Starting phenix.real_space_refine on Sat Mar 7 04:20:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j5j_0669/03_2026/6j5j_0669.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j5j_0669/03_2026/6j5j_0669.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6j5j_0669/03_2026/6j5j_0669.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j5j_0669/03_2026/6j5j_0669.map" model { file = "/net/cci-nas-00/data/ceres_data/6j5j_0669/03_2026/6j5j_0669.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j5j_0669/03_2026/6j5j_0669.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 145 5.16 5 C 24166 2.51 5 N 6600 2.21 5 O 7239 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38168 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3837 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 485} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3814 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain breaks: 1 Chain: "C" Number of atoms: 3722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3722 Classifications: {'peptide': 488} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain: "D" Number of atoms: 3555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3555 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "E" Number of atoms: 3522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3522 Classifications: {'peptide': 465} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 440} Chain: "F" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3527 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 441} Chain: "J" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 406 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'HIS:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 2112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2112 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 970 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'TRANS': 47} Chain: "S" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1429 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 177} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1478 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 5, 'TRANS': 203} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 229 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLU:plan': 5, 'HIS:plan': 2, 'ARG:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 3, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "c" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 428 Classifications: {'peptide': 70} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 64} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 4, 'ARG:plan': 1, 'PHE:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 99 Chain: "d" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 741 Classifications: {'peptide': 147} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 125} Link IDs: {'PTRANS': 8, 'TRANS': 138} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 472 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 398 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 10, 'TRP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 16, 'ASN:plan1': 6, 'GLN:plan1': 3, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 238 Chain: "e" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 315 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'TRANS': 62} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'UNK:plan-1': 63} Unresolved non-hydrogen planarities: 63 Chain: "f" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 530 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 82} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 5, 'GLU:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 112 Chain: "g" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 420 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'CIS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'UNK:plan-1': 84} Unresolved non-hydrogen planarities: 84 Chain: "i" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 301 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 40} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 145 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'UNK:plan-1': 29} Unresolved non-hydrogen planarities: 29 Chain: "8" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 374 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 52} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "a" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1702 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "M" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 510 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 513 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "u" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 210 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'UNK:plan-1': 42} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.54, per 1000 atoms: 0.22 Number of scatterers: 38168 At special positions: 0 Unit cell: (149.04, 231.84, 191.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 145 16.00 P 13 15.00 Mg 5 11.99 O 7239 8.00 N 6600 7.00 C 24166 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.3 seconds 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9538 Finding SS restraints... Secondary structure from input PDB file: 238 helices and 27 sheets defined 54.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 removed outlier: 3.590A pdb=" N ILE A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.898A pdb=" N LEU A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.527A pdb=" N ILE A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 182 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.786A pdb=" N LYS A 198 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.575A pdb=" N VAL A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.683A pdb=" N ALA A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.566A pdb=" N ASN A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.718A pdb=" N ALA A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.557A pdb=" N HIS A 302 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 removed outlier: 3.962A pdb=" N ILE A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.710A pdb=" N TYR A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.551A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA A 378 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 374 through 379' Processing helix chain 'A' and resid 380 through 398 removed outlier: 3.627A pdb=" N GLN A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.606A pdb=" N PHE A 403 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 404 " --> pdb=" O ALA A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.776A pdb=" N ARG A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 427 " --> pdb=" O ARG A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 450 removed outlier: 3.670A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 450 " --> pdb=" O TYR A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.648A pdb=" N SER A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.508A pdb=" N LEU A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 507 " --> pdb=" O ASN A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 removed outlier: 4.347A pdb=" N GLU B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 15 " --> pdb=" O ILE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.788A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 104 " --> pdb=" O GLU B 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 104' Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.634A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.714A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.718A pdb=" N ASP B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.643A pdb=" N LYS B 197 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 removed outlier: 3.656A pdb=" N VAL B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 removed outlier: 3.547A pdb=" N GLN B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 253 removed outlier: 3.576A pdb=" N MET B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 260 Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.597A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 277 " --> pdb=" O LYS B 273 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 removed outlier: 3.508A pdb=" N ALA B 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.521A pdb=" N LEU B 301 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.800A pdb=" N GLY B 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 373 through 377 removed outlier: 3.669A pdb=" N SER B 376 " --> pdb=" O ARG B 373 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA B 377 " --> pdb=" O VAL B 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 373 through 377' Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.808A pdb=" N VAL B 386 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 424 removed outlier: 4.182A pdb=" N VAL B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.664A pdb=" N LYS B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 removed outlier: 4.092A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR B 446 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 448 " --> pdb=" O VAL B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 473 removed outlier: 3.749A pdb=" N ASN B 466 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.506A pdb=" N GLY B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 505 removed outlier: 3.685A pdb=" N ALA B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 501 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 502 " --> pdb=" O LYS B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 156 removed outlier: 3.535A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.601A pdb=" N ILE C 178 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 184 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 194 through 197 removed outlier: 3.522A pdb=" N LYS C 197 " --> pdb=" O ASP C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 209 through 223 removed outlier: 4.608A pdb=" N GLN C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 229 removed outlier: 4.064A pdb=" N TYR C 228 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 229 " --> pdb=" O MET C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 225 through 229' Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 272 through 284 removed outlier: 3.747A pdb=" N TYR C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 298 through 303 removed outlier: 4.317A pdb=" N HIS C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.725A pdb=" N VAL C 342 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.523A pdb=" N PHE C 357 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C 358 " --> pdb=" O THR C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 358' Processing helix chain 'C' and resid 383 through 399 removed outlier: 3.856A pdb=" N GLY C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU C 393 " --> pdb=" O THR C 389 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLU C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 420 through 427 Processing helix chain 'C' and resid 437 through 450 removed outlier: 3.649A pdb=" N ALA C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY C 448 " --> pdb=" O VAL C 444 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG C 450 " --> pdb=" O TYR C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 460 through 476 removed outlier: 3.694A pdb=" N ASN C 466 " --> pdb=" O THR C 462 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER C 470 " --> pdb=" O ASN C 466 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 472 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 473 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN C 475 " --> pdb=" O HIS C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 removed outlier: 3.573A pdb=" N LEU C 480 " --> pdb=" O HIS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 509 removed outlier: 3.650A pdb=" N ALA C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL C 501 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.510A pdb=" N GLU D 127 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET D 128 " --> pdb=" O PHE D 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 124 through 128' Processing helix chain 'D' and resid 139 through 146 removed outlier: 3.513A pdb=" N LEU D 145 " --> pdb=" O VAL D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 179 removed outlier: 3.592A pdb=" N LEU D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN D 173 " --> pdb=" O MET D 169 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 176 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS D 177 " --> pdb=" O ASN D 173 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 removed outlier: 3.555A pdb=" N GLY D 195 " --> pdb=" O THR D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 248 removed outlier: 3.705A pdb=" N THR D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE D 245 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 265 removed outlier: 4.095A pdb=" N THR D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.722A pdb=" N ASP D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 331 removed outlier: 3.913A pdb=" N THR D 326 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N PHE D 328 " --> pdb=" O ALA D 325 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA D 329 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU D 331 " --> pdb=" O PHE D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 385 removed outlier: 4.179A pdb=" N HIS D 369 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 379 " --> pdb=" O GLY D 375 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 391 removed outlier: 3.561A pdb=" N ALA D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 417 removed outlier: 3.770A pdb=" N SER D 407 " --> pdb=" O LYS D 403 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER D 417 " --> pdb=" O GLN D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 428 Processing helix chain 'D' and resid 435 through 449 removed outlier: 3.700A pdb=" N ILE D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE D 443 " --> pdb=" O THR D 439 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 446 " --> pdb=" O GLY D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 460 removed outlier: 3.582A pdb=" N ALA D 458 " --> pdb=" O PRO D 455 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE D 459 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR D 460 " --> pdb=" O GLN D 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 455 through 460' Processing helix chain 'D' and resid 466 through 475 removed outlier: 3.691A pdb=" N ALA D 470 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 475 " --> pdb=" O LYS D 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 removed outlier: 3.880A pdb=" N THR E 92 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU E 93 " --> pdb=" O PRO E 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 93' Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.655A pdb=" N GLU E 127 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET E 128 " --> pdb=" O PHE E 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 128' Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.515A pdb=" N LEU E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 179 removed outlier: 4.161A pdb=" N LEU E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN E 173 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL E 175 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 204 removed outlier: 3.673A pdb=" N ASP E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 198 " --> pdb=" O GLU E 194 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 248 removed outlier: 3.861A pdb=" N LEU E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA E 242 " --> pdb=" O GLY E 238 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE E 245 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 265 Processing helix chain 'E' and resid 291 through 296 removed outlier: 3.707A pdb=" N GLN E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU E 296 " --> pdb=" O GLY E 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 291 through 296' Processing helix chain 'E' and resid 314 through 318 removed outlier: 3.914A pdb=" N ASP E 317 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 327 removed outlier: 3.766A pdb=" N THR E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 330 No H-bonds generated for 'chain 'E' and resid 328 through 330' Processing helix chain 'E' and resid 338 through 343 removed outlier: 3.752A pdb=" N ALA E 342 " --> pdb=" O SER E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 393 removed outlier: 4.476A pdb=" N HIS E 369 " --> pdb=" O VAL E 365 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY E 375 " --> pdb=" O ASP E 371 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP E 388 " --> pdb=" O LYS E 384 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE E 389 " --> pdb=" O SER E 385 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 416 removed outlier: 4.091A pdb=" N LEU E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR E 405 " --> pdb=" O GLU E 401 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG E 410 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 424 removed outlier: 3.949A pdb=" N GLU E 424 " --> pdb=" O GLN E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 447 removed outlier: 3.760A pdb=" N THR E 439 " --> pdb=" O PRO E 435 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 441 " --> pdb=" O LYS E 437 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E 447 " --> pdb=" O PHE E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 459 removed outlier: 3.773A pdb=" N ALA E 458 " --> pdb=" O PRO E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 473 removed outlier: 4.024A pdb=" N VAL E 469 " --> pdb=" O ILE E 465 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA E 470 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS E 471 " --> pdb=" O GLU E 467 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 472 " --> pdb=" O ALA E 468 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP E 473 " --> pdb=" O VAL E 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 465 through 473' Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.664A pdb=" N THR F 92 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU F 93 " --> pdb=" O PRO F 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 89 through 93' Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.665A pdb=" N GLU F 127 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 124 through 128' Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.560A pdb=" N LEU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 175 removed outlier: 3.522A pdb=" N ASN F 173 " --> pdb=" O MET F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 200 removed outlier: 3.508A pdb=" N TYR F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 236 through 248 removed outlier: 3.908A pdb=" N ALA F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 272 removed outlier: 3.884A pdb=" N THR F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY F 267 " --> pdb=" O PHE F 263 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA F 272 " --> pdb=" O SER F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 296 removed outlier: 3.803A pdb=" N GLY F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 318 removed outlier: 3.756A pdb=" N ASP F 317 " --> pdb=" O VAL F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 331 removed outlier: 3.723A pdb=" N HIS F 330 " --> pdb=" O THR F 327 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU F 331 " --> pdb=" O PHE F 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 327 through 331' Processing helix chain 'F' and resid 338 through 343 removed outlier: 3.730A pdb=" N ALA F 342 " --> pdb=" O SER F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 385 removed outlier: 3.746A pdb=" N GLN F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN F 381 " --> pdb=" O GLN F 377 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR F 383 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 394 removed outlier: 3.611A pdb=" N ALA F 391 " --> pdb=" O GLN F 387 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE F 392 " --> pdb=" O ASP F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 398 removed outlier: 3.540A pdb=" N LEU F 398 " --> pdb=" O MET F 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 395 through 398' Processing helix chain 'F' and resid 401 through 416 removed outlier: 3.756A pdb=" N THR F 405 " --> pdb=" O GLU F 401 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL F 406 " --> pdb=" O ASP F 402 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER F 407 " --> pdb=" O LYS F 403 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS F 411 " --> pdb=" O SER F 407 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 428 removed outlier: 3.822A pdb=" N THR F 427 " --> pdb=" O ALA F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 442 removed outlier: 3.968A pdb=" N LYS F 441 " --> pdb=" O LYS F 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 460 removed outlier: 3.574A pdb=" N ALA F 458 " --> pdb=" O PRO F 455 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR F 460 " --> pdb=" O GLN F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 470 removed outlier: 3.994A pdb=" N VAL F 469 " --> pdb=" O ILE F 465 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 19 removed outlier: 3.654A pdb=" N ALA J 18 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY J 19 " --> pdb=" O VAL J 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 14 through 19' Processing helix chain 'J' and resid 21 through 26 Processing helix chain 'J' and resid 26 through 34 removed outlier: 3.572A pdb=" N ARG J 32 " --> pdb=" O ALA J 28 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE J 34 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 44 removed outlier: 3.568A pdb=" N GLN J 41 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 55 removed outlier: 3.512A pdb=" N GLU J 52 " --> pdb=" O HIS J 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 37 removed outlier: 3.641A pdb=" N ARG G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE G 13 " --> pdb=" O ARG G 9 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA G 27 " --> pdb=" O MET G 23 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 33 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 54 removed outlier: 3.919A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR G 44 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER G 48 " --> pdb=" O TYR G 44 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 97 removed outlier: 3.552A pdb=" N SER G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 109 through 116 removed outlier: 3.718A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 148 removed outlier: 3.593A pdb=" N ALA G 141 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 191 removed outlier: 3.529A pdb=" N SER G 191 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 232 removed outlier: 3.513A pdb=" N GLU G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU G 209 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR G 222 " --> pdb=" O LYS G 218 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN G 225 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 271 removed outlier: 4.031A pdb=" N ALA G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE G 243 " --> pdb=" O ALA G 239 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP G 244 " --> pdb=" O SER G 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 246 " --> pdb=" O MET G 242 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 247 " --> pdb=" O ILE G 243 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR G 249 " --> pdb=" O LYS G 245 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU G 264 " --> pdb=" O LYS G 260 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 121 removed outlier: 3.736A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 115 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU H 120 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 145 removed outlier: 3.638A pdb=" N GLU H 136 " --> pdb=" O GLN H 132 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA H 137 " --> pdb=" O ILE H 133 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 22 removed outlier: 3.968A pdb=" N ILE I 18 " --> pdb=" O ARG I 14 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA I 20 " --> pdb=" O SER I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 32 through 39 removed outlier: 3.803A pdb=" N THR I 38 " --> pdb=" O ASN I 34 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER I 39 " --> pdb=" O ALA I 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 22 removed outlier: 3.514A pdb=" N ALA S 21 " --> pdb=" O ARG S 17 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU S 22 " --> pdb=" O TYR S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 27 Processing helix chain 'S' and resid 28 through 31 removed outlier: 4.149A pdb=" N LYS S 31 " --> pdb=" O LYS S 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 28 through 31' Processing helix chain 'S' and resid 33 through 43 removed outlier: 3.920A pdb=" N ARG S 41 " --> pdb=" O LYS S 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA S 43 " --> pdb=" O LEU S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 71 removed outlier: 3.757A pdb=" N LEU S 69 " --> pdb=" O LYS S 65 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP S 71 " --> pdb=" O LYS S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 76 removed outlier: 4.209A pdb=" N GLU S 76 " --> pdb=" O MET S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 92 removed outlier: 3.627A pdb=" N LEU S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU S 91 " --> pdb=" O ASN S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 93 through 96 removed outlier: 4.494A pdb=" N SER S 96 " --> pdb=" O GLY S 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 93 through 96' Processing helix chain 'S' and resid 97 through 111 removed outlier: 3.937A pdb=" N THR S 107 " --> pdb=" O SER S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 138 removed outlier: 3.681A pdb=" N LEU S 131 " --> pdb=" O ASP S 127 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU S 134 " --> pdb=" O THR S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 138 through 143 removed outlier: 4.221A pdb=" N SER S 143 " --> pdb=" O LYS S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 180 removed outlier: 3.614A pdb=" N ILE S 179 " --> pdb=" O ALA S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 185 Processing helix chain 'b' and resid 4 through 30 removed outlier: 3.906A pdb=" N HIS b 8 " --> pdb=" O PRO b 4 " (cutoff:3.500A) Proline residue: b 18 - end of helix Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 37 through 42 removed outlier: 3.917A pdb=" N LEU b 41 " --> pdb=" O LEU b 37 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 48 Processing helix chain 'b' and resid 49 through 51 No H-bonds generated for 'chain 'b' and resid 49 through 51' Processing helix chain 'b' and resid 61 through 138 removed outlier: 4.190A pdb=" N LEU b 67 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL b 68 " --> pdb=" O ILE b 64 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR b 69 " --> pdb=" O GLY b 65 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE b 70 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS b 72 " --> pdb=" O VAL b 68 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS b 73 " --> pdb=" O TYR b 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY b 75 " --> pdb=" O VAL b 71 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLY b 79 " --> pdb=" O GLY b 75 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA b 91 " --> pdb=" O GLU b 87 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN b 92 " --> pdb=" O GLN b 88 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS b 102 " --> pdb=" O GLN b 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA b 107 " --> pdb=" O GLN b 103 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU b 110 " --> pdb=" O ASP b 106 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN b 114 " --> pdb=" O LEU b 110 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN b 115 " --> pdb=" O GLU b 111 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU b 117 " --> pdb=" O SER b 113 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL b 118 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN b 119 " --> pdb=" O GLN b 115 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N HIS b 122 " --> pdb=" O VAL b 118 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP b 126 " --> pdb=" O HIS b 122 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG b 129 " --> pdb=" O PHE b 125 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE b 132 " --> pdb=" O GLN b 128 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA b 135 " --> pdb=" O ASN b 131 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU b 136 " --> pdb=" O ILE b 132 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU b 137 " --> pdb=" O ALA b 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 140 through 158 removed outlier: 3.602A pdb=" N VAL b 147 " --> pdb=" O ARG b 143 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE b 151 " --> pdb=" O VAL b 147 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG b 154 " --> pdb=" O GLU b 150 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 158 through 163 Processing helix chain 'b' and resid 163 through 181 removed outlier: 3.861A pdb=" N GLN b 167 " --> pdb=" O ASN b 163 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS b 168 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU b 169 " --> pdb=" O MET b 165 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE b 174 " --> pdb=" O GLN b 170 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP b 176 " --> pdb=" O HIS b 172 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL b 177 " --> pdb=" O MET b 173 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU b 178 " --> pdb=" O ILE b 174 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS b 179 " --> pdb=" O ARG b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 191 through 211 removed outlier: 3.991A pdb=" N CYS b 197 " --> pdb=" O THR b 193 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP b 200 " --> pdb=" O LYS b 196 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU b 201 " --> pdb=" O CYS b 197 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS b 202 " --> pdb=" O ILE b 198 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA b 208 " --> pdb=" O LEU b 204 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN b 209 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN b 211 " --> pdb=" O LYS b 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 23 removed outlier: 3.670A pdb=" N ASP c 13 " --> pdb=" O LYS c 9 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU c 17 " --> pdb=" O ASP c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 32 through 51 removed outlier: 3.650A pdb=" N GLN c 36 " --> pdb=" O GLY c 32 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU c 39 " --> pdb=" O TYR c 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP c 40 " --> pdb=" O GLN c 36 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET c 49 " --> pdb=" O LYS c 45 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 44 removed outlier: 3.820A pdb=" N ALA d 27 " --> pdb=" O GLN d 23 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN d 34 " --> pdb=" O LEU d 30 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR d 39 " --> pdb=" O GLU d 35 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 53 through 60 removed outlier: 3.760A pdb=" N LYS d 57 " --> pdb=" O TRP d 53 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA d 58 " --> pdb=" O ALA d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 73 removed outlier: 3.944A pdb=" N PHE d 69 " --> pdb=" O LEU d 65 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 100 removed outlier: 4.157A pdb=" N LEU d 88 " --> pdb=" O LYS d 84 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL d 89 " --> pdb=" O TYR d 85 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP d 90 " --> pdb=" O THR d 86 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU d 93 " --> pdb=" O VAL d 89 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN d 94 " --> pdb=" O ASP d 90 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU d 95 " --> pdb=" O ALA d 91 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS d 98 " --> pdb=" O GLN d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 101 through 125 removed outlier: 4.454A pdb=" N LYS d 108 " --> pdb=" O LEU d 104 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA d 109 " --> pdb=" O SER d 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG d 110 " --> pdb=" O LEU d 106 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU d 119 " --> pdb=" O GLU d 115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS d 122 " --> pdb=" O LEU d 118 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN d 123 " --> pdb=" O GLU d 119 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE d 125 " --> pdb=" O MET d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 137 removed outlier: 3.864A pdb=" N GLU d 137 " --> pdb=" O ASP d 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 34 removed outlier: 3.896A pdb=" N UNK e 12 " --> pdb=" O UNK e 8 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N UNK e 13 " --> pdb=" O UNK e 9 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N UNK e 27 " --> pdb=" O UNK e 23 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N UNK e 28 " --> pdb=" O UNK e 24 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 38 Processing helix chain 'e' and resid 39 through 58 removed outlier: 3.965A pdb=" N UNK e 46 " --> pdb=" O UNK e 42 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N UNK e 49 " --> pdb=" O UNK e 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 15 removed outlier: 3.501A pdb=" N LYS f 7 " --> pdb=" O VAL f 3 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP f 8 " --> pdb=" O VAL f 4 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG f 9 " --> pdb=" O PRO f 5 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU f 11 " --> pdb=" O LYS f 7 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL f 14 " --> pdb=" O ARG f 10 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS f 15 " --> pdb=" O LEU f 11 " (cutoff:3.500A) Processing helix chain 'f' and resid 27 through 35 removed outlier: 3.750A pdb=" N GLY f 32 " --> pdb=" O PHE f 28 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE f 33 " --> pdb=" O THR f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 36 through 41 Processing helix chain 'f' and resid 42 through 44 No H-bonds generated for 'chain 'f' and resid 42 through 44' Processing helix chain 'f' and resid 55 through 60 removed outlier: 3.616A pdb=" N LEU f 59 " --> pdb=" O SER f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 61 through 75 removed outlier: 3.527A pdb=" N VAL f 67 " --> pdb=" O LEU f 63 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL f 68 " --> pdb=" O ALA f 64 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N CYS f 72 " --> pdb=" O VAL f 68 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG f 73 " --> pdb=" O PHE f 69 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER f 74 " --> pdb=" O ASN f 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 32 removed outlier: 3.669A pdb=" N UNK g 7 " --> pdb=" O UNK g 3 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N UNK g 8 " --> pdb=" O UNK g 4 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N UNK g 18 " --> pdb=" O UNK g 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N UNK g 21 " --> pdb=" O UNK g 17 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N UNK g 24 " --> pdb=" O UNK g 20 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N UNK g 25 " --> pdb=" O UNK g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 65 Processing helix chain 'g' and resid 65 through 84 removed outlier: 3.565A pdb=" N UNK g 74 " --> pdb=" O UNK g 70 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N UNK g 77 " --> pdb=" O UNK g 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N UNK g 78 " --> pdb=" O UNK g 74 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N UNK g 79 " --> pdb=" O UNK g 75 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N UNK g 83 " --> pdb=" O UNK g 79 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N UNK g 84 " --> pdb=" O UNK g 80 " (cutoff:3.500A) Processing helix chain 'i' and resid 14 through 26 removed outlier: 3.976A pdb=" N ASN i 19 " --> pdb=" O LYS i 15 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER i 20 " --> pdb=" O LYS i 16 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU i 23 " --> pdb=" O ASN i 19 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N THR i 24 " --> pdb=" O SER i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 48 removed outlier: 4.281A pdb=" N LEU i 31 " --> pdb=" O MET i 27 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA i 38 " --> pdb=" O TYR i 34 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU i 40 " --> pdb=" O GLY i 36 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL i 41 " --> pdb=" O ILE i 37 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU i 42 " --> pdb=" O ALA i 38 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU i 46 " --> pdb=" O LEU i 42 " (cutoff:3.500A) Processing helix chain 'k' and resid 13 through 19 Processing helix chain '8' and resid 12 through 16 removed outlier: 3.667A pdb=" N SER 8 15 " --> pdb=" O THR 8 12 " (cutoff:3.500A) Processing helix chain '8' and resid 19 through 28 removed outlier: 3.705A pdb=" N LEU 8 23 " --> pdb=" O THR 8 19 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN 8 25 " --> pdb=" O PHE 8 21 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU 8 26 " --> pdb=" O ILE 8 22 " (cutoff:3.500A) Processing helix chain '8' and resid 35 through 60 removed outlier: 3.628A pdb=" N SER 8 39 " --> pdb=" O ALA 8 35 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE 8 40 " --> pdb=" O SER 8 36 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU 8 41 " --> pdb=" O PRO 8 37 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU 8 42 " --> pdb=" O GLU 8 38 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS 8 43 " --> pdb=" O SER 8 39 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR 8 44 " --> pdb=" O ILE 8 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN 8 45 " --> pdb=" O GLU 8 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER 8 48 " --> pdb=" O THR 8 44 " (cutoff:3.500A) Proline residue: 8 50 - end of helix Processing helix chain 'a' and resid 19 through 24 removed outlier: 4.165A pdb=" N ILE a 23 " --> pdb=" O ILE a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 29 Processing helix chain 'a' and resid 43 through 54 removed outlier: 3.795A pdb=" N LEU a 49 " --> pdb=" O ILE a 45 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN a 51 " --> pdb=" O GLN a 47 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR a 53 " --> pdb=" O LEU a 49 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 73 removed outlier: 3.737A pdb=" N LEU a 72 " --> pdb=" O TRP a 68 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET a 73 " --> pdb=" O SER a 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 68 through 73' Processing helix chain 'a' and resid 73 through 82 removed outlier: 3.813A pdb=" N MET a 77 " --> pdb=" O MET a 73 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 88 removed outlier: 3.818A pdb=" N LEU a 87 " --> pdb=" O ILE a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 96 Processing helix chain 'a' and resid 97 through 102 removed outlier: 4.552A pdb=" N ASN a 101 " --> pdb=" O GLN a 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU a 102 " --> pdb=" O LEU a 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 97 through 102' Processing helix chain 'a' and resid 105 through 117 removed outlier: 4.140A pdb=" N ALA a 111 " --> pdb=" O PRO a 107 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL a 113 " --> pdb=" O TRP a 109 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE a 114 " --> pdb=" O SER a 110 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR a 115 " --> pdb=" O ALA a 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY a 116 " --> pdb=" O THR a 112 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE a 117 " --> pdb=" O VAL a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 150 through 180 removed outlier: 4.580A pdb=" N VAL a 154 " --> pdb=" O PHE a 150 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG a 159 " --> pdb=" O ALA a 155 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN a 163 " --> pdb=" O ARG a 159 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR a 165 " --> pdb=" O THR a 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA a 166 " --> pdb=" O ALA a 162 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS a 168 " --> pdb=" O ILE a 164 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU a 170 " --> pdb=" O ALA a 166 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR a 178 " --> pdb=" O ILE a 174 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU a 179 " --> pdb=" O GLY a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 202 removed outlier: 4.207A pdb=" N PHE a 190 " --> pdb=" O THR a 186 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 206 through 222 removed outlier: 3.835A pdb=" N GLN a 210 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR a 212 " --> pdb=" O LEU a 208 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N THR a 215 " --> pdb=" O ALA a 211 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU a 216 " --> pdb=" O TYR a 212 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER a 219 " --> pdb=" O THR a 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 removed outlier: 3.699A pdb=" N ILE K 9 " --> pdb=" O ALA K 5 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY K 12 " --> pdb=" O PHE K 8 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR K 15 " --> pdb=" O ALA K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 37 removed outlier: 3.957A pdb=" N GLY K 26 " --> pdb=" O GLY K 22 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR K 27 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE K 29 " --> pdb=" O ILE K 25 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET K 32 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 73 removed outlier: 4.206A pdb=" N SER K 48 " --> pdb=" O GLN K 44 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE K 63 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS K 64 " --> pdb=" O MET K 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU K 72 " --> pdb=" O ALA K 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.631A pdb=" N ILE L 9 " --> pdb=" O ALA L 5 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA L 11 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA L 13 " --> pdb=" O ILE L 9 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR L 15 " --> pdb=" O ALA L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 24 Processing helix chain 'L' and resid 24 through 29 removed outlier: 4.194A pdb=" N VAL L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 35 removed outlier: 3.548A pdb=" N ILE L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 73 removed outlier: 4.139A pdb=" N SER L 48 " --> pdb=" O GLN L 44 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER L 57 " --> pdb=" O GLY L 53 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLY L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS L 64 " --> pdb=" O MET L 60 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA L 68 " --> pdb=" O CYS L 64 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 14 removed outlier: 3.536A pdb=" N LYS M 7 " --> pdb=" O ASP M 3 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY M 12 " --> pdb=" O PHE M 8 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA M 14 " --> pdb=" O GLY M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 17 through 29 removed outlier: 4.418A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA M 23 " --> pdb=" O ALA M 19 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY M 26 " --> pdb=" O GLY M 22 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 39 removed outlier: 3.555A pdb=" N ARG M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN M 39 " --> pdb=" O GLY M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 56 removed outlier: 4.172A pdb=" N SER M 48 " --> pdb=" O GLN M 44 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA M 50 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY M 53 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU M 56 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 71 removed outlier: 3.990A pdb=" N LEU M 65 " --> pdb=" O GLY M 61 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL M 67 " --> pdb=" O PHE M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.513A pdb=" N PHE N 8 " --> pdb=" O THR N 4 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY N 10 " --> pdb=" O ALA N 6 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA N 11 " --> pdb=" O LYS N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 19 removed outlier: 3.631A pdb=" N GLY N 17 " --> pdb=" O ALA N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 37 removed outlier: 3.569A pdb=" N ILE N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL N 28 " --> pdb=" O GLY N 24 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET N 32 " --> pdb=" O VAL N 28 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY N 35 " --> pdb=" O SER N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 63 removed outlier: 4.087A pdb=" N SER N 48 " --> pdb=" O GLN N 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE N 51 " --> pdb=" O PHE N 47 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY N 53 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 73 removed outlier: 3.511A pdb=" N PHE N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU N 70 " --> pdb=" O MET N 66 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE N 71 " --> pdb=" O VAL N 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 12 removed outlier: 3.697A pdb=" N PHE O 8 " --> pdb=" O THR O 4 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE O 9 " --> pdb=" O ALA O 5 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 31 removed outlier: 3.633A pdb=" N ILE O 25 " --> pdb=" O SER O 21 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR O 27 " --> pdb=" O ALA O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 37 Processing helix chain 'O' and resid 44 through 71 removed outlier: 3.966A pdb=" N SER O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA O 50 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU O 56 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET O 66 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL O 67 " --> pdb=" O PHE O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 14 removed outlier: 3.784A pdb=" N PHE P 8 " --> pdb=" O THR P 4 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE P 9 " --> pdb=" O ALA P 5 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY P 12 " --> pdb=" O PHE P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 26 removed outlier: 3.675A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY P 24 " --> pdb=" O GLY P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 44 through 73 removed outlier: 4.410A pdb=" N SER P 48 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA P 50 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA P 59 " --> pdb=" O ALA P 55 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU P 70 " --> pdb=" O MET P 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE P 71 " --> pdb=" O VAL P 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 15 removed outlier: 3.642A pdb=" N PHE Q 8 " --> pdb=" O THR Q 4 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA Q 11 " --> pdb=" O LYS Q 7 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA Q 13 " --> pdb=" O ILE Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 24 Processing helix chain 'Q' and resid 27 through 37 removed outlier: 3.952A pdb=" N MET Q 32 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE Q 33 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 73 removed outlier: 3.828A pdb=" N SER Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR Q 49 " --> pdb=" O GLN Q 45 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA Q 50 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA Q 68 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU Q 70 " --> pdb=" O MET Q 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.814A pdb=" N PHE R 8 " --> pdb=" O THR R 4 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE R 9 " --> pdb=" O ALA R 5 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY R 10 " --> pdb=" O ALA R 6 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA R 14 " --> pdb=" O GLY R 10 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 37 removed outlier: 4.293A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY R 26 " --> pdb=" O GLY R 22 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 73 removed outlier: 3.663A pdb=" N SER R 48 " --> pdb=" O GLN R 44 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 55 " --> pdb=" O ILE R 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL R 67 " --> pdb=" O PHE R 63 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA R 68 " --> pdb=" O CYS R 64 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE R 73 " --> pdb=" O PHE R 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 3 through 9 removed outlier: 3.631A pdb=" N UNK u 7 " --> pdb=" O UNK u 3 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 35 removed outlier: 4.470A pdb=" N UNK u 20 " --> pdb=" O UNK u 16 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N UNK u 21 " --> pdb=" O UNK u 17 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N UNK u 29 " --> pdb=" O UNK u 25 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.864A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 13 through 19 current: chain 'A' and resid 89 through 90 Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.864A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 60 through 66 current: chain 'E' and resid 38 through 41 removed outlier: 6.538A pdb=" N ARG E 61 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N HIS E 54 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR E 59 " --> pdb=" O HIS E 54 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL E 22 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL E 18 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP E 24 " --> pdb=" O VAL E 16 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 13 through 19 current: chain 'A' and resid 89 through 90 Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.756A pdb=" N VAL A 99 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.470A pdb=" N VAL A 108 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 202 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ASP A 269 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL A 204 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 266 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL A 326 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR A 268 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N GLU A 328 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A 351 " --> pdb=" O ASN A 366 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.665A pdb=" N THR B 91 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.733A pdb=" N SER B 33 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE F 15 " --> pdb=" O GLN F 26 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN F 26 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA F 17 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL F 23 " --> pdb=" O THR F 62 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL F 25 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR F 59 " --> pdb=" O HIS F 54 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N HIS F 54 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG F 61 " --> pdb=" O ALA F 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.557A pdb=" N ARG B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.626A pdb=" N CYS B 201 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL B 232 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TYR B 203 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ALA B 234 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA B 205 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 264 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 322 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 326 through 328 removed outlier: 6.372A pdb=" N ILE B 167 " --> pdb=" O ILE B 327 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.896A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS C 60 " --> pdb=" O PHE C 76 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.903A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 107 through 108 removed outlier: 8.874A pdb=" N ILE C 230 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 322 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 268 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 165 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 169 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 166 " --> pdb=" O GLY C 348 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 14 through 19 removed outlier: 5.523A pdb=" N ILE D 15 " --> pdb=" O GLN D 26 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN D 26 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 17 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR D 59 " --> pdb=" O HIS D 54 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N HIS D 54 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG D 61 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 85 through 88 removed outlier: 3.660A pdb=" N GLN D 114 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 96 through 97 removed outlier: 6.256A pdb=" N MET D 97 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 184 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 96 through 97 removed outlier: 6.256A pdb=" N MET D 97 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL D 184 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL D 309 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU D 255 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA D 311 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE D 257 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 85 through 87 removed outlier: 3.502A pdb=" N ALA E 116 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 96 through 97 removed outlier: 6.133A pdb=" N MET E 97 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLN E 223 " --> pdb=" O MET E 97 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER E 183 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N VAL E 220 " --> pdb=" O SER E 183 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE E 185 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLY E 222 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLY E 187 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 184 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL E 253 " --> pdb=" O THR E 307 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL E 309 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU E 255 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ALA E 311 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE E 257 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE E 154 " --> pdb=" O GLN E 310 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA E 333 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.164A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 85 through 88 removed outlier: 3.591A pdb=" N ALA F 116 " --> pdb=" O ILE F 86 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL F 88 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN F 114 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 96 through 97 removed outlier: 6.471A pdb=" N MET F 97 " --> pdb=" O TYR F 221 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR F 307 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE F 257 " --> pdb=" O VAL F 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 124 through 127 removed outlier: 8.022A pdb=" N ILE G 105 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR G 127 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY G 107 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU G 67 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE G 161 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE G 69 " --> pdb=" O ILE G 161 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ASN G 163 " --> pdb=" O ILE G 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 26 through 28 removed outlier: 6.398A pdb=" N PHE H 20 " --> pdb=" O PHE H 27 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 36 through 40 removed outlier: 3.556A pdb=" N VAL H 36 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL H 38 " --> pdb=" O PHE H 45 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE H 45 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY H 43 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 61 through 66 removed outlier: 3.781A pdb=" N GLY H 61 " --> pdb=" O VAL H 77 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 118 through 121 removed outlier: 5.681A pdb=" N CYS S 118 " --> pdb=" O GLU S 151 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'S' and resid 162 through 164 1333 hydrogen bonds defined for protein. 