Starting phenix.real_space_refine on Fri Dec 27 13:41:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wld_37616/12_2024/8wld_37616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wld_37616/12_2024/8wld_37616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wld_37616/12_2024/8wld_37616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wld_37616/12_2024/8wld_37616.map" model { file = "/net/cci-nas-00/data/ceres_data/8wld_37616/12_2024/8wld_37616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wld_37616/12_2024/8wld_37616.cif" } resolution = 3.48 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= -0.001 sd= 0.063 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: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 30774 2.51 5 N 8343 2.21 5 O 9074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 48292 Number of models: 1 Model: "" Number of chains: 15 Chain: "S" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2334 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 16, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 408 Unresolved non-hydrogen angles: 501 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 10, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 242 Chain: "T" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2654 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 18, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "K" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2051 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 16, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 825 Unresolved non-hydrogen dihedrals: 524 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 17, 'TYR:plan': 6, 'ASN:plan1': 16, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 362 Chain: "J" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2242 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 16, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 598 Unresolved non-hydrogen dihedrals: 395 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 290 Chain: "R" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2619 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 17, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "P" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2457 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain breaks: 3 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 173 Chain: "Q" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2345 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 18, 'TRANS': 323} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 519 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 14, 'TYR:plan': 3, 'ASN:plan1': 8, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 233 Chain: "O" Number of atoms: 4968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 4968 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 30, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 8, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 14, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 206 Chain: "A" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3259 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 21, 'TRANS': 459} Chain breaks: 3 Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 632 Unresolved non-hydrogen dihedrals: 424 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 14, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 312 Chain: "D" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 4840 Classifications: {'peptide': 660} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 29, 'TRANS': 630} Chain breaks: 3 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 460 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 5, 'TYR:plan': 7, 'ASN:plan1': 8, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 226 Chain: "L" Number of atoms: 4966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 4966 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 30, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 273 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 8, 'HIS:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 207 Chain: "M" Number of atoms: 4958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 4958 Classifications: {'peptide': 672} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 30, 'TRANS': 641} Chain breaks: 1 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 273 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 8, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 212 Chain: "N" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 3632 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 327} Link IDs: {'PTRANS': 25, 'TRANS': 587} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1237 Unresolved non-hydrogen angles: 1572 Unresolved non-hydrogen dihedrals: 1023 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 5, 'TYR:plan': 13, 'ASN:plan1': 22, 'TRP:plan': 5, 'ASP:plan': 29, 'PHE:plan': 18, 'GLU:plan': 37, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 756 Chain: "H" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2316 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 16, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 427 Unresolved non-hydrogen angles: 525 Unresolved non-hydrogen dihedrals: 345 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 11, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 256 Chain: "E" Number of atoms: 2651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2651 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 18, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 20.86, per 1000 atoms: 0.43 Number of scatterers: 48292 At special positions: 0 Unit cell: (167.156, 186.938, 229.469, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 9074 8.00 N 8343 7.00 C 30774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.74 Conformation dependent library (CDL) restraints added in 4.9 seconds 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12796 Finding SS restraints... Secondary structure from input PDB file: 278 helices and 47 sheets defined 42.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'S' and resid 11 through 24 removed outlier: 3.532A pdb=" N GLN S 15 " --> pdb=" O ASP S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 41 Processing helix chain 'S' and resid 52 through 63 Processing helix chain 'S' and resid 73 through 81 Processing helix chain 'S' and resid 87 through 101 removed outlier: 3.757A pdb=" N ILE S 101 " --> pdb=" O LEU S 97 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 108 removed outlier: 4.305A pdb=" N LYS S 106 " --> pdb=" O MET S 103 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE S 107 " --> pdb=" O SER S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 131 Processing helix chain 'S' and resid 139 through 151 removed outlier: 3.606A pdb=" N LYS S 143 " --> pdb=" O THR S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 166 through 175 Processing helix chain 'S' and resid 193 through 199 removed outlier: 4.188A pdb=" N GLU S 197 " --> pdb=" O ILE S 193 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN S 199 " --> pdb=" O THR S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 251 through 265 Processing helix chain 'S' and resid 280 through 294 removed outlier: 3.941A pdb=" N VAL S 286 " --> pdb=" O HIS S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 309 Processing helix chain 'S' and resid 310 through 320 Processing helix chain 'S' and resid 360 through 373 Processing helix chain 'T' and resid 11 through 24 removed outlier: 3.861A pdb=" N GLN T 15 " --> pdb=" O ASP T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 42 Processing helix chain 'T' and resid 52 through 64 Processing helix chain 'T' and resid 69 through 83 removed outlier: 4.151A pdb=" N ILE T 75 " --> pdb=" O LEU T 71 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE T 76 " --> pdb=" O LEU T 72 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR T 82 " --> pdb=" O ASN T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 101 removed outlier: 3.514A pdb=" N ILE T 101 " --> pdb=" O LEU T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 131 Processing helix chain 'T' and resid 139 through 149 removed outlier: 3.556A pdb=" N ASN T 149 " --> pdb=" O ALA T 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 166 through 175 removed outlier: 3.567A pdb=" N LEU T 175 " --> pdb=" O ALA T 171 " (cutoff:3.500A) Processing helix chain 'T' and resid 193 through 199 removed outlier: 3.760A pdb=" N GLU T 197 " --> pdb=" O ILE T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 252 through 265 Processing helix chain 'T' and resid 281 through 294 Processing helix chain 'T' and resid 306 through 309 Processing helix chain 'T' and resid 310 through 320 Processing helix chain 'T' and resid 356 through 359 removed outlier: 3.638A pdb=" N GLY T 359 " --> pdb=" O PHE T 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 356 through 359' Processing helix chain 'T' and resid 360 through 373 removed outlier: 3.712A pdb=" N GLN T 373 " --> pdb=" O GLU T 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 25 Processing helix chain 'K' and resid 36 through 42 Processing helix chain 'K' and resid 52 through 63 removed outlier: 3.510A pdb=" N SER K 63 " --> pdb=" O LYS K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 83 removed outlier: 4.383A pdb=" N THR K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 101 removed outlier: 3.553A pdb=" N ILE K 101 " --> pdb=" O LEU K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 131 removed outlier: 3.559A pdb=" N ALA K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 150 removed outlier: 3.739A pdb=" N LYS K 143 " --> pdb=" O THR K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 174 Processing helix chain 'K' and resid 193 through 199 removed outlier: 3.968A pdb=" N GLU K 197 " --> pdb=" O ILE K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 266 Processing helix chain 'K' and resid 280 through 294 Processing helix chain 'K' and resid 306 through 309 Processing helix chain 'K' and resid 310 through 320 Processing helix chain 'K' and resid 360 through 373 Processing helix chain 'J' and resid 14 through 25 removed outlier: 3.587A pdb=" N LEU J 18 " --> pdb=" O GLN J 14 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS J 21 " --> pdb=" O SER J 17 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL J 22 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 41 removed outlier: 3.678A pdb=" N VAL J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 36 through 41' Processing helix chain 'J' and resid 52 through 63 removed outlier: 3.513A pdb=" N SER J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 83 Processing helix chain 'J' and resid 87 through 101 removed outlier: 3.509A pdb=" N ILE J 101 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 113 through 131 Processing helix chain 'J' and resid 139 through 151 removed outlier: 3.747A pdb=" N LYS J 143 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 175 removed outlier: 3.512A pdb=" N LEU J 175 " --> pdb=" O ALA J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 199 removed outlier: 3.840A pdb=" N GLU J 197 " --> pdb=" O ILE J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 266 removed outlier: 3.749A pdb=" N VAL J 255 " --> pdb=" O MET J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 294 Processing helix chain 'J' and resid 306 through 309 Processing helix chain 'J' and resid 310 through 320 Processing helix chain 'J' and resid 360 through 373 Processing helix chain 'R' and resid 11 through 24 removed outlier: 3.676A pdb=" N GLN R 15 " --> pdb=" O ASP R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 42 Processing helix chain 'R' and resid 52 through 64 Processing helix chain 'R' and resid 70 through 81 Processing helix chain 'R' and resid 87 through 101 removed outlier: 3.622A pdb=" N ILE R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 131 removed outlier: 3.664A pdb=" N GLU R 120 " --> pdb=" O ASN R 116 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN R 131 " --> pdb=" O GLU R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 149 removed outlier: 3.518A pdb=" N ASN R 149 " --> pdb=" O ALA R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 175 removed outlier: 3.643A pdb=" N LEU R 175 " --> pdb=" O ALA R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 199 removed outlier: 3.756A pdb=" N ASN R 199 " --> pdb=" O THR R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 265 Processing helix chain 'R' and resid 281 through 294 Processing helix chain 'R' and resid 306 through 309 Processing helix chain 'R' and resid 310 through 320 Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.650A pdb=" N GLY R 359 " --> pdb=" O PHE R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 373 removed outlier: 3.888A pdb=" N GLN R 373 " --> pdb=" O GLU R 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 25 removed outlier: 3.598A pdb=" N GLN P 15 " --> pdb=" O ASP P 11 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU P 25 " --> pdb=" O HIS P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 41 removed outlier: 3.976A pdb=" N VAL P 40 " --> pdb=" O ALA P 36 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER P 41 " --> pdb=" O GLY P 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 36 through 41' Processing helix chain 'P' and resid 52 through 64 Processing helix chain 'P' and resid 71 through 81 removed outlier: 4.163A pdb=" N ILE P 75 " --> pdb=" O LEU P 71 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE P 76 " --> pdb=" O LEU P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 101 Processing helix chain 'P' and resid 113 through 131 removed outlier: 3.559A pdb=" N ALA P 117 " --> pdb=" O SER P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 151 removed outlier: 4.023A pdb=" N ILE P 151 " --> pdb=" O TRP P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 175 Processing helix chain 'P' and resid 193 through 199 removed outlier: 3.709A pdb=" N GLU P 197 " --> pdb=" O ILE P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 265 Processing helix chain 'P' and resid 281 through 294 Processing helix chain 'P' and resid 306 through 309 Processing helix chain 'P' and resid 310 through 320 Processing helix chain 'P' and resid 356 through 359 Processing helix chain 'P' and resid 360 through 373 Processing helix chain 'Q' and resid 11 through 24 removed outlier: 3.728A pdb=" N GLN Q 15 " --> pdb=" O ASP Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 42 Processing helix chain 'Q' and resid 52 through 64 Processing helix chain 'Q' and resid 69 through 83 removed outlier: 3.874A pdb=" N ILE Q 75 " --> pdb=" O LEU Q 71 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE Q 76 " --> pdb=" O LEU Q 72 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR Q 82 " --> pdb=" O ASN Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 101 removed outlier: 3.734A pdb=" N ILE Q 101 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 105 removed outlier: 4.525A pdb=" N GLY Q 105 " --> pdb=" O PRO Q 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 102 through 105' Processing helix chain 'Q' and resid 113 through 131 Processing helix chain 'Q' and resid 139 through 151 removed outlier: 3.684A pdb=" N ASN Q 149 " --> pdb=" O ALA Q 145 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE Q 151 " --> pdb=" O TRP Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 166 through 175 removed outlier: 3.657A pdb=" N LEU Q 175 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 199 Processing helix chain 'Q' and resid 252 through 265 removed outlier: 3.595A pdb=" N GLN Q 259 " --> pdb=" O VAL Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 294 Processing helix chain 'Q' and resid 306 through 309 removed outlier: 3.525A pdb=" N ASN Q 309 " --> pdb=" O VAL Q 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 306 through 309' Processing helix chain 'Q' and resid 310 through 320 Processing helix chain 'Q' and resid 356 through 359 removed outlier: 3.852A pdb=" N GLY Q 359 " --> pdb=" O PHE Q 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 356 through 359' Processing helix chain 'Q' and resid 360 through 373 Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'O' and resid 78 through 83 Processing helix chain 'O' and resid 122 through 130 Processing helix chain 'O' and resid 155 through 161 Processing helix chain 'O' and resid 168 through 171 Processing helix chain 'O' and resid 172 through 185 removed outlier: 3.520A pdb=" N THR O 176 " --> pdb=" O GLY O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 233 Processing helix chain 'O' and resid 234 through 242 Processing helix chain 'O' and resid 248 through 269 removed outlier: 4.120A pdb=" N ASN O 252 " --> pdb=" O GLY O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 288 through 302 