Starting phenix.real_space_refine on Fri Jan 19 06:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/01_2024/8hqo_34952.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/01_2024/8hqo_34952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/01_2024/8hqo_34952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/01_2024/8hqo_34952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/01_2024/8hqo_34952.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hqo_34952/01_2024/8hqo_34952.pdb" } resolution = 3.2 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= -0.017 sd= 0.972 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 S 300 5.16 5 C 38460 2.51 5 N 10209 2.21 5 O 11742 1.98 5 H 1902 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "x GLU 8": "OE1" <-> "OE2" Residue "x TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 8": "OE1" <-> "OE2" Residue "O TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 GLU 8": "OE1" <-> "OE2" Residue "3 TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 62613 Number of models: 1 Model: "" Number of chains: 33 Chain: "D" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "E" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "R" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "S" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "a" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 150} Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "P" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "Q" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "b" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 150} Chain: "x" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1233 Classifications: {'peptide': 80} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "A" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "F" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "G" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "H" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "I" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 150} Chain: "J" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "K" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "L" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "M" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "N" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 150} Chain: "O" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1233 Classifications: {'peptide': 80} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "T" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "U" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "V" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "W" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "X" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 150} Chain: "Y" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "Z" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2925 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "0" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "1" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1345 Classifications: {'peptide': 170} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 160} Chain: "2" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1279 Classifications: {'peptide': 160} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 150} Chain: "3" Number of atoms: 1233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1233 Classifications: {'peptide': 80} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Time building chain proxies: 23.43, per 1000 atoms: 0.37 Number of scatterers: 62613 At special positions: 0 Unit cell: (158.2, 159.6, 288.4, 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) S 300 16.00 O 11742 8.00 N 10209 7.00 C 38460 6.00 H 1902 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.84 Conformation dependent library (CDL) restraints added in 8.7 seconds 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14424 Finding SS restraints... Secondary structure from input PDB file: 291 helices and 99 sheets defined 47.7% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.85 Creating SS restraints... Processing helix chain 'D' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP D 20 " --> pdb=" O ARG D 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU D 22 " --> pdb=" O ILE D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 42 through 57 Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE D 98 " --> pdb=" O ASP D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 180 through 200 removed outlier: 3.508A pdb=" N LYS D 186 " --> pdb=" O ASP D 182 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU D 198 " --> pdb=" O LYS D 194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP D 261 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE D 284 " --> pdb=" O PRO D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 303 Proline residue: D 294 - end of helix removed outlier: 3.860A pdb=" N GLU D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET D 307 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 350 removed outlier: 3.594A pdb=" N ALA D 341 " --> pdb=" O LYS D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 362 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 22 " --> pdb=" O ILE E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 42 Processing helix chain 'E' and resid 42 through 57 Processing helix chain 'E' and resid 77 through 87 Processing helix chain 'E' and resid 94 through 109 removed outlier: 3.543A pdb=" N PHE E 98 " --> pdb=" O ASP E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 179 Processing helix chain 'E' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS E 186 " --> pdb=" O ASP E 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN E 231 " --> pdb=" O GLN E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 261 removed outlier: 4.127A pdb=" N ASP E 261 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 286 removed outlier: 3.700A pdb=" N ILE E 284 " --> pdb=" O PRO E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 303 Proline residue: E 294 - end of helix removed outlier: 3.860A pdb=" N GLU E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET E 307 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 362 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'R' and resid 5 through 14 Processing helix chain 'R' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA R 33 " --> pdb=" O THR R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 83 No H-bonds generated for 'chain 'R' and resid 81 through 83' Processing helix chain 'R' and resid 117 through 133 Processing helix chain 'R' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR R 162 " --> pdb=" O GLU R 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE R 163 " --> pdb=" O HIS R 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE R 164 " --> pdb=" O ILE R 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 14 Processing helix chain 'S' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA S 33 " --> pdb=" O THR S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 83 No H-bonds generated for 'chain 'S' and resid 81 through 83' Processing helix chain 'S' and resid 117 through 133 Processing helix chain 'S' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR S 162 " --> pdb=" O GLU S 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE S 163 " --> pdb=" O HIS S 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE S 164 " --> pdb=" O ILE S 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR S 167 " --> pdb=" O ILE S 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 20 Processing helix chain 'a' and resid 41 through 45 Processing helix chain 'a' and resid 85 through 103 Processing helix chain 'a' and resid 156 through 161 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP B 20 " --> pdb=" O ARG B 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 22 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 42 through 57 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'B' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP B 261 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 278 removed outlier: 3.639A pdb=" N PHE B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 303 Proline residue: B 294 - end of helix removed outlier: 3.859A pdb=" N GLU B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 350 removed outlier: 3.594A pdb=" N ALA B 341 " --> pdb=" O LYS B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 22 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 42 through 57 Processing helix chain 'C' and resid 77 through 87 Processing helix chain 'C' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'C' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS C 186 " --> pdb=" O ASP C 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 261 removed outlier: 4.126A pdb=" N ASP C 261 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 303 Proline residue: C 294 - end of helix removed outlier: 3.860A pdb=" N GLU C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET C 307 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 362 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'P' and resid 5 through 14 Processing helix chain 'P' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA P 33 " --> pdb=" O THR P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 83 No H-bonds generated for 'chain 'P' and resid 81 through 83' Processing helix chain 'P' and resid 117 through 133 Processing helix chain 'P' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR P 162 " --> pdb=" O GLU P 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE P 163 " --> pdb=" O HIS P 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE P 164 " --> pdb=" O ILE P 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR P 167 " --> pdb=" O ILE P 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 14 Processing helix chain 'Q' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA Q 33 " --> pdb=" O THR Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 83 No H-bonds generated for 'chain 'Q' and resid 81 through 83' Processing helix chain 'Q' and resid 117 through 133 Processing helix chain 'Q' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE Q 163 " --> pdb=" O HIS Q 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE Q 164 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR Q 167 " --> pdb=" O ILE Q 163 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 20 Processing helix chain 'b' and resid 41 through 45 Processing helix chain 'b' and resid 85 through 103 Processing helix chain 'b' and resid 156 through 161 Processing helix chain 'x' and resid 2 through 15 removed outlier: 3.636A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU x 9 " --> pdb=" O LEU x 5 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP x 12 " --> pdb=" O GLU x 8 " (cutoff:3.500A) Processing helix chain 'x' and resid 15 through 21 removed outlier: 4.495A pdb=" N THR x 19 " --> pdb=" O GLN x 15 " (cutoff:3.500A) Processing helix chain 'x' and resid 22 through 34 removed outlier: 3.695A pdb=" N GLU x 26 " --> pdb=" O ALA x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 36 through 46 removed outlier: 3.626A pdb=" N GLU x 40 " --> pdb=" O ALA x 36 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU x 44 " --> pdb=" O GLU x 40 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU x 46 " --> pdb=" O THR x 42 " (cutoff:3.500A) Processing helix chain 'x' and resid 49 through 80 removed outlier: 3.907A pdb=" N TYR x 54 " --> pdb=" O PRO x 50 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER x 55 " --> pdb=" O LYS x 51 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG x 58 " --> pdb=" O TYR x 54 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA x 63 " --> pdb=" O ALA x 59 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA x 64 " --> pdb=" O ALA x 60 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS x 65 " --> pdb=" O ASP x 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET x 76 " --> pdb=" O ALA x 72 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA x 77 " --> pdb=" O SER x 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 22 " --> pdb=" O ILE A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 42 through 57 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 179 Processing helix chain 'A' and resid 180 through 200 removed outlier: 3.508A pdb=" N LYS A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 4.126A pdb=" N ASP A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 303 Proline residue: A 294 - end of helix removed outlier: 3.860A pdb=" N GLU A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 350 removed outlier: 3.594A pdb=" N ALA A 341 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'F' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU F 22 " --> pdb=" O ILE F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 42 through 57 Processing helix chain 'F' and resid 77 through 87 Processing helix chain 'F' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 179 Processing helix chain 'F' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS F 186 " --> pdb=" O ASP F 182 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU F 198 " --> pdb=" O LYS F 194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 261 removed outlier: 4.127A pdb=" N ASP F 261 " --> pdb=" O LYS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE F 277 " --> pdb=" O ILE F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.700A pdb=" N ILE F 284 " --> pdb=" O PRO F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 303 Proline residue: F 294 - end of helix removed outlier: 3.860A pdb=" N GLU F 297 " --> pdb=" O ARG F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 320 removed outlier: 3.891A pdb=" N MET F 307 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA F 341 " --> pdb=" O LYS F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 362 Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'G' and resid 5 through 14 Processing helix chain 'G' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 83 No H-bonds generated for 'chain 'G' and resid 81 through 83' Processing helix chain 'G' and resid 117 through 133 Processing helix chain 'G' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR G 162 " --> pdb=" O GLU G 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE G 163 " --> pdb=" O HIS G 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR G 167 " --> pdb=" O ILE G 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 14 Processing helix chain 'H' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA H 33 " --> pdb=" O THR H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing helix chain 'H' and resid 117 through 133 Processing helix chain 'H' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR H 162 " --> pdb=" O GLU H 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE H 163 " --> pdb=" O HIS H 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE H 164 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR H 167 " --> pdb=" O ILE H 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 20 Processing helix chain 'I' and resid 41 through 45 Processing helix chain 'I' and resid 85 through 103 Processing helix chain 'I' and resid 156 through 161 Processing helix chain 'J' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU J 22 " --> pdb=" O ILE J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 42 Processing helix chain 'J' and resid 42 through 57 Processing helix chain 'J' and resid 77 through 87 Processing helix chain 'J' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 179 Processing helix chain 'J' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS J 186 " --> pdb=" O ASP J 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU J 198 " --> pdb=" O LYS J 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN J 231 " --> pdb=" O GLN J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP J 261 " --> pdb=" O LYS J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 262 through 278 removed outlier: 3.640A pdb=" N PHE J 277 " --> pdb=" O ILE J 273 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE J 284 " --> pdb=" O PRO J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 303 Proline residue: J 294 - end of helix removed outlier: 3.859A pdb=" N GLU J 297 " --> pdb=" O ARG J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 320 removed outlier: 3.891A pdb=" N MET J 307 " --> pdb=" O THR J 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 350 removed outlier: 3.594A pdb=" N ALA J 341 " --> pdb=" O LYS J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 354 through 362 Processing helix chain 'J' and resid 369 through 374 Processing helix chain 'K' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU K 22 " --> pdb=" O ILE K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 42 Processing helix chain 'K' and resid 42 through 57 Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE K 98 " --> pdb=" O ASP K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 179 Processing helix chain 'K' and resid 180 through 200 removed outlier: 3.510A pdb=" N LYS K 186 " --> pdb=" O ASP K 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU K 198 " --> pdb=" O LYS K 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 231 removed outlier: 3.707A pdb=" N ASN K 231 " --> pdb=" O GLN K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP K 261 " --> pdb=" O LYS K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE K 277 " --> pdb=" O ILE K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 286 removed outlier: 3.699A pdb=" N ILE K 284 " --> pdb=" O PRO K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 303 Proline residue: K 294 - end of helix removed outlier: 3.860A pdb=" N GLU K 297 " --> pdb=" O ARG K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET K 307 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA K 341 " --> pdb=" O LYS K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 362 Processing helix chain 'K' and resid 369 through 374 Processing helix chain 'L' and resid 5 through 14 Processing helix chain 'L' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA L 33 " --> pdb=" O THR L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 117 through 133 Processing helix chain 'L' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR L 162 " --> pdb=" O GLU L 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE L 163 " --> pdb=" O HIS L 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE L 164 " --> pdb=" O ILE L 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR L 167 " --> pdb=" O ILE L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 14 Processing helix chain 'M' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA M 33 " --> pdb=" O THR M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 83 No H-bonds generated for 'chain 'M' and resid 81 through 83' Processing helix chain 'M' and resid 117 through 133 Processing helix chain 'M' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR M 162 " --> pdb=" O GLU M 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE M 163 " --> pdb=" O HIS M 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE M 164 " --> pdb=" O ILE M 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR M 167 " --> pdb=" O ILE