3864 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: 7.91 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12547 1.34 - 1.46: 7163 1.46 - 1.58: 18696 1.58 - 1.70: 21 1.70 - 1.82: 270 Bond restraints: 38697 Sorted by residual: bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.99e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.68e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.68e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.41e+01 ... (remaining 38692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 52046 4.03 - 8.05: 351 8.05 - 12.08: 37 12.08 - 16.10: 2 16.10 - 20.13: 4 Bond angle restraints: 52440 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.74 20.13 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.98 18.89 1.00e+00 1.00e+00 3.57e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 121.61 18.26 1.00e+00 1.00e+00 3.33e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 119.05 17.78 1.00e+00 1.00e+00 3.16e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 120.85 15.98 1.00e+00 1.00e+00 2.55e+02 ... (remaining 52435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.47: 22818 33.47 - 66.94: 535 66.94 - 100.41: 52 100.41 - 133.88: 1 133.88 - 167.36: 2 Dihedral angle restraints: 23408 sinusoidal: 8551 harmonic: 14857 Sorted by residual: dihedral pdb=" CA GLU H 68 " pdb=" C GLU H 68 " pdb=" N ASP H 69 " pdb=" CA ASP H 69 " ideal model delta harmonic sigma weight residual 180.00 131.14 48.86 0 5.00e+00 4.00e-02 9.55e+01 dihedral pdb=" CA THR 8 6 " pdb=" C THR 8 6 " pdb=" N SER 8 7 " pdb=" CA SER 8 7 " ideal model delta harmonic sigma weight residual -180.00 -131.90 -48.10 0 5.00e+00 4.00e-02 9.25e+01 dihedral pdb=" CA ALA D 280 " pdb=" C ALA D 280 " pdb=" N VAL D 281 " pdb=" CA VAL D 281 " ideal model delta harmonic sigma weight residual -180.00 -131.97 -48.03 0 5.00e+00 4.00e-02 9.23e+01 ... (remaining 23405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5277 0.069 - 0.138: 839 0.138 - 0.206: 117 0.206 - 0.275: 14 0.275 - 0.344: 3 Chirality restraints: 6250 Sorted by residual: chirality pdb=" CA ALA H 49 " pdb=" N ALA H 49 " pdb=" C ALA H 49 " pdb=" CB ALA H 49 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ASN b 86 " pdb=" N ASN b 86 " pdb=" C ASN b 86 " pdb=" CB ASN b 86 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB ILE A 489 " pdb=" CA ILE A 489 " pdb=" CG1 ILE A 489 " pdb=" CG2 ILE A 489 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 6247 not shown) Planarity restraints: 6755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 39 " 0.062 5.00e-02 4.00e+02 9.45e-02 1.43e+01 pdb=" N PRO O 40 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO O 40 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO O 40 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 246 " -0.055 5.00e-02 4.00e+02 8.23e-02 1.08e+01 pdb=" N PRO A 247 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 240 " -0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO C 241 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 241 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 241 " -0.045 5.00e-02 4.00e+02 ... (remaining 6752 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 250 2.53 - 3.13: 25939 3.13 - 3.72: 56290 3.72 - 4.31: 78415 4.31 - 4.90: 129361 Nonbonded interactions: 290255 Sorted by model distance: nonbonded pdb=" NE ARG Q 38 " pdb=" NH1 ARG R 38 " model vdw 1.943 3.200 nonbonded pdb=" O2G ATP A 601 " pdb="MG MG A 602 " model vdw 2.051 2.170 nonbonded pdb=" O1B ADP D 501 " pdb="MG MG D 502 " model vdw 2.087 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 2.089 2.170 nonbonded pdb=" O2B ATP C 601 " pdb="MG MG C 602 " model vdw 2.101 2.170 ... (remaining 290250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 401 or resid 410 through 602)) selection = (chain 'B' and (resid 23 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 602)) selection = (chain 'C' and (resid 23 through 25 or (resid 26 and (name N or name CA or name \ C or name O or name CB )) or resid 27 through 401 or resid 410 through 602)) } ncs_group { reference = (chain 'D' and resid 12 through 476) selection = chain 'E' selection = (chain 'F' and resid 12 through 476) } ncs_group { reference = (chain 'K' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'L' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'M' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = chain 'N' selection = (chain 'O' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'P' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'Q' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) selection = (chain 'R' and (resid 2 through 59 or (resid 60 and (name N or name CA or name C \ or name O or name CB )) or resid 61 through 73)) } 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.640 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 38698 Z= 0.293 Angle : 1.012 20.127 52440 Z= 0.614 Chirality : 0.053 0.344 6250 Planarity : 0.007 0.094 6755 Dihedral : 15.158 167.355 13870 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.37 % Favored : 93.32 % Rotamer: Outliers : 0.46 % Allowed : 10.29 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.69 (0.08), residues: 4942 helix: -4.57 (0.05), residues: 2227 sheet: -2.55 (0.20), residues: 528 loop : -3.04 (0.10), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 159 TYR 0.030 0.002 TYR i 21 PHE 0.029 0.002 PHE A 406 TRP 0.016 0.002 TRP a 68 HIS 0.011 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00610 (38697) covalent geometry : angle 1.01235 (52440) hydrogen bonds : bond 0.32922 ( 1316) hydrogen bonds : angle 10.50080 ( 3864) Misc. bond : bond 0.00940 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 621 time to evaluate : 1.345 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: A 54 GLU cc_start: 0.7551 (pt0) cc_final: 0.7281 (pt0) REVERT: B 390 MET cc_start: 0.8653 (ttp) cc_final: 0.8265 (ttp) REVERT: B 393 GLU cc_start: 0.8120 (mp0) cc_final: 0.7911 (mp0) REVERT: C 140 ILE cc_start: 0.9090 (tp) cc_final: 0.8861 (tp) REVERT: C 226 MET cc_start: 0.7849 (mmm) cc_final: 0.7399 (mmm) REVERT: D 65 MET cc_start: 0.8567 (mmt) cc_final: 0.8297 (mmm) REVERT: E 169 MET cc_start: 0.8062 (mtm) cc_final: 0.7818 (mtp) REVERT: E 446 ILE cc_start: 0.8658 (mm) cc_final: 0.8454 (mt) REVERT: E 471 LYS cc_start: 0.8133 (tttt) cc_final: 0.7632 (ttmt) REVERT: F 170 GLU cc_start: 0.8183 (tp30) cc_final: 0.7829 (tp30) REVERT: G 204 TYR cc_start: 0.7772 (t80) cc_final: 0.7473 (t80) REVERT: G 229 MET cc_start: 0.8418 (ttp) cc_final: 0.8103 (ttp) REVERT: G 242 MET cc_start: 0.8454 (ttm) cc_final: 0.8225 (ttp) REVERT: H 111 ASN cc_start: 0.7377 (t0) cc_final: 0.6992 (t0) REVERT: H 135 ILE cc_start: 0.8080 (pt) cc_final: 0.7486 (mp) REVERT: H 139 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7773 (mt-10) REVERT: H 143 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7516 (mmtm) REVERT: I 21 LYS cc_start: 0.7664 (ttmm) cc_final: 0.7348 (tptm) REVERT: S 6 ARG cc_start: 0.7755 (mmt-90) cc_final: 0.7526 (mmm-85) REVERT: S 109 MET cc_start: 0.8563 (tpt) cc_final: 0.8205 (tpp) REVERT: b 129 ARG cc_start: 0.6771 (ttp80) cc_final: 0.6429 (tmm160) REVERT: b 143 ARG cc_start: 0.7252 (mtt-85) cc_final: 0.6990 (mtp180) REVERT: b 148 TYR cc_start: 0.7121 (t80) cc_final: 0.6792 (t80) REVERT: b 154 ARG cc_start: 0.6301 (mmt90) cc_final: 0.5785 (mmm160) REVERT: c 21 LYS cc_start: 0.6558 (tptt) cc_final: 0.6222 (mmmt) REVERT: c 29 VAL cc_start: 0.6057 (p) cc_final: 0.5761 (t) REVERT: i 27 MET cc_start: 0.6412 (mmp) cc_final: 0.6088 (tpp) REVERT: 8 5 ASP cc_start: 0.6296 (t70) cc_final: 0.6025 (m-30) REVERT: a 24 ILE cc_start: 0.6718 (mt) cc_final: 0.6242 (mt) REVERT: a 41 ARG cc_start: 0.5461 (ptt-90) cc_final: 0.5237 (ptt180) REVERT: a 185 ASN cc_start: 0.2752 (OUTLIER) cc_final: 0.1944 (p0) REVERT: M 60 MET cc_start: 0.6097 (tpp) cc_final: 0.5615 (mmt) REVERT: M 72 LEU cc_start: 0.6189 (tp) cc_final: 0.5772 (mt) REVERT: P 36 TYR cc_start: 0.4907 (t80) cc_final: 0.3503 (t80) REVERT: Q 60 MET cc_start: 0.5537 (mmp) cc_final: 0.5186 (mmt) REVERT: R 49 TYR cc_start: 0.5087 (m-10) cc_final: 0.4551 (m-10) REVERT: R 60 MET cc_start: 0.6294 (tpp) cc_final: 0.5842 (tpp) outliers start: 17 outliers final: 2 residues processed: 635 average time/residue: 0.2391 time to fit residues: 241.4688 Evaluate side-chains 434 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 431 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain a residue 185 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.0040 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 415 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 186 GLN C 190 ASN C 330 GLN C 341 ASN C 441 GLN ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 GLN C 503 ASN D 196 ASN D 479 HIS E 26 GLN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 53 GLN E 429 HIS F 179 HIS F 225 ASN F 363 ASN F 381 GLN J 27 GLN G 17 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN H 51 HIS H 56 GLN H 138 ASN I 17 GLN S 84 ASN b 162 GLN b 163 ASN 8 25 GLN a 47 GLN ** a 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 GLN a 66 GLN a 83 ASN a 90 HIS K 45 GLN ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.155517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118784 restraints weight = 60931.504| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.15 r_work: 0.3088 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 38698 Z= 0.166 Angle : 0.661 12.599 52440 Z= 0.346 Chirality : 0.043 0.163 6250 Planarity : 0.005 0.061 6755 Dihedral : 7.647 174.086 5667 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.44 % Favored : 94.29 % Rotamer: Outliers : 2.15 % Allowed : 14.81 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.46 (0.09), residues: 4942 helix: -3.19 (0.08), residues: 2353 sheet: -1.99 (0.21), residues: 532 loop : -2.75 (0.11), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 146 TYR 0.016 0.001 TYR f 71 PHE 0.020 0.002 PHE R 47 TRP 0.012 0.002 TRP 8 9 HIS 0.006 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00367 (38697) covalent geometry : angle 0.66138 (52440) hydrogen bonds : bond 0.06037 ( 1316) hydrogen bonds : angle 5.77957 ( 3864) Misc. bond : bond 0.00167 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 470 time to evaluate : 1.259 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: B 312 MET cc_start: 0.9102 (mmm) cc_final: 0.8760 (mmp) REVERT: B 436 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7352 (ttm) REVERT: C 281 MET cc_start: 0.9044 (tmm) cc_final: 0.8732 (ttt) REVERT: D 65 MET cc_start: 0.8582 (mmt) cc_final: 0.8351 (mmm) REVERT: D 234 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8446 (m) REVERT: E 169 MET cc_start: 0.8376 (mtm) cc_final: 0.8117 (mtp) REVERT: E 201 GLU cc_start: 0.8298 (tt0) cc_final: 0.8057 (tt0) REVERT: E 395 MET cc_start: 0.6853 (mpp) cc_final: 0.6268 (mpp) REVERT: G 5 ASP cc_start: 0.8194 (t0) cc_final: 0.7979 (m-30) REVERT: G 87 LYS cc_start: 0.8306 (ttpt) cc_final: 0.8100 (mtmt) REVERT: G 242 MET cc_start: 0.8754 (ttm) cc_final: 0.8549 (ttp) REVERT: H 45 PHE cc_start: 0.7353 (m-80) cc_final: 0.7145 (m-80) REVERT: H 111 ASN cc_start: 0.7274 (t0) cc_final: 0.6850 (t0) REVERT: H 128 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7155 (ttm-80) REVERT: H 135 ILE cc_start: 0.7930 (pt) cc_final: 0.7269 (mt) REVERT: H 139 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8029 (mt-10) REVERT: I 21 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7434 (tptm) REVERT: S 6 ARG cc_start: 0.7904 (mmt-90) cc_final: 0.7636 (mmm-85) REVERT: b 148 TYR cc_start: 0.7417 (t80) cc_final: 0.6993 (t80) REVERT: b 154 ARG cc_start: 0.5892 (mmt90) cc_final: 0.5675 (mmm160) REVERT: b 164 MET cc_start: 0.6723 (tmm) cc_final: 0.6468 (tmm) REVERT: b 165 MET cc_start: 0.7021 (mmm) cc_final: 0.6552 (mmm) REVERT: b 176 TRP cc_start: 0.7402 (t60) cc_final: 0.7062 (t-100) REVERT: c 21 LYS cc_start: 0.5897 (tptt) cc_final: 0.5457 (tppt) REVERT: f 66 TYR cc_start: 0.7517 (t80) cc_final: 0.7048 (t80) REVERT: f 78 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6719 (pp) REVERT: i 27 MET cc_start: 0.7082 (mmp) cc_final: 0.6461 (tpp) REVERT: 8 9 TRP cc_start: 0.4043 (OUTLIER) cc_final: 0.3097 (t60) REVERT: a 6 PHE cc_start: 0.2293 (m-10) cc_final: 0.1333 (m-10) REVERT: a 15 MET cc_start: 0.6909 (tpp) cc_final: 0.5988 (mmt) REVERT: a 39 ASN cc_start: 0.7206 (m-40) cc_final: 0.6928 (t0) REVERT: a 63 GLN cc_start: 0.6050 (mt0) cc_final: 0.5795 (mt0) REVERT: a 71 MET cc_start: 0.7958 (ttp) cc_final: 0.7696 (ptt) REVERT: a 168 HIS cc_start: 0.8283 (m-70) cc_final: 0.7819 (t70) REVERT: a 202 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8029 (mm) REVERT: L 32 MET cc_start: 0.5157 (tpp) cc_final: 0.4896 (tpp) REVERT: L 51 ILE cc_start: 0.5552 (OUTLIER) cc_final: 0.5219 (mm) REVERT: M 60 MET cc_start: 0.6019 (tpp) cc_final: 0.5362 (mmt) REVERT: M 72 LEU cc_start: 0.6032 (tp) cc_final: 0.5570 (mt) REVERT: N 2 ILE cc_start: 0.1778 (OUTLIER) cc_final: 0.1482 (tp) REVERT: N 44 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: N 47 PHE cc_start: 0.6223 (t80) cc_final: 0.5960 (t80) REVERT: O 66 MET cc_start: 0.0478 (ttt) cc_final: 0.0085 (mmm) REVERT: P 32 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5320 (ttm) REVERT: Q 45 GLN cc_start: 0.5578 (pm20) cc_final: 0.5111 (pm20) REVERT: Q 60 MET cc_start: 0.5189 (mmp) cc_final: 0.4945 (tpt) REVERT: R 39 ASN cc_start: 0.7280 (OUTLIER) cc_final: 0.6698 (p0) REVERT: R 56 LEU cc_start: 0.7659 (tp) cc_final: 0.7414 (tp) outliers start: 80 outliers final: 38 residues processed: 520 average time/residue: 0.2252 time to fit residues: 191.9056 Evaluate side-chains 480 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 432 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 18 ILE Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain b residue 69 TYR Chi-restraints excluded: chain c residue 17 GLU Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 90 HIS Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain P residue 32 MET Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 