removed outlier: 3.789A pdb=" N LEU O 292 " --> pdb=" O SER O 288 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU O 300 " --> pdb=" O LEU O 296 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE O 301 " --> pdb=" O TYR O 297 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER O 302 " --> pdb=" O ARG O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 311 through 315 removed outlier: 3.590A pdb=" N GLU O 315 " --> pdb=" O GLU O 312 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 373 Processing helix chain 'O' and resid 376 through 381 Processing helix chain 'O' and resid 396 through 406 removed outlier: 3.852A pdb=" N LEU O 400 " --> pdb=" O ASP O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 423 through 442 removed outlier: 3.783A pdb=" N SER O 442 " --> pdb=" O SER O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 472 through 488 removed outlier: 5.436A pdb=" N ARG O 485 " --> pdb=" O VAL O 481 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS O 486 " --> pdb=" O LYS O 482 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR O 487 " --> pdb=" O GLU O 483 " (cutoff:3.500A) Processing helix chain 'O' and resid 502 through 507 Processing helix chain 'O' and resid 519 through 528 removed outlier: 4.040A pdb=" N ARG O 523 " --> pdb=" O ASN O 519 " (cutoff:3.500A) Processing helix chain 'O' and resid 534 through 539 removed outlier: 3.896A pdb=" N GLY O 539 " --> pdb=" O GLU O 535 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 544 removed outlier: 3.568A pdb=" N LEU O 544 " --> pdb=" O LEU O 541 " (cutoff:3.500A) Processing helix chain 'O' and resid 579 through 586 removed outlier: 3.615A pdb=" N ASN O 586 " --> pdb=" O ALA O 582 " (cutoff:3.500A) Processing helix chain 'O' and resid 592 through 603 removed outlier: 3.968A pdb=" N VAL O 596 " --> pdb=" O ASP O 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 666 through 676 removed outlier: 3.807A pdb=" N HIS O 670 " --> pdb=" O PRO O 666 " (cutoff:3.500A) Processing helix chain 'O' and resid 681 through 687 Processing helix chain 'A' and resid 76 through 83 removed outlier: 3.805A pdb=" N GLU A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.719A pdb=" N VAL A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 250 through 269 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 362 through 373 Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.592A pdb=" N LEU A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 423 through 442 removed outlier: 3.653A pdb=" N GLY A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 472 through 488 removed outlier: 4.759A pdb=" N ARG A 485 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 519 through 528 removed outlier: 3.790A pdb=" N ARG A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 removed outlier: 4.375A pdb=" N GLY A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 544 Processing helix chain 'D' and resid 76 through 83 Processing helix chain 'D' and resid 122 through 131 Processing helix chain 'D' and resid 155 through 161 Processing helix chain 'D' and resid 168 through 171 Processing helix chain 'D' and resid 172 through 185 removed outlier: 3.555A pdb=" N THR D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 234 through 242 Processing helix chain 'D' and resid 248 through 269 removed outlier: 4.077A pdb=" N ASN D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 302 removed outlier: 3.991A pdb=" N LEU D 292 " --> pdb=" O SER D 288 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 301 " --> pdb=" O TYR D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 315 removed outlier: 3.549A pdb=" N GLU D 315 " --> pdb=" O GLU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 373 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.808A pdb=" N LEU D 400 " --> pdb=" O ASP D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 442 removed outlier: 3.871A pdb=" N SER D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 464 Processing helix chain 'D' and resid 472 through 488 removed outlier: 5.460A pdb=" N ARG D 485 " --> pdb=" O VAL D 481 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS D 486 " --> pdb=" O LYS D 482 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'D' and resid 502 through 507 Processing helix chain 'D' and resid 519 through 529 removed outlier: 3.964A pdb=" N ARG D 523 " --> pdb=" O ASN D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 539 removed outlier: 3.716A pdb=" N GLY D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 544 removed outlier: 3.607A pdb=" N LEU D 544 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 586 removed outlier: 3.530A pdb=" N LYS D 583 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 603 Processing helix chain 'D' and resid 666 through 675 removed outlier: 3.977A pdb=" N HIS D 670 " --> pdb=" O PRO D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 687 Processing helix chain 'L' and resid 78 through 83 Processing helix chain 'L' and resid 122 through 130 Processing helix chain 'L' and resid 155 through 161 Processing helix chain 'L' and resid 168 through 171 Processing helix chain 'L' and resid 172 through 185 Processing helix chain 'L' and resid 229 through 233 Processing helix chain 'L' and resid 234 through 243 Processing helix chain 'L' and resid 248 through 269 removed outlier: 3.939A pdb=" N ASN L 252 " --> pdb=" O GLY L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 302 removed outlier: 3.560A pdb=" N LEU L 292 " --> pdb=" O SER L 288 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU L 300 " --> pdb=" O LEU L 296 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER L 302 " --> pdb=" O ARG L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 315 removed outlier: 3.854A pdb=" N GLU L 315 " --> pdb=" O GLU L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 360 through 372 Processing helix chain 'L' and resid 373 through 375 No H-bonds generated for 'chain 'L' and resid 373 through 375' Processing helix chain 'L' and resid 376 through 381 Processing helix chain 'L' and resid 396 through 406 removed outlier: 3.933A pdb=" N LEU L 400 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 423 through 442 removed outlier: 3.853A pdb=" N SER L 442 " --> pdb=" O SER L 438 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 464 Processing helix chain 'L' and resid 472 through 488 removed outlier: 5.443A pdb=" N ARG L 485 " --> pdb=" O VAL L 481 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS L 486 " --> pdb=" O LYS L 482 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR L 487 " --> pdb=" O GLU L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 502 through 507 Processing helix chain 'L' and resid 519 through 529 removed outlier: 3.680A pdb=" N ARG L 523 " --> pdb=" O ASN L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 534 through 539 removed outlier: 4.026A pdb=" N GLY L 539 " --> pdb=" O GLU L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 544 removed outlier: 3.639A pdb=" N LEU L 544 " --> pdb=" O LEU L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 579 through 586 removed outlier: 3.591A pdb=" N ASN L 586 " --> pdb=" O ALA L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 592 through 603 removed outlier: 4.145A pdb=" N VAL L 596 " --> pdb=" O ASP L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 676 removed outlier: 3.653A pdb=" N HIS L 670 " --> pdb=" O PRO L 666 " (cutoff:3.500A) Processing helix chain 'L' and resid 680 through 687 Processing helix chain 'M' and resid 76 through 83 removed outlier: 3.953A pdb=" N LEU M 80 " --> pdb=" O PRO M 76 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU M 81 " --> pdb=" O ASP M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 131 Processing helix chain 'M' and resid 155 through 161 Processing helix chain 'M' and resid 168 through 171 Processing helix chain 'M' and resid 172 through 185 Processing helix chain 'M' and resid 229 through 233 removed outlier: 3.542A pdb=" N ALA M 232 " --> pdb=" O PRO M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 243 Processing helix chain 'M' and resid 248 through 269 removed outlier: 4.135A pdb=" N ASN M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 302 removed outlier: 3.618A pdb=" N LEU M 292 " --> pdb=" O SER M 288 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU M 300 " --> pdb=" O LEU M 296 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE M 301 " --> pdb=" O TYR M 297 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER M 302 " --> pdb=" O ARG M 298 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 315 Processing helix chain 'M' and resid 360 through 372 removed outlier: 3.508A pdb=" N LYS M 372 " --> pdb=" O ALA M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 375 No H-bonds generated for 'chain 'M' and resid 373 through 375' Processing helix chain 'M' and resid 376 through 381 Processing helix chain 'M' and resid 396 through 406 removed outlier: 3.902A pdb=" N LEU M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 422 No H-bonds generated for 'chain 'M' and resid 420 through 422' Processing helix chain 'M' and resid 423 through 442 removed outlier: 3.798A pdb=" N SER M 442 " --> pdb=" O SER M 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 464 removed outlier: 3.527A pdb=" N TYR M 464 " --> pdb=" O ALA M 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 461 through 464' Processing helix chain 'M' and resid 472 through 484 Processing helix chain 'M' and resid 502 through 508 removed outlier: 3.564A pdb=" N GLN M 508 " --> pdb=" O THR M 504 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 529 removed outlier: 3.822A pdb=" N ARG M 523 " --> pdb=" O ASN M 519 " (cutoff:3.500A) Processing helix chain 'M' and resid 534 through 539 Processing helix chain 'M' and resid 540 through 544 removed outlier: 3.619A pdb=" N LEU M 544 " --> pdb=" O LEU M 541 " (cutoff:3.500A) Processing helix chain 'M' and resid 579 through 586 removed outlier: 3.556A pdb=" N ASN M 586 " --> pdb=" O ALA M 582 " (cutoff:3.500A) Processing helix chain 'M' and resid 592 through 603 removed outlier: 4.288A pdb=" N VAL M 596 " --> pdb=" O ASP M 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 666 through 675 removed outlier: 3.646A pdb=" N HIS M 670 " --> pdb=" O PRO M 666 " (cutoff:3.500A) Processing helix chain 'M' and resid 681 through 687 Processing helix chain 'N' and resid 122 through 130 Processing helix chain 'N' and resid 155 through 161 Processing helix chain 'N' and resid 168 through 171 Processing helix chain 'N' and resid 172 through 185 Processing helix chain 'N' and resid 229 through 233 removed outlier: 3.527A pdb=" N ALA N 232 " --> pdb=" O PRO N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 242 Processing helix chain 'N' and resid 248 through 269 Processing helix chain 'N' and resid 289 through 299 Processing helix chain 'N' and resid 360 through 373 Processing helix chain 'N' and resid 376 through 381 Processing helix chain 'N' and resid 396 through 406 removed outlier: 3.583A pdb=" N LEU N 400 " --> pdb=" O ASP N 396 " (cutoff:3.500A) Processing helix chain 'N' and resid 423 through 442 removed outlier: 3.509A pdb=" N SER N 442 " --> pdb=" O SER N 438 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 464 Processing helix chain 'N' and resid 471 through 488 removed outlier: 4.069A pdb=" N ASP N 475 " --> pdb=" O GLY N 471 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ARG N 485 " --> pdb=" O VAL N 481 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS N 486 " --> pdb=" O LYS N 482 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR N 487 " --> pdb=" O GLU N 483 " (cutoff:3.500A) Processing helix chain 'N' and resid 497 through 501 Processing helix chain 'N' and resid 502 through 508 Processing helix chain 'N' and resid 519 through 528 removed outlier: 3.582A pdb=" N ARG N 523 " --> pdb=" O ASN N 519 " (cutoff:3.500A) Processing helix chain 'N' and resid 534 through 539 Processing helix chain 'N' and resid 540 through 544 removed outlier: 3.642A pdb=" N THR N 543 " --> pdb=" O MET N 540 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU N 544 " --> pdb=" O LEU N 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 540 through 544' Processing helix chain 'N' and resid 579 through 586 removed outlier: 3.999A pdb=" N ASN N 586 " --> pdb=" O ALA N 582 " (cutoff:3.500A) Processing helix chain 'N' and resid 592 through 603 removed outlier: 4.134A pdb=" N VAL N 596 " --> pdb=" O ASP N 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 666 through 676 removed outlier: 3.650A pdb=" N HIS N 670 " --> pdb=" O PRO N 666 " (cutoff:3.500A) Processing helix chain 'N' and resid 681 through 687 Processing helix chain 'H' and resid 12 through 24 Processing helix chain 'H' and resid 37 through 41 Processing helix chain 'H' and resid 52 through 63 Processing helix chain 'H' and resid 73 through 81 Processing helix chain 'H' and resid 87 through 101 removed outlier: 3.757A pdb=" N ILE H 101 " --> pdb=" O LEU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 108 removed outlier: 4.305A pdb=" N LYS H 106 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE H 107 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 131 Processing helix chain 'H' and resid 139 through 151 removed outlier: 3.607A pdb=" N LYS H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 175 Processing helix chain 'H' and resid 193 through 199 removed outlier: 4.189A pdb=" N GLU H 197 " --> pdb=" O ILE H 193 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN H 199 " --> pdb=" O THR H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 265 Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.941A pdb=" N VAL H 286 " --> pdb=" O HIS H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 309 Processing helix chain 'H' and resid 310 through 320 Processing helix chain 'H' and resid 360 through 373 Processing helix chain 'E' and resid 11 through 24 removed outlier: 3.862A pdb=" N GLN E 15 " --> pdb=" O ASP E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 42 Processing helix chain 'E' and resid 52 through 64 Processing helix chain 'E' and resid 69 through 83 removed outlier: 4.151A pdb=" N ILE E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 101 removed outlier: 3.514A pdb=" N ILE E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 131 Processing helix chain 'E' and resid 139 through 149 removed outlier: 3.557A pdb=" N ASN E 149 " --> pdb=" O ALA E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 removed outlier: 3.566A pdb=" N LEU E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 199 removed outlier: 3.759A pdb=" N GLU E 197 " --> pdb=" O ILE E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 265 Processing helix chain 'E' and resid 281 through 294 Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'E' and resid 310 through 320 Processing helix chain 'E' and resid 356 through 359 removed outlier: 3.638A pdb=" N GLY E 359 " --> pdb=" O PHE E 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 360 through 373 removed outlier: 3.713A pdb=" N GLN E 373 " --> pdb=" O GLU E 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S' and resid 207 through 210 removed outlier: 6.621A pdb=" N VAL S 157 " --> pdb=" O LYS S 207 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N TRP S 209 " --> pdb=" O VAL S 157 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE S 159 " --> pdb=" O TRP S 209 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE S 30 " --> pdb=" O GLU S 158 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE S 160 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE S 32 " --> pdb=" O PHE S 160 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA S 31 " --> pdb=" O ILE S 272 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N CYS S 274 " --> pdb=" O ALA S 31 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE S 33 " --> pdb=" O CYS S 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'S' and resid 43 through 44 Processing sheet with id=AA3, first strand: chain 'S' and resid 183 through 184 removed outlier: 3.897A pdb=" N VAL S 184 " --> pdb=" O PHE S 190 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE S 190 " --> pdb=" O VAL S 184 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 302 through 303 Processing sheet with id=AA5, first strand: chain 'T' and resid 9 through 10 removed outlier: 3.685A pdb=" N ALA T 331 " --> pdb=" O GLY T 338 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE T 33 " --> pdb=" O CYS T 274 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE T 32 " --> pdb=" O PHE T 160 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU T 208 " --> pdb=" O PHE T 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'T' and resid 217 through 219 Processing sheet with id=AA7, first strand: chain 'K' and resid 33 through 34 removed outlier: 5.939A pdb=" N PHE K 180 " --> pdb=" O LEU K 208 