M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 20 Processing helix chain 'N' and resid 41 through 45 Processing helix chain 'N' and resid 85 through 103 Processing helix chain 'N' and resid 156 through 161 Processing helix chain 'O' and resid 2 through 15 removed outlier: 3.635A pdb=" N GLU O 8 " --> pdb=" O LYS O 4 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU O 9 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP O 12 " --> pdb=" O GLU O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 21 removed outlier: 4.494A pdb=" N THR O 19 " --> pdb=" O GLN O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 34 removed outlier: 3.695A pdb=" N GLU O 26 " --> pdb=" O ALA O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 46 removed outlier: 3.626A pdb=" N GLU O 40 " --> pdb=" O ALA O 36 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU O 44 " --> pdb=" O GLU O 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU O 46 " --> pdb=" O THR O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 80 removed outlier: 3.907A pdb=" N TYR O 54 " --> pdb=" O PRO O 50 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER O 55 " --> pdb=" O LYS O 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG O 58 " --> pdb=" O TYR O 54 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA O 64 " --> pdb=" O ALA O 60 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA O 77 " --> pdb=" O SER O 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP T 20 " --> pdb=" O ARG T 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU T 22 " --> pdb=" O ILE T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 42 Processing helix chain 'T' and resid 42 through 57 Processing helix chain 'T' and resid 77 through 87 Processing helix chain 'T' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE T 98 " --> pdb=" O ASP T 94 " (cutoff:3.500A) Processing helix chain 'T' and resid 176 through 179 Processing helix chain 'T' and resid 180 through 200 removed outlier: 3.508A pdb=" N LYS T 186 " --> pdb=" O ASP T 182 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU T 198 " --> pdb=" O LYS T 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP T 199 " --> pdb=" O GLU T 195 " (cutoff:3.500A) Processing helix chain 'T' and resid 215 through 231 removed outlier: 3.707A pdb=" N ASN T 231 " --> pdb=" O GLN T 227 " (cutoff:3.500A) Processing helix chain 'T' and resid 256 through 261 removed outlier: 4.126A pdb=" N ASP T 261 " --> pdb=" O LYS T 258 " (cutoff:3.500A) Processing helix chain 'T' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE T 277 " --> pdb=" O ILE T 273 " (cutoff:3.500A) Processing helix chain 'T' and resid 280 through 286 removed outlier: 3.699A pdb=" N ILE T 284 " --> pdb=" O PRO T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 288 through 303 Proline residue: T 294 - end of helix removed outlier: 3.860A pdb=" N GLU T 297 " --> pdb=" O ARG T 293 " (cutoff:3.500A) Processing helix chain 'T' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET T 307 " --> pdb=" O THR T 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 336 through 350 removed outlier: 3.594A pdb=" N ALA T 341 " --> pdb=" O LYS T 337 " (cutoff:3.500A) Processing helix chain 'T' and resid 354 through 362 Processing helix chain 'T' and resid 369 through 374 Processing helix chain 'U' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU U 22 " --> pdb=" O ILE U 18 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 42 Processing helix chain 'U' and resid 42 through 57 Processing helix chain 'U' and resid 77 through 87 Processing helix chain 'U' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE U 98 " --> pdb=" O ASP U 94 " (cutoff:3.500A) Processing helix chain 'U' and resid 176 through 179 Processing helix chain 'U' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS U 186 " --> pdb=" O ASP U 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU U 198 " --> pdb=" O LYS U 194 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP U 199 " --> pdb=" O GLU U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 215 through 231 removed outlier: 3.707A pdb=" N ASN U 231 " --> pdb=" O GLN U 227 " (cutoff:3.500A) Processing helix chain 'U' and resid 256 through 261 removed outlier: 4.126A pdb=" N ASP U 261 " --> pdb=" O LYS U 258 " (cutoff:3.500A) Processing helix chain 'U' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE U 277 " --> pdb=" O ILE U 273 " (cutoff:3.500A) Processing helix chain 'U' and resid 280 through 286 removed outlier: 3.700A pdb=" N ILE U 284 " --> pdb=" O PRO U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 288 through 303 Proline residue: U 294 - end of helix removed outlier: 3.861A pdb=" N GLU U 297 " --> pdb=" O ARG U 293 " (cutoff:3.500A) Processing helix chain 'U' and resid 303 through 320 removed outlier: 3.891A pdb=" N MET U 307 " --> pdb=" O THR U 303 " (cutoff:3.500A) Processing helix chain 'U' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA U 341 " --> pdb=" O LYS U 337 " (cutoff:3.500A) Processing helix chain 'U' and resid 354 through 362 Processing helix chain 'U' and resid 369 through 374 Processing helix chain 'V' and resid 5 through 14 Processing helix chain 'V' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA V 33 " --> pdb=" O THR V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 83 No H-bonds generated for 'chain 'V' and resid 81 through 83' Processing helix chain 'V' and resid 117 through 133 Processing helix chain 'V' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR V 162 " --> pdb=" O GLU V 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE V 163 " --> pdb=" O HIS V 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE V 164 " --> pdb=" O ILE V 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR V 167 " --> pdb=" O ILE V 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 14 Processing helix chain 'W' and resid 21 through 39 removed outlier: 3.599A pdb=" N ALA W 33 " --> pdb=" O THR W 29 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 83 No H-bonds generated for 'chain 'W' and resid 81 through 83' Processing helix chain 'W' and resid 117 through 133 Processing helix chain 'W' and resid 157 through 168 removed outlier: 3.680A pdb=" N THR W 162 " --> pdb=" O GLU W 158 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE W 163 " --> pdb=" O HIS W 159 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE W 164 " --> pdb=" O ILE W 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR W 167 " --> pdb=" O ILE W 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 20 Processing helix chain 'X' and resid 41 through 45 Processing helix chain 'X' and resid 85 through 103 Processing helix chain 'X' and resid 156 through 161 Processing helix chain 'Y' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP Y 20 " --> pdb=" O ARG Y 16 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU Y 22 " --> pdb=" O ILE Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 42 Processing helix chain 'Y' and resid 42 through 57 Processing helix chain 'Y' and resid 77 through 87 Processing helix chain 'Y' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE Y 98 " --> pdb=" O ASP Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 176 through 179 Processing helix chain 'Y' and resid 180 through 200 removed outlier: 3.509A pdb=" N LYS Y 186 " --> pdb=" O ASP Y 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU Y 198 " --> pdb=" O LYS Y 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP Y 199 " --> pdb=" O GLU Y 195 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN Y 231 " --> pdb=" O GLN Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP Y 261 " --> pdb=" O LYS Y 258 " (cutoff:3.500A) Processing helix chain 'Y' and resid 262 through 278 removed outlier: 3.640A pdb=" N PHE Y 277 " --> pdb=" O ILE Y 273 " (cutoff:3.500A) Processing helix chain 'Y' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE Y 284 " --> pdb=" O PRO Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 303 Proline residue: Y 294 - end of helix removed outlier: 3.859A pdb=" N GLU Y 297 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 303 through 320 removed outlier: 3.891A pdb=" N MET Y 307 " --> pdb=" O THR Y 303 " (cutoff:3.500A) Processing helix chain 'Y' and resid 336 through 350 removed outlier: 3.595A pdb=" N ALA Y 341 " --> pdb=" O LYS Y 337 " (cutoff:3.500A) Processing helix chain 'Y' and resid 354 through 362 Processing helix chain 'Y' and resid 369 through 374 Processing helix chain 'Z' and resid 14 through 22 removed outlier: 3.909A pdb=" N ASP Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU Z 22 " --> pdb=" O ILE Z 18 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 42 Processing helix chain 'Z' and resid 42 through 57 Processing helix chain 'Z' and resid 77 through 87 Processing helix chain 'Z' and resid 94 through 109 removed outlier: 3.542A pdb=" N PHE Z 98 " --> pdb=" O ASP Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 176 through 179 Processing helix chain 'Z' and resid 180 through 200 removed outlier: 3.510A pdb=" N LYS Z 186 " --> pdb=" O ASP Z 182 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU Z 198 " --> pdb=" O LYS Z 194 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP Z 199 " --> pdb=" O GLU Z 195 " (cutoff:3.500A) Processing helix chain 'Z' and resid 215 through 231 removed outlier: 3.706A pdb=" N ASN Z 231 " --> pdb=" O GLN Z 227 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 261 removed outlier: 4.125A pdb=" N ASP Z 261 " --> pdb=" O LYS Z 258 " (cutoff:3.500A) Processing helix chain 'Z' and resid 262 through 278 removed outlier: 3.638A pdb=" N PHE Z 277 " --> pdb=" O ILE Z 273 " (cutoff:3.500A) Processing helix chain 'Z' and resid 280 through 286 removed outlier: 3.698A pdb=" N ILE Z 284 " --> pdb=" O PRO Z 280 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 303 Proline residue: Z 294 - end of helix removed outlier: 3.860A pdb=" N GLU Z 297 " --> pdb=" O ARG Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 303 through 320 removed outlier: 3.890A pdb=" N MET Z 307 " --> pdb=" O THR Z 303 " (cutoff:3.500A) Processing helix chain 'Z' and resid 336 through 350 removed outlier: 3.593A pdb=" N ALA Z 341 " --> pdb=" O LYS Z 337 " (cutoff:3.500A) Processing helix chain 'Z' and resid 354 through 362 Processing helix chain 'Z' and resid 369 through 374 Processing helix chain '0' and resid 5 through 14 Processing helix chain '0' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA 0 33 " --> pdb=" O THR 0 29 " (cutoff:3.500A) Processing helix chain '0' and resid 81 through 83 No H-bonds generated for 'chain '0' and resid 81 through 83' Processing helix chain '0' and resid 117 through 133 Processing helix chain '0' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR 0 162 " --> pdb=" O GLU 0 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE 0 164 " --> pdb=" O ILE 0 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR 0 167 " --> pdb=" O ILE 0 163 " (cutoff:3.500A) Processing helix chain '1' and resid 5 through 14 Processing helix chain '1' and resid 21 through 39 removed outlier: 3.598A pdb=" N ALA 1 33 " --> pdb=" O THR 1 29 " (cutoff:3.500A) Processing helix chain '1' and resid 81 through 83 No H-bonds generated for 'chain '1' and resid 81 through 83' Processing helix chain '1' and resid 117 through 133 Processing helix chain '1' and resid 157 through 168 removed outlier: 3.679A pdb=" N THR 1 162 " --> pdb=" O GLU 1 158 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ILE 1 163 " --> pdb=" O HIS 1 159 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE 1 164 " --> pdb=" O ILE 1 160 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR 1 167 " --> pdb=" O ILE 1 163 " (cutoff:3.500A) Processing helix chain '2' and resid 3 through 20 Processing helix chain '2' and resid 41 through 45 Processing helix chain '2' and resid 85 through 103 Processing helix chain '2' and resid 156 through 161 Processing helix chain '3' and resid 2 through 15 removed outlier: 3.635A pdb=" N GLU 3 8 " --> pdb=" O LYS 3 4 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU 3 9 " --> pdb=" O LEU 3 5 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP 3 12 " --> pdb=" O GLU 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 15 through 21 removed outlier: 4.495A pdb=" N THR 3 19 " --> pdb=" O GLN 3 15 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 34 removed outlier: 3.695A pdb=" N GLU 3 26 " --> pdb=" O ALA 3 22 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 46 removed outlier: 3.626A pdb=" N GLU 3 40 " --> pdb=" O ALA 3 36 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU 3 44 " --> pdb=" O GLU 3 40 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU 3 46 " --> pdb=" O THR 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 49 through 80 removed outlier: 3.907A pdb=" N TYR 3 54 " --> pdb=" O PRO 3 50 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG 3 58 " --> pdb=" O TYR 3 54 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA 3 63 " --> pdb=" O ALA 3 59 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS 3 65 " --> pdb=" O ASP 3 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET 3 76 " --> pdb=" O ALA 3 72 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA 3 77 " --> pdb=" O SER 3 73 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'D' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR D 61 " --> pdb=" O ASN D 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN D 326 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL D 63 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR D 324 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP D 65 " --> pdb=" O LYS D 322 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR D 113 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS D 141 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 163 through 164 Processing sheet with id= 5, first strand: chain 'D' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU D 206 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU E 242 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU D 208 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR E 61 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN E 326 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL E 63 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR E 324 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP E 65 " --> pdb=" O LYS E 322 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR E 113 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS E 141 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 163 through 164 Processing sheet with id= 10, first strand: chain 'E' and resid 247 through 248 removed outlier: 6.172A pdb=" N LEU E 206 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 242 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU E 208 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'R' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR R 103 " --> pdb=" O ILE R 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE R 75 " --> pdb=" O TYR R 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP R 105 " --> pdb=" O MET R 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET R 73 " --> pdb=" O ASP R 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU R 107 " --> pdb=" O THR R 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER R 69 " --> pdb=" O THR R 109 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'R' and resid 59 through 61 Processing sheet with id= 13, first strand: chain 'R' and resid 139 through 140 removed outlier: 3.811A pdb=" N ALA S 139 " --> pdb=" O THR R 148 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA P 139 " --> pdb=" O THR S 148 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA Q 139 " --> pdb=" O THR P 148 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'S' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR S 103 " --> pdb=" O ILE S 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE S 75 " --> pdb=" O TYR S 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP S 105 " --> pdb=" O MET S 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET S 73 " --> pdb=" O ASP S 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU S 107 " --> pdb=" O THR S 71 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER S 69 " --> pdb=" O THR S 109 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'S' and resid 59 through 61 Processing sheet with id= 16, first strand: chain 'a' and resid 35 through 36 removed outlier: 7.040A pdb=" N SER a 36 " --> pdb=" O VAL a 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY a 60 " --> pdb=" O THR b 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR b 129 " --> pdb=" O GLY a 60 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N TYR a 62 " --> pdb=" O SER b 127 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N SER b 127 " --> pdb=" O TYR a 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN b 147 " --> pdb=" O THR b 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL b 131 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU b 145 " --> pdb=" O VAL b 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR b 133 " --> pdb=" O LEU b 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU b 143 " --> pdb=" O THR b 133 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER b 36 " --> pdb=" O VAL b 53 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'a' and resid 125 through 133 removed outlier: 6.702A pdb=" N ASN a 147 " --> pdb=" O THR a 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL a 131 " --> pdb=" O GLU a 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU a 145 " --> pdb=" O VAL a 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR a 133 " --> pdb=" O LEU a 143 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU a 143 " --> pdb=" O THR a 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY a 60 " --> pdb=" O THR b 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR b 129 " --> pdb=" O GLY a 60 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N TYR a 62 " --> pdb=" O SER b 127 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N SER b 127 " --> pdb=" O TYR a 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN b 147 " --> pdb=" O THR b 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL b 131 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU b 145 " --> pdb=" O VAL b 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR b 133 " --> pdb=" O LEU b 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU b 143 " --> pdb=" O THR b 133 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'a' and resid 108 through 112 Processing sheet with id= 19, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR B 61 " --> pdb=" O ASN B 326 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN B 326 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL B 63 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR B 324 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP B 65 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'B' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR B 113 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS B 141 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 163 through 164 Processing sheet with id= 23, first strand: chain 'B' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU B 206 