39 ASN Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 87 optimal weight: 9.9990 chunk 314 optimal weight: 0.0870 chunk 204 optimal weight: 6.9990 chunk 495 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 290 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN J 27 GLN G 17 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 GLN b 158 HIS b 163 ASN a 61 HIS K 45 GLN L 44 GLN L 45 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.156592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.120557 restraints weight = 60678.097| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.86 r_work: 0.3109 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38698 Z= 0.123 Angle : 0.584 12.382 52440 Z= 0.301 Chirality : 0.042 0.294 6250 Planarity : 0.004 0.057 6755 Dihedral : 7.044 153.164 5665 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.96 % Favored : 94.80 % Rotamer: Outliers : 2.72 % Allowed : 16.27 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.10), residues: 4942 helix: -2.36 (0.09), residues: 2390 sheet: -1.62 (0.22), residues: 520 loop : -2.43 (0.12), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 146 TYR 0.033 0.001 TYR c 18 PHE 0.023 0.001 PHE L 47 TRP 0.012 0.001 TRP 8 9 HIS 0.025 0.001 HIS a 90 Details of bonding type rmsd covalent geometry : bond 0.00270 (38697) covalent geometry : angle 0.58413 (52440) hydrogen bonds : bond 0.04642 ( 1316) hydrogen bonds : angle 5.05262 ( 3864) Misc. bond : bond 0.00219 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 465 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9036 (t) REVERT: B 312 MET cc_start: 0.9090 (mmm) cc_final: 0.8763 (mmp) REVERT: D 234 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8464 (m) REVERT: E 169 MET cc_start: 0.8313 (mtm) cc_final: 0.8012 (mtp) REVERT: E 395 MET cc_start: 0.6883 (mpp) cc_final: 0.6337 (mpp) REVERT: E 471 LYS cc_start: 0.8090 (tttt) cc_final: 0.7531 (ttmt) REVERT: H 128 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7335 (ttm-80) REVERT: H 135 ILE cc_start: 0.7875 (pt) cc_final: 0.7235 (mt) REVERT: H 139 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7976 (mt-10) REVERT: I 14 ARG cc_start: 0.8846 (tpt90) cc_final: 0.8525 (mmm160) REVERT: I 21 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7434 (tptm) REVERT: I 27 LEU cc_start: 0.7782 (mt) cc_final: 0.7520 (mm) REVERT: I 32 LYS cc_start: 0.6927 (tptp) cc_final: 0.6710 (mmtm) REVERT: S 6 ARG cc_start: 0.7809 (mmt-90) cc_final: 0.7561 (mmm-85) REVERT: b 92 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: b 148 TYR cc_start: 0.7547 (t80) cc_final: 0.7082 (t80) REVERT: b 154 ARG cc_start: 0.6108 (mmt90) cc_final: 0.5791 (mmm160) REVERT: b 164 MET cc_start: 0.6719 (tmm) cc_final: 0.6389 (tmm) REVERT: b 176 TRP cc_start: 0.7196 (t60) cc_final: 0.6856 (t-100) REVERT: c 21 LYS cc_start: 0.5903 (tptt) cc_final: 0.5362 (tppt) REVERT: f 78 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6743 (pp) REVERT: i 14 ILE cc_start: 0.6066 (OUTLIER) cc_final: 0.5780 (pt) REVERT: i 27 MET cc_start: 0.6976 (mmp) cc_final: 0.6212 (tpp) REVERT: 8 9 TRP cc_start: 0.4197 (OUTLIER) cc_final: 0.3511 (t60) REVERT: a 6 PHE cc_start: 0.2320 (m-10) cc_final: 0.1493 (m-10) REVERT: a 15 MET cc_start: 0.6868 (tpp) cc_final: 0.5970 (mmt) REVERT: a 56 GLN cc_start: 0.6531 (mp-120) cc_final: 0.6066 (mp10) REVERT: a 58 MET cc_start: 0.5099 (tmm) cc_final: 0.4684 (tmm) REVERT: a 63 GLN cc_start: 0.6631 (mt0) cc_final: 0.6154 (mp10) REVERT: a 128 PHE cc_start: 0.6039 (m-80) cc_final: 0.5704 (m-80) REVERT: a 168 HIS cc_start: 0.8192 (m-70) cc_final: 0.7887 (t70) REVERT: a 173 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7539 (tp) REVERT: a 202 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7932 (mt) REVERT: L 32 MET cc_start: 0.5068 (tpp) cc_final: 0.4819 (tpp) REVERT: M 60 MET cc_start: 0.6477 (tpp) cc_final: 0.5659 (mmt) REVERT: M 72 LEU cc_start: 0.5851 (tp) cc_final: 0.5353 (mt) REVERT: N 2 ILE cc_start: 0.1807 (OUTLIER) cc_final: 0.1409 (tp) REVERT: N 44 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: N 47 PHE cc_start: 0.6342 (t80) cc_final: 0.6041 (t80) REVERT: O 25 ILE cc_start: 0.4144 (OUTLIER) cc_final: 0.3803 (tp) REVERT: P 32 MET cc_start: 0.6057 (OUTLIER) cc_final: 0.5510 (ttm) REVERT: R 39 ASN cc_start: 0.7199 (t0) cc_final: 0.6787 (p0) outliers start: 101 outliers final: 43 residues processed: 541 average time/residue: 0.2206 time to fit residues: 196.1180 Evaluate side-chains 470 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 415 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain S residue 98 THR Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 92 GLN Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain i residue 14 ILE Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain O residue 25 ILE Chi-restraints excluded: chain P residue 32 MET Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain R residue 67 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 214 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 442 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 254 optimal weight: 0.9990 chunk 294 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 297 optimal weight: 0.0010 chunk 451 optimal weight: 0.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 200 HIS G 17 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 GLN b 163 ASN 8 25 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.156712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123097 restraints weight = 60665.028| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.75 r_work: 0.3122 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38698 Z= 0.116 Angle : 0.567 11.551 52440 Z= 0.289 Chirality : 0.042 0.248 6250 Planarity : 0.004 0.054 6755 Dihedral : 6.548 124.220 5665 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.96 % Favored : 94.82 % Rotamer: Outliers : 2.85 % Allowed : 17.88 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.11), residues: 4942 helix: -1.74 (0.10), residues: 2383 sheet: -1.48 (0.22), residues: 520 loop : -2.23 (0.12), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 146 TYR 0.047 0.001 TYR c 18 PHE 0.032 0.001 PHE a 6 TRP 0.016 0.001 TRP 8 9 HIS 0.006 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00260 (38697) covalent geometry : angle 0.56657 (52440) hydrogen bonds : bond 0.03983 ( 1316) hydrogen bonds : angle 4.67812 ( 3864) Misc. bond : bond 0.00216 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 455 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9039 (t) REVERT: B 312 MET cc_start: 0.9066 (mmm) cc_final: 0.8734 (mmp) REVERT: B 390 MET cc_start: 0.8847 (ttp) cc_final: 0.8455 (ttp) REVERT: D 234 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8483 (m) REVERT: D 294 MET cc_start: 0.8702 (tmm) cc_final: 0.8332 (tmm) REVERT: D 433 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8314 (tt) REVERT: D 479 HIS cc_start: 0.7264 (m-70) cc_final: 0.6953 (m90) REVERT: E 169 MET cc_start: 0.8346 (mtm) cc_final: 0.7897 (mtp) REVERT: E 395 MET cc_start: 0.6867 (mpp) cc_final: 0.6392 (mpp) REVERT: E 471 LYS cc_start: 0.8046 (tttt) cc_final: 0.7498 (ttmt) REVERT: G 52 TYR cc_start: 0.7193 (m-80) cc_final: 0.6843 (m-80) REVERT: G 193 TYR cc_start: 0.6706 (m-80) cc_final: 0.6474 (m-80) REVERT: H 47 ILE cc_start: 0.7341 (mp) cc_final: 0.6940 (mt) REVERT: H 128 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.7403 (ttm-80) REVERT: H 135 ILE cc_start: 0.7801 (pt) cc_final: 0.7112 (mt) REVERT: H 139 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7762 (mt-10) REVERT: I 21 LYS cc_start: 0.7841 (ttmm) cc_final: 0.7406 (tptm) REVERT: S 6 ARG cc_start: 0.7832 (mmt-90) cc_final: 0.7552 (mmm-85) REVERT: b 92 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7567 (pm20) REVERT: b 129 ARG cc_start: 0.7712 (ttp-170) cc_final: 0.7341 (tpt90) REVERT: b 148 TYR cc_start: 0.7083 (t80) cc_final: 0.6655 (t80) REVERT: b 154 ARG cc_start: 0.6058 (mmt90) cc_final: 0.5698 (mmm160) REVERT: b 164 MET cc_start: 0.6873 (tmm) cc_final: 0.6633 (tmm) REVERT: f 78 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6118 (pt) REVERT: i 14 ILE cc_start: 0.6346 (OUTLIER) cc_final: 0.5529 (pt) REVERT: i 27 MET cc_start: 0.6898 (mmp) cc_final: 0.6156 (tpp) REVERT: 8 9 TRP cc_start: 0.4218 (OUTLIER) cc_final: 0.3409 (t60) REVERT: 8 31 TYR cc_start: 0.6252 (m-80) cc_final: 0.4542 (m-80) REVERT: a 15 MET cc_start: 0.6724 (tpp) cc_final: 0.5619 (mmt) REVERT: a 63 GLN cc_start: 0.6525 (mt0) cc_final: 0.6223 (pt0) REVERT: a 71 MET cc_start: 0.7088 (ptt) cc_final: 0.6521 (ppp) REVERT: a 168 HIS cc_start: 0.8218 (m-70) cc_final: 0.7842 (t70) REVERT: a 173 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7533 (tp) REVERT: M 60 MET cc_start: 0.6513 (tpp) cc_final: 0.6029 (mmt) REVERT: M 72 LEU cc_start: 0.5875 (tp) cc_final: 0.5605 (mt) REVERT: N 2 ILE cc_start: 0.2080 (OUTLIER) cc_final: 0.1722 (tp) REVERT: N 44 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7275 (tm-30) REVERT: N 47 PHE cc_start: 0.6452 (t80) cc_final: 0.6159 (t80) REVERT: N 63 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6655 (p90) REVERT: P 32 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5382 (ttm) REVERT: Q 36 TYR cc_start: 0.6065 (t80) cc_final: 0.5681 (t80) REVERT: Q 66 MET cc_start: 0.5232 (mmt) cc_final: 0.4802 (mtt) REVERT: R 39 ASN cc_start: 0.7148 (t0) cc_final: 0.6723 (p0) REVERT: R 72 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7091 (mm) outliers start: 106 outliers final: 60 residues processed: 537 average time/residue: 0.2175 time to fit residues: 193.3189 Evaluate side-chains 487 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 415 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain S residue 98 THR Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 92 GLN Chi-restraints excluded: chain b residue 163 ASN Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 59 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain i residue 14 ILE Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 90 HIS Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain P residue 32 MET Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 435 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 405 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 442 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 404 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 498 optimal weight: 20.0000 chunk 183 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 ASN G 17 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 GLN S 44 GLN b 128 GLN a 56 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.155558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.120270 restraints weight = 60769.926| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.11 r_work: 0.3088 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38698 Z= 0.143 Angle : 0.580 11.933 52440 Z= 0.295 Chirality : 0.043 0.279 6250 Planarity : 0.004 0.052 6755 Dihedral : 6.404 118.008 5665 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.50 % Rotamer: Outliers : 2.83 % Allowed : 18.91 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.11), residues: 4942 helix: -1.39 (0.10), residues: 2370 sheet: -1.44 (0.22), residues: 530 loop : -2.17 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 38 TYR 0.046 0.001 TYR c 18 PHE 0.024 0.001 PHE S 141 TRP 0.017 0.002 TRP 8 9 HIS 0.006 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00334 (38697) covalent geometry : angle 0.58025 (52440) hydrogen bonds : bond 0.03967 ( 1316) hydrogen bonds : angle 4.59459 ( 3864) Misc. bond : bond 0.00217 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 426 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9372 (OUTLIER) cc_final: 0.9062 (t) REVERT: A 197 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8535 (ttmm) REVERT: B 312 MET cc_start: 0.9098 (mmm) cc_final: 0.8774 (mmp) REVERT: B 390 MET cc_start: 0.8859 (ttp) cc_final: 0.8485 (ttp) REVERT: B 436 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7444 (ttm) REVERT: D 234 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8526 (m) REVERT: D 254 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8938 (mp) REVERT: D 433 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8331 (tt) REVERT: E 169 MET cc_start: 0.8418 (mtm) cc_final: 0.8013 (mtp) REVERT: E 395 MET cc_start: 0.6730 (mpp) cc_final: 0.6381 (mpp) REVERT: F 360 MET cc_start: 0.8303 (tpt) cc_final: 0.7727 (tpt) REVERT: G 52 TYR cc_start: 0.7240 (m-80) cc_final: 0.6916 (m-80) REVERT: H 128 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7350 (ttm-80) REVERT: H 135 ILE cc_start: 0.7695 (pt) cc_final: 0.7325 (mp) REVERT: H 139 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7778 (mt-10) REVERT: I 21 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7413 (tptm) REVERT: I 32 LYS cc_start: 0.7267 (tptp) cc_final: 0.6981 (mmtm) REVERT: I 34 ASN cc_start: 0.5673 (m-40) cc_final: 0.5136 (m-40) REVERT: S 6 ARG cc_start: 0.7869 (mmt-90) cc_final: 0.7564 (mmm-85) REVERT: b 92 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7446 (pm20) REVERT: b 129 ARG cc_start: 0.7595 (ttp-170) cc_final: 0.7244 (tpt90) REVERT: b 148 TYR cc_start: 0.7101 (t80) cc_final: 0.6648 (t80) REVERT: b 154 ARG cc_start: 0.6051 (mmt90) cc_final: 0.5532 (mmm160) REVERT: b 165 MET cc_start: 0.6902 (mmm) cc_final: 0.6340 (mmm) REVERT: c 14 LYS cc_start: 0.6456 (mttt) cc_final: 0.5980 (mtmm) REVERT: i 27 MET cc_start: 0.6873 (mmp) cc_final: 0.6074 (tpp) REVERT: 8 9 TRP cc_start: 0.4351 (OUTLIER) cc_final: 0.3449 (t60) REVERT: 8 31 TYR cc_start: 0.6323 (m-80) cc_final: 0.4790 (m-80) REVERT: a 15 MET cc_start: 0.6411 (tpp) cc_final: 0.5914 (mmt) REVERT: a 56 GLN cc_start: 0.6525 (mp-120) cc_final: 0.6254 (mp10) REVERT: a 63 GLN cc_start: 0.6568 (mt0) cc_final: 0.6136 (pt0) REVERT: a 71 MET cc_start: 0.7061 (ptt) cc_final: 0.6412 (ppp) REVERT: a 128 PHE cc_start: 0.5919 (m-80) cc_final: 0.5517 (m-80) REVERT: a 168 HIS cc_start: 0.8233 (m-70) cc_final: 0.7933 (t70) REVERT: M 60 MET cc_start: 0.6616 (tpp) cc_final: 0.6152 (mmt) REVERT: M 72 LEU cc_start: 0.5612 (tp) cc_final: 0.5211 (mt) REVERT: N 2 ILE cc_start: 0.1994 (OUTLIER) cc_final: 0.1639 (tp) REVERT: N 44 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7287 (tm-30) REVERT: N 63 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6361 (p90) REVERT: P 32 MET cc_start: 0.6103 (OUTLIER) cc_final: 0.5712 (ttm) REVERT: R 39 ASN cc_start: 0.7246 (t0) cc_final: 0.6645 (p0) REVERT: R 72 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6936 (mt) outliers start: 105 outliers final: 70 residues processed: 506 average time/residue: 0.2145 time to fit residues: 180.3879 Evaluate side-chains 496 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 414 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain S residue 98 THR Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 69 TYR Chi-restraints excluded: chain b residue 92 GLN Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 59 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 90 HIS Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain P residue 32 MET Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 35 optimal weight: 0.0060 chunk 432 optimal weight: 10.0000 chunk 275 optimal weight: 0.0010 chunk 273 optimal weight: 2.9990 chunk 493 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 448 optimal weight: 0.8980 chunk 338 optimal weight: 5.9990 chunk 503 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 overall best weight: 1.