Starting phenix.real_space_refine on Tue Sep 15 09:00:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6j5i_0677/09_2026/6j5i_0677.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j5i_0677/09_2026/6j5i_0677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6j5i_0677/09_2026/6j5i_0677.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6j5i_0677/09_2026/6j5i_0677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6j5i_0677/09_2026/6j5i_0677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j5i_0677/09_2026/6j5i_0677.map" model { file = "/net/cci-nas-00/data/ceres_data/6j5i_0677/09_2026/6j5i_0677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j5i_0677/09_2026/6j5i_0677.cif" } resolution = 3.34 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 143 5.16 5 C 24146 2.51 5 N 6603 2.21 5 O 7234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.08s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38144 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3873 Classifications: {'peptide': 509} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 490} Chain: "B" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3669 Classifications: {'peptide': 481} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 462} Chain breaks: 1 Chain: "C" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3821 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} 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: "D" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3564 Classifications: {'peptide': 471} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3532 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "F" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3536 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 411 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 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: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 973 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} 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: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1435 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain: "b" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1476 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 203} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 231 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 2, 'ARG:plan': 1, 'PHE:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 115 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: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 495 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 4, 'GLU:plan': 2, 'PHE:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 98 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: {'TRANS': 83} 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: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 303 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 41} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 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: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1687 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 210} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 25 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: 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: "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: 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: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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: 9.97, per 1000 atoms: 0.26 Number of scatterers: 38144 At special positions: 0 Unit cell: (182.16, 224.94, 168.36, 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 143 16.00 P 13 15.00 Mg 5 11.99 O 7234 8.00 N 6603 7.00 C 24146 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: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9532 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 26 sheets defined 52.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.941A pdb=" N GLU A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.607A pdb=" N ILE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 209 through 223 removed outlier: 3.753A pdb=" N VAL A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 247 through 254 removed outlier: 3.730A pdb=" N MET A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.661A 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 295 through 299 removed outlier: 3.818A pdb=" N VAL A 298 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 299 " --> pdb=" O GLY A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 299' Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.910A pdb=" N ARG A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 305' Processing helix chain 'A' and resid 337 through 346 removed outlier: 3.840A pdb=" N ILE A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.972A pdb=" N GLN A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.684A pdb=" N GLY A 388 " --> pdb=" O LYS A 384 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 removed outlier: 3.584A pdb=" N SER A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 449 removed outlier: 3.501A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 448 " --> pdb=" O VAL A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 475 removed outlier: 4.600A pdb=" N ASN A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 497 through 506 removed outlier: 3.663A pdb=" N THR A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN A 503 " --> pdb=" O GLU A 499 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.929A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) removed outlier: 3.616A 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 150 through 155 Processing helix chain 'B' and resid 175 through 186 removed outlier: 4.160A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.637A pdb=" N ASN B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 223 removed outlier: 4.513A pdb=" N LYS B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 removed outlier: 3.969A pdb=" N GLN B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 Processing helix chain 'B' and resid 253 through 259 removed outlier: 4.199A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 removed outlier: 3.920A pdb=" N MET B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 299 through 307 removed outlier: 3.532A pdb=" N ARG B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.545A pdb=" N ILE B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 360 removed outlier: 3.792A pdb=" N TYR B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.859A pdb=" N GLN B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 398 removed outlier: 3.870A pdb=" N LEU B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 425 removed outlier: 3.687A pdb=" N SER B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 450 removed outlier: 3.535A pdb=" N VAL B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 444 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY B 448 " --> pdb=" O VAL B 444 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG B 450 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 476 removed outlier: 3.562A pdb=" N SER B 470 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN B 475 " --> pdb=" O HIS B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.803A pdb=" N LYS B 482 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'C' and resid 10 through 18 removed outlier: 3.657A pdb=" N GLY C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 155 removed outlier: 3.685A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.787A pdb=" N ALA C 179 " --> pdb=" O LYS C 175 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 191 removed outlier: 3.614A pdb=" N ASN C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 186 through 191' Processing helix chain 'C' and resid 209 through 223 removed outlier: 3.571A pdb=" N VAL C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLN C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 227 removed outlier: 3.749A pdb=" N LYS C 227 " --> pdb=" O ASP C 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 239 through 245 removed outlier: 3.579A pdb=" N TYR C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.814A pdb=" N SER C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 282 removed outlier: 3.634A pdb=" N GLN C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.773A pdb=" N ALA C 293 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 336 through 344 removed outlier: 3.725A pdb=" N THR C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 342 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C 344 " --> pdb=" O THR C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 380 through 399 removed outlier: 3.761A pdb=" N GLN C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 429 removed outlier: 3.512A pdb=" N GLY C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 427 " --> pdb=" O ARG C 423 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 450 removed outlier: 3.785A pdb=" N VAL C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 448 " --> pdb=" O VAL C 444 " (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: 4.128A pdb=" N ASN C 466 " --> pdb=" O THR C 462 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 487 removed outlier: 3.617A pdb=" N LEU C 480 " --> pdb=" O HIS C 476 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS C 482 " --> pdb=" O ALA C 478 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 507 removed outlier: 3.520A pdb=" N LYS C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 501 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 502 " --> pdb=" O LYS C 498 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 507 " --> pdb=" O ASN C 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 163 through 175 removed outlier: 3.599A pdb=" N LEU D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 173 " --> pdb=" O MET D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.524A pdb=" N ASP D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 245 removed outlier: 3.567A pdb=" N GLY D 238 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 245 " --> pdb=" O VAL D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 265 removed outlier: 3.996A pdb=" N THR