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU C 242 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 208 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR C 61 " --> pdb=" O ASN C 326 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN C 326 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL C 63 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR C 324 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP C 65 " --> pdb=" O LYS C 322 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'C' and resid 121 through 124 removed outlier: 4.234A pdb=" N TYR C 113 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS C 141 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 163 through 164 Processing sheet with id= 28, first strand: chain 'C' and resid 208 through 209 Processing sheet with id= 29, first strand: chain 'P' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR P 103 " --> pdb=" O ILE P 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE P 75 " --> pdb=" O TYR P 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP P 105 " --> pdb=" O MET P 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET P 73 " --> pdb=" O ASP P 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU P 107 " --> pdb=" O THR P 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER P 69 " --> pdb=" O THR P 109 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 59 through 61 Processing sheet with id= 31, first strand: chain 'Q' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR Q 103 " --> pdb=" O ILE Q 75 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE Q 75 " --> pdb=" O TYR Q 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP Q 105 " --> pdb=" O MET Q 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET Q 73 " --> pdb=" O ASP Q 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU Q 107 " --> pdb=" O THR Q 71 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER Q 69 " --> pdb=" O THR Q 109 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 59 through 61 Processing sheet with id= 33, first strand: chain 'b' and resid 108 through 112 Processing sheet with id= 34, first strand: chain 'A' and resid 60 through 66 removed outlier: 4.922A pdb=" N TYR A 61 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN A 326 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL A 63 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR A 324 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP A 65 " --> pdb=" O LYS A 322 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'A' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR A 113 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'A' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS A 141 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'A' and resid 163 through 164 Processing sheet with id= 38, first strand: chain 'A' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU A 206 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU F 242 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 208 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'F' and resid 60 through 66 removed outlier: 4.922A pdb=" N TYR F 61 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN F 326 " --> pdb=" O TYR F 61 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL F 63 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR F 324 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP F 65 " --> pdb=" O LYS F 322 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'F' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR F 113 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'F' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS F 141 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'F' and resid 163 through 164 Processing sheet with id= 43, first strand: chain 'F' and resid 247 through 248 removed outlier: 6.172A pdb=" N LEU F 206 " --> pdb=" O LEU J 240 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU J 242 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU F 208 " --> pdb=" O LEU J 242 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'G' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR G 103 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE G 75 " --> pdb=" O TYR G 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP G 105 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET G 73 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU G 107 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER G 69 " --> pdb=" O THR G 109 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'G' and resid 59 through 61 Processing sheet with id= 46, first strand: chain 'G' and resid 139 through 140 removed outlier: 3.811A pdb=" N ALA H 139 " --> pdb=" O THR G 148 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA L 139 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA M 139 " --> pdb=" O THR L 148 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'H' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR H 103 " --> pdb=" O ILE H 75 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE H 75 " --> pdb=" O TYR H 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP H 105 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET H 73 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU H 107 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER H 69 " --> pdb=" O THR H 109 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'H' and resid 59 through 61 Processing sheet with id= 49, first strand: chain 'I' and resid 35 through 36 removed outlier: 7.040A pdb=" N SER I 36 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY I 60 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR N 129 " --> pdb=" O GLY I 60 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N TYR I 62 " --> pdb=" O SER N 127 " (cutoff:3.500A) removed outlier: 11.991A pdb=" N SER N 127 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN N 147 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL N 131 " --> pdb=" O GLU N 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU N 145 " --> pdb=" O VAL N 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR N 133 " --> pdb=" O LEU N 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU N 143 " --> pdb=" O THR N 133 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER N 36 " --> pdb=" O VAL N 53 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'I' and resid 125 through 133 removed outlier: 6.702A pdb=" N ASN I 147 " --> pdb=" O THR I 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL I 131 " --> pdb=" O GLU I 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU I 145 " --> pdb=" O VAL I 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR I 133 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU I 143 " --> pdb=" O THR I 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY I 60 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR N 129 " --> pdb=" O GLY I 60 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N TYR I 62 " --> pdb=" O SER N 127 " (cutoff:3.500A) removed outlier: 11.991A pdb=" N SER N 127 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN N 147 " --> pdb=" O THR N 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL N 131 " --> pdb=" O GLU N 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU N 145 " --> pdb=" O VAL N 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR N 133 " --> pdb=" O LEU N 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU N 143 " --> pdb=" O THR N 133 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'I' and resid 108 through 112 Processing sheet with id= 52, first strand: chain 'J' and resid 60 through 66 removed outlier: 4.922A pdb=" N TYR J 61 " --> pdb=" O ASN J 326 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN J 326 " --> pdb=" O TYR J 61 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL J 63 " --> pdb=" O THR J 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR J 324 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP J 65 " --> pdb=" O LYS J 322 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'J' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR J 113 " --> pdb=" O VAL J 124 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'J' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS J 141 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'J' and resid 163 through 164 Processing sheet with id= 56, first strand: chain 'J' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU J 206 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU K 242 " --> pdb=" O LEU J 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU J 208 " --> pdb=" O LEU K 242 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'K' and resid 60 through 66 removed outlier: 4.922A pdb=" N TYR K 61 " --> pdb=" O ASN K 326 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN K 326 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL K 63 " --> pdb=" O THR K 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR K 324 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP K 65 " --> pdb=" O LYS K 322 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'K' and resid 121 through 124 removed outlier: 4.234A pdb=" N TYR K 113 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'K' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS K 141 " --> pdb=" O GLU K 132 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'K' and resid 163 through 164 Processing sheet with id= 61, first strand: chain 'K' and resid 208 through 209 Processing sheet with id= 62, first strand: chain 'L' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR L 103 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE L 75 " --> pdb=" O TYR L 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP L 105 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET L 73 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU L 107 " --> pdb=" O THR L 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER L 69 " --> pdb=" O THR L 109 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'L' and resid 59 through 61 Processing sheet with id= 64, first strand: chain 'M' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR M 103 " --> pdb=" O ILE M 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE M 75 " --> pdb=" O TYR M 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP M 105 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET M 73 " --> pdb=" O ASP M 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU M 107 " --> pdb=" O THR M 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER M 69 " --> pdb=" O THR M 109 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'M' and resid 59 through 61 Processing sheet with id= 66, first strand: chain 'N' and resid 108 through 112 Processing sheet with id= 67, first strand: chain 'T' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR T 61 " --> pdb=" O ASN T 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN T 326 " --> pdb=" O TYR T 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL T 63 " --> pdb=" O THR T 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR T 324 " --> pdb=" O VAL T 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP T 65 " --> pdb=" O LYS T 322 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'T' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR T 113 " --> pdb=" O VAL T 124 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'T' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS T 141 " --> pdb=" O GLU T 132 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'T' and resid 163 through 164 Processing sheet with id= 71, first strand: chain 'T' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU T 206 " --> pdb=" O LEU U 240 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU U 242 " --> pdb=" O LEU T 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU T 208 " --> pdb=" O LEU U 242 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'U' and resid 60 through 66 removed outlier: 4.923A pdb=" N TYR U 61 " --> pdb=" O ASN U 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN U 326 " --> pdb=" O TYR U 61 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL U 63 " --> pdb=" O THR U 324 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR U 324 " --> pdb=" O VAL U 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP U 65 " --> pdb=" O LYS U 322 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'U' and resid 121 through 124 removed outlier: 4.234A pdb=" N TYR U 113 " --> pdb=" O VAL U 124 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'U' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS U 141 " --> pdb=" O GLU U 132 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'U' and resid 163 through 164 Processing sheet with id= 76, first strand: chain 'U' and resid 247 through 248 removed outlier: 6.172A pdb=" N LEU U 206 " --> pdb=" O LEU Y 240 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU Y 242 " --> pdb=" O LEU U 206 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU U 208 " --> pdb=" O LEU Y 242 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'V' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR V 103 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ILE V 75 " --> pdb=" O TYR V 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP V 105 " --> pdb=" O MET V 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET V 73 " --> pdb=" O ASP V 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU V 107 " --> pdb=" O THR V 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER V 69 " --> pdb=" O THR V 109 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'V' and resid 59 through 61 Processing sheet with id= 79, first strand: chain 'V' and resid 139 through 140 removed outlier: 3.810A pdb=" N ALA W 139 " --> pdb=" O THR V 148 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA 0 139 " --> pdb=" O THR W 148 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA 1 139 " --> pdb=" O THR 0 148 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'W' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR W 103 " --> pdb=" O ILE W 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE W 75 " --> pdb=" O TYR W 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP W 105 " --> pdb=" O MET W 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET W 73 " --> pdb=" O ASP W 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU W 107 " --> pdb=" O THR W 71 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER W 69 " --> pdb=" O THR W 109 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'W' and resid 59 through 61 Processing sheet with id= 82, first strand: chain 'X' and resid 35 through 36 removed outlier: 7.040A pdb=" N SER X 36 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY X 60 " --> pdb=" O THR 2 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR 2 129 " --> pdb=" O GLY X 60 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N TYR X 62 " --> pdb=" O SER 2 127 " (cutoff:3.500A) removed outlier: 11.991A pdb=" N SER 2 127 " --> pdb=" O TYR X 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN 2 147 " --> pdb=" O THR 2 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL 2 131 " --> pdb=" O GLU 2 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU 2 145 " --> pdb=" O VAL 2 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR 2 133 " --> pdb=" O LEU 2 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU 2 143 " --> pdb=" O THR 2 133 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER 2 36 " --> pdb=" O VAL 2 53 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'X' and resid 125 through 133 removed outlier: 6.702A pdb=" N ASN X 147 " --> pdb=" O THR X 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL X 131 " --> pdb=" O GLU X 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU X 145 " --> pdb=" O VAL X 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR X 133 " --> pdb=" O LEU X 143 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU X 143 " --> pdb=" O THR X 133 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY X 60 " --> pdb=" O THR 2 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR 2 129 " --> pdb=" O GLY X 60 " (cutoff:3.500A) removed outlier: 10.030A pdb=" N TYR X 62 " --> pdb=" O SER 2 127 " (cutoff:3.500A) removed outlier: 11.991A pdb=" N SER 2 127 " --> pdb=" O TYR X 62 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN 2 147 " --> pdb=" O THR 2 129 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL 2 131 " --> pdb=" O GLU 2 145 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU 2 145 " --> pdb=" O VAL 2 131 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR 2 133 " --> pdb=" O LEU 2 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU 2 143 " --> pdb=" O THR 2 133 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'X' and resid 108 through 112 Processing sheet with id= 85, first strand: chain 'Y' and resid 60 through 66 removed outlier: 4.922A pdb=" N TYR Y 61 " --> pdb=" O ASN Y 326 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASN Y 326 " --> pdb=" O TYR Y 61 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N VAL Y 63 " --> pdb=" O THR Y 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR Y 324 " --> pdb=" O VAL Y 63 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP Y 65 " --> pdb=" O LYS Y 322 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'Y' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR Y 113 " --> pdb=" O VAL Y 124 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'Y' and resid 129 through 133 removed outlier: 3.742A pdb=" N LYS Y 141 " --> pdb=" O GLU Y 132 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'Y' and resid 163 through 164 Processing sheet with id= 89, first strand: chain 'Y' and resid 247 through 248 removed outlier: 6.185A pdb=" N LEU Y 206 " --> pdb=" O LEU Z 240 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU Z 242 " --> pdb=" O LEU Y 206 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU Y 208 " --> pdb=" O LEU Z 242 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'Z' and resid 60 through 66 removed outlier: 4.924A pdb=" N TYR Z 61 " --> pdb=" O ASN Z 326 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ASN Z 326 " --> pdb=" O TYR Z 61 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL Z 63 " --> pdb=" O THR Z 324 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR Z 324 " --> pdb=" O VAL Z 63 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASP Z 65 " --> pdb=" O LYS Z 322 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'Z' and resid 121 through 124 removed outlier: 4.233A pdb=" N TYR Z 113 " --> pdb=" O VAL Z 124 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'Z' and resid 129 through 133 removed outlier: 3.743A pdb=" N LYS Z 141 " --> pdb=" O GLU Z 132 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'Z' and resid 163 through 164 Processing sheet with id= 94, first strand: chain 'Z' and resid 208 through 209 Processing sheet with id= 95, first strand: chain '0' and resid 46 through 53 removed outlier: 7.217A pdb=" N TYR 0 103 " --> pdb=" O ILE 0 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE 0 75 " --> pdb=" O TYR 0 103 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP 0 105 " --> pdb=" O MET 0 73 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N MET 0 73 " --> pdb=" O ASP 0 105 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLU 0 107 " --> pdb=" O THR 0 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER 0 69 " --> pdb=" O THR 0 109 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain '0' and resid 59 through 61 Processing sheet with id= 97, first strand: chain '1' and resid 46 through 53 removed outlier: 7.216A pdb=" N TYR 1 103 " --> pdb=" O ILE 1 75 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE 1 75 " --> pdb=" O TYR 1 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP 1 105 " --> pdb=" O MET 1 73 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET 1 73 " --> pdb=" O ASP 1 105 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU 1 107 " --> pdb=" O THR 1 71 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER 1 69 " --> pdb=" O THR 1 109 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain '1' and resid 59 through 61 Processing sheet with id= 99, first strand: chain '2' and resid 108 through 112 2967 hydrogen bonds defined for protein. 