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LYS K 210 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 43 through 44 Processing sheet with id=AA9, first strand: chain 'K' and resid 183 through 184 removed outlier: 3.747A pdb=" N VAL K 184 " --> pdb=" O PHE K 190 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE K 190 " --> pdb=" O VAL K 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 270 through 273 removed outlier: 7.466A pdb=" N LEU K 271 " --> pdb=" O TYR K 300 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU K 302 " --> pdb=" O LEU K 271 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR K 273 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE K 299 " --> pdb=" O ILE K 324 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU K 326 " --> pdb=" O ILE K 299 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY K 301 " --> pdb=" O LEU K 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 179 through 180 removed outlier: 5.850A pdb=" N PHE J 180 " --> pdb=" O LEU J 208 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LYS J 210 " --> pdb=" O PHE J 180 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE J 32 " --> pdb=" O PHE J 160 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA J 31 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N CYS J 274 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE J 33 " --> pdb=" O CYS J 274 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 43 through 44 Processing sheet with id=AB4, first strand: chain 'J' and resid 188 through 189 removed outlier: 3.624A pdb=" N ALA J 189 " --> pdb=" O ARG J 228 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 324 through 326 Processing sheet with id=AB6, first strand: chain 'R' and resid 9 through 10 removed outlier: 6.589A pdb=" N LEU R 271 " --> pdb=" O TYR R 300 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU R 302 " --> pdb=" O LEU R 271 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR R 273 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA R 31 " --> pdb=" O ILE R 272 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N CYS R 274 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE R 33 " --> pdb=" O CYS R 274 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE R 159 " --> pdb=" O TRP R 209 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 183 through 184 Processing sheet with id=AB8, first strand: chain 'R' and resid 217 through 219 removed outlier: 3.620A pdb=" N TRP R 227 " --> pdb=" O GLN R 218 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 9 through 10 removed outlier: 3.603A pdb=" N ILE P 332 " --> pdb=" O LEU P 325 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA P 31 " --> pdb=" O ILE P 272 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N CYS P 274 " --> pdb=" O ALA P 31 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE P 33 " --> pdb=" O CYS P 274 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE P 159 " --> pdb=" O TRP P 209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 217 through 219 removed outlier: 3.703A pdb=" N TRP P 227 " --> pdb=" O GLN P 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 9 through 10 removed outlier: 6.158A pdb=" N ALA Q 269 " --> pdb=" O LEU Q 298 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N TYR Q 300 " --> pdb=" O ALA Q 269 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU Q 271 " --> pdb=" O TYR Q 300 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU Q 302 " --> pdb=" O LEU Q 271 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR Q 273 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA Q 31 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N CYS Q 274 " --> pdb=" O ALA Q 31 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE Q 33 " --> pdb=" O CYS Q 274 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE Q 30 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N PHE Q 160 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE Q 32 " --> pdb=" O PHE Q 160 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE Q 159 " --> pdb=" O TRP Q 209 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 183 through 184 Processing sheet with id=AC4, first strand: chain 'Q' and resid 217 through 219 Processing sheet with id=AC5, first strand: chain 'O' and resid 13 through 20 removed outlier: 6.643A pdb=" N ARG O 26 " --> pdb=" O GLN O 18 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 25 through 29 current: chain 'O' and resid 61 through 71 removed outlier: 7.202A pdb=" N ASN O 62 " --> pdb=" O GLU O 97 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU O 97 " --> pdb=" O ASN O 62 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N PHE O 64 " --> pdb=" O VAL O 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL O 95 " --> pdb=" O PHE O 64 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER O 91 " --> pdb=" O SER O 68 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL O 70 " --> pdb=" O TRP O 89 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N TRP O 89 " --> pdb=" O VAL O 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 104 through 106 current: chain 'A' and resid 25 through 28 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 28 current: chain 'A' and resid 61 through 70 removed outlier: 7.206A pdb=" N ASN A 62 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU A 97 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE A 64 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER A 91 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL A 70 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TRP A 89 " --> pdb=" O VAL A 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 104 through 106 current: chain 'D' and resid 25 through 29 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 29 current: chain 'D' and resid 61 through 71 removed outlier: 7.067A pdb=" N ASN D 62 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU D 97 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE D 64 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER D 91 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL D 70 " --> pdb=" O TRP D 89 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N TRP D 89 " --> pdb=" O VAL D 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 104 through 106 current: chain 'L' and resid 25 through 29 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 25 through 29 current: chain 'L' and resid 61 through 71 removed outlier: 6.990A pdb=" N ASN L 62 " --> pdb=" O GLU L 97 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU L 97 " --> pdb=" O ASN L 62 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE L 64 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER L 91 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL L 70 " --> pdb=" O TRP L 89 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N TRP L 89 " --> pdb=" O VAL L 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 104 through 106 current: chain 'M' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 24 through 29 current: chain 'M' and resid 61 through 71 removed outlier: 6.898A pdb=" N LEU M 63 " --> pdb=" O GLU M 97 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU M 97 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY M 65 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL M 95 " --> pdb=" O GLY M 65 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL M 67 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN M 93 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN M 69 " --> pdb=" O SER M 91 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TRP M 89 " --> pdb=" O GLY M 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 104 through 106 current: chain 'N' and resid 24 through 28 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 24 through 28 current: chain 'N' and resid 61 through 71 removed outlier: 6.874A pdb=" N LEU N 63 " --> pdb=" O GLU N 97 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU N 97 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLY N 65 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL N 95 " --> pdb=" O GLY N 65 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL N 67 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLN N 93 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 39 through 40 Processing sheet with id=AC7, first strand: chain 'O' and resid 150 through 153 removed outlier: 6.533A pdb=" N ALA O 151 " --> pdb=" O LEU O 140 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU O 493 " --> pdb=" O SER O 163 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU O 459 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE O 195 " --> pdb=" O SER O 412 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N PHE O 414 " --> pdb=" O ILE O 195 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL O 197 " --> pdb=" O PHE O 414 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS O 213 " --> pdb=" O ILE O 413 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 303 through 304 removed outlier: 3.621A pdb=" N TYR O 352 " --> pdb=" O HIS O 304 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 616 through 618 removed outlier: 3.748A pdb=" N LEU O 617 " --> pdb=" O ILE O 641 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER O 640 " --> pdb=" O GLU O 653 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU O 651 " --> pdb=" O GLY O 642 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 150 through 154 removed outlier: 6.441A pdb=" N ALA A 151 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 164 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE A 195 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N PHE A 414 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 197 " --> pdb=" O PHE A 414 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 150 through 153 removed outlier: 6.627A pdb=" N ALA D 151 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA D 164 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 493 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 456 " --> pdb=" O MET D 492 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL D 494 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU D 458 " --> pdb=" O VAL D 494 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 459 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE D 195 " --> pdb=" O SER D 412 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE D 414 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 197 " --> pdb=" O PHE D 414 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU D 224 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL D 214 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 303 through 304 Processing sheet with id=AD4, first strand: chain 'D' and resid 616 through 618 Processing sheet with id=AD5, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.891A pdb=" N TYR L 45 " --> pdb=" O LYS L 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 150 through 153 removed outlier: 6.742A pdb=" N ALA L 151 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET L 560 " --> pdb=" O ILE L 551 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA L 514 " --> pdb=" O ILE L 550 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA L 164 " --> pdb=" O PHE L 513 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL L 456 " --> pdb=" O MET L 492 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL L 494 " --> pdb=" O VAL L 456 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU L 458 " --> pdb=" O VAL L 494 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU L 459 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE L 195 " --> pdb=" O SER L 412 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N PHE L 414 " --> pdb=" O ILE L 195 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL L 197 " --> pdb=" O PHE L 414 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N LEU L 224 " --> pdb=" O ALA L 212 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL L 214 " --> pdb=" O LEU L 224 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 303 through 304 Processing sheet with id=AD8, first strand: chain 'L' and resid 616 through 618 removed outlier: 3.893A pdb=" N LEU L 617 " --> pdb=" O ILE L 641 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU L 653 " --> pdb=" O LEU L 639 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE L 641 " --> pdb=" O GLU L 651 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU L 651 " --> pdb=" O ILE L 641 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 150 through 153 removed outlier: 3.982A pdb=" N GLY M 141 " --> pdb=" O ALA M 151 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL M 153 " --> pdb=" O SER M 139 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER M 139 " --> pdb=" O VAL M 153 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU M 459 " --> pdb=" O PHE M 198 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE M 195 " --> pdb=" O SER M 412 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE M 414 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL M 197 " --> pdb=" O PHE M 414 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS M 213 " --> pdb=" O ILE M 413 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASP M 415 " --> pdb=" O LYS M 213 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR M 215 " --> pdb=" O ASP M 415 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU M 224 " --> pdb=" O ALA M 212 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL M 214 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 638 through 642 removed outlier: 3.565A pdb=" N SER M 640 " --> pdb=" O GLU M 653 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE M 652 " --> pdb=" O TYR M 660 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 39 through 40 Processing sheet with id=AE3, first strand: chain 'N' and resid 150 through 154 removed outlier: 6.531A pdb=" N ALA N 151 " --> pdb=" O LEU N 140 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN N 142 " --> pdb=" O ILE N 563 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 224 through 225 removed outlier: 8.109A pdb=" N LEU N 224 " --> pdb=" O ALA N 212 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL N 214 " --> pdb=" O LEU N 224 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LYS N 213 " --> pdb=" O ILE N 413 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE N 195 " --> pdb=" O SER N 412 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE N 414 " --> pdb=" O ILE N 195 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL N 197 " --> pdb=" O PHE N 414 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU N 459 " --> pdb=" O PHE N 198 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU N 454 " --> pdb=" O GLY N 490 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N MET N 492 " --> pdb=" O LEU N 454 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL N 456 " --> pdb=" O MET N 492 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL N 494 " --> pdb=" O VAL N 456 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU N 458 " --> pdb=" O VAL N 494 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA N 164 " --> pdb=" O PHE N 513 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 641 through 642 Processing sheet with id=AE6, first strand: chain 'H' and resid 207 through 210 removed outlier: 6.620A pdb=" N VAL H 157 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N TRP H 209 " --> pdb=" O VAL H 157 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE H 159 " --> pdb=" O TRP H 209 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE H 30 " --> pdb=" O GLU H 158 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE H 160 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE H 32 " --> pdb=" O PHE H 160 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA H 31 " --> pdb=" O ILE H 272 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N CYS H 274 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE H 33 " --> pdb=" O CYS H 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 43 through 44 Processing sheet with id=AE8, first strand: chain 'H' and resid 183 through 184 removed outlier: 3.898A pdb=" N VAL H 184 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE H 190 " --> pdb=" O VAL H 184 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 302 through 303 Processing sheet with id=AF1, first strand: chain 'E' and resid 9 through 10 removed outlier: 3.686A pdb=" N ALA E 331 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE E 33 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE E 32 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 208 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 217 through 219 1982 hydrogen bonds defined for protein. 5634 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: 18.49 Time building geometry restraints manager: 10.