D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 275 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.119A pdb=" N GLY D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 318 removed outlier: 3.623A pdb=" N ASP D 317 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 345 removed outlier: 3.548A pdb=" N GLY D 345 " --> pdb=" O ALA D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 394 removed outlier: 3.779A pdb=" N GLY D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP D 388 " --> pdb=" O LYS D 384 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE D 389 " --> pdb=" O SER D 385 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 398 removed outlier: 3.632A pdb=" N LEU D 398 " --> pdb=" O MET D 395 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 395 through 398' Processing helix chain 'D' and resid 401 through 416 Processing helix chain 'D' and resid 420 through 424 removed outlier: 3.537A pdb=" N GLU D 424 " --> pdb=" O GLN D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 449 removed outlier: 3.602A pdb=" N LYS D 441 " --> pdb=" O LYS D 437 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 446 " --> pdb=" O GLY D 442 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 447 " --> pdb=" O PHE D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 459 Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 473 through 478 Processing helix chain 'E' and resid 139 through 146 removed outlier: 3.742A pdb=" N LEU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 176 removed outlier: 3.728A pdb=" N ALA E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 205 removed outlier: 3.813A pdb=" N ASN E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU E 204 " --> pdb=" O HIS E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 233 removed outlier: 3.565A pdb=" N ALA E 232 " --> pdb=" O PRO E 228 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG E 233 " --> pdb=" O GLY E 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 228 through 233' Processing helix chain 'E' and resid 233 through 241 removed outlier: 3.627A pdb=" N THR E 237 " --> pdb=" O ARG E 233 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 241 " --> pdb=" O THR E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.585A pdb=" N PHE E 263 " --> pdb=" O ASN E 259 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR E 264 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.640A pdb=" N MET E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 318 removed outlier: 3.789A pdb=" N ASP E 317 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 329 Processing helix chain 'E' and resid 338 through 344 removed outlier: 4.226A pdb=" N ALA E 342 " --> pdb=" O SER E 338 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU E 343 " --> pdb=" O ARG E 339 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU E 344 " --> pdb=" O ALA E 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 338 through 344' Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 366 through 374 removed outlier: 3.758A pdb=" N TYR E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 386 removed outlier: 3.813A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 393 Processing helix chain 'E' and resid 423 through 428 removed outlier: 3.973A pdb=" N THR E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 448 removed outlier: 3.634A pdb=" N ILE E 440 " --> pdb=" O LEU E 436 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY E 442 " --> pdb=" O GLU E 438 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE E 446 " --> pdb=" O GLY E 442 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU E 447 " --> pdb=" O PHE E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 464 through 475 removed outlier: 3.872A pdb=" N ALA E 468 " --> pdb=" O PRO E 464 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 469 " --> pdb=" O ILE E 465 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS E 474 " --> pdb=" O ALA E 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.880A pdb=" N LEU F 93 " --> pdb=" O PRO F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.995A pdb=" N GLU F 127 " --> pdb=" O GLU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 removed outlier: 3.691A pdb=" N LEU F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA F 146 " --> pdb=" O VAL F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 234 through 248 removed outlier: 3.615A pdb=" N GLY F 238 " --> pdb=" O VAL F 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU F 243 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 266 Processing helix chain 'F' and resid 286 through 295 removed outlier: 4.139A pdb=" N ASP F 290 " --> pdb=" O THR F 286 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET F 291 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 331 removed outlier: 3.727A pdb=" N LEU F 331 " --> pdb=" O PHE F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 385 removed outlier: 3.549A pdb=" N VAL F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE F 379 " --> pdb=" O GLY F 375 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR F 383 " --> pdb=" O ILE F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 393 Processing helix chain 'F' and resid 394 through 398 removed outlier: 3.933A pdb=" N GLU F 397 " --> pdb=" O GLY F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 415 removed outlier: 3.715A pdb=" N GLN F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 409 through 415' Processing helix chain 'F' and resid 423 through 428 removed outlier: 3.678A pdb=" N THR F 427 " --> pdb=" O ALA F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 448 removed outlier: 3.648A pdb=" N ILE F 440 " --> pdb=" O LEU F 436 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS F 441 " --> pdb=" O LYS F 437 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY F 442 " --> pdb=" O GLU F 438 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE F 446 " --> pdb=" O GLY F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 475 removed outlier: 3.619A pdb=" N VAL F 469 " --> pdb=" O ILE F 465 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 475 " --> pdb=" O LYS F 471 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 19 removed outlier: 4.102A pdb=" N GLY J 19 " --> pdb=" O VAL J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 28 Processing helix chain 'J' and resid 39 through 55 removed outlier: 3.768A pdb=" N ALA J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA J 44 " --> pdb=" O GLU J 40 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS J 47 " --> pdb=" O ALA J 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 35 removed outlier: 3.648A pdb=" N LYS G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS G 21 " --> pdb=" O GLN G 17 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA G 29 " --> pdb=" O MET G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 43 removed outlier: 3.655A pdb=" N ALA G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 55 removed outlier: 3.795A pdb=" N GLY G 47 " --> pdb=" O VAL G 43 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER G 48 " --> pdb=" O TYR G 44 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU G 49 " --> pdb=" O GLY G 45 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 94 removed outlier: 3.738A pdb=" N LYS G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLN G 88 " --> pdb=" O SER G 84 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA G 94 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 116 removed outlier: 4.279A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 148 removed outlier: 3.584A pdb=" N ILE G 144 " --> pdb=" O ASP G 140 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU G 146 " --> pdb=" O SER G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 187 through 192 removed outlier: 4.089A pdb=" N ILE G 192 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 215 removed outlier: 3.513A pdb=" N ASN G 203 " --> pdb=" O ASP G 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN G 205 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR G 207 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 270 removed outlier: 3.513A pdb=" N ALA G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG G 228 " --> pdb=" O GLU G 224 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR G 230 " --> pdb=" O SER G 226 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA G 231 " --> pdb=" O ALA G 227 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA G 235 " --> pdb=" O ALA G 231 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN G 238 " --> pdb=" O ASN G 234 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU G 241 " --> pdb=" O LYS G 237 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS G 245 " --> pdb=" O GLU G 241 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU G 248 " --> pdb=" O ASP G 244 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR G 249 " --> pdb=" O LYS G 245 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL G 257 " --> pdb=" O THR G 253 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS G 260 " --> pdb=" O ALA G 256 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE G 265 " --> pdb=" O GLU G 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 118 removed outlier: 3.649A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU H 113 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN H 116 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 122 removed outlier: 3.603A pdb=" N ALA H 122 " --> pdb=" O LEU H 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 119 through 122' Processing helix chain 'H' and resid 125 through 145 removed outlier: 3.939A pdb=" N ALA H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN H 132 " --> pdb=" O ARG H 128 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU H 141 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL H 142 " --> pdb=" O ASN H 138 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 24 removed outlier: 3.654A pdb=" N ILE I 17 " --> pdb=" O ARG I 13 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL I 22 " --> pdb=" O CYS I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 38 removed outlier: 3.784A pdb=" N THR I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER I 38 " --> pdb=" O ALA I 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 28 removed outlier: 4.067A pdb=" N GLY S 16 " --> pdb=" O TYR S 12 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR S 18 " --> pdb=" O ILE S 14 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR S 23 " --> pdb=" O ALA S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 46 removed outlier: 3.647A pdb=" N VAL S 35 " --> pdb=" O LYS S 31 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU S 36 " --> pdb=" O LEU S 32 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS S 37 " --> pdb=" O GLU S 33 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU S 38 " --> pdb=" O GLN S 34 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG S 41 " --> pdb=" O LYS S 37 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE S 45 " --> pdb=" O ARG S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 55 removed outlier: 3.903A pdb=" N ILE S 55 " --> pdb=" O ALA S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 76 removed outlier: 3.601A pdb=" N LYS S 67 " --> pdb=" O SER S 63 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU S 69 " --> pdb=" O LYS S 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA S 74 " --> pdb=" O SER S 70 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS S 75 " --> pdb=" O ASP S 71 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU S 76 " --> pdb=" O MET S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 93 Processing helix chain 'S' and resid 97 through 111 removed outlier: 3.742A pdb=" N ILE S 102 " --> pdb=" O THR S 98 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR S 107 " --> pdb=" O SER S 103 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL S 111 " --> pdb=" O THR S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 135 removed outlier: 4.050A pdb=" N LEU S 134 " --> pdb=" O THR S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 138 through 143 removed outlier: 4.602A pdb=" N LEU S 142 " --> pdb=" O LEU S 138 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER S 143 " --> pdb=" O LYS S 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 138 through 143' Processing helix chain 'S' and resid 174 through 183 removed outlier: 4.019A pdb=" N THR S 177 " --> pdb=" O SER S 174 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS S 178 " --> pdb=" O ALA S 175 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN S 180 " --> pdb=" O THR S 177 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER S 183 " --> pdb=" O GLN S 180 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 31 Proline residue: b 18 - end of helix Proline residue: b 27 - end of helix removed outlier: 3.505A pdb=" N VAL b 31 " --> pdb=" O PRO b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 42 removed outlier: 3.916A 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 84 removed outlier: 4.189A pdb=" N LEU b 67 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL b 68 " --> pdb=" O ILE b 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR b 69 " --> pdb=" O GLY b 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE b 70 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL b 71 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS b 72 " --> pdb=" O VAL b 68 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS b 73 " --> pdb=" O TYR b 69 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY b 75 " --> pdb=" O VAL b 71 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY b 79 " --> pdb=" O GLY b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 105 removed outlier: 4.497A pdb=" N GLU b 95 " --> pdb=" O ALA b 91 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL b 96 " --> pdb=" O GLN b 92 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER b 100 " --> pdb=" O VAL b 96 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE b 101 " --> pdb=" O LYS b 97 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN b 103 " --> pdb=" O ALA b 99 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN b 105 " --> pdb=" O ILE b 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 122 removed outlier: 3.732A pdb=" N GLU b 111 " --> pdb=" O ALA b 107 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN b 114 " --> pdb=" O LEU b 110 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL b 118 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN b 119 " --> pdb=" O GLN b 115 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS b 122 " --> pdb=" O VAL b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 187 removed outlier: 3.681A pdb=" N ALA b 133 " --> pdb=" O ARG b 129 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU b 137 " --> pdb=" O ALA b 133 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR b 139 " --> pdb=" O ALA b 135 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR b 140 " --> pdb=" O LEU b 136 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG b 141 " --> pdb=" O GLU b 137 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU b 142 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL b 147 " --> pdb=" O ARG b 143 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS b 152 " --> pdb=" O TYR b 148 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU b 155 " --> pdb=" O ILE b 151 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET b 164 " --> pdb=" O SER b 160 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG b 166 " --> pdb=" O GLN b 162 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU b 171 " --> pdb=" O GLN b 167 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS b 172 " --> pdb=" O LYS b 168 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL b 177 " --> pdb=" O MET b 173 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL b 181 " --> pdb=" O VAL b 177 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL b 182 " --> pdb=" O GLU b 178 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLN b 183 " --> pdb=" O LYS b 179 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER b 184 " --> pdb=" O HIS b 180 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 211 removed outlier: 3.678A pdb=" N ILE b 194 " --> pdb=" O GLU b 190 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS b 197 " --> pdb=" O THR b 193 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE b 198 " --> pdb=" O ILE b 194 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA b 208 " --> pdb=" O LEU b 204 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN b 209 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA b 210 " --> pdb=" O LYS b 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 20 removed outlier: 3.742A pdb=" N ASP c 13 " --> pdb=" O LYS c 9 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE c 15 " --> pdb=" O PHE c 11 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU c 17 " --> pdb=" O ASP c 13 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR c 20 " --> pdb=" O ARG c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 49 removed outlier: 3.639A pdb=" N GLN c 37 " --> pdb=" O PRO c 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP c 40 " --> pdb=" O GLN c 36 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS c 45 " --> pdb=" O ARG c 41 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS c 47 " --> pdb=" O LEU c 43 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N MET c 49 " --> pdb=" O LYS c 45 " (cutoff:3.500A) Processing helix chain 'd' and resid 14 through 18 removed outlier: 3.892A pdb=" N ILE d 18 " --> pdb=" O PHE d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 29 removed outlier: 4.015A pdb=" N ALA d 27 " --> pdb=" O GLN d 23 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 43 removed outlier: 4.093A pdb=" N THR d 36 " --> pdb=" O SER d 32 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER d 38 " --> pdb=" O ASN d 34 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR d 39 " --> pdb=" O GLU d 35 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG d 40 " --> pdb=" O THR d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 60 removed outlier: 4.231A pdb=" N TYR d 56 " --> pdb=" O ASP d 52 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS d 57 " --> pdb=" O TRP d 53 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA d 58 " --> pdb=" O ALA d 54 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR d 59 " --> pdb=" O TYR d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 73 Processing helix chain 'd' and resid 86 through 91 removed outlier: 3.978A pdb=" N ASP d 90 " --> pdb=" O THR d 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 120 removed outlier: 3.552A pdb=" N ALA d 101 " --> pdb=" O VAL d 97 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU d 102 " --> pdb=" O LYS d 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER d 105 " --> pdb=" O ALA d 101 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS d 108 " --> pdb=" O LEU d 104 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG d 110 " --> pdb=" O LEU d 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR d 114 " --> pdb=" O ARG d 110 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU d 118 " --> pdb=" O TYR d 114 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU d 119 " --> pdb=" O GLU d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 125 removed outlier: 3.557A pdb=" N ILE d 124 " --> pdb=" O LYS d 120 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE d 125 " --> pdb=" O MET d 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 120 through 125' Processing helix chain 'd' and resid 133 through 137 removed outlier: 3.865A pdb=" N GLU d 137 " --> pdb=" O ASP d 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 63 removed outlier: 3.502A pdb=" N UNK e 42 " --> pdb=" O UNK e 38 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 17 removed outlier: 3.502A pdb=" N LYS f 7 " --> pdb=" O VAL f 3 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP f 8 " --> pdb=" O VAL f 4 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG f 9 " --> pdb=" O PRO f 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU f 11 " --> pdb=" O LYS f 7 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 35 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: 3.617A pdb=" N LEU f 59 " --> pdb=" O SER f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 61 through 75 removed outlier: 3.526A 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: 4.384A 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: 3.668A 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: 