp) REVERT: R 182 MET cc_start: 0.8870 (mmm) cc_final: 0.8587 (mmm) REVERT: R 319 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6085 (tpp) REVERT: R 340 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.8007 (mtm-85) REVERT: R 444 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8699 (p) REVERT: R 478 MET cc_start: 0.8730 (mmt) cc_final: 0.8432 (mmp) REVERT: T 1 MET cc_start: 0.7049 (tmm) cc_final: 0.6789 (tmm) REVERT: T 396 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.7296 (t70) REVERT: T 555 LYS cc_start: 0.8060 (ptpp) cc_final: 0.7806 (mmtp) REVERT: V 537 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: X 385 LYS cc_start: 0.8110 (mttp) cc_final: 0.7792 (mmtp) REVERT: X 478 MET cc_start: 0.8731 (mmt) cc_final: 0.7931 (mmt) REVERT: X 555 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7874 (ptpt) outliers start: 148 outliers final: 87 residues processed: 1093 average time/residue: 1.8080 time to fit residues: 2543.2880 Evaluate side-chains 1130 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1007 time to evaluate : 6.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 51 LYS Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain D residue 555 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 311 GLU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 252 LEU Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 53 GLU Chi-restraints excluded: chain N residue 104 MET Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 252 LEU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 316 ASP Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 559 LYS Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 98 LYS Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 444 VAL Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 421 GLU Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 261 THR Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 319 MET Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain V residue 537 GLU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 182 MET Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 559 optimal weight: 6.9990 chunk 900 optimal weight: 8.9990 chunk 549 optimal weight: 5.9990 chunk 427 optimal weight: 2.9990 chunk 625 optimal weight: 7.9990 chunk 944 optimal weight: 0.5980 chunk 869 optimal weight: 5.9990 chunk 752 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 chunk 580 optimal weight: 5.9990 chunk 461 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 34 HIS ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN S 31 ASN W 208 ASN J 535 HIS D 309 ASN F 34 HIS F 333 GLN H 34 HIS H 309 ASN H 539 ASN L 34 HIS ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS R 34 HIS R 60 ASN ** R 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 60 ASN T 309 ASN T 314 HIS V 34 HIS V 314 HIS V 333 GLN V 544 HIS X 309 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 75888 Z= 0.334 Angle : 0.618 11.153 102348 Z= 0.335 Chirality : 0.050 0.226 11400 Planarity : 0.005 0.052 13404 Dihedral : 5.255 46.427 10359 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.72 % Allowed : 13.85 % Favored : 84.43 % 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: 0.32 (0.08), residues: 9600 helix: 1.13 (0.09), residues: 2916 sheet: 0.73 (0.15), residues: 1068 loop : -0.34 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP F 437 HIS 0.008 0.001 HIS X 248 PHE 0.020 0.002 PHE S 198 TYR 0.028 0.002 TYR I 15 ARG 0.010 0.001 ARG O 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 1143 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1007 time to evaluate : 6.496 Fit side-chains REVERT: A 58 MET cc_start: 0.7755 (mtt) cc_final: 0.7315 (mtm) REVERT: A 66 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7898 (mttm) REVERT: A 77 MET cc_start: 0.8302 (mtm) cc_final: 0.8047 (mtp) REVERT: A 80 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7759 (pt0) REVERT: A 130 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7865 (tptm) REVERT: A 219 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8145 (tppt) REVERT: B 394 LYS cc_start: 0.7674 (mtpt) cc_final: 0.7337 (ptpp) REVERT: C 80 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: C 130 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7659 (tttp) REVERT: E 125 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7761 (mmtm) REVERT: G 29 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8079 (mttt) REVERT: G 71 MET cc_start: 0.8697 (mtp) cc_final: 0.8436 (mtm) REVERT: I 25 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6865 (mt-10) REVERT: I 58 MET cc_start: 0.8079 (mtm) cc_final: 0.7790 (mtm) REVERT: K 80 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: K 125 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7797 (mmmt) REVERT: K 219 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8302 (tppt) REVERT: M 58 MET cc_start: 0.7849 (mtt) cc_final: 0.7611 (mtm) REVERT: M 71 MET cc_start: 0.8772 (mtp) cc_final: 0.8277 (mtp) REVERT: M 80 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: M 130 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7903 (ttmm) REVERT: O 72 ASP cc_start: 0.8184 (t0) cc_final: 0.7840 (t0) REVERT: O 160 LYS cc_start: 0.8201 (mmtm) cc_final: 0.7909 (mmmt) REVERT: Q 51 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8287 (mptp) REVERT: Q 60 GLU cc_start: 0.7901 (tt0) cc_final: 0.7643 (tt0) REVERT: Q 71 MET cc_start: 0.8827 (mtp) cc_final: 0.8526 (mtp) REVERT: Q 80 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: Q 134 VAL cc_start: 0.8169 (OUTLIER) cc_final: 0.7917 (t) REVERT: U 116 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7112 (mm-30) REVERT: U 209 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7973 (tp30) REVERT: W 21 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7541 (tmm-80) REVERT: J 1 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6216 (tmt) REVERT: J 103 ASP cc_start: 0.7858 (m-30) cc_final: 0.7616 (m-30) REVERT: D 1 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6893 (tmm) REVERT: F 154 THR cc_start: 0.8337 (p) cc_final: 0.8112 (p) REVERT: F 550 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7876 (mtpt) REVERT: H 27 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: H 65 GLU cc_start: 0.7764 (tt0) cc_final: 0.7498 (tt0) REVERT: H 182 MET cc_start: 0.8890 (mmm) cc_final: 0.8491 (mmm) REVERT: H 537 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: L 319 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7004 (mpp) REVERT: L 366 MET cc_start: 0.7220 (ptp) cc_final: 0.6774 (ptp) REVERT: L 448 MET cc_start: 0.8690 (ptp) cc_final: 0.8458 (ptp) REVERT: L 550 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7963 (mtmt) REVERT: L 555 LYS cc_start: 