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16139 1.34 - 1.46: 10250 1.46 - 1.58: 22656 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 49210 Sorted by residual: bond pdb=" N GLY N 680 " pdb=" CA GLY N 680 " ideal model delta sigma weight residual 1.447 1.476 -0.028 1.03e-02 9.43e+03 7.65e+00 bond pdb=" N LYS N 681 " pdb=" CA LYS N 681 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.93e+00 bond pdb=" N GLU N 677 " pdb=" CA GLU N 677 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.82e+00 bond pdb=" N SER N 678 " pdb=" CA SER N 678 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.11e+00 bond pdb=" C MET H 251 " pdb=" N PRO H 252 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.24e+00 ... (remaining 49205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 65694 1.41 - 2.82: 1229 2.82 - 4.22: 289 4.22 - 5.63: 62 5.63 - 7.04: 20 Bond angle restraints: 67294 Sorted by residual: angle pdb=" C ASP K 109 " pdb=" CA ASP K 109 " pdb=" CB ASP K 109 " ideal model delta sigma weight residual 116.63 110.61 6.02 1.16e+00 7.43e-01 2.69e+01 angle pdb=" C GLU P 111 " pdb=" CA GLU P 111 " pdb=" CB GLU P 111 " ideal model delta sigma weight residual 115.79 109.89 5.90 1.19e+00 7.06e-01 2.46e+01 angle pdb=" N VAL M 217 " pdb=" CA VAL M 217 " pdb=" C VAL M 217 " ideal model delta sigma weight residual 112.96 108.50 4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" N ILE T 115 " pdb=" CA ILE T 115 " pdb=" C ILE T 115 " ideal model delta sigma weight residual 111.90 108.55 3.35 8.10e-01 1.52e+00 1.72e+01 angle pdb=" N ILE E 115 " pdb=" CA ILE E 115 " pdb=" C ILE E 115 " ideal model delta sigma weight residual 111.90 108.56 3.34 8.10e-01 1.52e+00 1.70e+01 ... (remaining 67289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 27266 17.84 - 35.68: 1669 35.68 - 53.52: 244 53.52 - 71.37: 59 71.37 - 89.21: 19 Dihedral angle restraints: 29257 sinusoidal: 9470 harmonic: 19787 Sorted by residual: dihedral pdb=" CA GLU S 197 " pdb=" C GLU S 197 " pdb=" N GLU S 198 " pdb=" CA GLU S 198 " ideal model delta harmonic sigma weight residual 180.00 150.68 29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLU H 197 " pdb=" C GLU H 197 " pdb=" N GLU H 198 " pdb=" CA GLU H 198 " ideal model delta harmonic sigma weight residual 180.00 150.70 29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ARG O 161 " pdb=" C ARG O 161 " pdb=" N HIS O 162 " pdb=" CA HIS O 162 " ideal model delta harmonic sigma weight residual 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 29254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 5333 0.035 - 0.070: 1906 0.070 - 0.106: 589 0.106 - 0.141: 235 0.141 - 0.176: 14 Chirality restraints: 8077 Sorted by residual: chirality pdb=" CG LEU L 427 " pdb=" CB LEU L 427 " pdb=" CD1 LEU L 427 " pdb=" CD2 LEU L 427 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA GLU S 197 " pdb=" N GLU S 197 " pdb=" C GLU S 197 " pdb=" CB GLU S 197 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 8074 not shown) Planarity restraints: 8717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE T 83 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO T 84 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO T 84 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO T 84 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 83 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO E 84 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO E 84 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 84 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE P 83 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO P 84 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO P 84 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO P 84 " 0.028 5.00e-02 4.00e+02 ... (remaining 8714 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 431 2.62 - 3.19: 42986 3.19 - 3.76: 71005 3.76 - 4.33: 90955 4.33 - 4.90: 154327 Nonbonded interactions: 359704 Sorted by model distance: nonbonded pdb=" OD1 ASN M 154 " pdb=" OD1 ASP M 156 " model vdw 2.045 3.040 nonbonded pdb=" CG PRO R 202 " pdb=" O LYS H 200 " model vdw 2.148 3.440 nonbonded pdb=" O ASP R 165 " pdb=" NZ LYS R 210 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU R 169 " pdb=" OG SER H 186 " model vdw 2.209 3.040 nonbonded pdb=" O SER L 302 " pdb=" OG SER L 354 " model vdw 2.211 3.040 ... (remaining 359699 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 15 or (resid 16 through 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 or (resid 20 through 21 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 22 through 25 and (name N or na \ me CA or name C or name O or name CB )) or resid 26 through 28 or (resid 29 thro \ ugh 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 51 or (resid 52 and (name N or name CA or name C or name O or name CB )) or \ resid 53 or (resid 54 through 56 and (name N or name CA or name C or name O or n \ ame CB )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or \ name CB )) or resid 59 or (resid 60 and (name N or name CA or name C or name O \ or name CB )) or resid 61 or (resid 62 and (name N or name CA or name C or name \ O or name CB )) or resid 63 or (resid 64 and (name N or name CA or name C or nam \ e O or name CB )) or resid 65 through 67 or (resid 68 and (name N or name CA or \ name C or name O or name CB )) or resid 69 through 74 or (resid 75 and (name N o \ r name CA or name C or name O or name CB )) or resid 87 or (resid 88 through 89 \ and (name N or name CA or name C or name O or name CB )) or resid 90 through 91 \ or (resid 92 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 3 or (resid 94 and (name N or name CA or name C or name O or name CB )) or resid \ 95 through 96 or (resid 97 through 98 and (name N or name CA or name C or name \ O or name CB )) or (resid 99 through 104 and (name N or name CA or name C or nam \ e O or name CB )) or resid 105 or (resid 106 and (name N or name CA or name C or \ name O or name CB )) or resid 107 or (resid 108 through 110 and (name N or name \ CA or name C or name O or name CB )) or resid 111 through 112 or (resid 113 thr \ ough 114 and (name N or name CA or name C or name O or name CB )) or resid 115 o \ r (resid 116 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 17 through 119 or (resid 120 and (name N or name CA or name C or name O or name \ CB )) or resid 121 through 122 or (resid 123 and (name N or name CA or name C or \ name O or name CB )) or resid 124 or (resid 125 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 129 and \ (name N or name CA or name C or name O or name CB )) or resid 130 through 131 o \ r (resid 132 through 136 and (name N or name CA or name C or name O or name CB ) \ ) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or nam \ e O or name CB )) or resid 141 through 144 or (resid 145 and (name N or name CA \ or name C or name O or name CB )) or resid 146 through 147 or (resid 148 and (na \ me N or name CA or name C or name O or name CB )) or resid 149 through 151 or (r \ esid 152 and (name N or name CA or name C or name O or name CB )) or resid 153 o \ r (resid 154 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 55 or (resid 156 through 157 and (name N or name CA or name C or name O or name \ CB )) or resid 158 through 159 or (resid 160 through 161 and (name N or name CA \ or name C or name O or name CB )) or resid 162 through 170 or (resid 171 and (na \ me N or name CA or name C or name O or name CB )) or resid 172 through 175 or (r \ esid 176 through 177 and (name N or name CA or name C or name O or name CB )) or \ resid 178 through 179 or (resid 180 through 181 and (name N or name CA or name \ C or name O or name CB )) or resid 182 or (resid 183 through 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 through 186 or (resid 187 \ through 190 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 91 through 193 or (resid 194 and (name N or name CA or name C or name O or name \ CB )) or resid 195 through 196 or (resid 197 through 199 and (name N or name CA \ or name C or name O or name CB )) or resid 200 through 202 or (resid 203 and (na \ me N or name CA or name C or name O or name CB )) or resid 204 through 207 or (r \ esid 208 through 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 or (resid 211 through 212 and (name N or name CA or name C or name O \ or name CB )) or resid 213 through 215 or (resid 216 and (name N or name CA or n \ ame C or name O or name CB )) or resid 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB )) or resid 219 through 228 or (resid 229 and (na \ me N or name CA or name C or name O or name CB )) or resid 230 through 232 or (r \ esid 233 through 235 and (name N or name CA or name C or name O or name CB )) or \ resid 236 or (resid 237 through 238 and (name N or name CA or name C or name O \ or name CB )) or resid 239 through 242 or (resid 243 and (name N or name CA or n \ ame C or name O or name CB )) or resid 244 through 245 or (resid 246 through 247 \ and (name N or name CA or name C or name O or name CB )) or resid 248 or (resid \ 249 and (name N or name CA or name C or name O or name CB )) or resid 250 or (r \ esid 251 and (name N or name CA or name C or name O or name CB )) or resid 252 t \ hrough 253 or (resid 254 and (name N or name CA or name C or name O or name CB ) \ ) or resid 255 through 256 or (resid 257 through 272 and (name N or name CA or n \ ame C or name O or name CB )) or resid 273 or (resid 274 through 282 and (name N \ or name CA or name C or name O or name CB )) or resid 283 through 286 or (resid \ 287 through 307 and (name N or name CA or name C or name O or name CB )) or res \ id 308 or (resid 309 through 310 and (name N or name CA or name C or name O or n \ ame CB )) or resid 311 through 316 or resid 330 through 331 or (resid 332 throug \ h 335 and (name N or name CA or name C or name O or name CB )) or resid 336 thro \ ugh 337 or resid 352 through 355 or (resid 356 and (name N or name CA or name C \ or name O or name CB )) or (resid 357 through 362 and (name N or name CA or name \ C or name O or name CB )) or resid 363 or (resid 364 through 365 and (name N or \ name CA or name C or name O or name CB )) or resid 366 through 369 or (resid 37 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 371 through \ 372 or (resid 373 and (name N or name CA or name C or name O or name CB )) or re \ sid 374 or (resid 375 through 379 and (name N or name CA or name C or name O or \ name CB )) or resid 380 or (resid 381 through 384 and (name N or name CA or name \ C or name O or name CB )) or resid 385 through 387 or (resid 388 through 390 an \ d (name N or name CA or name C or name O or name CB )) or resid 391 or (resid 39 \ 2 through 399 and (name N or name CA or name C or name O or name CB )) or resid \ 400 through 401 or (resid 402 and (name N or name CA or name C or name O or name \ CB )) or resid 403 through 404 or (resid 405 and (name N or name CA or name C o \ r name O or name CB )) or resid 406 or (resid 407 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 413 or (resid 414 th \ rough 416 and (name N or name CA or name C or name O or name CB )) or resid 417 \ through 420 or (resid 421 and (name N or name CA or name C or name O or name CB \ )) or resid 422 or (resid 423 through 427 and (name N or name CA or name C or na \ me O or name CB )) or resid 428 through 431 or (resid 432 and (name N or name CA \ or name C or name O or name CB )) or resid 433 through 434 or (resid 435 throug \ h 437 and (name N or name CA or name C or name O or name CB )) or resid 438 thro \ ugh 439 or (resid 440 through 441 and (name N or name CA or name C or name O or \ name CB )) or resid 442 or (resid 443 through 445 and (name N or name CA or name \ C or name O or name CB )) or resid 446 or (resid 447 and (name N or name CA or \ name C or name O or name CB )) or resid 448 through 449 or (resid 450 through 45 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 453 through \ 458 or (resid 459 through 461 and (name N or name CA or name C or name O or name \ CB )) or resid 462 through 466 or (resid 467 through 468 and (name N or name CA \ or name C or name O or name CB )) or resid 469 or (resid 470 and (name N or nam \ e CA or name C or name O or name CB )) or resid 471 or (resid 472 through 473 an \ d (name N or name CA or name C or name O or name CB )) or resid 474 through 480 \ or (resid 481 through 483 and (name N or name CA or name C or name O or name CB \ )) or resid 484 or (resid 485 through 487 and (name N or name CA or name C or na \ me O or name CB )) or resid 488 through 490 or (resid 491 through 492 and (name \ N or name CA or name C or name O or name CB )) or resid 493 through 496 or (resi \ d 497 and (name N or name CA or name C or name O or name CB )) or resid 498 thro \ ugh 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) o \ r resid 501 through 507 or (resid 508 and (name N or name CA or name C or name O \ or name CB )) or resid 509 through 521 or (resid 522 and (name N or name CA or \ name C or name O or name CB )) or resid 523 through 530 or (resid 531 through 53 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 536 or (resi \ d 537 through 538 and (name N or name CA or name C or name O or name CB )) or re \ sid 539 or (resid 540 and (name N or name CA or name C or name O or name CB )) o \ r resid 541 through 547 or (resid 548 through 549 and (name N or name CA or name \ C or name O or name CB )) or resid 550 through 553 or (resid 554 through 558 an \ d (name N or name CA or name C or name O or name CB )) or resid 559 or (resid 56 \ 0 through 562 and (name N or name CA or name C or name O or name CB )) or resid \ 563 or (resid 564 and (name N or name CA or name C or name O or name CB )) or re \ sid 565 through 573 or (resid 574 through 577 and (name N or name CA or name C o \ r name O or name CB )) or resid 578 or (resid 579 through 580 and (name N or nam \ e CA or name C or name O or name CB )) or resid 581 through 582 or (resid 583 th \ rough 584 and (name N or name CA or name C or name O or name CB )) or resid 585 \ through 586 or (resid 587 through 590 and (name N or name CA or name C or name O \ or name CB )) or (resid 591 through 595 and (name N or name CA or name C or nam \ e O or name CB )) or resid 596 through 599 or (resid 600 and (name N or name CA \ or name C or name O or name CB )) or resid 601 or (resid 602 through 609 and (na \ me N or name CA or name C or name O or name CB )) or (resid 640 through 641 and \ (name N or name CA or name C or name O or name CB )) or (resid 642 through 653 a \ nd (name N or name CA or name C or name O or name CB )) or resid 654 through 657 \ or (resid 658 through 660 and (name N or name CA or name C or name O or name CB \ )) or resid 661 through 663 or (resid 664 through 665 and (name N or name CA or \ name C or name O or name CB )) or resid 666 through 667 or (resid 668 through 6 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 670 or (res \ id 671 through 679 and (name N or name CA or name C or name O or name CB )) or ( \ resid 680 through 684 and (name N or name CA or name C or name O or name CB )) o \ r resid 685 through 686 or (resid 687 through 695 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'L' and (resid 15 or (resid 16 through 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 or (resid 20 through 21 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 22 through 25 and (name N or na \ me CA or name C or name O or name CB )) or resid 26 through 28 or (resid 29 thro \ ugh 36 and (name N or name CA or name C or name O or name CB )) or (resid 45 thr \ ough 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thr \ ough 51 or (resid 52 and (name N or name CA or name C or name O or name CB )) or \ resid 53 or (resid 54 through 56 and (name N or name CA or name C or name O or \ name CB )) or resid 57 or (resid 58 and (name N or name CA or name C or name O o \ r name CB )) or resid 59 or (resid 60 and (name N or name CA or name C or name O \ or name CB )) or resid 61 or (resid 62 and (name N or name CA or name C or name \ O or name CB )) or resid 63 or (resid 64 and (name N or name CA or name C or na \ me O or name CB )) or resid 65 through 67 or (resid 68 and (name N or name CA or \ name C or name O or name CB )) or resid 69 through 74 or (resid 75 and (name N \ or name CA or name C or name O or name CB )) or resid 87 or (resid 88 through 89 \ and (name N or name CA or name C or name O or name CB )) or resid 90 through 91 \ or (resid 92 and (name N or name CA or name C or name O or name CB )) or resid \ 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) or resi \ d 95 through 96 or (resid 97 through 98 and (name N or name CA or name C or name \ O or name CB )) or (resid 99 through 104 and (name N or name CA or name C or na \ me O or name CB )) or resid 105 or (resid 106 and (name N or name CA or name C o \ r name O or name CB )) or resid 107 or (resid 108 through 110 and (name N or nam \ e CA or name C or name O or name CB )) or resid 