3.688A 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: 3.564A 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: 3.512A pdb=" N UNK g 78 " --> pdb=" O UNK g 74 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N UNK g 79 " --> pdb=" O UNK g 75 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N UNK g 83 " --> pdb=" O UNK g 79 " (cutoff:3.500A) removed outlier: 4.328A 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: 4.862A pdb=" N LEU i 23 " --> pdb=" O ASN i 19 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N THR i 24 " --> pdb=" O SER i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 48 removed outlier: 4.493A pdb=" N LEU i 31 " --> pdb=" O MET i 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 29 removed outlier: 3.818A pdb=" N UNK k 16 " --> pdb=" O UNK k 12 " (cutoff:3.500A) 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: 3.706A 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: 3.636A pdb=" N LEU 8 26 " --> pdb=" O ILE 8 22 " (cutoff:3.500A) Processing helix chain '8' and resid 34 through 39 Processing helix chain '8' and resid 44 through 60 removed outlier: 4.077A pdb=" N SER 8 48 " --> pdb=" O THR 8 44 " (cutoff:3.500A) Proline residue: 8 50 - end of helix removed outlier: 3.621A pdb=" N MET 8 53 " --> pdb=" O THR 8 49 " (cutoff:3.500A) 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: 3.796A pdb=" N LEU a 49 " --> pdb=" O ILE a 45 " (cutoff:3.500A) removed outlier: 3.656A 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: 3.770A 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: 3.814A 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: 3.820A 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: 4.551A pdb=" N ASN a 101 " --> pdb=" O GLN a 97 " (cutoff:3.500A) removed outlier: 3.607A 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: 4.138A 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: 3.658A pdb=" N VAL a 113 " --> pdb=" O TRP a 109 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE a 114 " --> pdb=" O SER a 110 " (cutoff:3.500A) removed outlier: 3.938A 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: 4.050A pdb=" N ARG a 159 " --> pdb=" O ALA a 155 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN a 163 " --> pdb=" O ARG a 159 " (cutoff:3.500A) removed outlier: 3.503A 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: 3.579A 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: 3.717A pdb=" N THR a 178 " --> pdb=" O ILE a 174 " (cutoff:3.500A) removed outlier: 3.732A 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: 4.032A pdb=" N THR a 200 " --> pdb=" O LEU a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 206 through 222 removed outlier: 3.834A pdb=" N GLN a 210 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) removed outlier: 4.174A 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: 3.700A 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: 3.636A 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: 3.867A 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: 3.792A 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: 4.189A pdb=" N ILE K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 73 removed outlier: 4.205A 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: 3.645A 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: 3.572A 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: 3.753A 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: 4.195A pdb=" N VAL L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 35 removed outlier: 3.546A pdb=" N ILE L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 73 removed outlier: 4.140A pdb=" N SER L 48 " --> pdb=" O GLN L 44 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA L 50 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 3.818A 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: 3.912A pdb=" N GLY L 61 " --> pdb=" O SER L 57 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE L 63 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 4.028A 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: 3.671A pdb=" N LEU L 72 " --> pdb=" O ALA L 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 14 removed outlier: 3.537A pdb=" N LYS M 7 " --> pdb=" O ASP M 3 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY M 12 " --> pdb=" O PHE M 8 " (cutoff:3.500A) removed outlier: 3.921A 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: 3.902A 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: 3.921A pdb=" N VAL M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE M 29 " --> pdb=" O ILE M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 39 removed outlier: 3.554A pdb=" N ARG M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN M 39 " --> pdb=" O GLY M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 56 removed outlier: 4.173A pdb=" N SER M 48 " --> pdb=" O GLN M 44 " (cutoff:3.500A) removed outlier: 5.070A 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: 3.513A pdb=" N GLY M 53 " --> pdb=" O TYR M 49 " (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: 3.912A 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: 3.630A 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: 3.764A pdb=" N VAL N 28 " --> pdb=" O GLY N 24 " (cutoff:3.500A) removed outlier: 3.686A 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: 4.085A 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: 3.648A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 4.182A 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: 3.544A 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: 3.695A 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: 3.935A 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: 3.883A 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: 3.667A pdb=" N PHE O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 4.205A 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: 4.068A 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: 4.383A pdb=" N ILE P 9 " --> pdb=" O ALA P 5 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA P 11 " --> pdb=" O LYS P 7 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY P 12 " --> pdb=" O PHE P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 26 removed outlier: 3.676A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.508A 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: 4.411A 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: 3.805A 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: 3.587A 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: 3.643A 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: 3.617A pdb=" N ILE Q 33 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 73 removed outlier: 3.829A pdb=" N SER Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR Q 49 " --> pdb=" O GLN Q 45 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA Q 50 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU Q 52 " --> pdb=" O SER Q 48 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.646A pdb=" N ALA Q 68 " --> pdb=" O CYS Q 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU Q 70 " --> pdb=" O MET Q 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 removed outlier: 3.812A 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: 3.656A pdb=" N GLY R 10 " --> pdb=" O ALA R 6 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA R 14 " --> pdb=" O GLY R 10 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 37 removed outlier: 4.294A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY R 26 " --> pdb=" O GLY R 22 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE R 29 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 73 removed outlier: 3.665A 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: 4.181A 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: 3.632A pdb=" N UNK u 7 " --> pdb=" O UNK u 3 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 35 removed outlier: 4.471A pdb=" N UNK u 20 " --> pdb=" O UNK u 16 " (cutoff:3.500A) removed outlier: 3.996A 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 30 through 35 removed outlier: 6.691A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE A 76 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLY A 61 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU E 39 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 50 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG E 61 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N HIS E 54 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR E 59 " --> pdb=" O HIS E 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 25 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 17 " --> pdb=" O ASP E 24 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLN E 26 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE E 15 " --> pdb=" O GLN E 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.846A pdb=" N CYS A 201 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL A 232 " --> pdb=" O CYS A 201 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR A 203 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA A 234 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ALA A 205 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N GLN A 349 " --> pdb=" O GLY A 368 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N GLY A 368 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE A 351 " --> pdb=" O ASN A 366 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.281A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 91 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA F 17 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLN F 26 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE F 15 " --> pdb=" O GLN F 26 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.987A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.516A pdb=" N VAL B 232 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR B 200 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE B 267 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE B 202 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR B 322 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 326 through 328 removed outlier: 6.588A pdb=" N ILE B 167 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.693A pdb=" N THR C 91 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N MET