8334 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: 24.79 Time building geometry restraints manager: 20.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1902 1.03 - 1.23: 81 1.23 - 1.42: 25014 1.42 - 1.61: 36165 1.61 - 1.81: 534 Bond restraints: 63696 Sorted by residual: bond pdb=" CB TRP L 131 " pdb=" CG TRP L 131 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.05e+00 bond pdb=" CB TRP V 131 " pdb=" CG TRP V 131 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.05e+00 bond pdb=" CB TRP R 131 " pdb=" CG TRP R 131 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.04e+00 bond pdb=" CB TRP P 131 " pdb=" CG TRP P 131 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.03e+00 bond pdb=" CB TRP G 131 " pdb=" CG TRP G 131 " ideal model delta sigma weight residual 1.498 1.454 0.044 3.10e-02 1.04e+03 2.03e+00 ... (remaining 63691 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.57: 1727 106.57 - 113.46: 37880 113.46 - 120.34: 24108 120.34 - 127.22: 23812 127.22 - 134.11: 406 Bond angle restraints: 87933 Sorted by residual: angle pdb=" CB ARG O 62 " pdb=" CG ARG O 62 " pdb=" CD ARG O 62 " ideal model delta sigma weight residual 111.30 120.53 -9.23 2.30e+00 1.89e-01 1.61e+01 angle pdb=" CB ARG x 62 " pdb=" CG ARG x 62 " pdb=" CD ARG x 62 " ideal model delta sigma weight residual 111.30 120.52 -9.22 2.30e+00 1.89e-01 1.61e+01 angle pdb=" CB ARG 3 62 " pdb=" CG ARG 3 62 " pdb=" CD ARG 3 62 " ideal model delta sigma weight residual 111.30 120.51 -9.21 2.30e+00 1.89e-01 1.60e+01 angle pdb=" N LYS B 263 " pdb=" CA LYS B 263 " pdb=" C LYS B 263 " ideal model delta sigma weight residual 111.33 115.81 -4.48 1.21e+00 6.83e-01 1.37e+01 angle pdb=" N LYS Y 263 " pdb=" CA LYS Y 263 " pdb=" C LYS Y 263 " ideal model delta sigma weight residual 111.33 115.80 -4.47 1.21e+00 6.83e-01 1.37e+01 ... (remaining 87928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 35481 17.96 - 35.92: 2496 35.92 - 53.88: 258 53.88 - 71.84: 78 71.84 - 89.80: 75 Dihedral angle restraints: 38388 sinusoidal: 15996 harmonic: 22392 Sorted by residual: dihedral pdb=" CA MET I 19 " pdb=" C MET I 19 " pdb=" N ASP I 20 " pdb=" CA ASP I 20 " ideal model delta harmonic sigma weight residual 180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA MET X 19 " pdb=" C MET X 19 " pdb=" N ASP X 20 " pdb=" CA ASP X 20 " ideal model delta harmonic sigma weight residual 180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA MET a 19 " pdb=" C MET a 19 " pdb=" N ASP a 20 " pdb=" CA ASP a 20 " ideal model delta harmonic sigma weight residual -180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 38385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 7033 0.054 - 0.107: 2055 0.107 - 0.161: 404 0.161 - 0.215: 12 0.215 - 0.268: 12 Chirality restraints: 9516 Sorted by residual: chirality pdb=" CA TYR B 230 " pdb=" N TYR B 230 " pdb=" C TYR B 230 " pdb=" CB TYR B 230 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA TYR Y 230 " pdb=" N TYR Y 230 " pdb=" C TYR Y 230 " pdb=" CB TYR Y 230 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA TYR J 230 " pdb=" N TYR J 230 " pdb=" C TYR J 230 " pdb=" CB TYR J 230 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 9513 not shown) Planarity restraints: 11052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 27 " 0.002 2.00e-02 2.50e+03 2.85e-02 1.62e+01 pdb=" CG TYR I 27 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR I 27 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR I 27 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR I 27 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR I 27 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR I 27 " -0.038 2.00e-02 2.50e+03 pdb=" OH TYR I 27 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 27 " -0.002 2.00e-02 2.50e+03 2.84e-02 1.61e+01 pdb=" CG TYR b 27 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR b 27 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR b 27 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR b 27 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR b 27 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR b 27 " 0.039 2.00e-02 2.50e+03 pdb=" OH TYR b 27 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 27 " -0.002 2.00e-02 2.50e+03 2.84e-02 1.61e+01 pdb=" CG TYR a 27 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR a 27 " -0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR a 27 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR a 27 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR a 27 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR a 27 " 0.038 2.00e-02 2.50e+03 pdb=" OH TYR a 27 " -0.041 2.00e-02 2.50e+03 ... (remaining 11049 not shown) Histogram of nonbonded interaction distances: 0.24 - 1.11: 138 1.11 - 1.98: 624 1.98 - 2.85: 31216 2.85 - 3.73: 131614 3.73 - 4.60: 236945 Warning: very small nonbonded interaction distances. Nonbonded interactions: 400537 Sorted by model distance: nonbonded pdb=" HA THR x 2 " pdb=" HZ2 LYS 3 4 " model vdw 0.237 2.270 nonbonded pdb=" HZ2 LYS O 4 " pdb=" HA THR 3 2 " model vdw 0.238 2.270 nonbonded pdb=" HZ2 LYS x 4 " pdb=" HA THR O 2 " model vdw 0.238 2.270 nonbonded pdb=" HD3 LYS O 23 " pdb=" HB1 ALA 3 18 " model vdw 0.250 2.440 nonbonded pdb=" HD3 LYS x 23 " pdb=" HB1 ALA O 18 " model vdw 0.250 2.440 ... (remaining 400532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' selection = chain 'W' } ncs_group { reference = chain '2' selection = chain 'I' selection = chain 'N' selection = chain 'X' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain '3' selection = chain 'O' selection = chain 'x' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' } 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: 1.190 Extract box with map and model: 8.010 Check model and map are aligned: 0.690 Set scattering table: 0.430 Process input model: 125.790 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5705 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 0.044 61794 Z= 0.411 Angle : 0.794 9.232 83604 Z= 0.478 Chirality : 0.051 0.268 9516 Planarity : 0.011 0.108 10818 Dihedral : 13.198 89.799 23460 Min Nonbonded Distance : 0.497 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.08), residues: 7590 helix: -0.79 (0.08), residues: 2997 sheet: -0.07 (0.16), residues: 948 loop : -1.22 (0.09), residues: 3645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 116 HIS 0.004 0.001 HIS N 54 PHE 0.027 0.002 PHE X 48 TYR 0.042 0.006 TYR I 27 ARG 0.023 0.004 ARG 2 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2426 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2426 time to evaluate : 5.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 260 LEU cc_start: 0.8657 (mt) cc_final: 0.8266 (mp) REVERT: E 29 ASN cc_start: 0.8665 (t0) cc_final: 0.8232 (t0) REVERT: E 54 ASP cc_start: 0.7662 (m-30) cc_final: 0.6409 (m-30) REVERT: R 142 ILE cc_start: 0.8615 (tt) cc_final: 0.8293 (tt) REVERT: R 170 VAL cc_start: 0.6797 (t) cc_final: 0.6488 (t) REVERT: S 133 LYS cc_start: 0.8487 (mmmt) cc_final: 0.8285 (mttm) REVERT: a 126 MET cc_start: 0.8464 (tmm) cc_final: 0.7511 (pmm) REVERT: a 134 ASP cc_start: 0.6539 (t70) cc_final: 0.6076 (t0) REVERT: B 330 VAL cc_start: 0.7821 (t) cc_final: 0.7592 (m) REVERT: B 372 MET cc_start: 0.8475 (tpt) cc_final: 0.7104 (tpp) REVERT: C 174 GLN cc_start: 0.7495 (tp40) cc_final: 0.7281 (tp-100) REVERT: C 196 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8396 (ttpt) REVERT: C 357 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7485 (mt-10) REVERT: P 72 LYS cc_start: 0.7619 (tttt) cc_final: 0.7292 (tptm) REVERT: P 80 ILE cc_start: 0.8797 (pt) cc_final: 0.8516 (pt) REVERT: P 110 GLN cc_start: 0.5795 (pt0) cc_final: 0.5581 (pp30) REVERT: Q 126 MET cc_start: 0.8837 (mtm) cc_final: 0.8477 (mtm) REVERT: Q 145 GLU cc_start: 0.7021 (pt0) cc_final: 0.6165 (mm-30) REVERT: b 32 TYR cc_start: 0.6598 (m-80) cc_final: 0.6089 (m-80) REVERT: b 113 LYS cc_start: 0.7324 (mmtp) cc_final: 0.7082 (mmtt) REVERT: A 34 THR cc_start: 0.5800 (p) cc_final: 0.5303 (p) REVERT: A 98 PHE cc_start: 0.4897 (t80) cc_final: 0.4428 (t80) REVERT: A 227 GLN cc_start: 0.5927 (tm-30) cc_final: 0.5654 (tt0) REVERT: A 372 MET cc_start: 0.6389 (tpt) cc_final: 0.6090 (mmm) REVERT: A 376 ARG cc_start: 0.5531 (mtt90) cc_final: 0.4751 (ptm-80) REVERT: F 216 LYS cc_start: 0.7830 (ttpt) cc_final: 0.6756 (mptt) REVERT: F 369 ASP cc_start: 0.5152 (t0) cc_final: 0.4740 (t70) REVERT: J 84 LEU cc_start: 0.5624 (mt) cc_final: 0.5404 (mt) REVERT: J 117 ASP cc_start: 0.3348 (t0) cc_final: 0.2620 (t0) REVERT: J 375 ILE cc_start: 0.7441 (mm) cc_final: 0.6690 (mm) REVERT: K 95 ILE cc_start: 0.6629 (tp) cc_final: 0.5940 (pt) REVERT: K 375 ILE cc_start: 0.5242 (mm) cc_final: 0.4772 (pt) REVERT: L 4 ILE cc_start: 0.2538 (pt) cc_final: 0.1605 (pt) REVERT: L 53 THR cc_start: 0.5843 (p) cc_final: 0.5445 (p) REVERT: M 32 ASN cc_start: 0.4730 (m-40) cc_final: 0.3942 (m-40) REVERT: M 142 ILE cc_start: 0.7842 (tt) cc_final: 0.7497 (mm) REVERT: T 141 LYS cc_start: 0.6832 (pttt) cc_final: 0.6097 (pttt) REVERT: V 4 ILE cc_start: 0.3935 (pt) cc_final: 0.3237 (tt) REVERT: X 19 MET cc_start: 0.4393 (mmt) cc_final: 0.4129 (mmt) REVERT: X 53 VAL cc_start: 0.7097 (t) cc_final: 0.6685 (p) REVERT: X 81 LYS cc_start: 0.5348 (tttt) cc_final: 0.4961 (pttt) REVERT: Y 97 THR cc_start: 0.7303 (m) cc_final: 0.6941 (p) REVERT: Y 145 ASN cc_start: 0.4249 (t0) cc_final: 0.3753 (t0) REVERT: Y 312 THR cc_start: 0.6288 (p) cc_final: 0.5966 (p) REVERT: Z 26 HIS cc_start: 0.6840 (p90) cc_final: 0.6513 (p90) REVERT: Z 90 ASN cc_start: 0.2504 (p0) cc_final: 0.1877 (p0) REVERT: 1 160 ILE cc_start: 0.6869 (mt) cc_final: 0.6637 (mt) outliers start: 0 outliers final: 0 residues processed: 2426 average time/residue: 0.6441 time to fit residues: 2528.4276 Evaluate side-chains 1205 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1205 time to evaluate : 5.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 9.9990 chunk 573 optimal weight: 7.9990 chunk 317 optimal weight: 5.9990 chunk 195 optimal weight: 0.0000 chunk 386 optimal weight: 10.0000 chunk 306 optimal weight: 5.9990 chunk 592 optimal weight: 0.6980 chunk 229 optimal weight: 6.9990 chunk 360 optimal weight: 0.0370 chunk 441 optimal weight: 10.0000 chunk 686 optimal weight: 9.9990 overall best weight: 2.5466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN D 223 GLN E 130 GLN E 174 GLN E 223 GLN R 49 GLN ** R 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS R 150 ASN ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 150 ASN ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 GLN a 153 GLN B 26 HIS ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 ASN P 150 ASN Q 49 GLN Q 132 HIS b 18 GLN b 153 GLN ** x 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN A 200 ASN F 74 ASN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 HIS G 150 ASN H 130 HIS ** H 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN I 23 GLN I 153 GLN ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 GLN J 281 GLN J 289 ASN ** J 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 ASN K 170 GLN K 174 GLN K 200 ASN ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 GLN ** K 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 ASN L 130 HIS ** L 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 HIS ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 GLN ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 37 GLN U 145 ASN U 200 ASN ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 227 GLN ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 289 ASN U 349 ASN ** U 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 49 GLN W 130 HIS ** W 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 150 ASN ** W 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 153 GLN Y 145 ASN ** Y 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 161 ASN Y 168 ASN Y 174 GLN Y 200 ASN Y 289 ASN Y 373 ASN ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 46 ASN ** Z 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 200 ASN Z 289 ASN ** Z 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 349 ASN ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 84 GLN 0 132 HIS ** 0 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 150 ASN ** 1 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 132 HIS ** 1 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 23 GLN ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 61794 Z= 0.250 Angle : 0.623 18.568 83604 Z= 0.335 Chirality : 0.042 0.266 9516 Planarity : 0.005 0.109 10818 Dihedral : 5.043 26.986 8313 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 34.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.32 % Allowed : 12.83 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: 0.04 (0.09), residues: 7590 helix: 0.81 (0.09), residues: 3273 sheet: 0.12 (0.15), residues: 960 loop : -0.71 (0.11), residues: 3357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 131 HIS 0.008 0.001 HIS A 123 PHE 0.023 0.002 PHE A 319 TYR 0.021 0.001 TYR J 230 ARG 0.013 0.001 ARG 0 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1826 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1534 time to evaluate : 5.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8091 (mmp) cc_final: 0.7444 (ttp) REVERT: D 211 ASP cc_start: 0.7607 (t0) cc_final: 0.7362 (t0) REVERT: D 260 LEU cc_start: 0.8857 (mt) cc_final: 0.8311 (mp) REVERT: D 329 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7596 (mp0) REVERT: R 93 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8743 (mt) REVERT: S 27 MET cc_start: 0.7790 (mtt) cc_final: 0.7499 (mtt) REVERT: S 96 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7789 (mtmm) REVERT: a 126 MET cc_start: 0.7976 (tmm) cc_final: 0.7376 (pmm) REVERT: a 134 ASP cc_start: 0.5620 (t70) cc_final: 0.5113 (p0) REVERT: a 151 ARG cc_start: 0.6873 (ttp80) cc_final: 0.6628 (ttp-110) REVERT: B 100 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.8110 (mtm-85) REVERT: B 372 MET cc_start: 0.8553 (tpt) cc_final: 0.6938 (tpp) REVERT: C 50 ASN cc_start: 0.6946 (m-40) cc_final: 0.6513 (t0) REVERT: C 54 ASP cc_start: 0.7772 (m-30) cc_final: 0.7536 (p0) REVERT: C 105 ASP cc_start: 0.8245 (t0) cc_final: 0.7992 (t0) REVERT: C 288 ASN cc_start: 0.5681 (t0) cc_final: 0.4898 (t0) REVERT: C 340 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8033 (pt0) REVERT: b 32 TYR cc_start: 0.6662 (m-80) cc_final: 0.6429 (m-80) REVERT: b 113 LYS cc_start: 0.7135 (mmtp) cc_final: 0.6909 (mmtt) REVERT: A 141 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.5756 (pttp) REVERT: A 227 GLN cc_start: 0.6038 (tm-30) cc_final: 0.5661 (tt0) REVERT: F 16 ARG cc_start: 0.7480 (ptp-170) cc_final: 0.7266 (ptp-170) REVERT: F 84 LEU cc_start: 0.7595 (mm) cc_final: 0.7274 (mm) REVERT: F 195 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.6312 (tp30) REVERT: F 353 MET cc_start: 0.5805 (ptm) cc_final: 0.5603 (ptp) REVERT: G 17 ARG cc_start: 0.7142 (mtt180) cc_final: 0.6543 (ttm110) REVERT: H 41 MET cc_start: 0.6545 (ptm) cc_final: 0.6208 (ppp) REVERT: I 128 ILE cc_start: 0.5545 (tt) cc_final: 0.4827 (mt) REVERT: J 84 LEU cc_start: 0.6287 (mt) cc_final: 0.5998 (mt) REVERT: J 259 ASP cc_start: 0.7513 (m-30) cc_final: 0.6956 (m-30) REVERT: K 136 ASN cc_start: 0.6310 (OUTLIER) cc_final: 0.6071 (t0) REVERT: K 307 MET cc_start: 0.7662 (mmm) cc_final: 0.6425 (mtt) REVERT: L 62 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6525 (mp) REVERT: M 26 MET cc_start: 0.6604 (tmm) cc_final: 0.6128 (ttm) REVERT: M 100 PRO cc_start: 0.7517 (Cg_exo) cc_final: 0.7296 (Cg_endo) REVERT: M 126 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6512 (ttp) REVERT: N 81 LYS cc_start: 0.5643 (tttm) cc_final: 0.4969 (tttm) REVERT: N 146 ILE cc_start: 0.7033 (mt) cc_final: 0.6784 (mp) REVERT: O 49 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6686 (mmm) REVERT: T 115 TYR cc_start: 0.7810 (t80) cc_final: 0.7390 (t80) REVERT: T 372 MET cc_start: 0.6839 (tpp) cc_final: 0.6436 (tpp) REVERT: U 129 MET cc_start: 0.5824 (OUTLIER) cc_final: 0.5539 (ttt) REVERT: V 80 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7151 (mp) REVERT: V 94 LEU cc_start: 0.7582 (tp) cc_final: 0.7142 (tp) REVERT: W 150 ASN cc_start: 0.6100 (m-40) cc_final: 0.5675 (m-40) REVERT: W 168 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7023 (ttm170) REVERT: X 30 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7164 (t0) REVERT: X 81 LYS cc_start: 0.6363 (tttt) cc_final: 0.5571 (pttt) REVERT: Y 95 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6826 (tp) REVERT: Y 97 THR cc_start: 0.7549 (m) cc_final: 0.7272 (p) REVERT: Y 145 ASN cc_start: 0.5682 (t0) cc_final: 0.5037 (t0) REVERT: Y 257 PHE cc_start: 0.7700 (t80) cc_final: 0.7293 (t80) REVERT: Y 372 MET cc_start: 0.6214 (tpp) cc_final: 0.5779 (ttm) REVERT: Z 140 LYS cc_start: 0.6640 (ttmt) cc_final: 0.6161 (mtmt) REVERT: Z 141 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7774 (ptpp) REVERT: Z 338 GLU cc_start: 0.7690 (tp30) cc_final: 0.6326 (mm-30) REVERT: 0 25 GLU cc_start: 0.8158 (tp30) cc_final: 0.7520 (tm-30) REVERT: 1 26 MET cc_start: 0.7588 (tmm) cc_final: 0.7250 (tmm) REVERT: 2 69 TRP cc_start: 0.7058 (m100) cc_final: 0.6794 (m100) REVERT: 2 98 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5341 (ptmt) outliers start: 292 outliers final: 172 residues processed: 1701 average time/residue: 0.6403 time to fit residues: 1838.7885 Evaluate side-chains 1375 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1188 time to evaluate : 5.