111 through 112 or (resid 113 th \ rough 114 and (name N or name CA or name C or name O or name CB )) or resid 115 \ or (resid 116 and (name N or name CA or name C or name O or name CB )) or resid \ 117 through 119 or (resid 120 and (name N or name CA or name C or name O or name \ CB )) or resid 121 through 122 or (resid 123 and (name N or name CA or name C o \ r name O or name CB )) or resid 124 or (resid 125 through 126 and (name N or nam \ e CA or name C or name O or name CB )) or resid 127 or (resid 128 through 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 131 \ or (resid 132 through 136 and (name N or name CA or name C or name O or name CB \ )) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or na \ me O or name CB )) or resid 141 through 144 or (resid 145 and (name N or name CA \ or name C or name O or name CB )) or resid 146 through 147 or (resid 148 and (n \ ame N or name CA or name C or name O or name CB )) or resid 149 through 151 or ( \ resid 152 and (name N or name CA or name C or name O or name CB )) or resid 153 \ or (resid 154 and (name N or name CA or name C or name O or name CB )) or resid \ 155 or (resid 156 through 157 and (name N or name CA or name C or name O or name \ CB )) or resid 158 through 159 or (resid 160 through 161 and (name N or name CA \ or name C or name O or name CB )) or resid 162 through 170 or (resid 171 and (n \ ame N or name CA or name C or name O or name CB )) or resid 172 through 175 or ( \ resid 176 through 177 and (name N or name CA or name C or name O or name CB )) o \ r resid 178 through 179 or (resid 180 through 181 and (name N or name CA or name \ C or name O or name CB )) or resid 182 or (resid 183 through 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 through 186 or (resid 18 \ 7 through 190 and (name N or name CA or name C or name O or name CB )) or resid \ 191 through 193 or (resid 194 and (name N or name CA or name C or name O or name \ CB )) or resid 195 through 196 or (resid 197 through 199 and (name N or name CA \ or name C or name O or name CB )) or resid 200 through 202 or (resid 203 and (n \ ame N or name CA or name C or name O or name CB )) or resid 204 through 207 or ( \ resid 208 through 209 and (name N or name CA or name C or name O or name CB )) o \ r resid 210 or (resid 211 through 212 and (name N or name CA or name C or name O \ or name CB )) or resid 213 through 215 or (resid 216 and (name N or name CA or \ name C or name O or name CB )) or resid 217 or (resid 218 and (name N or name CA \ or name C or name O or name CB )) or resid 219 through 228 or (resid 229 and (n \ ame N or name CA or name C or name O or name CB )) or resid 230 through 232 or ( \ resid 233 through 235 and (name N or name CA or name C or name O or name CB )) o \ r resid 236 or (resid 237 through 238 and (name N or name CA or name C or name O \ or name CB )) or resid 239 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 245 or (resid 246 through 24 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 248 or (resi \ d 249 and (name N or name CA or name C or name O or name CB )) or resid 250 or ( \ resid 251 and (name N or name CA or name C or name O or name CB )) or resid 252 \ through 253 or (resid 254 and (name N or name CA or name C or name O or name CB \ )) or resid 255 through 256 or (resid 257 through 272 and (name N or name CA or \ name C or name O or name CB )) or resid 273 or (resid 274 through 282 and (name \ N or name CA or name C or name O or name CB )) or resid 283 through 286 or (resi \ d 287 through 307 and (name N or name CA or name C or name O or name CB )) or re \ sid 308 or (resid 309 through 310 and (name N or name CA or name C or name O or \ name CB )) or resid 311 through 316 or resid 330 through 331 or (resid 332 throu \ gh 335 and (name N or name CA or name C or name O or name CB )) or resid 336 thr \ ough 337 or resid 352 through 355 or (resid 356 and (name N or name CA or name C \ or name O or name CB )) or (resid 357 through 362 and (name N or name CA or nam \ e C or name O or name CB )) or resid 363 or (resid 364 through 365 and (name N o \ r name CA or name C or name O or name CB )) or resid 366 through 369 or (resid 3 \ 70 and (name N or name CA or name C or name O or name CB )) or resid 371 or (res \ id 372 through 373 and (name N or name CA or name C or name O or name CB )) or r \ esid 374 or (resid 375 through 379 and (name N or name CA or name C or name O or \ name CB )) or resid 380 or (resid 381 through 384 and (name N or name CA or nam \ e C or name O or name CB )) or resid 385 through 387 or (resid 388 through 390 a \ nd (name N or name CA or name C or name O or name CB )) or resid 391 or (resid 3 \ 92 through 399 and (name N or name CA or name C or name O or name CB )) or resid \ 400 through 401 or (resid 402 and (name N or name CA or name C or name O or nam \ e CB )) or resid 403 through 404 or (resid 405 and (name N or name CA or name C \ or name O or name CB )) or resid 406 or (resid 407 through 410 and (name N or na \ me CA or name C or name O or name CB )) or resid 411 through 413 or (resid 414 t \ hrough 416 and (name N or name CA or name C or name O or name CB )) or resid 417 \ through 420 or (resid 421 and (name N or name CA or name C or name O or name CB \ )) or resid 422 or (resid 423 through 427 and (name N or name CA or name C or n \ ame O or name CB )) or resid 428 through 431 or (resid 432 and (name N or name C \ A or name C or name O or name CB )) or resid 433 through 434 or (resid 435 throu \ gh 437 and (name N or name CA or name C or name O or name CB )) or resid 438 thr \ ough 439 or (resid 440 through 441 and (name N or name CA or name C or name O or \ name CB )) or resid 442 or (resid 443 through 445 and (name N or name CA or nam \ e C or name O or name CB )) or resid 446 or (resid 447 and (name N or name CA or \ name C or name O or name CB )) or resid 448 through 449 or (resid 450 through 4 \ 52 and (name N or name CA or name C or name O or name CB )) or resid 453 through \ 458 or (resid 459 through 461 and (name N or name CA or name C or name O or nam \ e CB )) or resid 462 through 466 or (resid 467 through 468 and (name N or name C \ A or name C or name O or name CB )) or resid 469 or (resid 470 and (name N or na \ me CA or name C or name O or name CB )) or resid 471 or (resid 472 through 473 a \ nd (name N or name CA or name C or name O or name CB )) or resid 474 through 480 \ or (resid 481 through 483 and (name N or name CA or name C or name O or name CB \ )) or resid 484 or (resid 485 through 487 and (name N or name CA or name C or n \ ame O or name CB )) or resid 488 through 490 or (resid 491 through 492 and (name \ N or name CA or name C or name O or name CB )) or resid 493 through 496 or (res \ id 497 and (name N or name CA or name C or name O or name CB )) or resid 498 thr \ ough 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) \ or resid 501 through 507 or (resid 508 and (name N or name CA or name C or name \ O or name CB )) or resid 509 through 521 or (resid 522 and (name N or name CA or \ name C or name O or name CB )) or resid 523 through 530 or (resid 531 through 5 \ 35 and (name N or name CA or name C or name O or name CB )) or resid 536 or (res \ id 537 through 538 and (name N or name CA or name C or name O or name CB )) or r \ esid 539 or (resid 540 and (name N or name CA or name C or name O or name CB )) \ or resid 541 through 547 or (resid 548 through 549 and (name N or name CA or nam \ e C or name O or name CB )) or resid 550 through 553 or (resid 554 through 558 a \ nd (name N or name CA or name C or name O 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through 209 or (r \ esid 210 through 211 and (name N or name CA or name C or name O or name CB )) or \ resid 212 through 214 or (resid 215 through 216 and (name N or name CA or name \ C or name O or name CB )) or resid 217 or (resid 218 through 226 and (name N or \ name CA or name C or name O or name CB )) or resid 227 through 231 or (resid 232 \ through 233 and (name N or name CA or name C or name O or name CB )) or (resid \ 234 through 239 and (name N or name CA or name C or name O or name CB )) or resi \ d 240 through 241 or (resid 242 through 251 and (name N or name CA or name C or \ name O or name CB )) or resid 252 or (resid 253 through 254 and (name N or name \ CA or name C or name O or name CB )) or resid 255 or (resid 256 through 258 and \ (name N or name CA or name C or name O or name CB )) or resid 259 through 263 or \ (resid 264 through 266 and (name N or name CA or name C or name O or name CB )) \ or resid 267 through 269 or (resid 270 and (name N or name CA or name C or name \ O or name CB )) or resid 271 or (resid 272 through 273 and (name N or name CA o \ r name C or name O or name CB )) or resid 274 through 277 or (resid 278 through \ 281 and (name N or name CA or name C or name O or name CB )) or resid 282 or (re \ sid 283 through 287 and (name N or name CA or name C or name O or name CB )) or \ resid 288 through 291 or (resid 292 and (name N or name CA or name C or name O o \ r name CB )) or resid 293 through 295 or (resid 296 through 299 and (name N or n \ ame CA or name C or name O or name CB )) or resid 300 through 303 or (resid 304 \ through 333 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 4 through 338 or (resid 359 through 365 and (name N or name CA or name C or name \ O or name CB )) or resid 366 or (resid 367 through 371 and (name N or name CA o \ r name C or name O or name CB )) or resid 372 or (resid 373 and (name N or name \ CA or name C or name O or name CB )))) selection = (chain 'R' and ((resid 13 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 or (resid 20 through 21 and (name N or na \ me CA or name C or name O or name CB )) or resid 22 through 23 or (resid 24 thro \ ugh 28 and (name N or name CA or name C or name O or name CB )) or resid 29 or ( \ resid 30 through 36 and (name N or name CA or name C or name O or name CB )) or \ resid 37 through 38 or (resid 39 through 47 and (name N or name CA or name C or \ name O or name CB )) or resid 48 or (resid 49 through 50 and (name N or name CA \ or name C or name O or name CB )) or resid 51 or (resid 52 through 54 and (name \ N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 through \ 60 and (name N or name CA or name C or name O or name CB )) or resid 61 or (resi \ d 62 through 63 and (name N or name CA or name C or name O or name CB )) or (res \ id 72 through 83 and (name N or name CA or name C or name O or name CB )) or res \ id 84 through 86 or (resid 87 through 91 and (name N or name CA or name C or nam \ e O or name CB )) or resid 92 through 93 or (resid 94 and (name N or name CA or \ name C or name O or name CB )) or resid 95 or (resid 96 and (name N or name CA o \ r name C or name O or name CB )) or resid 97 or (resid 98 through 101 and (name \ N or name CA or name C or name O or name CB )) or resid 102 through 103 or (resi \ d 104 and (name N or name CA or name C or name O or name CB )) or resid 105 thro \ ugh 113 or (resid 114 through 120 and (name N or name CA or name C or name O or \ name CB )) or resid 121 or (resid 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 or (resid 124 through 129 and (name N or name CA or \ name C or name O or name CB )) or resid 130 through 131 or (resid 132 through 13 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 134 through \ 136 or (resid 137 through 139 and (name N or name CA or name C or name O or name \ CB )) or resid 140 through 142 or (resid 143 and (name N or name CA or name C o \ r name O or name CB )) or resid 144 through 146 or (resid 147 and (name N or nam \ e CA or name C or name O or name CB )) or resid 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 or (resid 151 through 15 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 159 or (resi \ d 160 and (name N or name CA or name C or name O or name CB )) or resid 161 thro \ ugh 162 or (resid 163 through 166 and (name N or name CA or name C or name O or \ name CB )) or resid 167 or (resid 168 through 171 and (name N or name CA or name \ C or name O or name CB )) or resid 172 or (resid 173 through 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 185 or (resid 18 \ 6 through 190 and (name N or name CA or name C or name O or name CB )) or resid \ 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or re \ sid 193 or (resid 194 and (name N or name CA or name C or name O or name CB )) o \ r resid 195 through 196 or (resid 197 through 201 and (name N or name CA or name \ C or name O or name CB )) or resid 202 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 209 or (resid 21 \ 0 through 211 and (name N or name CA or name C or name O or name CB )) or resid \ 212 through 214 or (resid 215 through 216 and (name N or name CA or name C or na \ me O or name CB )) or resid 217 or (resid 218 through 226 and (name N or name CA \ or name C or name O or name CB )) or resid 227 through 229 or (resid 230 and (n \ ame N or name CA or name C or name O or name CB )) or resid 231 or (resid 232 th \ rough 233 and (name N or name CA or name C or name O or name CB )) or (resid 234 \ through 239 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 40 through 241 or (resid 242 and (name N or name CA or name C or name O or name \ CB )) or resid 251 through 252 or (resid 253 through 254 and (name N or name CA \ or name C or name O or name CB )) or resid 255 or (resid 256 through 258 and (na \ me N or name CA or name C or name O or name CB )) or resid 259 through 263 or (r \ esid 264 through 266 and (name N or name CA or name C or name O or name CB )) or \ resid 267 through 269 or (resid 270 and (name N or name CA or name C or name O \ or name CB )) or resid 271 or (resid 272 through 273 and (name N or name CA or n \ ame C or name O or name CB )) or resid 274 through 277 or (resid 278 through 281 \ and (name N or name CA or name C or name O or name CB )) or resid 282 or (resid \ 283 through 287 and (name N or name CA or name C or name O or name CB )) or res \ id 288 or (resid 289 and (name N or name CA or name C or name O or name CB )) or \ resid 290 through 291 or (resid 292 and (name N or name CA or name C or name O \ or name CB )) or resid 293 or (resid 294 and (name N or name CA or name C or nam \ e O or name CB )) or resid 295 or (resid 296 through 299 and (name N or name CA \ or name C or name O or name CB )) or resid 300 through 302 or (resid 303 through \ 333 and (name N or name CA or name C or name O or name CB )) or resid 334 or (r \ esid 335 through 337 and (name N or name CA or name C or name O or name CB )) or \ resid 338 or resid 359 or (resid 360 through 365 and (name N or name CA or name \ C or name O or name CB )) or resid 366 or (resid 367 through 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372 or (resid 373 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'S' and ((resid 13 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 or (resid 20 through 21 and (name N or na \ me CA or name C or name O or name CB )) or resid 22 through 29 or (resid 30 thro \ ugh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 thro \ ugh 38 or (resid 39 through 47 and (name N or name CA or name C or name O or nam \ e CB )) or resid 48 or (resid 49 through 50 and (name N or name CA or name C or \ name O or name CB )) or resid 51 through 52 or (resid 53 through 54 and (name N \ or name CA or name C or name O or name CB )) or resid 55 or (resid 56 through 60 \ and (name N or name CA or name C or name O or name CB )) or resid 61 or (resid \ 62 through 83 and (name N or name CA or name C or name O or name CB )) or resid \ 84 through 86 or (resid 87 through 91 and (name N or name CA or name C or name O \ or name CB )) or resid 92 through 93 or (resid 94 and (name N or name CA or nam \ e C or name O or name CB )) or resid 95 or (resid 96 and (name N or name CA or n \ ame C or name O or name CB )) or resid 97 or (resid 98 through 101 and (name N o \ r name CA or name C or name O or name CB )) or resid 102 through 103 or (resid 1 \ 04 and (name N or name CA or name C or name O or name CB )) or (resid 105 throug \ h 112 and (name N or name CA or name C or name O or name CB )) or resid 113 thro \ ugh 115 or (resid 116 through 120 and (name N or name CA or name C or name O or \ name CB )) or resid 121 or (resid 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 or (resid 124 through 129 and (name N or name CA or \ name C or name O or name CB )) or resid 130 or (resid 131 through 133 and (name \ N or name CA or name C or name O or name CB )) or resid 134 through 138 or (resi \ d 139 and (name N or name CA or name C or name O or name CB )) or resid 140 thro \ ugh 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) o \ r resid 148 or (resid 149 and (name N or name CA or name C or name O or name CB \ )) or resid 150 or (resid 151 through 158 and (name N or name CA or name C or na \ me O or name CB )) or resid 159 or (resid 160 