C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU C 51 " --> pdb=" O SER C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.273A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 106 through 109 removed outlier: 3.982A pdb=" N ARG C 106 " --> pdb=" O THR C 229 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE C 202 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASP C 269 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL C 204 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR C 268 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLU C 328 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AB4, first strand: chain 'D' and resid 13 through 18 removed outlier: 6.759A pdb=" N ASP D 24 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL D 23 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE D 63 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL D 51 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU D 39 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 85 through 88 removed outlier: 3.528A pdb=" N ILE D 86 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 4.435A 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: 6.100A pdb=" N MET D 97 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TYR D 182 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE D 256 " --> pdb=" O TYR D 182 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL D 184 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL D 253 " --> pdb=" O THR D 307 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N VAL D 309 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU D 255 " --> pdb=" O VAL D 309 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA D 311 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE D 257 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 85 through 87 removed outlier: 3.510A pdb=" N ALA E 116 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 96 through 97 removed outlier: 6.097A pdb=" N MET E 97 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLN E 223 " --> pdb=" O MET E 97 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE E 185 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY E 222 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLY E 187 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP E 258 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE E 257 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 252 through 253 removed outlier: 3.537A pdb=" N VAL E 253 " --> pdb=" O SER E 305 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 85 through 88 removed outlier: 3.555A pdb=" N VAL F 88 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN F 114 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 155 through 158 removed outlier: 7.513A pdb=" N VAL F 253 " --> pdb=" O THR F 307 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL F 309 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU F 255 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ALA F 311 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE F 257 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N TYR F 313 " --> pdb=" O ILE F 257 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 184 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER F 183 " --> pdb=" O ALA F 218 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N VAL F 220 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE F 185 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLY F 222 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY F 187 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 171 through 179 removed outlier: 6.071A pdb=" N ILE G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ILE G 105 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR G 127 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY G 107 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LYS G 129 " --> pdb=" O GLY G 107 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 31 through 32 removed outlier: 3.587A pdb=" N ALA H 31 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER H 81 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 64 through 65 removed outlier: 3.664A pdb=" N VAL H 65 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER H 73 " --> pdb=" O VAL H 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 76 through 77 Processing sheet with id=AC7, first strand: chain 'S' and resid 118 through 120 removed outlier: 6.142A pdb=" N CYS S 118 " --> pdb=" O GLU S 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'S' and resid 162 through 164 removed outlier: 3.647A pdb=" N MET S 173 " --> pdb=" O MET S 162 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL S 164 " --> pdb=" O VAL S 171 " (cutoff:3.500A) 1306 hydrogen bonds defined for protein. 3753 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: 7.81 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9945 1.33 - 1.45: 7076 1.45 - 1.58: 21364 1.58 - 1.70: 22 1.70 - 1.82: 266 Bond restraints: 38673 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.60e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.63e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.53e+01 bond pdb=" C5 ATP C 601 " pdb=" C6 ATP C 601 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.53e+01 ... (remaining 38668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 51886 4.02 - 8.04: 452 8.04 - 12.06: 60 12.06 - 16.09: 4 16.09 - 20.11: 3 Bond angle restraints: 52405 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 119.76 20.11 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 121.00 18.87 1.00e+00 1.00e+00 3.56e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 121.19 18.68 1.00e+00 1.00e+00 3.49e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 120.89 15.94 1.00e+00 1.00e+00 2.54e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 124.52 12.31 1.00e+00 1.00e+00 1.52e+02 ... (remaining 52400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 22735 34.61 - 69.22: 525 69.22 - 103.84: 30 103.84 - 138.45: 2 138.45 - 173.06: 2 Dihedral angle restraints: 23294 sinusoidal: 8445 harmonic: 14849 Sorted by residual: dihedral pdb=" CA ALA E 280 " pdb=" C ALA E 280 " pdb=" N VAL E 281 " pdb=" CA VAL E 281 " ideal model delta harmonic sigma weight residual -180.00 -128.27 -51.73 0 5.00e+00 4.00e-02 1.07e+02 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 -131.74 -48.26 0 5.00e+00 4.00e-02 9.32e+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 -132.40 -47.60 0 5.00e+00 4.00e-02 9.06e+01 ... (remaining 23291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 5209 0.077 - 0.154: 926 0.154 - 0.231: 92 0.231 - 0.309: 11 0.309 - 0.386: 4 Chirality restraints: 6242 Sorted by residual: chirality pdb=" CA LEU b 85 " pdb=" N LEU b 85 " pdb=" C LEU b 85 " pdb=" CB LEU b 85 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CB ILE C 489 " pdb=" CA ILE C 489 " pdb=" CG1 ILE C 489 " pdb=" CG2 ILE C 489 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB VAL B 157 " pdb=" CA VAL B 157 " pdb=" CG1 VAL B 157 " pdb=" CG2 VAL B 157 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 6239 not shown) Planarity restraints: 6752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 246 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO A 247 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN O 39 " 0.062 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO O 40 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO O 40 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO O 40 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 40 " 0.017 2.00e-02 2.50e+03 3.54e-02 1.26e+01 pdb=" C GLU J 40 " -0.061 2.00e-02 2.50e+03 pdb=" O GLU J 40 " 0.023 2.00e-02 2.50e+03 pdb=" N GLN J 41 " 0.021 2.00e-02 2.50e+03 ... (remaining 6749 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 7 2.07 - 2.77: 9169 2.77 - 3.48: 47996 3.48 - 4.19: 85364 4.19 - 4.90: 150953 Nonbonded interactions: 293489 Sorted by model distance: nonbonded pdb=" CB LEU H 48 " pdb=" OD1 ASN R 39 " model vdw 1.358 3.440 nonbonded pdb=" O VAL E 469 " pdb=" OD1 ASP E 473 " model vdw 1.789 3.040 nonbonded pdb=" O LYS f 53 " pdb=" O ARG a 41 " model vdw 1.880 3.040 nonbonded pdb=" OG1 THR G 2 " pdb=" OD2 ASP G 5 " model vdw 2.016 3.040 nonbonded pdb=" CD2 LEU H 48 " pdb=" CB SER R 41 " model vdw 2.033 3.860 ... (remaining 293484 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 22 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)) selection = (chain 'B' and (resid 22 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 22 through 401 or resid 410 through 602)) } ncs_group { reference = (chain 'D' and resid 10 through 476) selection = chain 'E' selection = (chain 'F' and resid 10 through 476) } ncs_group { reference = (chain 'K' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'L' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'M' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'N' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 65 or (resid 66 and (name N or name C \ A or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'O' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 73)) selection = (chain 'P' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 through 73)) selection = (chain 'Q' and (resid 2 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 59 or (resid 60 and (name N or name C \ A or name C or name O or name CB )) or resid 61 through 65 or (resid 66 and (nam \ e N or name CA or name C or name O or name CB )) or resid 67 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 65 or (resid 66 and (name N or name \ CA or name C or name O or name CB )) or resid 67 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 36.970 Find NCS groups from input model: 0.830 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: 0.000 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: 41.