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS G 17 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 146 GLN b 163 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119087 restraints weight = 60662.687| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.96 r_work: 0.3108 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38698 Z= 0.125 Angle : 0.564 11.515 52440 Z= 0.286 Chirality : 0.042 0.283 6250 Planarity : 0.004 0.052 6755 Dihedral : 6.220 112.294 5665 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.96 % Favored : 94.90 % Rotamer: Outliers : 3.23 % Allowed : 19.15 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.11), residues: 4942 helix: -1.06 (0.10), residues: 2370 sheet: -1.33 (0.22), residues: 530 loop : -2.05 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 22 TYR 0.043 0.001 TYR c 18 PHE 0.035 0.001 PHE i 18 TRP 0.018 0.001 TRP 8 9 HIS 0.006 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00290 (38697) covalent geometry : angle 0.56354 (52440) hydrogen bonds : bond 0.03706 ( 1316) hydrogen bonds : angle 4.45292 ( 3864) Misc. bond : bond 0.00245 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 436 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.9122 (t) REVERT: B 312 MET cc_start: 0.9071 (mmm) cc_final: 0.8730 (mmp) REVERT: B 390 MET cc_start: 0.8808 (ttp) cc_final: 0.8447 (ttp) REVERT: B 436 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7460 (ttm) REVERT: D 234 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8486 (m) REVERT: D 254 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8886 (mp) REVERT: D 433 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8299 (tt) REVERT: D 479 HIS cc_start: 0.7204 (m-70) cc_final: 0.6900 (m90) REVERT: E 169 MET cc_start: 0.8386 (mtm) cc_final: 0.7943 (mtp) REVERT: F 360 MET cc_start: 0.8259 (tpt) cc_final: 0.7658 (tpt) REVERT: H 128 ARG cc_start: 0.7758 (ttm-80) cc_final: 0.7250 (ttm-80) REVERT: H 135 ILE cc_start: 0.7702 (pt) cc_final: 0.7330 (mp) REVERT: H 139 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7587 (mt-10) REVERT: I 21 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7418 (tptm) REVERT: I 32 LYS cc_start: 0.7143 (tptp) cc_final: 0.6908 (mmtm) REVERT: I 34 ASN cc_start: 0.5754 (m-40) cc_final: 0.5181 (m-40) REVERT: S 6 ARG cc_start: 0.7840 (mmt-90) cc_final: 0.7548 (mmm-85) REVERT: b 129 ARG cc_start: 0.7588 (ttp-170) cc_final: 0.7198 (tpt170) REVERT: b 148 TYR cc_start: 0.6899 (t80) cc_final: 0.6365 (t80) REVERT: b 154 ARG cc_start: 0.6114 (mmt90) cc_final: 0.5586 (mmm160) REVERT: c 14 LYS cc_start: 0.6558 (mttt) cc_final: 0.6108 (mttp) REVERT: i 27 MET cc_start: 0.6908 (mmp) cc_final: 0.6087 (tpp) REVERT: 8 9 TRP cc_start: 0.4841 (OUTLIER) cc_final: 0.3259 (t60) REVERT: 8 18 MET cc_start: 0.7871 (mpp) cc_final: 0.6974 (tpp) REVERT: 8 31 TYR cc_start: 0.6403 (m-80) cc_final: 0.5989 (m-80) REVERT: a 14 MET cc_start: 0.7840 (pmm) cc_final: 0.7468 (tpp) REVERT: a 15 MET cc_start: 0.6317 (tpp) cc_final: 0.5404 (mmt) REVERT: a 68 TRP cc_start: 0.7899 (m100) cc_final: 0.7617 (m100) REVERT: a 71 MET cc_start: 0.7040 (ptt) cc_final: 0.6445 (ppp) REVERT: a 168 HIS cc_start: 0.8203 (m-70) cc_final: 0.7885 (t70) REVERT: a 173 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7735 (tp) REVERT: M 60 MET cc_start: 0.6617 (tpp) cc_final: 0.6208 (mmt) REVERT: M 66 MET cc_start: 0.6149 (ppp) cc_final: 0.5827 (ppp) REVERT: N 2 ILE cc_start: 0.2026 (OUTLIER) cc_final: 0.1663 (tp) REVERT: N 44 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7216 (tm-30) REVERT: N 63 PHE cc_start: 0.7070 (OUTLIER) cc_final: 0.6107 (p90) REVERT: P 32 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5983 (ttm) REVERT: R 39 ASN cc_start: 0.7120 (t0) cc_final: 0.6475 (p0) REVERT: R 49 TYR cc_start: 0.6428 (m-80) cc_final: 0.6133 (m-80) REVERT: R 72 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7039 (mt) outliers start: 120 outliers final: 79 residues processed: 528 average time/residue: 0.2104 time to fit residues: 186.2395 Evaluate side-chains 500 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 410 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain S residue 98 THR Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 69 TYR Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 59 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 90 HIS Chi-restraints excluded: chain a residue 99 SER Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain a residue 214 PHE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain P residue 32 MET Chi-restraints excluded: chain P residue 44 GLN Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 31 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 379 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 287 optimal weight: 0.0980 chunk 399 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 HIS ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 163 ASN a 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.154056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118899 restraints weight = 60777.281| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.38 r_work: 0.3070 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 38698 Z= 0.182 Angle : 0.618 13.503 52440 Z= 0.312 Chirality : 0.044 0.252 6250 Planarity : 0.004 0.052 6755 Dihedral : 6.333 101.606 5665 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.79 % Rotamer: Outliers : 3.29 % Allowed : 19.66 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.11), residues: 4942 helix: -0.98 (0.10), residues: 2373 sheet: -1.43 (0.22), residues: 527 loop : -2.09 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 146 TYR 0.044 0.002 TYR c 18 PHE 0.023 0.002 PHE S 141 TRP 0.018 0.001 TRP 8 9 HIS 0.008 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00438 (38697) covalent geometry : angle 0.61812 (52440) hydrogen bonds : bond 0.04041 ( 1316) hydrogen bonds : angle 4.56612 ( 3864) Misc. bond : bond 0.00266 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 409 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.9098 (t) REVERT: B 312 MET cc_start: 0.9111 (mmm) cc_final: 0.8785 (mmp) REVERT: B 390 MET cc_start: 0.8832 (ttp) cc_final: 0.8461 (ttp) REVERT: D 234 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8546 (m) REVERT: D 254 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8901 (mp) REVERT: D 433 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8311 (tt) REVERT: E 169 MET cc_start: 0.8398 (mtm) cc_final: 0.7969 (mtp) REVERT: F 145 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9001 (mp) REVERT: F 170 GLU cc_start: 0.8590 (tp30) cc_final: 0.8151 (tp30) REVERT: F 360 MET cc_start: 0.8278 (tpt) cc_final: 0.7522 (tpt) REVERT: G 161 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.7023 (mt) REVERT: H 128 ARG cc_start: 0.7706 (ttm-80) cc_final: 0.7206 (ttm-80) REVERT: H 135 ILE cc_start: 0.7742 (pt) cc_final: 0.7420 (mp) REVERT: H 139 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7641 (mt-10) REVERT: I 21 LYS cc_start: 0.7845 (ttmm) cc_final: 0.7327 (tptm) REVERT: I 34 ASN cc_start: 0.5836 (m-40) cc_final: 0.5243 (m-40) REVERT: S 6 ARG cc_start: 0.7890 (mmt-90) cc_final: 0.7570 (mmm-85) REVERT: b 129 ARG cc_start: 0.7617 (ttp-170) cc_final: 0.7258 (tpt170) REVERT: b 148 TYR cc_start: 0.7337 (t80) cc_final: 0.6775 (t80) REVERT: b 154 ARG cc_start: 0.6038 (mmt90) cc_final: 0.5513 (mmm160) REVERT: c 14 LYS cc_start: 0.6536 (mttt) cc_final: 0.6044 (mtmm) REVERT: i 27 MET cc_start: 0.6956 (mmp) cc_final: 0.6179 (tpp) REVERT: 8 9 TRP cc_start: 0.4747 (OUTLIER) cc_final: 0.3191 (t60) REVERT: 8 18 MET cc_start: 0.7831 (mpp) cc_final: 0.6926 (tpp) REVERT: 8 31 TYR cc_start: 0.6443 (m-80) cc_final: 0.5942 (m-80) REVERT: a 14 MET cc_start: 0.7922 (pmm) cc_final: 0.7427 (tpp) REVERT: a 15 MET cc_start: 0.6250 (tpp) cc_final: 0.5147 (mmt) REVERT: a 56 GLN cc_start: 0.6362 (mp-120) cc_final: 0.6052 (tt0) REVERT: a 71 MET cc_start: 0.7121 (ptt) cc_final: 0.6339 (ppp) REVERT: a 73 MET cc_start: 0.5204 (mtm) cc_final: 0.4890 (mtm) REVERT: a 168 HIS cc_start: 0.8244 (m-70) cc_final: 0.7910 (t70) REVERT: a 173 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7863 (tp) REVERT: K 32 MET cc_start: 0.7716 (tmm) cc_final: 0.7447 (tmm) REVERT: M 60 MET cc_start: 0.7008 (tpp) cc_final: 0.6379 (mmt) REVERT: M 66 MET cc_start: 0.6269 (ppp) cc_final: 0.5907 (ppp) REVERT: M 69 PHE cc_start: 0.6124 (OUTLIER) cc_final: 0.5284 (m-80) REVERT: M 72 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5308 (pp) REVERT: N 2 ILE cc_start: 0.1861 (OUTLIER) cc_final: 0.1543 (tp) REVERT: N 44 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7365 (tm-30) REVERT: N 63 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6005 (p90) REVERT: O 62 LEU cc_start: 0.3956 (OUTLIER) cc_final: 0.3491 (tt) REVERT: Q 32 MET cc_start: 0.7100 (mmm) cc_final: 0.6760 (mmm) REVERT: R 39 ASN cc_start: 0.7162 (t0) cc_final: 0.6375 (p0) REVERT: R 72 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6994 (mt) outliers start: 122 outliers final: 95 residues processed: 501 average time/residue: 0.2129 time to fit residues: 178.5027 Evaluate side-chains 505 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 396 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain S residue 98 THR Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 163 ASN Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 59 LEU Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 90 HIS Chi-restraints excluded: chain a residue 99 SER Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 187 MET Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain a residue 214 PHE Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 44 GLN Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 72 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.0770 chunk 332 optimal weight: 0.9980 chunk 412 optimal weight: 30.0000 chunk 276 optimal weight: 2.9990 chunk 483 optimal weight: 20.0000 chunk 446 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 450 optimal weight: 10.0000 chunk 428 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.155709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121125 restraints weight = 60328.788| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.78 r_work: 0.3118 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 38698 Z= 0.118 Angle : 0.575 13.893 52440 Z= 0.290 Chirality : 0.042 0.202 6250 Planarity : 0.004 0.053 6755 Dihedral : 6.142 97.298 5665 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 2.99 % Allowed : 20.25 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.12), residues: 4942 helix: -0.74 (0.11), residues: 2364 sheet: -1.27 (0.22), residues: 529 loop : -1.96 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 38 TYR 0.044 0.001 TYR c 18 PHE 0.030 0.001 PHE f 69 TRP 0.019 0.001 TRP 8 9 HIS 0.003 0.000 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00273 (38697) covalent geometry : angle 0.57495 (52440) hydrogen bonds : bond 0.03630 ( 1316) hydrogen bonds : angle 4.39712 ( 3864) Misc. bond : bond 0.00270 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 419 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9145 (t) REVERT: B 312 MET cc_start: 0.9084 (mmm) cc_final: 0.8739 (mmp) REVERT: B 390 MET cc_start: 0.8794 (ttp) cc_final: 0.8475 (ttp) REVERT: D 234 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8480 (m) REVERT: D 433 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8240 (tt) REVERT: D 479 HIS cc_start: 0.7300 (m-70) cc_final: 0.6891 (m90) REVERT: E 169 MET cc_start: 0.8336 (mtm) cc_final: 0.7877 (mtp) REVERT: E 471 LYS cc_start: 0.8023 (tttt) cc_final: 0.7538 (ttmt) REVERT: F 145 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9022 (mp) REVERT: F 170 GLU cc_start: 0.8518 (tp30) cc_final: 0.8135 (tp30) REVERT: F 360 MET cc_start: 0.8244 (tpt) cc_final: 0.7523 (tpt) REVERT: G 61 GLU cc_start: 0.4282 (OUTLIER) cc_final: 0.3726 (pp20) REVERT: H 128 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7231 (ttm-80) REVERT: H 135 ILE cc_start: 0.7830 (pt) cc_final: 0.7447 (mp) REVERT: H 139 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7630 (mt-10) REVERT: I 21 LYS cc_start: 0.7818 (ttmm) cc_final: 0.7400 (tptm) REVERT: I 32 LYS cc_start: 0.7143 (tptp) cc_final: 0.6932 (mmtm) REVERT: I 34 ASN cc_start: 0.5820 (m-40) cc_final: 0.5247 (m-40) REVERT: S 6 ARG cc_start: 0.7828 (mmt-90) cc_final: 0.7600 (mmm-85) REVERT: b 129 ARG cc_start: 0.7570 (ttp-170) cc_final: 0.7219 (tpt170) REVERT: b 148 TYR cc_start: 0.7349 (t80) cc_final: 0.6747 (t80) REVERT: b 154 ARG cc_start: 0.6361 (mmt90) cc_final: 0.5697 (mmm160) REVERT: c 14 LYS cc_start: 0.6557 (mttt) cc_final: 0.6029 (mtmm) REVERT: i 27 MET cc_start: 0.6960 (mmp) cc_final: 0.6129 (tpp) REVERT: 8 9 TRP cc_start: 0.4671 (OUTLIER) cc_final: 0.3113 (t60) REVERT: 8 18 MET cc_start: 0.7799 (mpp) cc_final: 0.6927 (tpp) REVERT: 8 31 TYR cc_start: 0.6393 (m-80) cc_final: 0.5911 (m-80) REVERT: a 15 MET cc_start: 0.6011 (tpp) cc_final: 0.5436 (mmt) REVERT: a 56 GLN cc_start: 0.6631 (mp-120) cc_final: 0.6278 (tt0) REVERT: a 71 MET cc_start: 0.6877 (ptt) cc_final: 0.6394 (ppp) REVERT: a 168 HIS cc_start: 0.8291 (m-70) cc_final: 0.7966 (t70) REVERT: a 173 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7765 (tp) REVERT: K 32 MET cc_start: 0.7924 (tmm) cc_final: 0.7679 (tmm) REVERT: K 51 ILE cc_start: 0.7249 (mm) cc_final: 0.6995 (mm) REVERT: M 60 MET