and (name N or name CA or name C o \ r name O or name CB )) or resid 161 through 162 or (resid 163 through 166 and (n \ ame N or name CA or name C or name O or name CB )) or resid 167 or (resid 168 th \ rough 171 and (name N or name CA or name C or name O or name CB )) or resid 172 \ through 185 or (resid 186 through 190 and (name N or name CA or name C or name O \ or name CB )) or resid 191 through 193 or (resid 194 and (name N or name CA or \ name C or name O or name CB )) or resid 195 through 196 or (resid 197 through 20 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 202 through \ 203 or (resid 204 and (name N or name CA or name C or name O or name CB )) or re \ sid 205 through 209 or (resid 210 through 211 and (name N or name CA or name C o \ r name O or name CB )) or resid 212 through 214 or (resid 215 through 216 and (n \ ame N or name CA or name C or name O or name CB )) or resid 217 through 222 or ( \ resid 223 through 226 and (name N or name CA or name C or name O or name CB )) o \ r resid 227 through 231 or (resid 232 through 233 and (name N or name CA or name \ C or name O or name CB )) or (resid 234 through 239 and (name N or name CA or n \ ame C or name O or name CB )) or resid 240 through 242 or resid 251 through 252 \ or (resid 253 through 254 and (name N or name CA or name C or name O or name CB \ )) or resid 255 through 256 or (resid 257 through 258 and (name N or name CA or \ name C or name O or name CB )) or resid 259 through 271 or (resid 272 through 27 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 274 through \ 277 or (resid 278 through 281 and (name N or name CA or name C or name O or name \ CB )) or resid 282 or (resid 283 through 287 and (name N or name CA or name C o \ r name O or name CB )) or resid 288 through 303 or (resid 304 through 333 and (n \ ame N or name CA or name C or name O or name CB )) or resid 334 through 338 or r \ esid 359 or (resid 360 through 365 and (name N or name CA or name C or name O or \ name CB )) or resid 366 through 367 or (resid 368 through 371 and (name N or na \ me CA or name C or name O or name CB )) or resid 372 through 373)) selection = (chain 'T' and ((resid 13 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 or (resid 20 through 21 and (name N or na \ me CA or name C or name O or name CB )) or resid 22 through 23 or (resid 24 thro \ ugh 28 and (name N or name CA or name C or name O or name CB )) or resid 29 or ( \ resid 30 through 36 and (name N or name CA or name C or name O or name CB )) or \ resid 37 through 38 or (resid 39 through 47 and (name N or name CA or name C or \ name O or name CB )) or resid 48 or (resid 49 through 50 and (name N or name CA \ or name C or name O or name CB )) or resid 51 or (resid 52 through 54 and (name \ N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 through \ 60 and (name N or name CA or name C or name O or name CB )) or resid 61 or (resi \ d 62 through 63 and (name N or name CA or name C or name O or name CB )) or (res \ id 72 through 83 and (name N or name CA or name C or name O or name CB )) or res \ id 84 through 86 or (resid 87 through 91 and (name N or name CA or name C or nam \ e O or name CB )) or resid 92 through 93 or (resid 94 and (name N or name CA or \ name C or name O or name CB )) or resid 95 or (resid 96 and (name N or name CA o \ r name C or name O or name CB )) or resid 97 or (resid 98 through 101 and (name \ N or name CA or name C or name O or name CB )) or resid 102 through 103 or (resi \ d 104 and (name N or name CA or name C or name O or name CB )) or resid 105 thro \ ugh 114 or (resid 115 through 120 and (name N or name CA or name C or name O or \ name CB )) or resid 121 or (resid 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 or (resid 124 through 129 and (name N or name CA or \ name C or name O or name CB )) or resid 130 through 131 or (resid 132 through 13 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 134 through \ 136 or (resid 137 through 139 and (name N or name CA or name C or name O or name \ CB )) or resid 140 through 142 or (resid 143 and (name N or name CA or name C o \ r name O or name CB )) or resid 144 through 146 or (resid 147 and (name N or nam \ e CA or name C or name O or name CB )) or resid 148 or (resid 149 and (name N or \ name CA or name C or name O or name CB )) or resid 150 or (resid 151 through 15 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 159 or (resi \ d 160 and (name N or name CA or name C or name O or name CB )) or resid 161 thro \ ugh 162 or (resid 163 through 166 and (name N or name CA or name C or name O or \ name CB )) or resid 167 or (resid 168 through 171 and (name N or name CA or name \ C or name O or name CB )) or resid 172 or (resid 173 through 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 through 185 or (resid 18 \ 6 through 190 and (name N or name CA or name C or name O or name CB )) or resid \ 191 or (resid 192 and (name N or name CA or name C or name O or name CB )) or re \ sid 193 or (resid 194 and (name N or name CA or name C or name O or name CB )) o \ r resid 195 through 196 or (resid 197 through 201 and (name N or name CA or name \ C or name O or name CB )) or resid 202 through 203 or (resid 204 and (name N or \ name CA or name C or name O or name CB )) or resid 205 through 206 or (resid 20 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 208 through \ 209 or (resid 210 through 211 and (name N or name CA or name C or name O or name \ CB )) or resid 212 through 214 or (resid 215 through 216 and (name N or name CA \ or name C or name O or name CB )) or resid 217 or (resid 218 through 226 and (n \ ame N or name CA or name C or name O or name CB )) or resid 227 through 229 or ( \ resid 230 and (name N or name CA or name C or name O or name CB )) or resid 231 \ or (resid 232 through 233 and (name N or name CA or name C or name O or name CB \ )) or (resid 234 through 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 242 or resid 251 through 252 or (resid 253 through 25 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 255 or (resi \ d 256 through 258 and (name N or name CA or name C or name O or name CB )) or re \ sid 259 through 263 or (resid 264 through 266 and (name N or name CA or name C o \ r name O or name CB )) or resid 267 through 269 or (resid 270 and (name N or nam \ e CA or name C or name O or name CB )) or resid 271 or (resid 272 through 273 an \ d (name N or name CA or name C or name O or name CB )) or resid 274 through 277 \ or (resid 278 through 281 and (name N or name CA or name C or name O or name CB \ )) or resid 282 or (resid 283 through 287 and (name N or name CA or name C or na \ me O or name CB )) or resid 288 or (resid 289 and (name N or name CA or name C o \ r name O or name CB )) or resid 290 through 291 or (resid 292 and (name N or nam \ e CA or name C or name O or name CB )) or resid 293 or (resid 294 and (name N or \ name CA or name C or name O or name CB )) or resid 295 or (resid 296 through 29 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 300 through \ 302 or (resid 303 through 333 and (name N or name CA or name C or name O or name \ CB )) or resid 334 or (resid 335 through 337 and (name N or name CA or name C o \ r name O or name CB )) or resid 338 or resid 359 or (resid 360 through 365 and ( \ name N or name CA or name C or name O or name CB )) or resid 366 or (resid 367 t \ hrough 371 and (name N or name CA or name C or name O or name CB )) or resid 372 \ or (resid 373 and (name N or name CA or name C or name O or name CB )))) } 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 83.050 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.002 0.053 49210 Z= 0.147 Angle : 0.516 7.041 67294 Z= 0.282 Chirality : 0.043 0.176 8077 Planarity : 0.004 0.065 8717 Dihedral : 12.163 89.208 16461 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.53 % Favored : 94.31 % Rotamer: Outliers : 0.02 % Allowed : 0.52 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 6748 helix: 1.51 (0.11), residues: 2514 sheet: -0.89 (0.18), residues: 873 loop : -1.12 (0.11), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 584 HIS 0.005 0.001 HIS M 162 PHE 0.016 0.001 PHE Q 367 TYR 0.015 0.001 TYR J 253 ARG 0.009 0.000 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 598 time to evaluate : 4.188 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: S 198 GLU cc_start: 0.8789 (mp0) cc_final: 0.8477 (mp0) REVERT: S 258 ASP cc_start: 0.8448 (m-30) cc_final: 0.8026 (m-30) REVERT: S 259 GLN cc_start: 0.9319 (mm110) cc_final: 0.8800 (mm-40) REVERT: J 169 GLU cc_start: 0.9060 (pm20) cc_final: 0.8704 (pm20) REVERT: J 170 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8571 (tm-30) REVERT: P 181 ASP cc_start: 0.8762 (p0) cc_final: 0.8488 (p0) REVERT: P 210 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7611 (mtpt) REVERT: Q 192 ASP cc_start: 0.8469 (t0) cc_final: 0.8051 (t0) REVERT: Q 258 ASP cc_start: 0.7818 (p0) cc_final: 0.7588 (p0) REVERT: Q 369 GLU cc_start: 0.8351 (pp20) cc_final: 0.8074 (pp20) REVERT: O 69 GLN cc_start: 0.8102 (tt0) cc_final: 0.7784 (tt0) REVERT: O 560 MET cc_start: 0.8581 (ptp) cc_final: 0.8356 (ptt) REVERT: A 97 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7227 (tm-30) REVERT: A 98 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6975 (tm-30) REVERT: A 437 ASP cc_start: 0.9182 (m-30) cc_final: 0.8979 (m-30) REVERT: A 509 CYS cc_start: 0.8806 (m) cc_final: 0.8494 (m) REVERT: D 256 ASP cc_start: 0.8794 (m-30) cc_final: 0.8543 (m-30) REVERT: D 468 ASP cc_start: 0.8060 (p0) cc_final: 0.7802 (p0) REVERT: M 259 TYR cc_start: 0.8350 (t80) cc_final: 0.8006 (t80) REVERT: H 58 ARG cc_start: 0.7716 (pmt-80) cc_final: 0.6633 (tpp-160) REVERT: H 98 LEU cc_start: 0.5653 (mt) cc_final: 0.5431 (mt) REVERT: H 130 VAL cc_start: 0.5071 (t) cc_final: 0.4497 (m) REVERT: H 257 MET cc_start: 0.7899 (mtt) cc_final: 0.7520 (mtp) REVERT: H 304 TYR cc_start: 0.5379 (t80) cc_final: 0.5116 (p90) REVERT: H 360 ASP cc_start: 0.6235 (t0) cc_final: 0.5789 (t0) REVERT: E 12 THR cc_start: 0.4787 (p) cc_final: 0.4516 (t) REVERT: E 151 ILE cc_start: 0.5297 (mt) cc_final: 0.5089 (tp) REVERT: E 161 THR cc_start: 0.3247 (p) cc_final: 0.3018 (m) REVERT: E 198 GLU cc_start: 0.1681 (pp20) cc_final: 0.1385 (mm-30) REVERT: E 314 LYS cc_start: 0.4168 (ttmt) cc_final: 0.3918 (mtmm) outliers start: 1 outliers final: 1 residues processed: 598 average time/residue: 0.4945 time to fit residues: 496.7558 Evaluate side-chains 433 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 162 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 574 optimal weight: 6.9990 chunk 515 optimal weight: 5.9990 chunk 285 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 347 optimal weight: 7.9990 chunk 275 optimal weight: 3.9990 chunk 532 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 324 optimal weight: 6.9990 chunk 396 optimal weight: 5.9990 chunk 617 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 116 ASN T 212 HIS ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN P 218 GLN ** P 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 110 GLN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 670 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN N 119 HIS N 462 HIS ** N 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN H 21 HIS ** H 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN E 116 ASN E 156 GLN E 212 HIS ** E 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 49210 Z= 0.330 Angle : 0.576 8.237 67294 Z= 0.300 Chirality : 0.045 0.183 8077 Planarity : 0.004 0.059 8717 Dihedral : 4.057 32.614 7201 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.82 % Favored : 93.03 % Rotamer: Outliers : 1.30 % Allowed : 6.97 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.11), residues: 6748 helix: 1.51 (0.11), residues: 2547 sheet: -1.00 (0.18), residues: 878 loop : -1.19 (0.11), residues: 3323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 227 HIS 0.009 0.001 HIS D 670 PHE 0.019 0.002 PHE H 361 TYR 0.016 0.001 TYR N 230 ARG 0.009 0.000 ARG N 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 448 time to evaluate : 4.155 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: S 258 ASP cc_start: 0.8506 (m-30) cc_final: 0.8173 (m-30) REVERT: K 261 LYS cc_start: 0.9470 (ttpp) cc_final: 0.9164 (mmtt) REVERT: J 169 GLU cc_start: 0.9218 (pm20) cc_final: 0.8951 (pm20) REVERT: J 170 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8576 (tm-30) REVERT: R 194 ARG cc_start: 0.8691 (tpt170) cc_final: 0.8303 (tpm170) REVERT: P 181 ASP cc_start: 0.8789 (p0) cc_final: 0.8460 (p0) REVERT: P 210 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7856 (mttm) REVERT: Q 129 GLU cc_start: 0.8897 (tp30) cc_final: 0.8332 (pt0) REVERT: Q 191 PHE cc_start: 0.8179 (t80) cc_final: 0.7748 (t80) REVERT: Q 369 GLU cc_start: 0.8509 (pp20) cc_final: 0.8221 (pp20) REVERT: O 69 GLN cc_start: 0.8128 (tt0) cc_final: 0.7781 (tt0) REVERT: O 78 LYS cc_start: 0.8142 (tppt) cc_final: 0.7800 (ttpt) REVERT: A 97 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7021 (tm-30) REVERT: A 437 ASP cc_start: 0.9101 (m-30) cc_final: 0.8888 (m-30) REVERT: A 441 TRP cc_start: 0.8617 (m100) cc_final: 0.7944 (m100) REVERT: A 491 MET cc_start: 0.8398 (tpp) cc_final: 0.7802 (tpp) REVERT: A 509 CYS cc_start: 0.8912 (m) cc_final: 0.8607 (m) REVERT: D 256 ASP cc_start: 0.8846 (m-30) cc_final: 0.8609 (m-30) REVERT: M 259 TYR cc_start: 0.8358 (t80) cc_final: 0.8011 (t80) REVERT: H 58 ARG cc_start: 0.8207 (pmt-80) cc_final: 0.7348 (tpp-160) REVERT: H 62 ASP cc_start: 0.5371 (p0) cc_final: 0.5143 (p0) REVERT: H 120 GLU cc_start: 0.7746 (mp0) cc_final: 0.7291 (tm-30) REVERT: H 204 ARG cc_start: 0.6980 (ttt180) cc_final: 0.6703 (ttt90) REVERT: H 304 TYR cc_start: 0.5448 (t80) cc_final: 0.5104 (p90) REVERT: H 360 ASP cc_start: 0.6026 (t0) cc_final: 0.5710 (t0) REVERT: H 368 LEU cc_start: 0.7124 (mm) cc_final: 0.6804 (tp) REVERT: E 12 THR cc_start: 0.4816 (p) cc_final: 0.3953 (t) REVERT: E 330 ARG cc_start: 0.5038 (mpp-170) cc_final: 0.4829 (mtm180) outliers start: 57 outliers final: 34 residues processed: 485 average time/residue: 0.4538 time to fit residues: 374.2987 Evaluate side-chains 442 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 408 time to evaluate : 4.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain K residue 123 CYS Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 256 MET Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain O residue 438 SER Chi-restraints excluded: chain A residue 32 ASN Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 480 ILE Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 162 HIS Chi-restraints excluded: chain N residue 240 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 464 TYR Chi-restraints excluded: chain N residue 517 MET Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 286 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 343 optimal weight: 6.9990 chunk 191 optimal weight: 6.9990 chunk 513 optimal weight: 10.0000 chunk 420 optimal weight: 2.9990 chunk 170 optimal weight: 0.3980 chunk 618 optimal weight: 0.7980 chunk 668 optimal weight: 20.0000 chunk 550 optimal weight: 6.9990 chunk 613 optimal weight: 2.9990 chunk 210 optimal weight: 6.9990 chunk 496 optimal weight: 0.0020 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 282 HIS ** P 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 670 HIS ** N 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 ASN E 15 GLN E 21 HIS E 282 HIS E 289 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 49210 Z= 0.184 Angle : 0.517 8.991 67294 Z= 0.267 Chirality : 0.043 0.174 8077 Planarity : 0.004 0.054 8717 Dihedral : 3.938 30.949 7201 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.88 % Favored : 94.00 % Rotamer: Outliers : 1.28 % Allowed : 9.05 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 6748 helix: 1.58 (0.11), residues: 2537 sheet: -0.89 (0.18), residues: 872 loop : -1.14 (0.11), residues: 3339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 227 HIS 0.009 0.001 HIS E 21 PHE 0.014 0.001 PHE P 367 TYR 0.015 0.001 TYR N 230 ARG 0.005 0.000 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 448 time to evaluate : 4.243 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: S 258 ASP cc_start: 0.8396 (m-30) cc_final: 0.8103 (m-30) REVERT: K 261 LYS cc_start: 0.9442 (ttpp) cc_final: 0.9190 (mptt) REVERT: J 169 GLU cc_start: 0.9198 (pm20) cc_final: 0.8908 (pm20) REVERT: J 170 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8548 (tm-30) REVERT: R 194 ARG cc_start: 0.8834 (tpt170) cc_final: 0.8290 (tpm170) REVERT: P 181 ASP cc_start: 0.8741 (p0) cc_final: 0.8419 (p0) REVERT: P 210 LYS cc_start: 0.8161 (mtmm) cc_final: 0.7849 (mttm) REVERT: Q 124 GLU cc_start: 0.5962 (mm-30) cc_final: 0.5446 (mm-30) REVERT: Q 129 GLU cc_start: 0.9002 (tp30) cc_final: 0.8242 (pt0) REVERT: Q 192 ASP cc_start: 0.8270 (t0) cc_final: 0.8040 (t70) REVERT: Q 369 GLU cc_start: 0.8558 (pp20) cc_final: 0.8262 (pp20) REVERT: O 69 GLN cc_start: 0.8050 (tt0) cc_final: 0.7641 (tt0) REVERT: A 97 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6968 (tm-30) REVERT: A 162 HIS cc_start: 0.7003 (m-70) cc_final: 0.6743 (m-70) REVERT: A 491 MET cc_start: 0.8361 (tpp) cc_final: 0.7717 (tpp) REVERT: A 509 CYS cc_start: 0.8921 (m) cc_final: 0.8637 (m) REVERT: D 256 ASP cc_start: 0.8821 (m-30) cc_final: 0.8600 (m-30) REVERT: D 468 ASP cc_start: 0.8042 (p0) cc_final: 0.7814 (p0) REVERT: M 259 TYR cc_start: 0.8362 (t80) cc_final: 0.8044 (t80) REVERT: H 58 ARG cc_start: 0.8295 (pmt-80) cc_final: 0.7470 (tpp-160) REVERT: H 120 GLU cc_start: 0.7872 (mp0) cc_final: 0.7508 (tm-30) REVERT: H 124 GLU cc_start: 0.6816 (pp20) cc_final: 0.6591 (pp20) REVERT: H 204 ARG cc_start: 0.6992 (ttt180) cc_final: 0.6711 (ttt90) REVERT: H 212 HIS cc_start: 0.8539 (OUTLIER) cc_final: 0.8249 (t70) REVERT: H 260 LEU cc_start: 0.9228 (mt) cc_final: 0.9011 (pp) REVERT: H 304 TYR cc_start: 0.5466 (t80) cc_final: 0.5101 (p90) REVERT: H 360 ASP cc_start: 0.6020 (t0) cc_final: 0.5691 (t0) REVERT: H 368 LEU cc_start: 0.7170 (mm) cc_final: 0.6816 (tp) REVERT: E 12 THR cc_start: 0.4492 (p) cc_final: 0.4267 (t) REVERT: E 15 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6901 (pt0) REVERT: E 282 HIS cc_start: 0.5945 (OUTLIER) cc_final: 0.5649 (p-80) outliers start: 56 outliers final: 34 residues processed: 487 average time/residue: 0.4542 time to fit residues: 376.7253 Evaluate side-chains 452 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 415 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 256 MET Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain O residue 438 SER Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 480 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 162 HIS Chi-restraints excluded: chain N residue 240 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 464 TYR Chi-restraints excluded: chain N residue 517 MET Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 212 HIS Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 282 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 611 optimal weight: 7.9990 chunk 465 optimal weight: 1.9990 chunk 321 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 295 optimal weight: 2.9990 chunk 415 optimal weight: 20.0000 chunk 620 optimal weight: 20.0000 chunk 657 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 chunk 588 optimal weight: 3.9990 chunk 177 optimal weight: 0.2980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 HIS R 282 HIS ** P 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 ASN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 HIS ** N 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 GLN E 289 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 49210 Z= 0.231 Angle : 0.521 9.051 67294 Z= 0.268 Chirality : 0.043 0.160 8077 Planarity : 0.004 0.053 8717 Dihedral : 3.927 30.351 7201 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.61 % Favored : 93.32 % Rotamer: Outliers : 1.55 % Allowed : 10.46 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 6748 helix: 1.61 (0.11), residues: 2553 sheet: -0.89 (0.18), residues: 890 loop : -1.11 (0.11), residues: 3305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 227 HIS 0.019 0.001 HIS E 282 PHE 0.015 0.001 PHE P 367 TYR 0.020 0.001 TYR E 253 ARG 0.005 0.000 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 432 time to evaluate : 4.416 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: S 258 ASP cc_start: 0.8389 (m-30) cc_final: 0.8087 (m-30) REVERT: K 261 LYS cc_start: 0.9420 (ttpp) cc_final: 0.9175 (mptt) REVERT: J 169 GLU cc_start: 0.9147 (pm20) cc_final: 0.8826 (pm20) REVERT: J 170 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8527 (tm-30) REVERT: R 194 ARG cc_start: 0.8816 (tpt170) cc_final: 0.8271 (tpm170) REVERT: R 205 TRP cc_start: 0.7122 (m100) cc_final: 0.6881 (m100) REVERT: P 181 ASP cc_start: 0.8773 (p0) cc_final: 0.8455 (p0) REVERT: P 210 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7860 (mttm) REVERT: Q 192 ASP cc_start: 0.8164 (t0) cc_final: 0.7791 (m-30) REVERT: Q 208 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6981 (tp) REVERT: Q 278 TYR cc_start: 0.8351 (m-80) cc_final: 0.7954 (t80) REVERT: Q 369 GLU cc_start: 0.8551 (pp20) cc_final: 0.8246 (pp20) REVERT: O 69 GLN cc_start: 0.8056 (tt0) cc_final: 0.7630 (tt0) REVERT: O 560 MET cc_start: 0.8322 (ptp) cc_final: 0.8117 (ptp) REVERT: A 97 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7050 (tm-30) REVERT: A 441 TRP cc_start: 0.8653 (m100) cc_final: 0.7901 (m100) REVERT: A 491 MET cc_start: 0.8388 (tpp) cc_final: 0.7784 (tpp) REVERT: A 509 CYS cc_start: 0.8942 (m) cc_final: 0.8676 (m) REVERT: D 256 ASP cc_start: 0.8826 (m-30) cc_final: 0.8616 (m-30) REVERT: M 259 TYR cc_start: 0.8314 (t80) cc_final: 0.7991 (t80) REVERT: H 58 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7304 (tpp-160) REVERT: H 62 ASP cc_start: 0.4952 (p0) cc_final: 0.4529 (m-30) REVERT: H 120 GLU cc_start: 0.7911 (mp0) cc_final: 0.7556 (tm-30) REVERT: H 282 HIS cc_start: 0.5929 (m170) cc_final: 0.5549 (p-80) REVERT: H 304 TYR cc_start: 0.5549 (t80) cc_final: 0.5060 (p90) REVERT: H 360 ASP cc_start: 0.6024 (t0) cc_final: 0.5692 (t0) REVERT: H 368 LEU cc_start: 0.7146 (mm) cc_final: 0.6782 (tp) outliers start: 68 outliers final: 47 residues processed: 475 average time/residue: 0.4498 time to fit residues: 365.8172 Evaluate side-chains 460 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 411 time to evaluate : 4.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 256 MET Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain O residue 438 SER Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 480 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain N residue 240 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 517 MET Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 161 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 547 optimal weight: 7.9990 chunk 373 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 489 optimal weight: 5.9990 chunk 271 optimal weight: 0.7980 chunk 560 optimal weight: 6.9990 chunk 454 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 335 optimal weight: 9.9990 chunk 589 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 116 ASN R 242 HIS R 282 HIS ** P 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 49210 Z= 0.371 Angle : 0.584 8.640 67294 Z= 0.301 Chirality : 0.045 0.161 8077 Planarity : 0.004 0.051 8717 Dihedral : 4.272 32.466 7199 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.63 % Favored : 92.28 % Rotamer: Outliers : 2.05 % Allowed : 11.37 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.20 (0.11), residues: 6748 helix: 1.53 (0.11), residues: 2537 sheet: -1.05 (0.18), residues: 881 loop : -1.21 (0.11), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 227 HIS 0.009 0.001 HIS O 162 PHE 0.019 0.002 PHE L 39 TYR 0.017 0.001 TYR N 230 ARG 0.007 0.000 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 412 time to evaluate : 4.152 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: S 124 GLU cc_start: 0.7769 (pm20) cc_final: 0.7487 (pm20) REVERT: S 127 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: K 261 LYS cc_start: 0.9411 (ttpp) cc_final: 0.9184 (tptt) REVERT: J 169 GLU cc_start: 0.9212 (pm20) cc_final: 0.8843 (pm20) REVERT: R 194 ARG cc_start: 0.8838 (tpt170) cc_final: 0.8291 (tpt170) REVERT: R 205 TRP cc_start: 0.7463 (m100) cc_final: 0.7178 (m100) REVERT: P 181 ASP cc_start: 0.8801 (p0) cc_final: 0.8497 (p0) REVERT: P 210 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7892 (mttm) REVERT: Q 129 GLU cc_start: 0.8856 (tp30) cc_final: 0.8267 (pt0) REVERT: Q 208 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6810 (tp) REVERT: Q 278 TYR cc_start: 0.8427 (m-80) cc_final: 0.8067 (t80) REVERT: Q 369 GLU cc_start: 0.8610 (pp20) cc_final: 0.8299 (pp20) REVERT: O 69 GLN cc_start: 0.8112 (tt0) cc_final: 0.7727 (tt0) REVERT: O 78 LYS cc_start: 0.8313 (tttt) cc_final: 0.8020 (ttpt) REVERT: A 97 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7109 (tm-30) REVERT: A 491 MET cc_start: 0.8471 (tpp) cc_final: 0.7802 (tpp) REVERT: A 509 CYS cc_start: 0.8965 (m) cc_final: 0.8679 (m) REVERT: M 259 TYR cc_start: 0.8457 (t80) cc_final: 0.8093 (t80) REVERT: H 58 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7332 (tpp-160) REVERT: H 120 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: H 260 LEU cc_start: 0.9189 (mt) cc_final: 0.8881 (pp) REVERT: H 261 LYS cc_start: 0.8154 (pttm) cc_final: 0.7529 (tppp) REVERT: H 304 TYR cc_start: 0.5631 (t80) cc_final: 0.4855 (p90) REVERT: H 360 ASP cc_start: 0.6089 (t0) cc_final: 0.5780 (t0) REVERT: H 361 PHE cc_start: 0.7617 (t80) cc_final: 0.7203 (t80) REVERT: H 368 LEU cc_start: 0.7119 (mm) cc_final: 0.6751 (tp) outliers start: 90 outliers final: 60 residues processed: 478 average time/residue: 0.4582 time to fit residues: 376.1957 Evaluate side-chains 456 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 392 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 127 GLU Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 126 ILE Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 184 VAL Chi-restraints excluded: chain P residue 256 MET Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 438 SER Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 480 ILE Chi-restraints excluded: chain L residue 481 VAL Chi-restraints excluded: chain L residue 665 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain M residue 562 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain N residue 240 SER Chi-restraints excluded: chain N residue 434 ILE Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 517 MET Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 212 HIS Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 161 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 221 optimal weight: 9.9990 chunk 591 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 385 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 657 optimal weight: 0.6980 chunk 546 optimal weight: 2.9990 chunk 304 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 345 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 116 ASN R 242 HIS R 282 HIS ** P 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 212 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 HIS E 282 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 49210 Z= 0.328 Angle : 0.566 9.564 67294 Z= 0.292 Chirality : 0.045 0.237 8077 Planarity : 0.004 0.054 8717 Dihedral : 4.253 31.112 7199 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.08 % Favored : 92.84 % Rotamer: Outliers : 1.96 % Allowed : 12.63 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.25 (0.11), residues: 6748 helix: 1.51 (0.11), residues: 2543 sheet: -1.06 (0.18), residues: 856 loop : -1.26 (0.11), residues: 3349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 227 HIS 0.010 0.001 HIS O 162 PHE 0.015 0.001 PHE L 513 TYR 0.013 0.001 TYR J 164 ARG 0.007 0.000 ARG E 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 415 time to evaluate : 4.213 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: K 119 GLU cc_start: 0.8596 (pp20) cc_final: 0.7748 (pt0) REVERT: K 261 LYS cc_start: 0.9414 (ttpp) cc_final: 0.9181 (tptt) REVERT: J 165 ASP cc_start: 0.7536 (p0) cc_final: 0.7215 (p0) REVERT: J 169 GLU cc_start: 0.9227 (pm20) cc_final: 0.8828 (pm20) REVERT: R 194 ARG cc_start: 0.8828 (tpt170) cc_final: 0.8205 (tpm170) REVERT: R 205 TRP cc_start: 0.7454 (m100) cc_final: 0.7194 (m100) REVERT: P 181 ASP cc_start: 0.8762 (p0) cc_final: 0.8456 (p0) REVERT: P 210 LYS cc_start: 0.8324 (mtmm) cc_final: 0.7902 (mttm) REVERT: Q 278 TYR cc_start: 0.8400 (m-80) cc_final: 0.8017 (t80) REVERT: O 69 GLN cc_start: 0.8102 (tt0) cc_final: 0.7715 (tt0) REVERT: O 574 ASP cc_start: 0.8274 (t0) cc_final: 0.7994 (t0) REVERT: A 97 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6974 (tm-30) REVERT: A 441 TRP cc_start: 0.8684 (m100) cc_final: 0.7850 (m100) REVERT: A 491 MET cc_start: 0.8413 (tpp) cc_final: 0.7770 (tpp) REVERT: A 509 CYS cc_start: 0.8970 (m) cc_final: 0.8703 (m) REVERT: M 259 TYR cc_start: 0.8458 (t80) cc_final: 0.8076 (t80) REVERT: M 430 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.9008 (mp) REVERT: H 58 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7290 (tpp-160) REVERT: H 62 ASP cc_start: 0.4721 (p0) cc_final: 0.4472 (m-30) REVERT: H 99 GLN cc_start: 0.6276 (pt0) cc_final: 0.5983 (mm-40) REVERT: H 120 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7614 (tm-30) REVERT: H 205 TRP cc_start: 0.7368 (m100) cc_final: 0.6873 (m100) REVERT: H 262 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8366 (mm) REVERT: H 304 TYR cc_start: 0.5664 (t80) cc_final: 0.4781 (p90) REVERT: H 360 ASP cc_start: 0.6035 (t0) cc_final: 0.5732 (t0) REVERT: H 361 PHE cc_start: 0.7650 (t80) cc_final: 0.7276 (t80) REVERT: H 368 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6662 (tp) REVERT: E 282 HIS cc_start: 0.6091 (OUTLIER) cc_final: 0.5825 (p-80) outliers start: 86 outliers final: 62 residues processed: 474 average time/residue: 0.4382 time to fit residues: 356.9517 Evaluate side-chains 460 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 392 time to evaluate : 4.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 116 ASN Chi-restraints excluded: chain T residue 126 ILE Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain T residue 323 LEU Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 256 MET Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain O residue 438 SER Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 480 ILE Chi-restraints excluded: chain L residue 481 VAL Chi-restraints excluded: chain L residue 665 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 430 ILE Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain M residue 562 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain N residue 240 SER Chi-restraints excluded: chain N residue 434 ILE Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 464 TYR Chi-restraints excluded: chain N residue 501 ILE Chi-restraints excluded: chain N residue 517 MET Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 212 HIS Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 282 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 634 optimal weight: 50.0000 chunk 74 optimal weight: 10.0000 chunk 374 optimal weight: 5.9990 chunk 480 optimal weight: 5.9990 chunk 372 optimal weight: 0.6980 chunk 553 optimal weight: 9.9990 chunk 367 optimal weight: 0.7980 chunk 655 optimal weight: 30.0000 chunk 410 optimal weight: 3.9990 chunk 399 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 HIS R 282 HIS ** P 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 212 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 49210 Z= 0.277 Angle : 0.557 10.944 67294 Z= 0.286 Chirality : 0.044 0.207 8077 Planarity : 0.004 0.053 8717 Dihedral : 4.193 30.888 7199 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.29 % Favored : 92.63 % Rotamer: Outliers : 2.01 % Allowed : 13.20 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.21 (0.11), residues: 6748 helix: 1.55 (0.11), residues: 2543 sheet: -1.09 (0.18), residues: 852 loop : -1.23 (0.11), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP H 217 HIS 0.025 0.001 HIS E 282 PHE 0.018 0.001 PHE P 367 TYR 0.020 0.001 TYR D 204 ARG 0.008 0.000 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 407 time to evaluate : 4.195 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: S 127 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7805 (pt0) REVERT: K 119 GLU cc_start: 0.8544 (pp20) cc_final: 0.7704 (pt0) REVERT: K 261 LYS cc_start: 0.9395 (ttpp) cc_final: 0.9167 (tptt) REVERT: J 169 GLU cc_start: 0.9212 (pm20) cc_final: 0.8795 (pm20) REVERT: R 194 ARG cc_start: 0.8791 (tpt170) cc_final: 0.8197 (tpm170) REVERT: R 205 TRP cc_start: 0.7450 (m100) cc_final: 0.7188 (m100) REVERT: P 181 ASP cc_start: 0.8776 (p0) cc_final: 0.8460 (p0) REVERT: P 210 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7886 (mttm) REVERT: Q 129 GLU cc_start: 0.8851 (tp30) cc_final: 0.8143 (pt0) REVERT: Q 278 TYR cc_start: 0.8415 (m-80) cc_final: 0.8006 (t80) REVERT: O 69 GLN cc_start: 0.8083 (tt0) cc_final: 0.7708 (tt0) REVERT: O 574 ASP cc_start: 0.8282 (t0) cc_final: 0.7983 (t0) REVERT: A 97 GLU cc_start: 0.7527 (tm-30) cc_final: 0.6954 (tm-30) REVERT: A 441 TRP cc_start: 0.8692 (m100) cc_final: 0.7833 (m100) REVERT: A 491 MET cc_start: 0.8412 (tpp) cc_final: 0.7754 (tpp) REVERT: A 509 CYS cc_start: 0.8966 (m) cc_final: 0.8689 (m) REVERT: M 259 TYR cc_start: 0.8444 (t80) cc_final: 0.8060 (t80) REVERT: M 554 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: H 58 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7389 (tpp-160) REVERT: H 99 GLN cc_start: 0.6244 (pt0) cc_final: 0.6003 (mm-40) REVERT: H 120 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: H 260 LEU cc_start: 0.9199 (mt) cc_final: 0.8906 (pp) REVERT: H 261 LYS cc_start: 0.8425 (pttm) cc_final: 0.7830 (tptm) REVERT: H 304 TYR cc_start: 0.5690 (t80) cc_final: 0.4777 (p90) REVERT: H 360 ASP cc_start: 0.5930 (t0) cc_final: 0.5631 (t0) REVERT: H 361 PHE cc_start: 0.7728 (t80) cc_final: 0.7361 (t80) REVERT: H 368 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6648 (tp) REVERT: E 282 HIS cc_start: 0.6100 (OUTLIER) cc_final: 0.5817 (p-80) outliers start: 88 outliers final: 67 residues processed: 469 average time/residue: 0.4545 time to fit residues: 365.3835 Evaluate side-chains 458 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 385 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain S residue 127 GLU Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 126 ILE Chi-restraints excluded: chain T residue 139 THR Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 256 MET Chi-restraints excluded: chain Q residue 19 LEU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 438 SER Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 480 ILE Chi-restraints excluded: chain L residue 481 VAL Chi-restraints excluded: chain L residue 665 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 554 GLU Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain M residue 562 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain N residue 240 SER Chi-restraints excluded: chain N residue 434 ILE Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 517 MET Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 181 ASP Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 209 TRP Chi-restraints excluded: chain H residue 212 HIS Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 312 GLU Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 282 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 405 optimal weight: 0.0050 chunk 261 optimal weight: 0.9990 chunk 391 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 416 optimal weight: 6.9990 chunk 446 optimal weight: 0.0270 chunk 324 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 515 optimal weight: 8.9990 overall best weight: 0.5454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 HIS Q 212 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 508 GLN ** N 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 49210 Z= 0.138 Angle : 0.525 11.081 67294 Z= 0.269 Chirality : 0.043 0.224 8077 Planarity : 0.004 0.052 8717 Dihedral : 3.843 28.858 7199 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 1.23 % Allowed : 14.27 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.11), residues: 6748 helix: 1.69 (0.11), residues: 2542 sheet: -0.94 (0.18), residues: 865 loop : -1.13 (0.11), residues: 3341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP H 217 HIS 0.030 0.001 HIS E 282 PHE 0.031 0.001 PHE K 263 TYR 0.021 0.001 TYR D 60 ARG 0.009 0.000 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 435 time to evaluate : 4.168 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: S 21 HIS cc_start: 0.8171 (m-70) cc_final: 0.7898 (m-70) REVERT: S 127 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: K 119 GLU cc_start: 0.8613 (pp20) cc_final: 0.7758 (pt0) REVERT: K 261 LYS cc_start: 0.9362 (ttpp) cc_final: 0.9141 (tptt) REVERT: J 169 GLU cc_start: 0.9177 (pm20) cc_final: 0.8769 (pm20) REVERT: R 194 ARG cc_start: 0.8786 (tpt170) cc_final: 0.8518 (tpm170) REVERT: P 181 ASP cc_start: 0.8720 (p0) cc_final: 0.8473 (p0) REVERT: P 210 LYS cc_start: 0.8237 (mtmm) cc_final: 0.7892 (mttm) REVERT: Q 32 PHE cc_start: 0.8655 (m-80) cc_final: 0.8369 (m-80) REVERT: Q 278 TYR cc_start: 0.8323 (m-80) cc_final: 0.7937 (t80) REVERT: Q 369 GLU cc_start: 0.8554 (pp20) cc_final: 0.8245 (pp20) REVERT: O 69 GLN cc_start: 0.8003 (tt0) cc_final: 0.7596 (tt0) REVERT: O 574 ASP cc_start: 0.8228 (t0) cc_final: 0.7936 (t0) REVERT: A 97 GLU cc_start: 0.7469 (tm-30) cc_final: 0.6933 (tm-30) REVERT: A 162 HIS cc_start: 0.6657 (m-70) cc_final: 0.6267 (m-70) REVERT: A 441 TRP cc_start: 0.8628 (m100) cc_final: 0.7679 (m100) REVERT: A 491 MET cc_start: 0.8344 (tpp) cc_final: 0.7712 (tpp) REVERT: A 508 GLN cc_start: 0.9116 (mp10) cc_final: 0.8871 (mp10) REVERT: A 509 CYS cc_start: 0.8948 (m) cc_final: 0.8657 (m) REVERT: M 259 TYR cc_start: 0.8345 (t80) cc_final: 0.7981 (t80) REVERT: H 58 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7242 (tpp-160) REVERT: H 99 GLN cc_start: 0.6244 (pt0) cc_final: 0.5950 (mm110) REVERT: H 100 GLN cc_start: 0.5776 (mt0) cc_final: 0.5271 (mm-40) REVERT: H 120 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: H 205 TRP cc_start: 0.7479 (m100) cc_final: 0.7071 (m100) REVERT: H 304 TYR cc_start: 0.5650 (t80) cc_final: 0.4741 (p90) REVERT: H 360 ASP cc_start: 0.5945 (t0) cc_final: 0.5655 (t0) REVERT: H 361 PHE cc_start: 0.7680 (t80) cc_final: 0.7287 (t80) REVERT: H 368 LEU cc_start: 0.7026 (mm) cc_final: 0.6793 (pp) REVERT: E 198 GLU cc_start: 0.0810 (OUTLIER) cc_final: 0.0136 (mm-30) REVERT: E 253 TYR cc_start: 0.3617 (t80) cc_final: 0.3248 (t80) REVERT: E 282 HIS cc_start: 0.6121 (OUTLIER) cc_final: 0.5837 (p-80) outliers start: 54 outliers final: 37 residues processed: 469 average time/residue: 0.4478 time to fit residues: 363.9594 Evaluate side-chains 447 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 405 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 124 GLU Chi-restraints excluded: chain S residue 127 GLU Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 148 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 126 ILE Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 665 VAL Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 240 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 209 TRP Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 312 GLU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 282 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 596 optimal weight: 8.9990 chunk 627 optimal weight: 20.0000 chunk 572 optimal weight: 5.9990 chunk 610 optimal weight: 0.0030 chunk 367 optimal weight: 4.9990 chunk 266 optimal weight: 20.0000 chunk 479 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 551 optimal weight: 20.0000 chunk 577 optimal weight: 7.9990 chunk 608 optimal weight: 20.0000 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 HIS ** P 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 212 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** N 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 49210 Z= 0.284 Angle : 0.562 11.333 67294 Z= 0.288 Chirality : 0.044 0.161 8077 Planarity : 0.004 0.052 8717 Dihedral : 4.019 30.355 7199 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.10 % Favored : 92.83 % Rotamer: Outliers : 1.44 % Allowed : 14.84 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.05 (0.11), residues: 6748 helix: 1.67 (0.11), residues: 2548 sheet: -0.99 (0.18), residues: 864 loop : -1.14 (0.11), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP H 217 HIS 0.010 0.001 HIS H 239 PHE 0.021 0.001 PHE P 367 TYR 0.027 0.001 TYR D 60 ARG 0.004 0.000 ARG D 470 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 397 time to evaluate : 5.163 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: S 127 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: K 119 GLU cc_start: 0.8579 (pp20) cc_final: 0.7783 (pt0) REVERT: K 261 LYS cc_start: 0.9379 (ttpp) cc_final: 0.9158 (tptt) REVERT: J 165 ASP cc_start: 0.7463 (p0) cc_final: 0.7181 (p0) REVERT: J 169 GLU cc_start: 0.9205 (pm20) cc_final: 0.8773 (pm20) REVERT: R 205 TRP cc_start: 0.7345 (m100) cc_final: 0.7031 (m100) REVERT: P 181 ASP cc_start: 0.8775 (p0) cc_final: 0.8465 (p0) REVERT: P 210 LYS cc_start: 0.8348 (mtmm) cc_final: 0.7894 (mttm) REVERT: Q 32 PHE cc_start: 0.8614 (m-80) cc_final: 0.8322 (m-80) REVERT: Q 129 GLU cc_start: 0.8785 (tp30) cc_final: 0.8018 (pt0) REVERT: Q 192 ASP cc_start: 0.8012 (t0) cc_final: 0.7546 (m-30) REVERT: Q 278 TYR cc_start: 0.8363 (m-80) cc_final: 0.7984 (t80) REVERT: Q 369 GLU cc_start: 0.8549 (pp20) cc_final: 0.8240 (pp20) REVERT: O 69 GLN cc_start: 0.8081 (tt0) cc_final: 0.7688 (tt0) REVERT: O 574 ASP cc_start: 0.8286 (t0) cc_final: 0.7962 (t0) REVERT: A 97 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6972 (tm-30) REVERT: A 117 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8760 (mmtt) REVERT: A 162 HIS cc_start: 0.6903 (m-70) cc_final: 0.6627 (m-70) REVERT: A 491 MET cc_start: 0.8416 (tpp) cc_final: 0.7772 (tpp) REVERT: A 508 GLN cc_start: 0.9132 (mp10) cc_final: 0.8869 (mp10) REVERT: A 509 CYS cc_start: 0.8929 (m) cc_final: 0.8600 (m) REVERT: M 259 TYR cc_start: 0.8358 (t80) cc_final: 0.8023 (t80) REVERT: H 58 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7249 (tpp-160) REVERT: H 62 ASP cc_start: 0.4011 (m-30) cc_final: 0.3675 (m-30) REVERT: H 99 GLN cc_start: 0.6204 (pt0) cc_final: 0.5997 (mm-40) REVERT: H 100 GLN cc_start: 0.5925 (mt0) cc_final: 0.5388 (mm-40) REVERT: H 120 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: H 205 TRP cc_start: 0.7449 (m100) cc_final: 0.7087 (m100) REVERT: H 260 LEU cc_start: 0.9173 (mt) cc_final: 0.8903 (pp) REVERT: H 304 TYR cc_start: 0.5619 (t80) cc_final: 0.4794 (p90) REVERT: H 360 ASP cc_start: 0.5956 (t0) cc_final: 0.5675 (t0) REVERT: H 361 PHE cc_start: 0.7755 (t80) cc_final: 0.7455 (t80) REVERT: E 198 GLU cc_start: 0.0841 (OUTLIER) cc_final: 0.0182 (mm-30) REVERT: E 253 TYR cc_start: 0.3674 (t80) cc_final: 0.3292 (t80) REVERT: E 282 HIS cc_start: 0.6206 (t-170) cc_final: 0.5934 (p90) outliers start: 63 outliers final: 48 residues processed: 440 average time/residue: 0.4872 time to fit residues: 368.9345 Evaluate side-chains 437 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 384 time to evaluate : 4.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 127 GLU Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 148 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 126 ILE Chi-restraints excluded: chain T residue 168 MET Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain P residue 256 MET Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain O residue 438 SER Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 665 VAL Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 240 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 464 TYR Chi-restraints excluded: chain N residue 517 MET Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 209 TRP Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 312 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 401 optimal weight: 3.9990 chunk 645 optimal weight: 10.0000 chunk 394 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 chunk 448 optimal weight: 9.9990 chunk 677 optimal weight: 0.0870 chunk 623 optimal weight: 30.0000 chunk 539 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 416 optimal weight: 5.9990 chunk 330 optimal weight: 4.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 212 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 GLN ** N 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 49210 Z= 0.215 Angle : 0.548 11.200 67294 Z= 0.280 Chirality : 0.044 0.211 8077 Planarity : 0.004 0.052 8717 Dihedral : 3.957 29.517 7199 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.21 % Favored : 93.72 % Rotamer: Outliers : 1.30 % Allowed : 15.06 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.11), residues: 6748 helix: 1.69 (0.11), residues: 2545 sheet: -0.97 (0.18), residues: 849 loop : -1.10 (0.11), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.001 TRP H 217 HIS 0.009 0.001 HIS H 239 PHE 0.035 0.001 PHE K 263 TYR 0.023 0.001 TYR D 60 ARG 0.011 0.000 ARG D 470 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13496 Ramachandran restraints generated. 6748 Oldfield, 0 Emsley, 6748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 404 time to evaluate : 4.189 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: S 127 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: K 119 GLU cc_start: 0.8587 (pp20) cc_final: 0.7801 (pt0) REVERT: K 261 LYS cc_start: 0.9365 (ttpp) cc_final: 0.9148 (tptt) REVERT: J 165 ASP cc_start: 0.7444 (p0) cc_final: 0.7137 (p0) REVERT: J 169 GLU cc_start: 0.9199 (pm20) cc_final: 0.8773 (pm20) REVERT: R 205 TRP cc_start: 0.7401 (m100) cc_final: 0.7100 (m100) REVERT: P 181 ASP cc_start: 0.8763 (p0) cc_final: 0.8476 (p0) REVERT: P 210 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7862 (mttm) REVERT: Q 32 PHE cc_start: 0.8643 (m-80) cc_final: 0.8356 (m-80) REVERT: Q 192 ASP cc_start: 0.8034 (t0) cc_final: 0.7613 (m-30) REVERT: Q 278 TYR cc_start: 0.8356 (m-80) cc_final: 0.7969 (t80) REVERT: Q 369 GLU cc_start: 0.8549 (pp20) cc_final: 0.8235 (pp20) REVERT: O 69 GLN cc_start: 0.8058 (tt0) cc_final: 0.7670 (tt0) REVERT: O 78 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7739 (ttpt) REVERT: O 574 ASP cc_start: 0.8290 (t0) cc_final: 0.7987 (t0) REVERT: A 97 GLU cc_start: 0.7490 (tm-30) cc_final: 0.6928 (tm-30) REVERT: A 117 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8754 (mmtt) REVERT: A 162 HIS cc_start: 0.6762 (m-70) cc_final: 0.6400 (m-70) REVERT: A 491 MET cc_start: 0.8328 (tpp) cc_final: 0.7683 (tpp) REVERT: A 508 GLN cc_start: 0.9148 (mp10) cc_final: 0.8906 (mp10) REVERT: A 509 CYS cc_start: 0.8907 (m) cc_final: 0.8628 (m) REVERT: M 259 TYR cc_start: 0.8371 (t80) cc_final: 0.8015 (t80) REVERT: H 58 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7247 (tpp-160) REVERT: H 62 ASP cc_start: 0.3998 (m-30) cc_final: 0.3660 (m-30) REVERT: H 99 GLN cc_start: 0.6186 (pt0) cc_final: 0.5843 (mm110) REVERT: H 100 GLN cc_start: 0.5790 (mt0) cc_final: 0.5273 (mm-40) REVERT: H 120 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: H 205 TRP cc_start: 0.7436 (m100) cc_final: 0.7069 (m100) REVERT: H 260 LEU cc_start: 0.9167 (mt) cc_final: 0.8836 (pp) REVERT: H 261 LYS cc_start: 0.8628 (pttm) cc_final: 0.7960 (tptm) REVERT: H 304 TYR cc_start: 0.5227 (t80) cc_final: 0.4559 (p90) REVERT: H 360 ASP cc_start: 0.5941 (t0) cc_final: 0.5638 (t0) REVERT: H 361 PHE cc_start: 0.7756 (t80) cc_final: 0.7441 (t80) REVERT: E 198 GLU cc_start: 0.0897 (OUTLIER) cc_final: 0.0226 (mm-30) REVERT: E 253 TYR cc_start: 0.3675 (t80) cc_final: 0.3287 (t80) REVERT: E 282 HIS cc_start: 0.6146 (t-170) cc_final: 0.5895 (p90) REVERT: E 325 LEU cc_start: 0.4980 (tt) cc_final: 0.4677 (mp) REVERT: E 330 ARG cc_start: 0.4899 (ptt-90) cc_final: 0.4324 (mtm180) outliers start: 57 outliers final: 48 residues processed: 445 average time/residue: 0.4462 time to fit residues: 340.4579 Evaluate side-chains 448 residues out of total 6060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 395 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 127 GLU Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 148 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 126 ILE Chi-restraints excluded: chain T residue 168 MET Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 562 THR Chi-restraints excluded: chain L residue 184 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 665 VAL Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 562 THR Chi-restraints excluded: chain N residue 240 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 464 TYR Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 196 ILE Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 209 TRP Chi-restraints excluded: chain H residue 212 HIS Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 312 GLU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 680 random chunks: chunk 428 optimal weight: 2.9990 chunk 574 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 497 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 540 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 554 optimal weight: 10.0000 chunk 68 optimal weight: 0.0000 chunk 99 optimal weight: 8.9990 overall best weight: 3.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 ASN R 242 HIS ** P 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 212 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.113538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072212 restraints weight = 137254.873| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.30 r_work: 0.2924 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 49210 Z= 0.360 Angle : 0.605 11.274 67294 Z= 0.311 Chirality : 0.045 0.292 8077 Planarity : 0.004 0.052 8717 Dihedral : 4.266 31.264 7199 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.06 % Favored : 91.86 % Rotamer: Outliers : 1.53 % Allowed : 14.97 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.18 (0.11), residues: 6748 helix: 1.54 (0.11), residues: 2550 sheet: -1.09 (0.18), residues: 855 loop : -1.19 (0.11), residues: 3343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP H 217 HIS 0.010 0.001 HIS O 162 PHE 0.024 0.002 PHE N 513 TYR 0.026 0.001 TYR D 60 ARG 0.010 0.000 ARG D 470 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8535.59 seconds wall clock time: 150 minutes 37.28 seconds (9037.28 seconds total)