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 151 ASN Chi-restraints excluded: chain R residue 153 LYS Chi-restraints excluded: chain S residue 96 LYS Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 104 MET Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 104 MET Chi-restraints excluded: chain b residue 128 ILE Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 49 MET Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain G residue 131 TRP Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 74 ASN Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 155 ILE Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 174 GLN Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 279 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 136 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 241 ILE Chi-restraints excluded: chain K residue 345 THR Chi-restraints excluded: chain K residue 349 ASN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain L residue 165 GLU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 49 GLN Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 126 MET Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 92 PHE Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 155 ILE Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 282 VAL Chi-restraints excluded: chain T residue 338 GLU Chi-restraints excluded: chain T residue 374 ARG Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 93 MET Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 129 MET Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 279 VAL Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 336 ASP Chi-restraints excluded: chain U residue 349 ASN Chi-restraints excluded: chain U residue 367 LEU Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 80 ILE Chi-restraints excluded: chain V residue 104 MET Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 156 ILE Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain Y residue 50 ASN Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 114 ILE Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Y residue 158 ILE Chi-restraints excluded: chain Y residue 162 SER Chi-restraints excluded: chain Y residue 233 SER Chi-restraints excluded: chain Y residue 256 SER Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 330 VAL Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 46 ASN Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 141 LYS Chi-restraints excluded: chain Z residue 143 ILE Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 204 ILE Chi-restraints excluded: chain Z residue 330 VAL Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain Z residue 377 ILE Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 0 residue 42 ASP Chi-restraints excluded: chain 0 residue 78 LYS Chi-restraints excluded: chain 0 residue 84 GLN Chi-restraints excluded: chain 0 residue 95 LEU Chi-restraints excluded: chain 0 residue 128 VAL Chi-restraints excluded: chain 1 residue 35 ILE Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 1 residue 73 MET Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 116 ILE Chi-restraints excluded: chain 1 residue 154 SER Chi-restraints excluded: chain 2 residue 71 PHE Chi-restraints excluded: chain 2 residue 98 LYS Chi-restraints excluded: chain 2 residue 124 THR Chi-restraints excluded: chain 2 residue 150 VAL Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 49 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 571 optimal weight: 0.0050 chunk 467 optimal weight: 0.0770 chunk 189 optimal weight: 0.2980 chunk 687 optimal weight: 9.9990 chunk 742 optimal weight: 30.0000 chunk 612 optimal weight: 0.0070 chunk 682 optimal weight: 7.9990 chunk 234 optimal weight: 0.3980 chunk 551 optimal weight: 20.0000 overall best weight: 0.1570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 289 ASN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN Q 130 HIS x 71 GLN ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN F 74 ASN ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 GLN ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 130 GLN K 136 ASN K 168 ASN ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 373 ASN ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 GLN ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 281 GLN ** U 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 349 ASN ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 371 GLN ** 0 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 159 HIS ** 1 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 138 GLN ** 1 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 61794 Z= 0.106 Angle : 0.440 10.378 83604 Z= 0.236 Chirality : 0.039 0.163 9516 Planarity : 0.003 0.046 10818 Dihedral : 4.163 24.141 8313 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 34.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.20 % Allowed : 17.74 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: 0.97 (0.10), residues: 7590 helix: 1.75 (0.09), residues: 3213 sheet: 0.44 (0.15), residues: 936 loop : -0.32 (0.11), residues: 3441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 131 HIS 0.009 0.001 HIS A 123 PHE 0.021 0.001 PHE K 257 TYR 0.018 0.001 TYR 1 85 ARG 0.009 0.000 ARG U 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1272 time to evaluate : 5.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8130 (mmp) cc_final: 0.7475 (ttp) REVERT: D 61 TYR cc_start: 0.7590 (m-80) cc_final: 0.7305 (m-80) REVERT: D 329 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7527 (mp0) REVERT: E 264 GLU cc_start: 0.7003 (mp0) cc_final: 0.6762 (mp0) REVERT: S 96 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7750 (mtmm) REVERT: a 126 MET cc_start: 0.8021 (tmm) cc_final: 0.7445 (pmm) REVERT: a 134 ASP cc_start: 0.5778 (t70) cc_final: 0.5356 (p0) REVERT: a 149 THR cc_start: 0.8455 (m) cc_final: 0.8119 (p) REVERT: B 100 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.8136 (mtm-85) REVERT: B 372 MET cc_start: 0.8616 (tpt) cc_final: 0.6893 (tpp) REVERT: C 150 TYR cc_start: 0.8046 (m-80) cc_final: 0.6827 (m-80) REVERT: C 196 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7303 (ttpp) REVERT: C 224 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: P 98 SER cc_start: 0.8733 (m) cc_final: 0.8493 (p) REVERT: Q 27 MET cc_start: 0.7592 (mtt) cc_final: 0.7222 (mtt) REVERT: Q 145 GLU cc_start: 0.7172 (pt0) cc_final: 0.6882 (pm20) REVERT: A 131 VAL cc_start: 0.6133 (t) cc_final: 0.5763 (t) REVERT: A 227 GLN cc_start: 0.5842 (tm-30) cc_final: 0.5550 (tt0) REVERT: F 163 TYR cc_start: 0.3224 (t80) cc_final: 0.2894 (t80) REVERT: F 216 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7301 (mppt) REVERT: F 353 MET cc_start: 0.5388 (ptm) cc_final: 0.5082 (ptp) REVERT: H 41 MET cc_start: 0.6224 (ptm) cc_final: 0.5942 (ppp) REVERT: I 128 ILE cc_start: 0.5498 (tt) cc_final: 0.4537 (mt) REVERT: J 37 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7079 (tt0) REVERT: J 317 PHE cc_start: 0.6391 (t80) cc_final: 0.6070 (t80) REVERT: K 114 ILE cc_start: 0.6805 (mp) cc_final: 0.6340 (mt) REVERT: K 307 MET cc_start: 0.7619 (mmm) cc_final: 0.7314 (mpp) REVERT: L 121 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7362 (mtpp) REVERT: M 26 MET cc_start: 0.6564 (tmm) cc_final: 0.6213 (ttm) REVERT: M 100 PRO cc_start: 0.7375 (Cg_exo) cc_final: 0.7155 (Cg_endo) REVERT: M 126 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6158 (ttp) REVERT: N 81 LYS cc_start: 0.5887 (tttm) cc_final: 0.4965 (tttm) REVERT: N 146 ILE cc_start: 0.6713 (mt) cc_final: 0.6398 (mp) REVERT: T 115 TYR cc_start: 0.7841 (t80) cc_final: 0.7374 (t80) REVERT: T 195 GLU cc_start: 0.6409 (tp30) cc_final: 0.5896 (tp30) REVERT: T 372 MET cc_start: 0.6806 (tpp) cc_final: 0.6457 (tpp) REVERT: U 37 GLN cc_start: 0.8224 (pp30) cc_final: 0.7563 (mt0) REVERT: W 41 MET cc_start: 0.7491 (mpp) cc_final: 0.7181 (mpp) REVERT: X 81 LYS cc_start: 0.6275 (tttt) cc_final: 0.5654 (pttt) REVERT: Y 145 ASN cc_start: 0.5343 (t0) cc_final: 0.4736 (t0) REVERT: Y 257 PHE cc_start: 0.7686 (t80) cc_final: 0.7276 (t80) REVERT: Y 372 MET cc_start: 0.6379 (tpp) cc_final: 0.6048 (ttm) REVERT: Z 337 LYS cc_start: 0.7414 (mttp) cc_final: 0.7080 (mmmt) REVERT: Z 338 GLU cc_start: 0.7614 (tp30) cc_final: 0.6307 (mm-30) REVERT: 0 25 GLU cc_start: 0.8142 (tp30) cc_final: 0.7591 (tm-30) REVERT: 0 120 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6773 (mm) REVERT: 0 169 ARG cc_start: 0.6948 (tpp80) cc_final: 0.6640 (mmt90) REVERT: 1 26 MET cc_start: 0.7627 (tmm) cc_final: 0.7320 (tmm) REVERT: 2 45 ILE cc_start: 0.8189 (mp) cc_final: 0.7965 (mp) REVERT: 2 69 TRP cc_start: 0.7008 (m100) cc_final: 0.6531 (m100) REVERT: 2 81 LYS cc_start: 0.6699 (ttpt) cc_final: 0.6485 (ttpt) outliers start: 149 outliers final: 92 residues processed: 1348 average time/residue: 0.5654 time to fit residues: 1297.5821 Evaluate side-chains 1234 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1136 time to evaluate : 5.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 96 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain P residue 104 MET Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain x residue 46 LEU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 343 HIS Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain G residue 131 TRP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 20 ASP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 155 ILE Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 136 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 121 LYS Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 126 MET Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 159 LYS Chi-restraints excluded: chain U residue 279 VAL Chi-restraints excluded: chain U residue 336 ASP Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 104 MET Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 143 LEU Chi-restraints excluded: chain Y residue 50 ASN Chi-restraints excluded: chain Y residue 93 MET Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 114 ILE Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 158 ILE Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Z residue 11 LEU Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 214 LEU Chi-restraints excluded: chain Z residue 274 CYS Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 35 ILE Chi-restraints excluded: chain 0 residue 42 ASP Chi-restraints excluded: chain 0 residue 78 LYS Chi-restraints excluded: chain 0 residue 84 GLN Chi-restraints excluded: chain 0 residue 120 LEU Chi-restraints excluded: chain 1 residue 35 ILE Chi-restraints excluded: chain 1 residue 93 ILE Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 116 ILE Chi-restraints excluded: chain 1 residue 135 ASP Chi-restraints excluded: chain 1 residue 145 GLU Chi-restraints excluded: chain 2 residue 71 PHE Chi-restraints excluded: chain 2 residue 73 GLU Chi-restraints excluded: chain 3 residue 15 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 9.9990 chunk 517 optimal weight: 6.9990 chunk 356 optimal weight: 0.0060 chunk 76 optimal weight: 9.9990 chunk 328 optimal weight: 0.8980 chunk 461 optimal weight: 0.0060 chunk 690 optimal weight: 9.9990 chunk 730 optimal weight: 1.9990 chunk 360 optimal weight: 9.9990 chunk 654 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 overall best weight: 1.9816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 291 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 132 HIS ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 HIS S 132 HIS ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 54 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN C 223 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 ASN x 15 GLN A 145 ASN A 170 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 ASN F 74 ASN ** F 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 ASN K 168 ASN ** K 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 GLN M 134 GLN ** M 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 223 GLN ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 281 GLN ** V 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 29 ASN X 30 ASN ** X 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 215 ASN Y 295 ASN Z 145 ASN ** Z 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 371 GLN ** 0 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 52 ASN ** 0 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 130 HIS ** 0 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 150 ASN ** 1 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 15 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.8362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 61794 Z= 0.207 Angle : 0.575 19.994 83604 Z= 0.308 Chirality : 0.042 0.274 9516 Planarity : 0.005 0.067 10818 Dihedral : 4.244 24.956 8313 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 38.25 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.25 % Favored : 96.73 % Rotamer: Outliers : 4.54 % Allowed : 17.62 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: 0.88 (0.10), residues: 7590 helix: 1.66 (0.09), residues: 3132 sheet: 0.59 (0.16), residues: 960 loop : -0.38 (0.11), residues: 3498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 131 HIS 0.009 0.001 HIS B 343 PHE 0.027 0.002 PHE F 299 TYR 0.046 0.002 TYR 0 88 ARG 0.014 0.001 ARG G 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1715 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1408 time to evaluate : 5.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8129 (mmp) cc_final: 0.7351 (ttp) REVERT: D 61 TYR cc_start: 0.7905 (m-80) cc_final: 0.7534 (m-80) REVERT: D 160 ASP cc_start: 0.7883 (t0) cc_final: 0.7586 (t0) REVERT: D 329 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7551 (mp0) REVERT: D 357 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7355 (mt-10) REVERT: D 372 MET cc_start: 0.8874 (mmm) cc_final: 0.8466 (mmm) REVERT: E 352 ILE cc_start: 0.8974 (mt) cc_final: 0.8702 (tp) REVERT: R 113 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.5925 (m-10) REVERT: S 96 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7467 (mtmm) REVERT: a 57 THR cc_start: 0.8616 (OUTLIER) cc_final: 0.8275 (t) REVERT: a 126 MET cc_start: 0.8049 (tmm) cc_final: 0.7479 (pmm) REVERT: a 134 ASP cc_start: 0.6447 (t70) cc_final: 0.6070 (p0) REVERT: a 149 THR cc_start: 0.8353 (m) cc_final: 0.7892 (p) REVERT: B 100 ARG cc_start: 0.8365 (mtm-85) cc_final: 0.8019 (mtm-85) REVERT: B 372 MET cc_start: 0.8760 (tpt) cc_final: 0.7316 (tpp) REVERT: C 150 TYR cc_start: 0.8368 (m-80) cc_final: 0.7158 (m-80) REVERT: C 224 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: P 27 MET cc_start: 0.8211 (mtt) cc_final: 0.8008 (mtt) REVERT: P 96 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8609 (ttmm) REVERT: P 98 SER cc_start: 0.8698 (m) cc_final: 0.8485 (p) REVERT: Q 151 ASN cc_start: 0.8459 (t0) cc_final: 0.8231 (t0) REVERT: A 353 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6763 (tmm) REVERT: F 50 ASN cc_start: 0.7529 (t0) cc_final: 0.7109 (m110) REVERT: F 53 ILE cc_start: 0.8830 (mt) cc_final: 0.8557 (mm) REVERT: F 300 TYR cc_start: 0.7275 (m-80) cc_final: 0.7047 (m-80) REVERT: G 27 MET cc_start: 0.7530 (mmp) cc_final: 0.6726 (mmm) REVERT: H 41 MET cc_start: 0.6892 (ptm) cc_final: 0.6406 (ppp) REVERT: H 145 GLU cc_start: 0.7116 (pt0) cc_final: 0.6886 (pt0) REVERT: H 151 ASN cc_start: 0.7777 (t0) cc_final: 0.7222 (p0) REVERT: I 19 MET cc_start: 0.6188 (tpp) cc_final: 0.5969 (tpp) REVERT: I 128 ILE cc_start: 0.6956 (tt) cc_final: 0.6261 (mt) REVERT: J 17 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.7968 (mt) REVERT: J 21 MET cc_start: 0.7497 (tpp) cc_final: 0.7044 (tpp) REVERT: J 254 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8549 (pt) REVERT: J 315 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7796 (mt) REVERT: K 46 ASN cc_start: 0.7910 (t0) cc_final: 0.7254 (t0) REVERT: K 115 TYR cc_start: 0.7805 (t80) cc_final: 0.7555 (t80) REVERT: K 116 TRP cc_start: 0.7072 (OUTLIER) cc_final: 0.5829 (t60) REVERT: K 307 MET cc_start: 0.7809 (mmm) cc_final: 0.6648 (mtt) REVERT: K 372 MET cc_start: 0.5271 (tpt) cc_final: 0.4894 (tpt) REVERT: L 82 PRO cc_start: 0.8099 (Cg_exo) cc_final: 0.7889 (Cg_endo) REVERT: L 128 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8655 (t) REVERT: M 126 MET cc_start: 0.7006 (tmm) cc_final: 0.6695 (ttp) REVERT: N 81 LYS cc_start: 0.6636 (tttm) cc_final: 0.5861 (tttm) REVERT: N 148 VAL cc_start: 0.7722 (t) cc_final: 0.7329 (t) REVERT: O 8 GLU cc_start: 0.2279 (OUTLIER) cc_final: 0.1391 (pt0) REVERT: T 51 MET cc_start: 0.7163 (tmm) cc_final: 0.6924 (ptm) REVERT: T 61 TYR cc_start: 0.7528 (m-80) cc_final: 0.7261 (m-80) REVERT: T 109 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7281 (mm-30) REVERT: T 321 TYR cc_start: 0.6957 (m-80) cc_final: 0.6747 (m-10) REVERT: T 372 MET cc_start: 0.7333 (tpp) cc_final: 0.6683 (tpp) REVERT: U 29 ASN cc_start: 0.5989 (t0) cc_final: 0.5551 (p0) REVERT: U 87 VAL cc_start: 0.8002 (t) cc_final: 0.7795 (t) REVERT: U 140 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7828 (mtpp) REVERT: U 213 ILE cc_start: 0.6383 (mt) cc_final: 0.6052 (mt) REVERT: V 43 ASP cc_start: 0.6413 (t0) cc_final: 0.5824 (t70) REVERT: V 62 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7660 (mm) REVERT: W 7 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: W 73 MET cc_start: 0.6686 (ttp) cc_final: 0.6251 (ttp) REVERT: W 151 ASN cc_start: 0.7596 (t0) cc_final: 0.7361 (p0) REVERT: W 168 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7530 (ttm170) REVERT: X 113 LYS cc_start: 0.4231 (mmtp) cc_final: 0.3765 (mttt) REVERT: Y 265 ASP cc_start: 0.7724 (m-30) cc_final: 0.7164 (p0) REVERT: Y 302 MET cc_start: 0.6780 (mmp) cc_final: 0.6357 (tpp) REVERT: Y 307 MET cc_start: 0.7607 (mtp) cc_final: 0.7391 (mtm) REVERT: Y 377 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7320 (tp) REVERT: Z 93 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.8001 (ttm) REVERT: Z 141 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8151 (ptpp) REVERT: Z 145 ASN cc_start: 0.7262 (t160) cc_final: 0.6621 (t0) REVERT: Z 150 TYR cc_start: 0.7495 (m-80) cc_final: 0.7020 (m-80) REVERT: Z 265 ASP cc_start: 0.7305 (m-30) cc_final: 0.7103 (m-30) REVERT: Z 300 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.7011 (t80) REVERT: Z 372 MET cc_start: 0.6201 (tpp) cc_final: 0.5976 (tpp) REVERT: 0 25 GLU cc_start: 0.8382 (tp30) cc_final: 0.7870 (tm-30) REVERT: 0 157 PRO cc_start: 0.7087 (Cg_exo) cc_final: 0.6700 (Cg_endo) outliers start: 307 outliers final: 151 residues processed: 1587 average time/residue: 0.5631 time to fit residues: 1520.4689 Evaluate side-chains 1290 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1120 time to evaluate : 5.