cc_start: 0.7045 (tpp) cc_final: 0.6323 (mmt) REVERT: M 66 MET cc_start: 0.6581 (ppp) cc_final: 0.6198 (ppp) REVERT: M 69 PHE cc_start: 0.6196 (OUTLIER) cc_final: 0.5329 (m-80) REVERT: M 72 LEU cc_start: 0.5278 (OUTLIER) cc_final: 0.4944 (pp) REVERT: N 2 ILE cc_start: 0.1833 (OUTLIER) cc_final: 0.1509 (tp) REVERT: N 44 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7438 (tm-30) REVERT: N 63 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6024 (p90) REVERT: O 32 MET cc_start: 0.7160 (tmm) cc_final: 0.6887 (tmm) REVERT: O 60 MET cc_start: 0.5888 (tpt) cc_final: 0.5637 (tpt) REVERT: O 62 LEU cc_start: 0.3954 (OUTLIER) cc_final: 0.3479 (tt) REVERT: R 39 ASN cc_start: 0.7088 (t0) cc_final: 0.6370 (p0) REVERT: R 72 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6978 (mt) outliers start: 111 outliers final: 77 residues processed: 503 average time/residue: 0.2206 time to fit residues: 185.5391 Evaluate side-chains 494 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 404 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 196 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain S residue 98 THR Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain 8 residue 9 TRP Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 90 HIS Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 44 GLN Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 72 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 46 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 499 optimal weight: 7.9990 chunk 316 optimal weight: 1.9990 chunk 377 optimal weight: 20.0000 chunk 252 optimal weight: 0.7980 chunk 395 optimal weight: 40.0000 chunk 283 optimal weight: 1.9990 chunk 309 optimal weight: 8.9990 chunk 293 optimal weight: 0.9980 chunk 471 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.153855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117461 restraints weight = 60432.819| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.03 r_work: 0.3077 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38698 Z= 0.178 Angle : 0.617 14.066 52440 Z= 0.311 Chirality : 0.044 0.185 6250 Planarity : 0.004 0.053 6755 Dihedral : 6.266 94.490 5665 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.79 % Rotamer: Outliers : 3.02 % Allowed : 20.31 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.12), residues: 4942 helix: -0.77 (0.11), residues: 2368 sheet: -1.42 (0.22), residues: 535 loop : -2.02 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 38 TYR 0.044 0.002 TYR c 18 PHE 0.023 0.002 PHE O 47 TRP 0.018 0.001 TRP 8 9 HIS 0.003 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00427 (38697) covalent geometry : angle 0.61740 (52440) hydrogen bonds : bond 0.04014 ( 1316) hydrogen bonds : angle 4.52340 ( 3864) Misc. bond : bond 0.00304 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 406 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 VAL cc_start: 0.9412 (OUTLIER) cc_final: 0.9155 (t) REVERT: B 312 MET cc_start: 0.9094 (mmm) cc_final: 0.8758 (mmp) REVERT: B 390 MET cc_start: 0.8793 (ttp) cc_final: 0.8442 (ttp) REVERT: D 234 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8534 (m) REVERT: D 433 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8341 (tt) REVERT: E 169 MET cc_start: 0.8384 (mtm) cc_final: 0.7938 (mtp) REVERT: F 170 GLU cc_start: 0.8499 (tp30) cc_final: 0.8241 (tp30) REVERT: J 24 LYS cc_start: 0.8908 (mttm) cc_final: 0.8698 (mttm) REVERT: G 61 GLU cc_start: 0.4439 (OUTLIER) cc_final: 0.3871 (pp20) REVERT: G 95 ASN cc_start: 0.7654 (t0) cc_final: 0.7034 (t0) REVERT: G 140 ASP cc_start: 0.8211 (m-30) cc_final: 0.7814 (m-30) REVERT: G 161 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.7009 (mt) REVERT: H 128 ARG cc_start: 0.7685 (ttm-80) cc_final: 0.7231 (ttm-80) REVERT: H 135 ILE cc_start: 0.7794 (pt) cc_final: 0.7471 (mp) REVERT: H 139 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7662 (mt-10) REVERT: I 21 LYS cc_start: 0.7828 (ttmm) cc_final: 0.7387 (tptm) REVERT: I 34 ASN cc_start: 0.5886 (m-40) cc_final: 0.5259 (m-40) REVERT: b 129 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7415 (tpt170) REVERT: b 148 TYR cc_start: 0.7346 (t80) cc_final: 0.6775 (t80) REVERT: b 154 ARG cc_start: 0.6356 (mmt90) cc_final: 0.5681 (mmm160) REVERT: c 14 LYS cc_start: 0.6383 (mttt) cc_final: 0.5876 (mtmm) REVERT: i 17 TYR cc_start: 0.7715 (m-80) cc_final: 0.7319 (m-80) REVERT: i 27 MET cc_start: 0.7022 (mmp) cc_final: 0.6226 (tpp) REVERT: a 14 MET cc_start: 0.7706 (pmm) cc_final: 0.7306 (tpt) REVERT: a 15 MET cc_start: 0.6069 (tpp) cc_final: 0.5199 (mmt) REVERT: a 56 GLN cc_start: 0.6762 (mp-120) cc_final: 0.6297 (tt0) REVERT: a 71 MET cc_start: 0.6956 (ptt) cc_final: 0.6230 (ppp) REVERT: a 117 PHE cc_start: 0.5479 (m-10) cc_final: 0.5278 (m-80) REVERT: a 168 HIS cc_start: 0.8350 (m-70) cc_final: 0.7927 (t70) REVERT: a 173 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7863 (tp) REVERT: K 32 MET cc_start: 0.7912 (tmm) cc_final: 0.7613 (tmm) REVERT: K 36 TYR cc_start: 0.6866 (t80) cc_final: 0.6360 (t80) REVERT: K 51 ILE cc_start: 0.7238 (mm) cc_final: 0.7024 (mm) REVERT: M 42 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6421 (pt) REVERT: M 60 MET cc_start: 0.7045 (tpp) cc_final: 0.6416 (mmt) REVERT: M 66 MET cc_start: 0.6212 (ppp) cc_final: 0.5852 (ppp) REVERT: M 69 PHE cc_start: 0.6186 (OUTLIER) cc_final: 0.5348 (m-80) REVERT: M 72 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5501 (pp) REVERT: N 2 ILE cc_start: 0.1857 (OUTLIER) cc_final: 0.1542 (tp) REVERT: N 44 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7406 (tm-30) REVERT: N 63 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.5951 (p90) REVERT: O 32 MET cc_start: 0.7148 (tmm) cc_final: 0.6887 (tmm) REVERT: O 62 LEU cc_start: 0.3835 (OUTLIER) cc_final: 0.3405 (tt) REVERT: P 31 SER cc_start: 0.7860 (m) cc_final: 0.7524 (p) REVERT: P 52 LEU cc_start: 0.7484 (tt) cc_final: 0.6586 (mm) REVERT: R 39 ASN cc_start: 0.7100 (t0) cc_final: 0.6337 (p0) REVERT: R 72 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7024 (mt) outliers start: 112 outliers final: 84 residues processed: 494 average time/residue: 0.2173 time to fit residues: 179.2143 Evaluate side-chains 499 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 402 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 271 SER Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain G residue 229 MET Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 136 GLU Chi-restraints excluded: chain S residue 98 THR Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 112 HIS Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 163 ASN Chi-restraints excluded: chain c residue 9 LYS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 60 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 154 VAL Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 44 GLN Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 217 optimal weight: 0.9980 chunk 408 optimal weight: 20.0000 chunk 453 optimal weight: 8.9990 chunk 359 optimal weight: 5.9990 chunk 332 optimal weight: 2.9990 chunk 439 optimal weight: 0.0870 chunk 444 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 261 optimal weight: 0.1980 chunk 79 optimal weight: 0.8980 chunk 221 optimal weight: 0.0970 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 HIS D 479 HIS ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 10 GLN b 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.157546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120273 restraints weight = 59618.051| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.91 r_work: 0.3138 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 38698 Z= 0.098 Angle : 0.569 14.705 52440 Z= 0.285 Chirality : 0.042 0.203 6250 Planarity : 0.004 0.055 6755 Dihedral : 5.930 89.409 5665 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.13 % Favored : 95.73 % Rotamer: Outliers : 1.97 % Allowed : 21.55 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.12), residues: 4942 helix: -0.43 (0.11), residues: 2338 sheet: -1.10 (0.22), residues: 532 loop : -1.78 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 38 TYR 0.041 0.001 TYR c 18 PHE 0.040 0.001 PHE f 69 TRP 0.061 0.003 TRP 8 9 HIS 0.003 0.000 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00209 (38697) covalent geometry : angle 0.56854 (52440) hydrogen bonds : bond 0.03346 ( 1316) hydrogen bonds : angle 4.27378 ( 3864) Misc. bond : bond 0.00307 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9884 Ramachandran restraints generated. 4942 Oldfield, 0 Emsley, 4942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 441 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 312 MET cc_start: 0.9123 (mmm) cc_final: 0.8763 (mmp) REVERT: B 390 MET cc_start: 0.8897 (ttp) cc_final: 0.8627 (ttp) REVERT: C 328 GLU cc_start: 0.8969 (tp30) cc_final: 0.8741 (tm-30) REVERT: D 234 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8454 (m) REVERT: D 254 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8964 (mp) REVERT: D 433 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8102 (tt) REVERT: D 479 HIS cc_start: 0.7594 (m-70) cc_final: 0.7049 (m90) REVERT: E 169 MET cc_start: 0.8413 (mtm) cc_final: 0.8005 (mtp) REVERT: E 471 LYS cc_start: 0.8006 (tttt) cc_final: 0.7519 (ttmt) REVERT: F 360 MET cc_start: 0.8211 (tpt) cc_final: 0.7865 (tpt) REVERT: G 61 GLU cc_start: 0.4311 (OUTLIER) cc_final: 0.3738 (pp20) REVERT: G 161 ILE cc_start: 0.7448 (OUTLIER) cc_final: 0.7236 (mt) REVERT: H 91 GLN cc_start: 0.8109 (mp10) cc_final: 0.7877 (mp10) REVERT: H 128 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7227 (ttm-80) REVERT: H 135 ILE cc_start: 0.7854 (pt) cc_final: 0.7406 (mp) REVERT: H 139 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7507 (mt-10) REVERT: I 21 LYS cc_start: 0.7697 (ttmm) cc_final: 0.7307 (tptm) REVERT: I 34 ASN cc_start: 0.5970 (m-40) cc_final: 0.5310 (m-40) REVERT: b 129 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.7376 (tpt170) REVERT: b 148 TYR cc_start: 0.6916 (t80) cc_final: 0.6313 (t80) REVERT: b 154 ARG cc_start: 0.6244 (mmt90) cc_final: 0.5611 (mmm160) REVERT: c 14 LYS cc_start: 0.6379 (mttt) cc_final: 0.5878 (mtmm) REVERT: c 22 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.6859 (ttp-110) REVERT: i 17 TYR cc_start: 0.7665 (m-80) cc_final: 0.7252 (m-80) REVERT: i 27 MET cc_start: 0.7032 (mmp) cc_final: 0.6239 (tpp) REVERT: 8 18 MET cc_start: 0.7918 (mpp) cc_final: 0.6880 (tpp) REVERT: a 14 MET cc_start: 0.7706 (pmm) cc_final: 0.7275 (tpt) REVERT: a 15 MET cc_start: 0.5969 (tpp) cc_final: 0.5108 (mmt) REVERT: a 56 GLN cc_start: 0.6758 (mp-120) cc_final: 0.6300 (tt0) REVERT: a 68 TRP cc_start: 0.8213 (m100) cc_final: 0.8004 (m100) REVERT: a 71 MET cc_start: 0.6849 (ptt) cc_final: 0.6464 (ppp) REVERT: a 168 HIS cc_start: 0.8318 (m-70) cc_final: 0.7714 (t70) REVERT: a 173 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7777 (tp) REVERT: K 32 MET cc_start: 0.7955 (tmm) cc_final: 0.7667 (tmm) REVERT: M 66 MET cc_start: 0.6255 (ppp) cc_final: 0.5898 (ppp) REVERT: M 69 PHE cc_start: 0.6012 (OUTLIER) cc_final: 0.5220 (m-80) REVERT: M 72 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5425 (pp) REVERT: N 2 ILE cc_start: 0.2066 (OUTLIER) cc_final: 0.1784 (tp) REVERT: N 44 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7431 (tm-30) REVERT: N 63 PHE cc_start: 0.6933 (OUTLIER) cc_final: 0.5945 (p90) REVERT: O 32 MET cc_start: 0.7227 (tmm) cc_final: 0.6974 (tmm) REVERT: P 31 SER cc_start: 0.7808 (m) cc_final: 0.7475 (p) REVERT: Q 66 MET cc_start: 0.4344 (mmt) cc_final: 0.4132 (mtt) REVERT: R 39 ASN cc_start: 0.7132 (t0) cc_final: 0.6428 (p0) REVERT: R 49 TYR cc_start: 0.7024 (m-80) cc_final: 0.6754 (m-80) REVERT: R 72 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.6962 (mt) outliers start: 73 outliers final: 54 residues processed: 499 average time/residue: 0.2181 time to fit residues: 180.6429 Evaluate side-chains 475 residues out of total 4034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 410 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 HIS Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 425 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain S residue 98 THR Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 122 THR Chi-restraints excluded: chain b residue 163 ASN Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 99 SER Chi-restraints excluded: chain a residue 163 ASN Chi-restraints excluded: chain a residue 173 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 201 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 45 GLN Chi-restraints excluded: chain K residue 54 PHE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain N residue 2 ILE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain P residue 44 GLN Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 67 VAL Chi-restraints excluded: chain R residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 79 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 373 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 491 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 494 optimal weight: 6.9990 chunk 369 optimal weight: 8.9990 chunk 172 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 393 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.155056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118934 restraints weight = 60631.539| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.47 r_work: 0.3119 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 38698 Z= 0.148 Angle : 0.598 13.997 52440 Z= 0.300 Chirality : 0.043 0.169 6250 Planarity : 0.004 0.055 6755 Dihedral : 5.975 91.279 5665 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.12 % Favored : 94.74 % Rotamer: Outliers : 2.10 % Allowed : 21.79 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.26 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.12), residues: 4942 helix: -0.42 (0.11), residues: 2348 sheet: -1.23 (0.22), residues: 537 loop : -1.83 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 146 TYR 0.041 0.001 TYR c 18 PHE 0.032 0.001 PHE f 69 TRP 0.057 0.003 TRP 8 9 HIS 0.003 0.001 HIS F 369 Details of bonding type rmsd covalent geometry : bond 0.00352 (38697) covalent geometry : angle 0.59802 (52440) hydrogen bonds : bond 0.03676 ( 1316) hydrogen bonds : angle 4.34993 ( 3864) Misc. bond : bond 0.00238 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10136.07 seconds wall clock time: 173 minutes 25.07 seconds (10405.07 seconds total)