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.009 0.103 38674 Z= 0.390 Angle : 1.141 20.108 52405 Z= 0.676 Chirality : 0.059 0.386 6242 Planarity : 0.007 0.095 6752 Dihedral : 15.524 173.062 13762 Min Nonbonded Distance : 1.358 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.67 % Favored : 92.08 % Rotamer: Outliers : 0.89 % Allowed : 13.16 % Favored : 85.95 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % 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: -5.57 (0.09), residues: 4939 helix: -4.28 (0.06), residues: 2255 sheet: -2.27 (0.23), residues: 482 loop : -3.25 (0.10), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 373 TYR 0.054 0.003 TYR A 337 PHE 0.029 0.003 PHE C 403 TRP 0.023 0.003 TRP I 4 HIS 0.008 0.002 HIS F 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00882 / 0.39 (38673) covalent geometry : angle 1.14051 / 0.68 (52405) hydrogen bonds : bond 0.32574 / 21.68 ( 1306) hydrogen bonds : angle 10.66082 / 7.20 ( 3753) Misc. bond : bond 0.01444 / 0.76 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 513 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: A 446 TYR cc_start: 0.7165 (t80) cc_final: 0.6965 (t80) REVERT: B 390 MET cc_start: 0.7304 (ttp) cc_final: 0.6902 (ttp) REVERT: B 430 GLN cc_start: 0.7263 (tt0) cc_final: 0.6875 (tt0) REVERT: C 292 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7288 (mt-10) REVERT: C 373 ARG cc_start: 0.6975 (tmm160) cc_final: 0.6616 (mtt-85) REVERT: C 390 MET cc_start: 0.7831 (ttt) cc_final: 0.7361 (ttt) REVERT: D 168 ILE cc_start: 0.8682 (tt) cc_final: 0.8476 (tt) REVERT: D 202 MET cc_start: 0.7078 (mtm) cc_final: 0.6768 (mtm) REVERT: D 358 ARG cc_start: 0.6742 (mtt-85) cc_final: 0.6427 (mtt90) REVERT: D 395 MET cc_start: 0.7836 (tpt) cc_final: 0.7078 (tpp) REVERT: E 204 GLU cc_start: 0.7936 (pt0) cc_final: 0.7579 (pt0) REVERT: E 260 ILE cc_start: 0.8583 (tp) cc_final: 0.8252 (tp) REVERT: F 28 ASP cc_start: 0.7592 (t0) cc_final: 0.7147 (t0) REVERT: F 63 ILE cc_start: 0.8659 (mt) cc_final: 0.8271 (mt) REVERT: F 126 MET cc_start: 0.7427 (mmm) cc_final: 0.7167 (mmt) REVERT: F 395 MET cc_start: 0.8151 (tpp) cc_final: 0.7795 (tpp) REVERT: F 441 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8213 (ttpt) REVERT: F 474 LYS cc_start: 0.8147 (tptp) cc_final: 0.7914 (tptm) REVERT: H 55 LEU cc_start: 0.7432 (mt) cc_final: 0.7143 (pp) REVERT: S 162 MET cc_start: 0.7021 (ptm) cc_final: 0.5729 (pmm) REVERT: b 169 GLU cc_start: 0.7258 (tt0) cc_final: 0.7030 (tm-30) REVERT: b 171 GLU cc_start: 0.7988 (pp20) cc_final: 0.7292 (pp20) REVERT: c 23 GLN cc_start: 0.7170 (mm110) cc_final: 0.6916 (mm-40) REVERT: a 104 MET cc_start: 0.2375 (mtp) cc_final: 0.1108 (mmm) REVERT: a 114 PHE cc_start: 0.3336 (m-10) cc_final: 0.3027 (t80) REVERT: P 32 MET cc_start: 0.4917 (tmm) cc_final: 0.4197 (tpp) outliers start: 33 outliers final: 16 residues processed: 542 average time/residue: 0.2619 time to fit residues: 228.1829 Evaluate side-chains 387 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 370 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain C residue 69 ASP Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain a residue 142 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 ASN A 415 GLN B 215 GLN B 366 ASN B 415 GLN C 190 ASN C 330 GLN C 341 ASN C 432 GLN C 441 GLN C 471 HIS C 503 ASN D 179 HIS D 225 ASN D 310 GLN D 369 HIS E 132 GLN E 179 HIS ** E 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 ASN F 225 ASN F 295 GLN G 82 HIS G 211 ASN G 234 ASN H 132 GLN H 138 ASN I 16 GLN b 188 GLN a 39 ASN a 61 HIS a 63 GLN a 83 ASN a 97 GLN L 44 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.195353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.159868 restraints weight = 49150.430| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.07 r_work: 0.3479 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 38674 Z= 0.166 Angle : 0.678 10.077 52405 Z= 0.354 Chirality : 0.044 0.243 6242 Planarity : 0.005 0.075 6752 Dihedral : 7.732 178.873 5592 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.30 % Favored : 93.48 % Rotamer: Outliers : 2.83 % Allowed : 16.59 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.50 (0.10), residues: 4939 helix: -3.15 (0.08), residues: 2353 sheet: -1.85 (0.23), residues: 497 loop : -2.92 (0.12), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 17 TYR 0.021 0.002 TYR A 337 PHE 0.016 0.001 PHE R 47 TRP 0.011 0.002 TRP 8 9 HIS 0.004 0.001 HIS D 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (38673) covalent geometry : angle 0.67814 / 0.35 (52405) hydrogen bonds : bond 0.05169 / 3.45 ( 1306) hydrogen bonds : angle 5.72239 / 3.86 ( 3753) Misc. bond : bond 0.00396 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 407 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 TYR cc_start: 0.7607 (t80) cc_final: 0.7359 (t80) REVERT: B 67 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: B 216 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8202 (tp) REVERT: B 312 MET cc_start: 0.8299 (mmt) cc_final: 0.8065 (mmt) REVERT: B 390 MET cc_start: 0.7719 (ttp) cc_final: 0.7327 (ttp) REVERT: B 430 GLN cc_start: 0.7373 (tt0) cc_final: 0.6951 (tt0) REVERT: C 13 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7332 (tm-30) REVERT: C 292 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7988 (mt-10) REVERT: C 390 MET cc_start: 0.8017 (ttt) cc_final: 0.7628 (ttt) REVERT: D 168 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8468 (tt) REVERT: D 202 MET cc_start: 0.7583 (mtm) cc_final: 0.7140 (mtp) REVERT: D 395 MET cc_start: 0.8185 (tpt) cc_final: 0.7501 (tpp) REVERT: E 204 GLU cc_start: 0.8289 (pt0) cc_final: 0.7897 (pt0) REVERT: E 474 LYS cc_start: 0.7714 (mmtt) cc_final: 0.7488 (ttpt) REVERT: F 28 ASP cc_start: 0.8670 (t0) cc_final: 0.8208 (t0) REVERT: F 63 ILE cc_start: 0.8754 (mt) cc_final: 0.8493 (mt) REVERT: F 360 MET cc_start: 0.8278 (tpp) cc_final: 0.8045 (tpp) REVERT: I 26 LEU cc_start: 0.6252 (mp) cc_final: 0.6013 (mp) REVERT: I 44 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7446 (mp) REVERT: S 89 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8460 (mt) REVERT: S 162 MET cc_start: 0.6848 (ptm) cc_final: 0.5324 (pmm) REVERT: b 176 TRP cc_start: 0.6695 (t60) cc_final: 0.6130 (t60) REVERT: a 43 ILE cc_start: 0.3584 (OUTLIER) cc_final: 0.3166 (mt) REVERT: a 104 MET cc_start: 0.1599 (mtp) cc_final: 0.0480 (mmm) REVERT: a 114 PHE cc_start: 0.2677 (m-10) cc_final: 0.2065 (t80) REVERT: K 32 MET cc_start: 0.6592 (ttt) cc_final: 0.6316 (ttm) REVERT: L 60 MET cc_start: 0.3515 (mmm) cc_final: 0.3046 (tpp) REVERT: N 32 MET cc_start: 0.5120 (ppp) cc_final: 0.4897 (ppp) REVERT: P 32 MET cc_start: 0.5070 (tmm) cc_final: 0.4124 (tpp) REVERT: R 66 MET cc_start: 0.4062 (ppp) cc_final: 0.2753 (ttt) outliers start: 105 outliers final: 57 residues processed: 490 average time/residue: 0.2479 time to fit residues: 197.8800 Evaluate side-chains 414 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 351 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 155 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 142 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 3 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 423 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 189 optimal weight: 0.5980 chunk 417 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 388 optimal weight: 0.0060 chunk 268 optimal weight: 0.7980 chunk 457 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN B 415 GLN E 251 GLN H 116 GLN a 47 GLN K 39 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.195637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157248 restraints weight = 48871.461| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.07 r_work: 0.3421 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 38674 Z= 0.113 Angle : 0.584 9.970 52405 Z= 0.301 Chirality : 0.042 0.214 6242 Planarity : 0.004 0.061 6752 Dihedral : 6.857 168.906 5579 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.28 % Favored : 94.51 % Rotamer: Outliers : 2.62 % Allowed : 18.07 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % 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: -3.60 (0.11), residues: 4939 helix: -2.29 (0.09), residues: 2357 sheet: -1.52 (0.23), residues: 521 loop : -2.61 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 414 TYR 0.017 0.001 TYR I 14 PHE 0.016 0.001 PHE G 155 TRP 0.019 0.001 TRP 8 9 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (38673) covalent geometry : angle 0.58412 / 0.30 (52405) hydrogen bonds : bond 0.04065 / 2.73 ( 1306) hydrogen bonds : angle 4.92329 / 3.31 ( 3753) Misc. bond : bond 0.00464 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 396 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 446 TYR cc_start: 0.7558 (t80) cc_final: 0.7254 (t80) REVERT: B 216 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8050 (tp) REVERT: B 381 ARG cc_start: 0.7161 (tpp-160) cc_final: 0.6939 (tpp-160) REVERT: B 390 MET cc_start: 0.7776 (ttp) cc_final: 0.7244 (ttp) REVERT: B 430 GLN cc_start: 0.7380 (tt0) cc_final: 0.7005 (tt0) REVERT: C 13 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7083 (tm-30) REVERT: C 50 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7123 (mm-30) REVERT: C 90 ARG cc_start: 0.7188 (mtp-110) cc_final: 0.6654 (mtp85) REVERT: C 186 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7930 (mm-40) REVERT: C 292 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7954 (mt-10) REVERT: C 390 MET cc_start: 0.8047 (ttt) cc_final: 0.7694 (ttt) REVERT: D 202 MET cc_start: 0.7414 (mtm) cc_final: 0.6851 (mtp) REVERT: D 395 MET cc_start: 0.8095 (tpt) cc_final: 0.7531 (tpp) REVERT: E 173 ASN cc_start: 0.7636 (t0) cc_final: 0.7407 (t0) REVERT: E 474 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7422 (ttpt) REVERT: F 28 ASP cc_start: 0.8414 (t0) cc_final: 0.7993 (t0) REVERT: F 239 LEU cc_start: 0.8964 (tp) cc_final: 0.8711 (tt) REVERT: G 20 THR cc_start: 0.9316 (m) cc_final: 0.9112 (m) REVERT: G 39 LYS cc_start: 0.6781 (OUTLIER) cc_final: 0.6497 (mttt) REVERT: G 124 PHE cc_start: 0.7144 (m-80) cc_final: 0.6711 (m-80) REVERT: I 4 TRP cc_start: 0.5997 (p90) cc_final: 0.5563 (p90) REVERT: I 44 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7443 (mp) REVERT: S 56 MET cc_start: 0.7714 (mtt) cc_final: 0.7322 (mpp) REVERT: S 77 LYS cc_start: 0.5932 (tttm) cc_final: 0.5541 (ttpp) REVERT: S 162 MET cc_start: 0.6992 (ptm) cc_final: 0.5161 (pmm) REVERT: a 71 MET cc_start: 0.3903 (ppp) cc_final: 0.3326 (ppp) REVERT: a 104 MET cc_start: 0.1291 (mtp) cc_final: 0.0644 (mmm) REVERT: a 114 PHE cc_start: 0.2834 (m-10) cc_final: 0.1949 (t80) REVERT: K 32 MET cc_start: 0.6401 (ttt) cc_final: 0.6185 (ttm) REVERT: L 60 MET cc_start: 0.3549 (mmm) cc_final: 0.3214 (tpp) REVERT: M 51 ILE cc_start: 0.4282 (OUTLIER) cc_final: 0.3308 (pt) REVERT: M 66 MET cc_start: 0.4086 (ppp) cc_final: 0.3559 (pmm) REVERT: O 32 MET cc_start: 0.5418 (mpp) cc_final: 0.3462 (tpt) REVERT: P 32 MET cc_start: 0.5151 (tmm) cc_final: 0.4020 (tpp) REVERT: Q 65 LEU cc_start: 0.0491 (OUTLIER) cc_final: 0.0226 (mp) REVERT: R 66 MET cc_start: 0.4520 (ppp) cc_final: 0.3343 (ttp) outliers start: 97 outliers final: 57 residues processed: 476 average time/residue: 0.2449 time to fit residues: 191.3380 Evaluate side-chains 419 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 356 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 142 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain Q residue 65 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 309 optimal weight: 0.7980 chunk 509 optimal weight: 40.0000 chunk 229 optimal weight: 3.9990 chunk 120 optimal weight: 0.2980 chunk 94 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 438 optimal weight: 10.0000 chunk 174 optimal weight: 8.9990 chunk 219 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 343 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN B 415 GLN E 54 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.193927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.158148 restraints weight = 49013.605| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 3.05 r_work: 0.3583 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38674 Z= 0.142 Angle : 0.595 11.265 52405 Z= 0.304 Chirality : 0.043 0.271 6242 Planarity : 0.004 0.055 6752 Dihedral : 6.561 168.654 5576 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.16 % Favored : 93.70 % Rotamer: Outliers : 3.75 % Allowed : 18.75 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.14 (0.11), residues: 4939 helix: -1.82 (0.10), residues: 2344 sheet: -1.36 (0.23), residues: 512 loop : -2.48 (0.12), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 414 TYR 0.018 0.001 TYR i 21 PHE 0.020 0.001 PHE C 464 TRP 0.019 0.001 TRP 8 9 HIS 0.004 0.001 HIS D 429 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (38673) covalent geometry : angle 0.59541 / 0.30 (52405) hydrogen bonds : bond 0.03789 / 2.56 ( 1306) hydrogen bonds : angle 4.70888 / 3.18 ( 3753) Misc. bond : bond 0.00365 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 368 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7191 (mt) REVERT: A 14 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: A 394 LEU cc_start: 0.7733 (tt) cc_final: 0.7525 (tp) REVERT: A 446 TYR cc_start: 0.7315 (t80) cc_final: 0.7023 (t80) REVERT: B 216 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8073 (tp) REVERT: B 390 MET cc_start: 0.7680 (ttp) cc_final: 0.7243 (ttp) REVERT: B 430 GLN cc_start: 0.7364 (tt0) cc_final: 0.7087 (tt0) REVERT: C 90 ARG cc_start: 0.7444 (mtp-110) cc_final: 0.7028 (mtp85) REVERT: C 186 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7962 (mm-40) REVERT: C 473 ILE cc_start: 0.7388 (mt) cc_final: 0.7063 (mt) REVERT: D 202 MET cc_start: 0.7494 (mtm) cc_final: 0.7010 (mtp) REVERT: D 395 MET cc_start: 0.8011 (tpt) cc_final: 0.7557 (tpp) REVERT: D 433 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6493 (tt) REVERT: F 28 ASP cc_start: 0.8122 (t0) cc_final: 0.7742 (t0) REVERT: G 39 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.6029 (mttt) REVERT: I 44 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7694 (mp) REVERT: S 41 ARG cc_start: 0.7570 (ttp-110) cc_final: 0.7157 (ttp-110) REVERT: S 89 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8393 (mt) REVERT: S 162 MET cc_start: 0.6866 (ptm) cc_final: 0.5498 (pmm) REVERT: a 43 ILE cc_start: 0.3945 (OUTLIER) cc_final: 0.3276 (mt) REVERT: a 71 MET cc_start: 0.4615 (ppp) cc_final: 0.4003 (ppp) REVERT: a 104 MET cc_start: 0.2279 (mtp) cc_final: 0.1205 (mmm) REVERT: a 114 PHE cc_start: 0.3449 (m-10) cc_final: 0.3193 (t80) REVERT: L 60 MET cc_start: 0.3469 (mmm) cc_final: 0.3092 (tpp) REVERT: M 66 MET cc_start: 0.3697 (ppp) cc_final: 0.3470 (pmm) REVERT: N 32 MET cc_start: 0.5338 (ppp) cc_final: 0.5125 (ppp) REVERT: O 32 MET cc_start: 0.5138 (mpp) cc_final: 0.3795 (tpt) REVERT: P 32 MET cc_start: 0.5237 (tmm) cc_final: 0.4317 (tpp) REVERT: R 66 MET cc_start: 0.3817 (ppp) cc_final: 0.3037 (ttp) outliers start: 139 outliers final: 96 residues processed: 483 average time/residue: 0.2294 time to fit residues: 183.1003 Evaluate side-chains 451 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 346 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 186 GLN Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 155 ASP Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 8 SER Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 142 VAL Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain R residue 27 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 259 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 441 optimal weight: 0.0970 chunk 120 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 245 optimal weight: 0.7980 chunk 367 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN B 415 GLN ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.196106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.154628 restraints weight = 48688.117| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 3.25 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3947 r_free = 0.3947 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 38674 Z= 0.100 Angle : 0.551 9.844 52405 Z= 0.280 Chirality : 0.042 0.253 6242 Planarity : 0.004 0.054 6752 Dihedral : 6.060 161.052 5576 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 2.89 % Allowed : 20.37 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.59 (0.11), residues: 4939 helix: -1.32 (0.10), residues: 2324 sheet: -1.20 (0.23), residues: 522 loop : -2.22 (0.12), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 414 TYR 0.019 0.001 TYR I 14 PHE 0.022 0.001 PHE a 78 TRP 0.022 0.001 TRP 8 9 HIS 0.003 0.000 HIS D 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (38673) covalent geometry : angle 0.55052 / 0.28 (52405) hydrogen bonds : bond 0.03263 / 2.21 ( 1306) hydrogen bonds : angle 4.40532 / 2.97 ( 3753) Misc. bond : bond 0.00408 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 387 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 MET cc_start: 0.8628 (tpt) cc_final: 0.8405 (tpt) REVERT: A 446 TYR cc_start: 0.6758 (t80) cc_final: 0.6451 (t80) REVERT: B 216 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8017 (tp) REVERT: B 312 MET cc_start: 0.8221 (mmt) cc_final: 0.7894 (mmm) REVERT: B 390 MET cc_start: 0.7166 (ttp) cc_final: 0.6712 (ttp) REVERT: B 430 GLN cc_start: 0.7192 (tt0) cc_final: 0.6920 (tt0) REVERT: C 50 GLU cc_start: 0.6488 (mm-30) cc_final: 0.6155 (mm-30) REVERT: C 90 ARG cc_start: 0.7467 (mtp-110) cc_final: 0.7132 (mtp85) REVERT: C 473 ILE cc_start: 0.7134 (mt) cc_final: 0.6812 (mt) REVERT: D 202 MET cc_start: 0.7397 (mtm) cc_final: 0.6992 (mtp) REVERT: D 433 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6248 (tt) REVERT: E 374 ARG cc_start: 0.6969 (tpp-160) cc_final: 0.6622 (tpp80) REVERT: F 28 ASP cc_start: 0.7379 (t0) cc_final: 0.6995 (t0) REVERT: F 387 GLN cc_start: 0.7353 (mm-40) cc_final: 0.7102 (mm-40) REVERT: G 39 LYS cc_start: 0.6296 (OUTLIER) cc_final: 0.6013 (mttt) REVERT: I 44 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7817 (mp) REVERT: S 41 ARG cc_start: 0.7039 (ttp-110) cc_final: 0.6687 (ttp-110) REVERT: S 162 MET cc_start: 0.6520 (ptm) cc_final: 0.5037 (pmm) REVERT: S 163 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.5975 (pt) REVERT: a 43 ILE cc_start: 0.4032 (OUTLIER) cc_final: 0.3330 (mt) REVERT: a 71 MET cc_start: 0.5140 (ppp) cc_final: 0.4340 (ppp) REVERT: a 104 MET cc_start: 0.2282 (mtp) cc_final: 0.1155 (mmm) REVERT: a 114 PHE cc_start: 0.3724 (m-10) cc_final: 0.3369 (t80) REVERT: a 140 MET cc_start: 0.1573 (ttp) cc_final: 0.0883 (ptm) REVERT: a 187 MET cc_start: -0.1174 (tmm) cc_final: -0.1913 (tpt) REVERT: L 60 MET cc_start: 0.3440 (mmm) cc_final: 0.3129 (tpp) REVERT: M 66 MET cc_start: 0.3641 (ppp) cc_final: 0.3433 (pmm) REVERT: P 32 MET cc_start: 0.5524 (tmm) cc_final: 0.4750 (tpp) REVERT: R 66 MET cc_start: 0.3642 (ppp) cc_final: 0.2962 (ttp) REVERT: R 72 LEU cc_start: 0.3411 (OUTLIER) cc_final: 0.2954 (pt) outliers start: 107 outliers final: 70 residues processed: 473 average time/residue: 0.2314 time to fit residues: 181.4220 Evaluate side-chains 433 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 356 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 291 MET Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 142 VAL Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 66 MET Chi-restraints excluded: chain R residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 262 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 0.0670 chunk 295 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 257 optimal weight: 1.9990 chunk 349 optimal weight: 8.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 132 GLN H 85 ASN a 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.196004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.156905 restraints weight = 48970.147| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 3.16 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3965 r_free = 0.3965 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3965 r_free = 0.3965 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 38674 Z= 0.114 Angle : 0.555 11.161 52405 Z= 0.281 Chirality : 0.042 0.232 6242 Planarity : 0.004 0.056 6752 Dihedral : 5.948 158.146 5575 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.35 % Favored : 94.53 % Rotamer: Outliers : 3.10 % Allowed : 20.31 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.38 (0.11), residues: 4939 helix: -1.06 (0.11), residues: 2336 sheet: -1.27 (0.23), residues: 531 loop : -2.17 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 414 TYR 0.020 0.001 TYR A 256 PHE 0.024 0.001 PHE a 78 TRP 0.029 0.002 TRP 8 9 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (38673) covalent geometry : angle 0.55472 / 0.28 (52405) hydrogen bonds : bond 0.03218 / 2.17 ( 1306) hydrogen bonds : angle 4.33038 / 2.93 ( 3753) Misc. bond : bond 0.00365 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 375 time to evaluate : 1.475 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 446 TYR cc_start: 0.6719 (t80) cc_final: 0.6353 (t80) REVERT: B 216 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7949 (tp) REVERT: B 390 MET cc_start: 0.7116 (ttp) cc_final: 