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 151 ASN Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain S residue 90 ASP Chi-restraints excluded: chain S residue 96 LYS Chi-restraints excluded: chain a residue 57 THR Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain b residue 128 ILE Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 15 GLN Chi-restraints excluded: chain x residue 46 LEU Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain H residue 156 ILE Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 24 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 315 LEU Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain K residue 41 LYS Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 84 GLN Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 125 CYS Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 92 PHE Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 207 ILE Chi-restraints excluded: chain T residue 251 TYR Chi-restraints excluded: chain T residue 274 CYS Chi-restraints excluded: chain T residue 282 VAL Chi-restraints excluded: chain T residue 338 GLU Chi-restraints excluded: chain T residue 354 THR Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 85 LEU Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain U residue 159 LYS Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 279 VAL Chi-restraints excluded: chain U residue 336 ASP Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 362 LEU Chi-restraints excluded: chain V residue 2 GLN Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 58 LYS Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain W residue 7 GLU Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 93 ILE Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 123 HIS Chi-restraints excluded: chain Y residue 128 LEU Chi-restraints excluded: chain Y residue 297 GLU Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 330 VAL Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain Z residue 93 MET Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 141 LYS Chi-restraints excluded: chain Z residue 204 ILE Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain Z residue 364 LEU Chi-restraints excluded: chain 0 residue 5 THR Chi-restraints excluded: chain 0 residue 35 ILE Chi-restraints excluded: chain 0 residue 129 ASP Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 1 residue 73 MET Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 116 ILE Chi-restraints excluded: chain 1 residue 145 GLU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 15 GLN Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 6.9990 chunk 414 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 544 optimal weight: 10.0000 chunk 301 optimal weight: 0.8980 chunk 623 optimal weight: 8.9990 chunk 505 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 373 optimal weight: 10.0000 chunk 655 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 30 ASN a 87 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 ASN A 223 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN G 84 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN ** J 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 343 HIS ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 ASN M 84 GLN M 132 HIS ** M 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 363 ASN U 74 ASN ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 130 HIS ** V 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 GLN X 54 HIS X 87 GLN X 153 GLN Y 145 ASN Y 223 GLN Y 270 ASN ** Y 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 46 ASN Z 123 HIS ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 114 ASN ** 1 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 54 HIS ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 1.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 61794 Z= 0.343 Angle : 0.676 14.513 83604 Z= 0.364 Chirality : 0.046 0.346 9516 Planarity : 0.005 0.094 10818 Dihedral : 5.074 32.277 8313 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 38.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.57 % Allowed : 19.65 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.04 (0.09), residues: 7590 helix: 0.96 (0.09), residues: 3129 sheet: 0.31 (0.16), residues: 954 loop : -0.89 (0.10), residues: 3507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP W 131 HIS 0.009 0.002 HIS A 343 PHE 0.040 0.003 PHE M 149 TYR 0.027 0.002 TYR Z 61 ARG 0.011 0.001 ARG J 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1612 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 377 poor density : 1235 time to evaluate : 5.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8248 (mmp) cc_final: 0.7381 (ttp) REVERT: D 93 MET cc_start: 0.8437 (ttp) cc_final: 0.8063 (ttm) REVERT: D 329 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7627 (mp0) REVERT: E 352 ILE cc_start: 0.9070 (mt) cc_final: 0.8840 (tp) REVERT: E 372 MET cc_start: 0.8531 (tpt) cc_final: 0.8133 (tpp) REVERT: R 27 MET cc_start: 0.7988 (mtm) cc_final: 0.7382 (mtp) REVERT: R 113 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6297 (m-10) REVERT: a 126 MET cc_start: 0.8228 (tmm) cc_final: 0.7319 (pmm) REVERT: a 134 ASP cc_start: 0.6343 (t70) cc_final: 0.5935 (p0) REVERT: a 149 THR cc_start: 0.8467 (m) cc_final: 0.7968 (p) REVERT: B 372 MET cc_start: 0.8380 (tpt) cc_final: 0.7362 (tpp) REVERT: C 224 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: C 271 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8044 (mppt) REVERT: P 96 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8563 (ttmm) REVERT: x 57 GLU cc_start: 0.9049 (pt0) cc_final: 0.8815 (pt0) REVERT: A 247 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7676 (mtpp) REVERT: A 260 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8668 (mp) REVERT: F 192 ASN cc_start: 0.8548 (m-40) cc_final: 0.8033 (m-40) REVERT: F 274 CYS cc_start: 0.7615 (t) cc_final: 0.7388 (t) REVERT: H 114 ASN cc_start: 0.7438 (m-40) cc_final: 0.7106 (p0) REVERT: J 21 MET cc_start: 0.7950 (tpp) cc_final: 0.7390 (tpp) REVERT: J 26 HIS cc_start: 0.7411 (p90) cc_final: 0.7176 (p90) REVERT: J 88 ARG cc_start: 0.7272 (ttt90) cc_final: 0.6995 (ttp80) REVERT: J 164 VAL cc_start: 0.8665 (t) cc_final: 0.8455 (m) REVERT: J 187 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7376 (tmm-80) REVERT: J 188 SER cc_start: 0.8160 (m) cc_final: 0.7324 (p) REVERT: J 192 ASN cc_start: 0.8902 (m-40) cc_final: 0.8483 (m-40) REVERT: J 199 ASP cc_start: 0.7772 (m-30) cc_final: 0.7536 (m-30) REVERT: J 228 LEU cc_start: 0.8826 (tp) cc_final: 0.8626 (tp) REVERT: J 246 MET cc_start: 0.8943 (mtp) cc_final: 0.8359 (mtm) REVERT: J 333 LEU cc_start: 0.8365 (tp) cc_final: 0.8129 (tt) REVERT: K 21 MET cc_start: 0.8158 (mmm) cc_final: 0.7655 (ttm) REVERT: K 40 SER cc_start: 0.8796 (t) cc_final: 0.8349 (m) REVERT: K 116 TRP cc_start: 0.7529 (OUTLIER) cc_final: 0.6708 (t60) REVERT: K 307 MET cc_start: 0.7820 (mmm) cc_final: 0.7432 (mtm) REVERT: L 73 MET cc_start: 0.7409 (ptp) cc_final: 0.7196 (ptp) REVERT: L 84 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: L 118 GLU cc_start: 0.6706 (tp30) cc_final: 0.6498 (tp30) REVERT: L 133 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8464 (ttpp) REVERT: M 27 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7797 (mpp) REVERT: M 81 ASP cc_start: 0.8658 (p0) cc_final: 0.8066 (p0) REVERT: M 84 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8086 (tp40) REVERT: M 94 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8468 (mm) REVERT: O 70 MET cc_start: 0.7263 (mmm) cc_final: 0.7032 (mmm) REVERT: T 61 TYR cc_start: 0.8204 (m-80) cc_final: 0.7798 (m-80) REVERT: T 333 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8245 (mm) REVERT: U 96 SER cc_start: 0.8391 (m) cc_final: 0.7806 (p) REVERT: U 101 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8444 (mp) REVERT: U 211 ASP cc_start: 0.7411 (m-30) cc_final: 0.7174 (t0) REVERT: U 213 ILE cc_start: 0.8020 (mt) cc_final: 0.7670 (mm) REVERT: U 336 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7393 (t0) REVERT: V 101 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7235 (tm-30) REVERT: V 145 GLU cc_start: 0.6523 (pt0) cc_final: 0.6013 (mt-10) REVERT: W 27 MET cc_start: 0.8158 (tpp) cc_final: 0.7930 (mmt) REVERT: W 38 LEU cc_start: 0.9033 (mt) cc_final: 0.8744 (mt) REVERT: W 105 ASP cc_start: 0.7749 (t0) cc_final: 0.7225 (t0) REVERT: W 168 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7401 (ttm170) REVERT: X 134 ASP cc_start: 0.5864 (t70) cc_final: 0.5283 (t0) REVERT: Y 44 ILE cc_start: 0.8447 (tt) cc_final: 0.8222 (tt) REVERT: Y 150 TYR cc_start: 0.7437 (m-80) cc_final: 0.6537 (m-80) REVERT: Y 190 MET cc_start: 0.7398 (mmm) cc_final: 0.6922 (mtt) REVERT: Y 265 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7151 (p0) REVERT: Y 319 PHE cc_start: 0.7756 (m-80) cc_final: 0.7412 (m-80) REVERT: Y 327 THR cc_start: 0.7904 (OUTLIER) cc_final: 0.7421 (m) REVERT: Y 338 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8195 (tm-30) REVERT: Y 340 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7254 (mt-10) REVERT: Z 26 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.7150 (p90) REVERT: Z 93 MET cc_start: 0.8564 (ttp) cc_final: 0.8310 (ttm) REVERT: Z 150 TYR cc_start: 0.7931 (m-80) cc_final: 0.7148 (m-80) REVERT: Z 288 ASN cc_start: 0.6038 (t0) cc_final: 0.5816 (m-40) REVERT: Z 300 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7172 (t80) REVERT: Z 326 ASN cc_start: 0.7893 (m-40) cc_final: 0.7024 (t0) REVERT: 0 25 GLU cc_start: 0.8669 (tp30) cc_final: 0.8399 (tm-30) REVERT: 0 79 GLU cc_start: 0.8512 (tp30) cc_final: 0.8086 (tp30) REVERT: 0 98 SER cc_start: 0.7947 (m) cc_final: 0.7351 (p) REVERT: 1 1 MET cc_start: 0.5753 (tpp) cc_final: 0.5209 (ttm) REVERT: 1 27 MET cc_start: 0.7868 (ttp) cc_final: 0.7649 (mtt) REVERT: 1 50 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8552 (tp) REVERT: 1 84 GLN cc_start: 0.8605 (mm110) cc_final: 0.8338 (mm-40) REVERT: 2 151 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.5998 (tpp80) outliers start: 377 outliers final: 218 residues processed: 1475 average time/residue: 0.5719 time to fit residues: 1441.8327 Evaluate side-chains 1215 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 975 time to evaluate : 5.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 123 HIS Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 274 CYS Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain R residue 54 LYS Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 151 ASN Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain a residue 145 GLU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 77 ASP Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 41 MET Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 126 MET Chi-restraints excluded: chain b residue 128 ILE Chi-restraints excluded: chain x residue 8 GLU Chi-restraints excluded: chain x residue 46 LEU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 291 ASN Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 155 ILE Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 224 GLU Chi-restraints excluded: chain K residue 227 GLN Chi-restraints excluded: chain K residue 238 SER Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 84 GLN Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 133 LYS Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 84 GLN Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 125 CYS Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 128 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 34 ASN Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 45 GLN Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 59 CYS Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 155 ILE Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 233 SER Chi-restraints excluded: chain T residue 246 MET Chi-restraints excluded: chain T residue 333 LEU Chi-restraints excluded: chain T residue 334 THR Chi-restraints excluded: chain T residue 374 ARG Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 85 LEU Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 336 ASP Chi-restraints excluded: chain U residue 342 LYS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 154 SER Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain Y residue 59 CYS Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 157 PHE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 213 ILE Chi-restraints excluded: chain Y residue 238 SER Chi-restraints excluded: chain Y residue 256 SER Chi-restraints excluded: chain Y residue 265 ASP Chi-restraints excluded: chain Y residue 311 LEU Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Z residue 26 HIS Chi-restraints excluded: chain Z residue 59 CYS Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 182 ASP Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 274 CYS Chi-restraints excluded: chain Z residue 292 ILE Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain Z residue 377 ILE Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 35 ILE Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 41 MET Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 50 LEU Chi-restraints excluded: chain 1 residue 93 ILE Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 116 ILE Chi-restraints excluded: chain 1 residue 128 VAL Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 100 VAL Chi-restraints excluded: chain 2 residue 151 ARG Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 15 GLN Chi-restraints excluded: chain 3 residue 46 LEU Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 10.0000 chunk 658 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 429 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 731 optimal weight: 3.9990 chunk 607 optimal weight: 6.9990 chunk 338 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 384 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN J 200 ASN ** J 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 GLN ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 HIS ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 223 GLN V 110 GLN ** V 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 151 ASN ** W 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 30 ASN Y 50 ASN ** Y 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 123 HIS ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 145 ASN ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 15 GLN ** 3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 1.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 61794 Z= 0.206 Angle : 0.496 8.914 83604 Z= 0.269 Chirality : 0.040 0.157 9516 Planarity : 0.004 0.060 10818 Dihedral : 4.372 26.918 8313 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 37.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.75 % Allowed : 22.66 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: 0.46 (0.10), residues: 7590 helix: 1.50 (0.10), residues: 3114 sheet: 0.35 (0.16), residues: 936 loop : -0.79 (0.10), residues: 3540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 116 HIS 0.007 0.001 HIS C 343 PHE 0.017 0.001 PHE M 149 TYR 0.022 0.001 TYR K 115 ARG 0.005 0.000 ARG T 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1071 time to evaluate : 5.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8168 (mmp) cc_final: 0.7363 (ttp) REVERT: D 93 MET cc_start: 0.8397 (ttp) cc_final: 0.8185 (ttm) REVERT: D 329 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7680 (mp0) REVERT: E 352 ILE cc_start: 0.9035 (mt) cc_final: 0.8771 (tp) REVERT: E 372 MET cc_start: 0.8421 (tpt) cc_final: 0.8045 (tpp) REVERT: R 27 MET cc_start: 0.7983 (mtm) cc_final: 0.7427 (mtp) REVERT: R 113 PHE cc_start: 0.7058 (OUTLIER) cc_final: 0.6255 (m-10) REVERT: a 126 MET cc_start: 0.8151 (tmm) cc_final: 0.7281 (pmm) REVERT: a 149 THR cc_start: 0.8317 (m) cc_final: 0.7840 (p) REVERT: B 190 MET cc_start: 0.7206 (mtp) cc_final: 0.6759 (ttp) REVERT: B 372 MET cc_start: 0.8418 (tpt) cc_final: 0.7324 (tpp) REVERT: C 224 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: P 96 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8572 (ttmm) REVERT: x 57 GLU cc_start: 0.9144 (pt0) cc_final: 0.8905 (pt0) REVERT: A 247 LYS cc_start: 0.7882 (mmtp) cc_final: 0.7492 (mtpp) REVERT: A 337 LYS cc_start: 0.5714 (pptt) cc_final: 0.5372 (ptpp) REVERT: A 357 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7686 (mt-10) REVERT: F 192 ASN cc_start: 0.8531 (m-40) cc_final: 0.7940 (m-40) REVERT: G 84 GLN cc_start: 0.6817 (mt0) cc_final: 0.6476 (mt0) REVERT: H 114 ASN cc_start: 0.7641 (m-40) cc_final: 0.7250 (p0) REVERT: H 168 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7967 (ttt-90) REVERT: J 26 HIS cc_start: 0.7479 (p90) cc_final: 0.7256 (p90) REVERT: J 88 ARG cc_start: 0.7361 (ttt90) cc_final: 0.7142 (ttp80) REVERT: J 164 VAL cc_start: 0.8734 (t) cc_final: 0.8472 (m) REVERT: J 187 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7057 (tmm-80) REVERT: J 228 LEU cc_start: 0.8852 (tp) cc_final: 0.8608 (tp) REVERT: J 246 MET cc_start: 0.8912 (mtp) cc_final: 0.8602 (mtm) REVERT: J 291 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7068 (m-40) REVERT: J 333 LEU cc_start: 0.8382 (tp) cc_final: 0.8052 (tp) REVERT: K 21 MET cc_start: 0.7991 (mmm) cc_final: 0.7707 (ttt) REVERT: K 40 SER cc_start: 0.8733 (t) cc_final: 0.8351 (m) REVERT: K 43 GLU cc_start: 0.5932 (mt-10) cc_final: 0.5687 (mt-10) REVERT: K 343 HIS cc_start: 0.7003 (t70) cc_final: 0.6793 (t70) REVERT: L 50 LEU cc_start: 0.6971 (pp) cc_final: 0.6627 (tp) REVERT: N 54 HIS cc_start: 0.6820 (OUTLIER) cc_final: 0.6531 (m-70) REVERT: T 27 ARG cc_start: 0.7493 (ttt180) cc_final: 0.7152 (mtp180) REVERT: T 61 TYR cc_start: 0.8260 (m-80) cc_final: 0.7826 (m-80) REVERT: T 212 GLU cc_start: 0.8513 (mp0) cc_final: 0.8296 (mp0) REVERT: T 333 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8472 (mm) REVERT: U 101 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8646 (mp) REVERT: U 213 ILE cc_start: 0.8203 (mt) cc_final: 0.7929 (mm) REVERT: U 353 MET cc_start: 0.7985 (mtm) cc_final: 0.7719 (mtm) REVERT: W 16 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7327 (pttt) REVERT: W 168 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7588 (ttm170) REVERT: X 30 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8523 (t0) REVERT: Y 150 TYR cc_start: 0.7432 (m-80) cc_final: 0.6576 (m-80) REVERT: Y 265 ASP cc_start: 0.7516 (m-30) cc_final: 0.7204 (p0) REVERT: Y 319 PHE cc_start: 0.7845 (m-80) cc_final: 0.7438 (m-80) REVERT: Y 338 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7957 (tp30) REVERT: Z 54 ASP cc_start: 0.7330 (m-30) cc_final: 0.7015 (m-30) REVERT: Z 93 MET cc_start: 0.8484 (ttp) cc_final: 0.8175 (ttm) REVERT: Z 150 TYR cc_start: 0.7971 (m-80) cc_final: 0.7161 (m-80) REVERT: Z 300 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7261 (t80) REVERT: Z 326 ASN cc_start: 0.7908 (m-40) cc_final: 0.7042 (t0) REVERT: 0 98 SER cc_start: 0.8241 (m) cc_final: 0.7799 (p) REVERT: 1 27 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7620 (mtt) REVERT: 2 70 MET cc_start: 0.8606 (mmm) cc_final: 0.8147 (mmm) REVERT: 2 151 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6027 (tpp80) outliers start: 254 outliers final: 172 residues processed: 1226 average time/residue: 0.5588 time to fit residues: 1169.5332 Evaluate side-chains 1147 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 961 time to evaluate : 5.