0.8312 (ptpt) cc_final: 0.8093 (mttt) REVERT: N 182 MET cc_start: 0.8794 (mmm) cc_final: 0.8548 (mmm) REVERT: N 191 MET cc_start: 0.8790 (tpp) cc_final: 0.8336 (tpp) REVERT: N 319 MET cc_start: 0.6676 (mmm) cc_final: 0.6137 (tpp) REVERT: N 396 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7244 (t70) REVERT: N 537 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7100 (mm-30) REVERT: P 27 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: P 276 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: P 319 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6656 (mpp) REVERT: P 396 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7181 (t70) REVERT: P 421 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7253 (pt0) REVERT: P 551 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: R 27 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: R 98 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7534 (tptp) REVERT: R 182 MET cc_start: 0.8870 (mmm) cc_final: 0.8556 (mmm) REVERT: R 319 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.6095 (tpp) REVERT: R 340 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.8017 (mtm-85) REVERT: R 478 MET cc_start: 0.8817 (mmt) cc_final: 0.8553 (mmp) REVERT: R 537 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: T 1 MET cc_start: 0.7098 (tmm) cc_final: 0.6824 (tmm) REVERT: T 396 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7316 (t70) REVERT: T 559 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8031 (tttm) REVERT: V 537 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: X 385 LYS cc_start: 0.8202 (mttp) cc_final: 0.7884 (mmtp) REVERT: X 555 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7868 (ptpt) outliers start: 136 outliers final: 86 residues processed: 1068 average time/residue: 1.8024 time to fit residues: 2476.8057 Evaluate side-chains 1119 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 995 time to evaluate : 6.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 80 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 125 LYS Chi-restraints excluded: chain K residue 219 LYS Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 130 LYS Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain O residue 44 MET Chi-restraints excluded: chain O residue 128 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain Q residue 51 LYS Chi-restraints excluded: chain Q residue 80 GLU Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 170 SER Chi-restraints excluded: chain S residue 128 SER Chi-restraints excluded: chain S residue 134 VAL Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 116 GLU Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 209 GLU Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 316 ASP Chi-restraints excluded: chain J residue 396 ASP Chi-restraints excluded: chain J residue 433 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 316 ASP Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 421 GLU Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 537 GLU Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 252 LEU Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 319 MET Chi-restraints excluded: chain L residue 396 ASP Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 212 GLU Chi-restraints excluded: chain N residue 240 LYS Chi-restraints excluded: chain N residue 396 ASP Chi-restraints excluded: chain N residue 421 GLU Chi-restraints excluded: chain N residue 444 VAL Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 537 GLU Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 252 LEU Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 316 ASP Chi-restraints excluded: chain P residue 319 MET Chi-restraints excluded: chain P residue 366 MET Chi-restraints excluded: chain P residue 396 ASP Chi-restraints excluded: chain P residue 421 GLU Chi-restraints excluded: chain P residue 551 GLU Chi-restraints excluded: chain P residue 559 LYS Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 98 LYS Chi-restraints excluded: chain R residue 212 GLU Chi-restraints excluded: chain R residue 319 MET Chi-restraints excluded: chain R residue 391 LYS Chi-restraints excluded: chain R residue 396 ASP Chi-restraints excluded: chain R residue 517 LYS Chi-restraints excluded: chain R residue 537 GLU Chi-restraints excluded: chain R residue 565 LEU Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 396 ASP Chi-restraints excluded: chain T residue 477 GLU Chi-restraints excluded: chain T residue 559 LYS Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 261 THR Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 396 ASP Chi-restraints excluded: chain V residue 421 GLU Chi-restraints excluded: chain V residue 444 VAL Chi-restraints excluded: chain V residue 537 GLU Chi-restraints excluded: chain X residue 8 GLU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 182 MET Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain X residue 396 ASP Chi-restraints excluded: chain X residue 555 LYS Chi-restraints excluded: chain X residue 565 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 597 optimal weight: 0.3980 chunk 801 optimal weight: 7.9990 chunk 230 optimal weight: 0.8980 chunk 693 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 753 optimal weight: 3.9990 chunk 315 optimal weight: 10.0000 chunk 773 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN K 79 HIS S 31 ASN W 208 ASN ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 535 HIS D 34 HIS D 309 ASN F 34 HIS F 333 GLN H 34 HIS H 309 ASN H 539 ASN L 34 HIS ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 HIS N 314 HIS R 34 HIS ** R 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 HIS T 60 ASN T 314 HIS V 34 HIS ** V 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 HIS V 333 GLN V 544 HIS X 309 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099818 restraints weight = 76268.145| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.43 r_work: 0.3099 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 75888 Z= 0.214 Angle : 0.554 10.295 102348 Z= 0.301 Chirality : 0.046 0.225 11400 Planarity : 0.004 0.053 13404 Dihedral : 5.090 47.998 10359 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.62 % Allowed : 14.01 % Favored : 84.37 % 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: 0.48 (0.08), residues: 9600 helix: 1.44 (0.10), residues: 2844 sheet: 0.50 (0.14), residues: 1260 loop : -0.29 (0.08), residues: 5496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 181 HIS 0.007 0.001 HIS B 248 PHE 0.020 0.001 PHE O 198 TYR 0.025 0.002 TYR G 15 ARG 0.010 0.000 ARG O 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34211.90 seconds wall clock time: 585 minutes 37.20 seconds (35137.20 seconds total)