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 300 TYR Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 151 ASN Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 126 MET Chi-restraints excluded: chain x residue 46 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 ASN Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 111 CYS Chi-restraints excluded: chain J residue 123 HIS Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 350 ASN Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 125 CYS Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 119 ASP Chi-restraints excluded: chain M residue 125 CYS Chi-restraints excluded: chain N residue 54 HIS Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 105 ASP Chi-restraints excluded: chain T residue 141 LYS Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 233 SER Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain T residue 333 LEU Chi-restraints excluded: chain T residue 365 GLU Chi-restraints excluded: chain T residue 374 ARG Chi-restraints excluded: chain U residue 53 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 223 GLN Chi-restraints excluded: chain U residue 242 LEU Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 151 ASN Chi-restraints excluded: chain V residue 154 SER Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 97 THR Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 59 CYS Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 274 CYS Chi-restraints excluded: chain Z residue 291 ASN Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 5 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 41 MET Chi-restraints excluded: chain 0 residue 90 ASP Chi-restraints excluded: chain 1 residue 27 MET Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 128 VAL Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 151 ARG Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 416 optimal weight: 20.0000 chunk 534 optimal weight: 9.9990 chunk 413 optimal weight: 10.0000 chunk 615 optimal weight: 20.0000 chunk 408 optimal weight: 9.9990 chunk 728 optimal weight: 3.9990 chunk 456 optimal weight: 8.9990 chunk 444 optimal weight: 9.9990 chunk 336 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN E 288 ASN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN C 281 GLN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 HIS I 68 GLN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 170 GLN K 174 GLN ** K 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 134 GLN ** M 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 350 ASN ** U 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 159 HIS ** X 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 153 GLN ** Y 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 161 ASN Y 168 ASN Y 270 ASN ** Y 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 350 ASN ** Y 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 26 HIS ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 145 ASN ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 150 ASN ** 1 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 1.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 61794 Z= 0.424 Angle : 0.714 10.446 83604 Z= 0.382 Chirality : 0.046 0.197 9516 Planarity : 0.006 0.072 10818 Dihedral : 5.196 29.421 8313 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 42.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.28 % Favored : 94.70 % Rotamer: Outliers : 5.29 % Allowed : 21.69 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: -0.44 (0.09), residues: 7590 helix: 0.77 (0.09), residues: 3078 sheet: -0.02 (0.16), residues: 990 loop : -1.32 (0.10), residues: 3522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP K 116 HIS 0.032 0.002 HIS N 54 PHE 0.030 0.003 PHE A 299 TYR 0.026 0.002 TYR Z 61 ARG 0.008 0.001 ARG I 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 940 time to evaluate : 5.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 365 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7616 (tm-30) REVERT: E 352 ILE cc_start: 0.9067 (mt) cc_final: 0.8843 (tp) REVERT: R 27 MET cc_start: 0.8003 (mtm) cc_final: 0.7270 (mtp) REVERT: R 113 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6770 (m-10) REVERT: a 126 MET cc_start: 0.8264 (tmm) cc_final: 0.7440 (pmm) REVERT: a 149 THR cc_start: 0.8440 (m) cc_final: 0.8013 (p) REVERT: B 372 MET cc_start: 0.8350 (tpt) cc_final: 0.7310 (tpp) REVERT: C 224 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: C 271 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8076 (mppt) REVERT: P 96 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8513 (ttmm) REVERT: x 70 MET cc_start: 0.8014 (mmm) cc_final: 0.7811 (mmm) REVERT: A 51 MET cc_start: 0.8207 (mtt) cc_final: 0.7843 (mtm) REVERT: A 337 LYS cc_start: 0.6038 (pptt) cc_final: 0.5765 (ptpp) REVERT: A 357 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7816 (mt-10) REVERT: F 130 GLN cc_start: 0.8250 (tt0) cc_final: 0.7939 (tt0) REVERT: G 27 MET cc_start: 0.8068 (mmm) cc_final: 0.7740 (mmm) REVERT: G 73 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7189 (ptm) REVERT: G 104 MET cc_start: 0.7742 (ppp) cc_final: 0.6895 (ppp) REVERT: H 76 ASN cc_start: 0.8296 (m-40) cc_final: 0.8023 (m110) REVERT: I 122 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7891 (pp20) REVERT: I 126 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.6773 (pmm) REVERT: J 88 ARG cc_start: 0.7623 (ttt90) cc_final: 0.7060 (ttp80) REVERT: J 150 TYR cc_start: 0.7892 (m-80) cc_final: 0.7688 (m-10) REVERT: J 187 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.6980 (tmm-80) REVERT: J 246 MET cc_start: 0.9141 (mtp) cc_final: 0.8865 (mtm) REVERT: J 333 LEU cc_start: 0.8683 (tp) cc_final: 0.8349 (tp) REVERT: K 116 TRP cc_start: 0.7845 (OUTLIER) cc_final: 0.7406 (t60) REVERT: K 171 ILE cc_start: 0.8533 (mt) cc_final: 0.8306 (mt) REVERT: K 190 MET cc_start: 0.7877 (mtt) cc_final: 0.7660 (ttm) REVERT: M 27 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7685 (mpp) REVERT: M 94 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8601 (mm) REVERT: T 61 TYR cc_start: 0.8365 (m-80) cc_final: 0.7970 (m-80) REVERT: T 212 GLU cc_start: 0.8461 (mp0) cc_final: 0.8253 (mp0) REVERT: T 233 SER cc_start: 0.8531 (OUTLIER) cc_final: 0.8316 (p) REVERT: T 333 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8422 (mm) REVERT: T 342 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8456 (mmmt) REVERT: T 361 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8070 (tm-30) REVERT: U 96 SER cc_start: 0.8666 (m) cc_final: 0.8064 (p) REVERT: U 101 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8611 (mp) REVERT: U 174 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: V 103 TYR cc_start: 0.7522 (m-80) cc_final: 0.7321 (m-10) REVERT: W 1 MET cc_start: 0.7906 (ptt) cc_final: 0.7659 (ptt) REVERT: W 16 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7866 (mttp) REVERT: W 168 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8378 (ttp80) REVERT: Y 150 TYR cc_start: 0.7635 (m-80) cc_final: 0.6705 (m-80) REVERT: Z 93 MET cc_start: 0.8561 (ttp) cc_final: 0.8335 (ttm) REVERT: Z 150 TYR cc_start: 0.8054 (m-80) cc_final: 0.6970 (m-80) REVERT: Z 300 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7816 (m-80) REVERT: Z 344 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9033 (mm) REVERT: 0 98 SER cc_start: 0.8651 (m) cc_final: 0.8442 (p) REVERT: 1 64 SER cc_start: 0.8692 (m) cc_final: 0.8034 (p) REVERT: 1 97 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8106 (p90) REVERT: 1 113 PHE cc_start: 0.6603 (OUTLIER) cc_final: 0.6390 (m-80) REVERT: 2 151 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7215 (ttp80) outliers start: 358 outliers final: 254 residues processed: 1181 average time/residue: 0.5557 time to fit residues: 1122.8738 Evaluate side-chains 1141 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 865 time to evaluate : 5.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 199 ASP Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 360 LEU Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 151 ASN Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 73 MET Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 77 ASP Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain Q residue 136 TYR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 126 MET Chi-restraints excluded: chain x residue 8 GLU Chi-restraints excluded: chain x residue 27 ASN Chi-restraints excluded: chain x residue 46 LEU Chi-restraints excluded: chain x residue 61 ASP Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 122 GLU Chi-restraints excluded: chain I residue 126 MET Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 188 SER Chi-restraints excluded: chain J residue 190 MET Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 254 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 311 LEU Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 350 ASN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 195 GLU Chi-restraints excluded: chain K residue 209 GLU Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 265 ASP Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 377 ILE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 77 ASP Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 66 SER Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 119 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 59 CYS Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 124 VAL Chi-restraints excluded: chain T residue 141 LYS Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 233 SER Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain T residue 327 THR Chi-restraints excluded: chain T residue 333 LEU Chi-restraints excluded: chain T residue 350 ASN Chi-restraints excluded: chain T residue 374 ARG Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 50 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 85 LEU Chi-restraints excluded: chain U residue 95 ILE Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 174 GLN Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 265 ASP Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 151 ASN Chi-restraints excluded: chain V residue 154 SER Chi-restraints excluded: chain W residue 11 LEU Chi-restraints excluded: chain W residue 16 LYS Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 59 CYS Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 97 THR Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 155 ILE Chi-restraints excluded: chain Y residue 157 PHE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 340 GLU Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 59 CYS Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain Z residue 195 GLU Chi-restraints excluded: chain Z residue 204 ILE Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 271 LYS Chi-restraints excluded: chain Z residue 274 CYS Chi-restraints excluded: chain Z residue 288 ASN Chi-restraints excluded: chain Z residue 291 ASN Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 344 LEU Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain Z residue 362 LEU Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 41 MET Chi-restraints excluded: chain 0 residue 43 ASP Chi-restraints excluded: chain 0 residue 72 LYS Chi-restraints excluded: chain 0 residue 90 ASP Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 97 PHE Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 128 VAL Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 151 ARG Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 46 LEU Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 5.9990 chunk 290 optimal weight: 0.0570 chunk 435 optimal weight: 0.3980 chunk 219 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 463 optimal weight: 7.9990 chunk 496 optimal weight: 5.9990 chunk 360 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 572 optimal weight: 5.9990 overall best weight: 3.6904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 GLN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 HIS I 68 GLN ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 HIS ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 54 HIS N 87 GLN ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 153 GLN ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 223 GLN V 52 ASN ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 149 ASN Y 223 GLN ** Y 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 350 ASN ** Y 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 281 GLN ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 150 ASN 0 151 ASN ** 1 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 1.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 61794 Z= 0.219 Angle : 0.500 9.147 83604 Z= 0.272 Chirality : 0.040 0.166 9516 Planarity : 0.004 0.067 10818 Dihedral : 4.490 26.217 8313 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 38.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 4.02 % Allowed : 23.37 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.10), residues: 7590 helix: 1.31 (0.10), residues: 3135 sheet: 0.12 (0.17), residues: 912 loop : -1.13 (0.10), residues: 3543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP T 116 HIS 0.009 0.001 HIS A 343 PHE 0.016 0.001 PHE M 149 TYR 0.021 0.001 TYR 1 85 ARG 0.009 0.000 ARG I 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 949 time to evaluate : 5.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8101 (mmp) cc_final: 0.7385 (ttp) REVERT: D 365 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7668 (tm-30) REVERT: E 352 ILE cc_start: 0.9030 (mt) cc_final: 0.8770 (tp) REVERT: E 372 MET cc_start: 0.8428 (tpt) cc_final: 0.7956 (tpp) REVERT: R 27 MET cc_start: 0.7974 (mtm) cc_final: 0.7330 (mtp) REVERT: R 113 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6580 (m-10) REVERT: a 126 MET cc_start: 0.8219 (tmm) cc_final: 0.7331 (pmm) REVERT: a 149 THR cc_start: 0.8339 (m) cc_final: 0.7906 (p) REVERT: B 372 MET cc_start: 0.8385 (tpt) cc_final: 0.7314 (tpp) REVERT: C 224 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: C 271 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7962 (mppt) REVERT: P 96 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8575 (ttmm) REVERT: x 70 MET cc_start: 0.7958 (mmm) cc_final: 0.7302 (mmm) REVERT: A 21 MET cc_start: 0.7660 (tpp) cc_final: 0.6903 (ttp) REVERT: A 51 MET cc_start: 0.7718 (mtt) cc_final: 0.7517 (mtm) REVERT: A 54 ASP cc_start: 0.7960 (p0) cc_final: 0.7748 (p0) REVERT: A 101 LEU cc_start: 0.9049 (mt) cc_final: 0.8768 (mt) REVERT: A 220 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: A 225 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7715 (tt0) REVERT: A 337 LYS cc_start: 0.6053 (pptt) cc_final: 0.5802 (ptpp) REVERT: A 357 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7837 (mt-10) REVERT: F 163 TYR cc_start: 0.7203 (t80) cc_final: 0.6690 (t80) REVERT: F 199 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7847 (m-30) REVERT: G 27 MET cc_start: 0.8102 (mmm) cc_final: 0.7748 (mmm) REVERT: H 76 ASN cc_start: 0.8305 (m-40) cc_final: 0.8098 (m110) REVERT: H 105 ASP cc_start: 0.8163 (m-30) cc_final: 0.7698 (t0) REVERT: H 114 ASN cc_start: 0.7799 (m-40) cc_final: 0.7091 (p0) REVERT: H 168 ARG cc_start: 0.8332 (ttt-90) cc_final: 0.7990 (ttt-90) REVERT: I 126 MET cc_start: 0.7684 (tmm) cc_final: 0.6754 (pmm) REVERT: J 187 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.6907 (tmm-80) REVERT: J 246 MET cc_start: 0.9024 (mtp) cc_final: 0.8732 (mtm) REVERT: J 270 ASN cc_start: 0.8110 (m-40) cc_final: 0.7688 (m-40) REVERT: K 116 TRP cc_start: 0.7647 (OUTLIER) cc_final: 0.7300 (t60) REVERT: K 369 ASP cc_start: 0.6552 (OUTLIER) cc_final: 0.5866 (t0) REVERT: T 61 TYR cc_start: 0.8258 (m-80) cc_final: 0.7847 (m-80) REVERT: T 333 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8316 (mm) REVERT: T 342 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8196 (mmmt) REVERT: T 374 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7093 (ptm-80) REVERT: U 29 ASN cc_start: 0.8956 (t0) cc_final: 0.8690 (t0) REVERT: U 35 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8463 (t) REVERT: U 96 SER cc_start: 0.8590 (m) cc_final: 0.8043 (p) REVERT: U 101 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8630 (mp) REVERT: U 174 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: U 261 ASP cc_start: 0.7842 (p0) cc_final: 0.7487 (p0) REVERT: U 361 GLU cc_start: 0.8612 (tp30) cc_final: 0.8392 (tt0) REVERT: V 43 ASP cc_start: 0.6501 (t0) cc_final: 0.6218 (t70) REVERT: W 1 MET cc_start: 0.7818 (ptt) cc_final: 0.7570 (ptt) REVERT: W 168 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8386 (ttt-90) REVERT: Y 43 GLU cc_start: 0.5120 (tm-30) cc_final: 0.4865 (tm-30) REVERT: Y 150 TYR cc_start: 0.7563 (m-80) cc_final: 0.6671 (m-80) REVERT: Y 229 ASP cc_start: 0.7768 (m-30) cc_final: 0.7513 (m-30) REVERT: Z 81 LEU cc_start: 0.9224 (tp) cc_final: 0.8973 (tp) REVERT: Z 93 MET cc_start: 0.8527 (ttp) cc_final: 0.8170 (ttm) REVERT: Z 150 TYR cc_start: 0.7956 (m-80) cc_final: 0.6915 (m-80) REVERT: Z 300 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7727 (m-80) REVERT: Z 372 MET cc_start: 0.6280 (tpp) cc_final: 0.5799 (mmm) REVERT: 1 97 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7950 (p90) REVERT: 1 113 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.6075 (m-80) outliers start: 272 outliers final: 204 residues processed: 1122 average time/residue: 0.5831 time to fit residues: 1122.9502 Evaluate side-chains 1116 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 894 time to evaluate : 5.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 151 ASN Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 21 GLU Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 126 MET Chi-restraints excluded: chain x residue 46 LEU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 49 GLN Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 152 VAL Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 229 ASP Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 246 MET Chi-restraints excluded: chain K residue 265 ASP Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 49 MET Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 59 CYS Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 141 LYS Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain T residue 333 LEU Chi-restraints excluded: chain T residue 374 ARG Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 85 LEU Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 174 GLN Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 265 ASP Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 342 LYS Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 135 ASP Chi-restraints excluded: chain V residue 151 ASN Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain X residue 55 ILE Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 97 THR Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 157 PHE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 314 SER Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 18 ILE Chi-restraints excluded: chain Z residue 59 CYS Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 132 GLU Chi-restraints excluded: chain Z residue 210 THR Chi-restraints excluded: chain Z residue 274 CYS Chi-restraints excluded: chain Z residue 282 VAL Chi-restraints excluded: chain Z residue 291 ASN Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain 0 residue 5 THR Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 90 ASP Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 97 PHE Chi-restraints excluded: chain 1 residue 113 PHE Chi-restraints excluded: chain 1 residue 128 VAL Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 151 ARG Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 662 optimal weight: 0.6980 chunk 698 optimal weight: 5.9990 chunk 636 optimal weight: 9.9990 chunk 679 optimal weight: 8.9990 chunk 697 optimal weight: 0.1980 chunk 408 optimal weight: 8.9990 chunk 295 optimal weight: 7.9990 chunk 533 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 613 optimal weight: 20.0000 chunk 642 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 GLN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 350 ASN U 223 GLN ** U 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 270 ASN ** Y 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 350 ASN ** 0 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 49 GLN 1 84 GLN ** 1 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 ASN ** 3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 1.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 61794 Z= 0.206 Angle : 0.489 8.538 83604 Z= 0.264 Chirality : 0.040 0.171 9516 Planarity : 0.004 0.063 10818 Dihedral : 4.268 25.686 8313 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 38.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.43 % Favored : 95.55 % Rotamer: Outliers : 3.58 % Allowed : 23.95 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: 0.30 (0.10), residues: 7590 helix: 1.51 (0.09), residues: 3189 sheet: 0.16 (0.17), residues: 912 loop : -1.03 (0.10), residues: 3489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 116 HIS 0.010 0.001 HIS A 343 PHE 0.016 0.001 PHE M 149 TYR 0.021 0.001 TYR 1 85 ARG 0.005 0.000 ARG I 4 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 910 time to evaluate : 5.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8114 (mmp) cc_final: 0.7387 (ttp) REVERT: D 365 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7649 (tm-30) REVERT: E 229 ASP cc_start: 0.8443 (m-30) cc_final: 0.8188 (t0) REVERT: E 352 ILE cc_start: 0.9029 (mt) cc_final: 0.8771 (tp) REVERT: E 372 MET cc_start: 0.8458 (tpt) cc_final: 0.7988 (tpp) REVERT: R 27 MET cc_start: 0.7970 (mtm) cc_final: 0.7334 (mtp) REVERT: R 113 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6628 (m-10) REVERT: a 126 MET cc_start: 0.8170 (tmm) cc_final: 0.7282 (pmm) REVERT: a 149 THR cc_start: 0.8325 (m) cc_final: 0.7870 (p) REVERT: B 372 MET cc_start: 0.8408 (tpt) cc_final: 0.7377 (tpp) REVERT: C 224 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: C 271 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8000 (mppt) REVERT: P 96 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8435 (ttmm) REVERT: x 57 GLU cc_start: 0.9127 (pt0) cc_final: 0.8919 (pt0) REVERT: x 70 MET cc_start: 0.7962 (mmm) cc_final: 0.7307 (mmm) REVERT: A 101 LEU cc_start: 0.9039 (mt) cc_final: 0.8771 (mt) REVERT: A 220 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: A 307 MET cc_start: 0.8390 (mtm) cc_final: 0.8121 (mtm) REVERT: A 357 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7937 (mt-10) REVERT: F 163 TYR cc_start: 0.7093 (t80) cc_final: 0.6653 (t80) REVERT: F 199 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: G 27 MET cc_start: 0.8102 (mmm) cc_final: 0.7791 (mmm) REVERT: H 76 ASN cc_start: 0.8299 (m-40) cc_final: 0.8098 (m110) REVERT: H 114 ASN cc_start: 0.7829 (m-40) cc_final: 0.7068 (p0) REVERT: H 168 ARG cc_start: 0.8320 (ttt-90) cc_final: 0.8042 (ttt-90) REVERT: I 126 MET cc_start: 0.7404 (tmm) cc_final: 0.6564 (pmm) REVERT: J 187 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.6844 (tmm-80) REVERT: J 246 MET cc_start: 0.9016 (mtp) cc_final: 0.8701 (mtm) REVERT: J 270 ASN cc_start: 0.8077 (m-40) cc_final: 0.7614 (m-40) REVERT: K 116 TRP cc_start: 0.7604 (OUTLIER) cc_final: 0.7250 (t60) REVERT: K 190 MET cc_start: 0.7548 (ttm) cc_final: 0.7255 (ttm) REVERT: K 369 ASP cc_start: 0.6016 (OUTLIER) cc_final: 0.5642 (t0) REVERT: K 370 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8211 (pp20) REVERT: T 61 TYR cc_start: 0.8247 (m-80) cc_final: 0.7823 (m-80) REVERT: T 333 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8308 (mm) REVERT: T 342 LYS cc_start: 0.8360 (mmmm) cc_final: 0.8048 (mmmt) REVERT: U 35 THR cc_start: 0.8948 (OUTLIER) cc_final: 0.8659 (t) REVERT: U 96 SER cc_start: 0.8592 (m) cc_final: 0.8059 (p) REVERT: U 101 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8742 (mp) REVERT: U 174 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: U 361 GLU cc_start: 0.8622 (tp30) cc_final: 0.8419 (tt0) REVERT: W 1 MET cc_start: 0.7740 (ptt) cc_final: 0.7439 (ptt) REVERT: W 168 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8355 (ttt-90) REVERT: Y 43 GLU cc_start: 0.5264 (tm-30) cc_final: 0.5036 (tm-30) REVERT: Y 150 TYR cc_start: 0.7606 (m-80) cc_final: 0.6540 (m-80) REVERT: Y 229 ASP cc_start: 0.7759 (m-30) cc_final: 0.7506 (m-30) REVERT: Z 31 LYS cc_start: 0.8581 (mmmt) cc_final: 0.7894 (mmmt) REVERT: Z 81 LEU cc_start: 0.9222 (tp) cc_final: 0.8956 (tp) REVERT: Z 93 MET cc_start: 0.8533 (ttp) cc_final: 0.8152 (ttm) REVERT: Z 150 TYR cc_start: 0.8056 (m-80) cc_final: 0.7016 (m-80) REVERT: Z 300 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: 0 36 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8707 (p) REVERT: 1 64 SER cc_start: 0.8611 (m) cc_final: 0.7926 (p) REVERT: 2 151 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7046 (ttm110) outliers start: 242 outliers final: 199 residues processed: 1074 average time/residue: 0.5555 time to fit residues: 1021.1157 Evaluate side-chains 1089 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 873 time to evaluate : 5.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 225 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 151 ASN Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 21 GLU Chi-restraints excluded: chain S residue 104 MET Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 LYS Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 128 VAL Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain x residue 8 GLU Chi-restraints excluded: chain x residue 46 LEU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 123 HIS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 113 PHE Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain J residue 350 ASN Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 209 GLU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 377 ILE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 136 TYR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 SER Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain T residue 17 ILE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 59 CYS Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 141 LYS Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain T residue 333 LEU Chi-restraints excluded: chain T residue 350 ASN Chi-restraints excluded: chain T residue 365 GLU Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 85 LEU Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 174 GLN Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 265 ASP Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 342 LYS Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 151 ASN Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 97 THR Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 157 PHE Chi-restraints excluded: chain Y residue 204 ILE Chi-restraints excluded: chain Y residue 314 SER Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 132 GLU Chi-restraints excluded: chain Z residue 274 CYS Chi-restraints excluded: chain Z residue 291 ASN Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain 0 residue 5 THR Chi-restraints excluded: chain 0 residue 11 LEU Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 90 ASP Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 128 VAL Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 146 ILE Chi-restraints excluded: chain 2 residue 151 ARG Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 61 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 7.9990 chunk 445 optimal weight: 0.0060 chunk 718 optimal weight: 9.9990 chunk 438 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 chunk 499 optimal weight: 1.9990 chunk 753 optimal weight: 10.0000 chunk 693 optimal weight: 9.9990 chunk 599 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 463 optimal weight: 10.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN C 281 GLN ** C 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN I 54 HIS ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 123 HIS K 145 ASN K 223 GLN K 236 GLN ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 350 ASN ** U 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 ASN ** V 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 1.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 61794 Z= 0.177 Angle : 0.466 8.528 83604 Z= 0.252 Chirality : 0.040 0.159 9516 Planarity : 0.004 0.059 10818 Dihedral : 4.091 24.788 8313 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 37.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.78 % Favored : 96.21 % Rotamer: Outliers : 3.27 % Allowed : 24.49 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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 (0.10), residues: 7590 helix: 1.63 (0.09), residues: 3216 sheet: 0.23 (0.16), residues: 1032 loop : -0.96 (0.11), residues: 3342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP T 116 HIS 0.010 0.001 HIS A 343 PHE 0.019 0.001 PHE K 33 TYR 0.021 0.001 TYR 1 85 ARG 0.004 0.000 ARG T 376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15180 Ramachandran restraints generated. 7590 Oldfield, 0 Emsley, 7590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 899 time to evaluate : 5.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 21 MET cc_start: 0.8090 (mmp) cc_final: 0.7385 (ttp) REVERT: D 284 ILE cc_start: 0.8319 (mm) cc_final: 0.8055 (mt) REVERT: D 365 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7633 (tm-30) REVERT: E 41 LYS cc_start: 0.8305 (mmtp) cc_final: 0.8086 (mmtt) REVERT: E 229 ASP cc_start: 0.8395 (m-30) cc_final: 0.8133 (t0) REVERT: E 352 ILE cc_start: 0.9010 (mt) cc_final: 0.8760 (tp) REVERT: E 372 MET cc_start: 0.8583 (tpt) cc_final: 0.8203 (tpp) REVERT: R 27 MET cc_start: 0.7960 (mtm) cc_final: 0.7316 (mtp) REVERT: R 113 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6766 (m-10) REVERT: a 126 MET cc_start: 0.8137 (tmm) cc_final: 0.7248 (pmm) REVERT: a 149 THR cc_start: 0.8345 (m) cc_final: 0.7885 (p) REVERT: B 271 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8361 (mmmt) REVERT: B 372 MET cc_start: 0.8411 (tpt) cc_final: 0.7368 (tpp) REVERT: C 224 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: C 271 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7989 (mppt) REVERT: x 57 GLU cc_start: 0.9262 (pt0) cc_final: 0.8442 (pt0) REVERT: x 58 ARG cc_start: 0.8867 (mmt180) cc_final: 0.8565 (mmt180) REVERT: x 70 MET cc_start: 0.7936 (mmm) cc_final: 0.7309 (mmm) REVERT: A 101 LEU cc_start: 0.9022 (mt) cc_final: 0.8757 (mt) REVERT: A 220 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: A 307 MET cc_start: 0.8283 (mtm) cc_final: 0.8028 (mtm) REVERT: A 357 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7887 (mt-10) REVERT: F 163 TYR cc_start: 0.7078 (t80) cc_final: 0.6607 (t80) REVERT: F 199 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: G 27 MET cc_start: 0.8071 (mmm) cc_final: 0.7793 (mmm) REVERT: H 114 ASN cc_start: 0.7792 (m-40) cc_final: 0.7053 (p0) REVERT: H 168 ARG cc_start: 0.8328 (ttt-90) cc_final: 0.8070 (ttt-90) REVERT: I 80 ASP cc_start: 0.7348 (p0) cc_final: 0.6198 (p0) REVERT: I 126 MET cc_start: 0.7460 (tmm) cc_final: 0.6616 (pmm) REVERT: J 187 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.6969 (tmm-80) REVERT: J 246 MET cc_start: 0.8974 (mtp) cc_final: 0.8670 (mtm) REVERT: J 288 ASN cc_start: 0.7328 (t0) cc_final: 0.7100 (t0) REVERT: K 116 TRP cc_start: 0.7577 (OUTLIER) cc_final: 0.7224 (t60) REVERT: K 190 MET cc_start: 0.7616 (ttm) cc_final: 0.7329 (ttm) REVERT: K 369 ASP cc_start: 0.5971 (OUTLIER) cc_final: 0.5646 (t0) REVERT: K 370 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8087 (pp20) REVERT: M 27 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.6729 (mpp) REVERT: T 61 TYR cc_start: 0.8260 (m-80) cc_final: 0.7903 (m-80) REVERT: T 333 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8300 (mm) REVERT: T 342 LYS cc_start: 0.8362 (mmmm) cc_final: 0.8060 (mmmt) REVERT: T 374 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7239 (ptm-80) REVERT: U 96 SER cc_start: 0.8592 (m) cc_final: 0.8065 (p) REVERT: U 101 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8725 (mp) REVERT: U 174 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: U 261 ASP cc_start: 0.7782 (p0) cc_final: 0.7452 (p0) REVERT: V 2 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7932 (mm-40) REVERT: W 1 MET cc_start: 0.7718 (ptt) cc_final: 0.7405 (ptt) REVERT: W 168 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8314 (ttt-90) REVERT: Y 21 MET cc_start: 0.7379 (mmp) cc_final: 0.7024 (ptm) REVERT: Y 150 TYR cc_start: 0.7668 (m-80) cc_final: 0.6595 (m-80) REVERT: Y 229 ASP cc_start: 0.7753 (m-30) cc_final: 0.7502 (m-30) REVERT: Y 336 ASP cc_start: 0.7155 (t0) cc_final: 0.6944 (t0) REVERT: Z 31 LYS cc_start: 0.8593 (mmmt) cc_final: 0.7924 (mmmt) REVERT: Z 81 LEU cc_start: 0.9201 (tp) cc_final: 0.8942 (tp) REVERT: Z 93 MET cc_start: 0.8508 (ttp) cc_final: 0.8201 (ttm) REVERT: Z 150 TYR cc_start: 0.8026 (m-80) cc_final: 0.6998 (m-80) REVERT: Z 300 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: 0 36 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8693 (p) REVERT: 1 64 SER cc_start: 0.8623 (m) cc_final: 0.7962 (p) REVERT: 2 151 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7192 (ttm110) outliers start: 221 outliers final: 178 residues processed: 1054 average time/residue: 0.5621 time to fit residues: 1013.6859 Evaluate side-chains 1057 residues out of total 6765 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 861 time to evaluate : 5.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 CYS Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 275 LEU Chi-restraints excluded: chain E residue 353 MET Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 113 PHE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 151 ASN Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 21 GLU Chi-restraints excluded: chain a residue 70 MET Chi-restraints excluded: chain a residue 128 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 274 CYS Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 142 ILE Chi-restraints excluded: chain Q residue 58 LYS Chi-restraints excluded: chain Q residue 64 SER Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain x residue 46 LEU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 264 GLU Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 89 SER Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 136 TYR Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 164 ILE Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain I residue 69 TRP Chi-restraints excluded: chain I residue 143 LEU Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 187 ARG Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 330 VAL Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 116 TRP Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 246 MET Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 300 TYR Chi-restraints excluded: chain K residue 311 LEU Chi-restraints excluded: chain K residue 327 THR Chi-restraints excluded: chain K residue 360 LEU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 MET Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 105 ASP Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 136 TYR Chi-restraints excluded: chain N residue 100 VAL Chi-restraints excluded: chain N residue 112 SER Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 43 GLU Chi-restraints excluded: chain T residue 68 ASN Chi-restraints excluded: chain T residue 70 VAL Chi-restraints excluded: chain T residue 97 THR Chi-restraints excluded: chain T residue 141 LYS Chi-restraints excluded: chain T residue 202 THR Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain T residue 333 LEU Chi-restraints excluded: chain T residue 365 GLU Chi-restraints excluded: chain T residue 374 ARG Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 85 LEU Chi-restraints excluded: chain U residue 101 LEU Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 123 HIS Chi-restraints excluded: chain U residue 143 ILE Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain U residue 164 VAL Chi-restraints excluded: chain U residue 174 GLN Chi-restraints excluded: chain U residue 254 ILE Chi-restraints excluded: chain U residue 265 ASP Chi-restraints excluded: chain U residue 291 ASN Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 342 LYS Chi-restraints excluded: chain U residue 360 LEU Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 50 LEU Chi-restraints excluded: chain V residue 114 ASN Chi-restraints excluded: chain V residue 120 LEU Chi-restraints excluded: chain V residue 151 ASN Chi-restraints excluded: chain V residue 154 SER Chi-restraints excluded: chain W residue 43 ASP Chi-restraints excluded: chain W residue 90 ASP Chi-restraints excluded: chain W residue 128 VAL Chi-restraints excluded: chain W residue 154 SER Chi-restraints excluded: chain W residue 168 ARG Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 95 ILE Chi-restraints excluded: chain Y residue 97 THR Chi-restraints excluded: chain Y residue 120 SER Chi-restraints excluded: chain Y residue 131 VAL Chi-restraints excluded: chain Y residue 157 PHE Chi-restraints excluded: chain Y residue 314 SER Chi-restraints excluded: chain Y residue 377 ILE Chi-restraints excluded: chain Z residue 42 ILE Chi-restraints excluded: chain Z residue 59 CYS Chi-restraints excluded: chain Z residue 70 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 132 GLU Chi-restraints excluded: chain Z residue 274 CYS Chi-restraints excluded: chain Z residue 291 ASN Chi-restraints excluded: chain Z residue 300 TYR Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 360 LEU Chi-restraints excluded: chain 0 residue 5 THR Chi-restraints excluded: chain 0 residue 29 THR Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 142 ILE Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 1 residue 128 VAL Chi-restraints excluded: chain 1 residue 164 ILE Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 151 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 0.9990 chunk 476 optimal weight: 10.0000 chunk 638 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 553 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 600 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 616 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** C 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN C 281 GLN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 HIS ** J 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 GLN ** K 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 114 ASN ** V 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 23 GLN ** 2 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.108250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095338 restraints weight = 183580.664| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.10 r_work: 0.3422 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 1.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 61794 Z= 0.425 Angle : 0.657 9.566 83604 Z= 0.352 Chirality : 0.044 0.185 9516 Planarity : 0.005 0.065 10818 Dihedral : 4.808 26.495 8313 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 41.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.35 % Favored : 93.61 % Rotamer: Outliers : 4.04 % Allowed : 24.02 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.96 % 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: -0.30 (0.10), residues: 7590 helix: 1.07 (0.09), residues: 3096 sheet: -0.10 (0.16), residues: 1086 loop : -1.45 (0.10), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP K 116 HIS 0.009 0.002 HIS C 343 PHE 0.025 0.002 PHE A 299 TYR 0.026 0.002 TYR 1 85 ARG 0.006 0.001 ARG Z 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19529.44 seconds wall clock time: 342 minutes 5.17 seconds (20525.17 seconds total)