0.6683 (ttp) REVERT: B 430 GLN cc_start: 0.7203 (tt0) cc_final: 0.6978 (tt0) REVERT: C 50 GLU cc_start: 0.6434 (mm-30) cc_final: 0.6076 (mm-30) REVERT: C 90 ARG cc_start: 0.7312 (mtp-110) cc_final: 0.7037 (mtp85) REVERT: C 473 ILE cc_start: 0.7021 (mt) cc_final: 0.6704 (mt) REVERT: D 202 MET cc_start: 0.7428 (mtm) cc_final: 0.7063 (mtp) REVERT: D 433 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6249 (tt) REVERT: E 374 ARG cc_start: 0.6796 (tpp-160) cc_final: 0.6478 (tpp80) REVERT: F 28 ASP cc_start: 0.6924 (t0) cc_final: 0.6555 (t0) REVERT: F 371 ASP cc_start: 0.7288 (m-30) cc_final: 0.7031 (m-30) REVERT: F 387 GLN cc_start: 0.7120 (mm-40) cc_final: 0.6877 (mm-40) REVERT: G 124 PHE cc_start: 0.7206 (m-80) cc_final: 0.6912 (m-80) REVERT: I 44 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7852 (mp) REVERT: S 41 ARG cc_start: 0.6968 (ttp-110) cc_final: 0.6734 (ttp-110) REVERT: S 89 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8283 (mt) REVERT: S 163 ILE cc_start: 0.6718 (OUTLIER) cc_final: 0.6121 (pt) REVERT: b 171 GLU cc_start: 0.7996 (pp20) cc_final: 0.7791 (pp20) REVERT: a 43 ILE cc_start: 0.4624 (OUTLIER) cc_final: 0.3825 (mt) REVERT: a 100 MET cc_start: 0.3972 (ptm) cc_final: 0.3516 (ttt) REVERT: a 104 MET cc_start: 0.2309 (mtp) cc_final: 0.1542 (mmt) REVERT: M 69 PHE cc_start: 0.2504 (OUTLIER) cc_final: 0.1071 (m-10) REVERT: P 32 MET cc_start: 0.5469 (tmm) cc_final: 0.4756 (tpp) REVERT: R 66 MET cc_start: 0.3298 (ppp) cc_final: 0.2791 (ttp) outliers start: 115 outliers final: 89 residues processed: 472 average time/residue: 0.2284 time to fit residues: 178.3484 Evaluate side-chains 449 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 353 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 291 MET Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 155 ASP Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 142 VAL Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain R residue 27 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 292 optimal weight: 0.9990 chunk 492 optimal weight: 0.0040 chunk 155 optimal weight: 0.7980 chunk 337 optimal weight: 3.9990 chunk 461 optimal weight: 20.0000 chunk 473 optimal weight: 0.9980 chunk 462 optimal weight: 20.0000 chunk 181 optimal weight: 0.7980 chunk 281 optimal weight: 3.9990 chunk 299 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN F 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.196921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.156998 restraints weight = 48908.591| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 3.16 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3969 r_free = 0.3969 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 38674 Z= 0.099 Angle : 0.549 18.016 52405 Z= 0.277 Chirality : 0.041 0.260 6242 Planarity : 0.004 0.053 6752 Dihedral : 5.729 148.742 5575 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.33 % Favored : 95.55 % Rotamer: Outliers : 2.89 % Allowed : 21.20 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 4939 helix: -0.82 (0.11), residues: 2336 sheet: -1.14 (0.23), residues: 542 loop : -2.03 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 164 TYR 0.019 0.001 TYR I 14 PHE 0.024 0.001 PHE a 78 TRP 0.028 0.002 TRP 8 9 HIS 0.002 0.000 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (38673) covalent geometry : angle 0.54860 / 0.28 (52405) hydrogen bonds : bond 0.03030 / 2.06 ( 1306) hydrogen bonds : angle 4.20104 / 2.85 ( 3753) Misc. bond : bond 0.00373 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 367 time to evaluate : 1.404 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 226 MET cc_start: 0.8623 (tpt) cc_final: 0.8395 (tpt) REVERT: A 446 TYR cc_start: 0.6786 (t80) cc_final: 0.6447 (t80) REVERT: B 216 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7999 (tp) REVERT: B 312 MET cc_start: 0.8256 (mmt) cc_final: 0.7927 (mmm) REVERT: B 390 MET cc_start: 0.7128 (ttp) cc_final: 0.6672 (ttp) REVERT: B 430 GLN cc_start: 0.7200 (tt0) cc_final: 0.6948 (tt0) REVERT: C 50 GLU cc_start: 0.6375 (mm-30) cc_final: 0.6038 (mm-30) REVERT: C 90 ARG cc_start: 0.7352 (mtp-110) cc_final: 0.7067 (mtp85) REVERT: C 215 GLN cc_start: 0.7376 (tt0) cc_final: 0.7172 (tt0) REVERT: C 392 LEU cc_start: 0.8041 (mt) cc_final: 0.7828 (tp) REVERT: C 473 ILE cc_start: 0.6911 (mt) cc_final: 0.6587 (mt) REVERT: D 202 MET cc_start: 0.7336 (mtm) cc_final: 0.6975 (mtp) REVERT: E 374 ARG cc_start: 0.6888 (tpp-160) cc_final: 0.6559 (tpp80) REVERT: F 28 ASP cc_start: 0.6952 (t0) cc_final: 0.6575 (t0) REVERT: F 360 MET cc_start: 0.7747 (tpp) cc_final: 0.7541 (tpp) REVERT: F 371 ASP cc_start: 0.7192 (m-30) cc_final: 0.6955 (m-30) REVERT: F 387 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6896 (mm-40) REVERT: G 124 PHE cc_start: 0.7305 (m-80) cc_final: 0.6954 (m-80) REVERT: I 44 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7893 (mp) REVERT: S 89 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8343 (mt) REVERT: b 171 GLU cc_start: 0.7909 (pp20) cc_final: 0.7663 (pp20) REVERT: a 43 ILE cc_start: 0.4574 (OUTLIER) cc_final: 0.3799 (mt) REVERT: a 71 MET cc_start: 0.5355 (ppp) cc_final: 0.4536 (ppp) REVERT: a 100 MET cc_start: 0.3879 (ptm) cc_final: 0.3527 (ttt) REVERT: a 187 MET cc_start: -0.0790 (tmm) cc_final: -0.1488 (tpt) REVERT: M 32 MET cc_start: 0.4923 (OUTLIER) cc_final: 0.4669 (mtt) REVERT: O 32 MET cc_start: 0.5518 (mpp) cc_final: 0.3827 (tpp) REVERT: P 32 MET cc_start: 0.5512 (tmm) cc_final: 0.4936 (tpp) REVERT: R 66 MET cc_start: 0.3014 (ppp) cc_final: 0.2780 (ttp) outliers start: 107 outliers final: 89 residues processed: 460 average time/residue: 0.2366 time to fit residues: 180.6256 Evaluate side-chains 443 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 349 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 61 LYS Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain M residue 32 MET Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain R residue 27 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 452 optimal weight: 0.8980 chunk 193 optimal weight: 0.7980 chunk 250 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 220 optimal weight: 5.9990 chunk 121 optimal weight: 0.0010 chunk 150 optimal weight: 4.9990 chunk 427 optimal weight: 50.0000 chunk 232 optimal weight: 0.0870 chunk 212 optimal weight: 4.9990 chunk 509 optimal weight: 40.0000 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN F 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.198942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.163255 restraints weight = 48544.332| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 3.14 r_work: 0.3557 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3582 r_free = 0.3582 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 38674 Z= 0.092 Angle : 0.533 11.247 52405 Z= 0.269 Chirality : 0.041 0.264 6242 Planarity : 0.003 0.053 6752 Dihedral : 5.412 131.913 5574 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.31 % Favored : 95.57 % Rotamer: Outliers : 2.59 % Allowed : 21.66 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.80 (0.12), residues: 4939 helix: -0.55 (0.11), residues: 2344 sheet: -1.03 (0.23), residues: 543 loop : -1.93 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 164 TYR 0.025 0.001 TYR F 370 PHE 0.029 0.001 PHE a 78 TRP 0.028 0.002 TRP 8 9 HIS 0.003 0.000 HIS F 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (38673) covalent geometry : angle 0.53316 / 0.27 (52405) hydrogen bonds : bond 0.02788 / 1.90 ( 1306) hydrogen bonds : angle 4.03379 / 2.74 ( 3753) Misc. bond : bond 0.00375 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 380 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7674 (tt0) REVERT: A 446 TYR cc_start: 0.7414 (t80) cc_final: 0.7080 (t80) REVERT: B 216 LEU cc_start: 0.8206 (tt) cc_final: 0.7925 (tp) REVERT: B 312 MET cc_start: 0.8384 (mmt) cc_final: 0.8052 (mmm) REVERT: B 390 MET cc_start: 0.7507 (ttp) cc_final: 0.7112 (ttp) REVERT: B 430 GLN cc_start: 0.7437 (tt0) cc_final: 0.7188 (tt0) REVERT: C 50 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6487 (mm-30) REVERT: C 90 ARG cc_start: 0.7343 (mtp-110) cc_final: 0.7135 (mtp85) REVERT: C 426 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: C 473 ILE cc_start: 0.6989 (mt) cc_final: 0.6686 (mt) REVERT: D 202 MET cc_start: 0.7461 (mtm) cc_final: 0.7004 (mtp) REVERT: E 100 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8315 (mt) REVERT: E 374 ARG cc_start: 0.7153 (tpp-160) cc_final: 0.6791 (tpp80) REVERT: F 28 ASP cc_start: 0.8106 (t0) cc_final: 0.7733 (t0) REVERT: F 65 MET cc_start: 0.8042 (mmm) cc_final: 0.7741 (mmm) REVERT: F 371 ASP cc_start: 0.7905 (m-30) cc_final: 0.7650 (m-30) REVERT: G 124 PHE cc_start: 0.7583 (m-80) cc_final: 0.7134 (m-80) REVERT: G 224 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6792 (tt0) REVERT: H 134 ARG cc_start: 0.7075 (mtp180) cc_final: 0.6555 (tpt-90) REVERT: I 44 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7794 (mp) REVERT: S 89 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8337 (mt) REVERT: b 171 GLU cc_start: 0.7859 (pp20) cc_final: 0.7539 (pp20) REVERT: a 43 ILE cc_start: 0.4407 (OUTLIER) cc_final: 0.3726 (mt) REVERT: a 100 MET cc_start: 0.4158 (ptm) cc_final: 0.3561 (ttt) REVERT: a 187 MET cc_start: -0.1042 (tmm) cc_final: -0.1671 (tpt) REVERT: M 32 MET cc_start: 0.5107 (OUTLIER) cc_final: 0.4631 (mtp) REVERT: O 32 MET cc_start: 0.6014 (mpp) cc_final: 0.4163 (tpp) REVERT: P 32 MET cc_start: 0.5827 (tmm) cc_final: 0.4912 (tpp) REVERT: R 66 MET cc_start: 0.3963 (ppp) cc_final: 0.3163 (ttp) outliers start: 96 outliers final: 72 residues processed: 459 average time/residue: 0.2403 time to fit residues: 182.3206 Evaluate side-chains 430 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 351 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 224 GLU Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 61 LYS Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 49 LEU Chi-restraints excluded: chain a residue 114 PHE Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain M residue 32 MET Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 16 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 323 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 437 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 319 optimal weight: 6.9990 chunk 291 optimal weight: 0.9980 chunk 358 optimal weight: 0.0870 chunk 188 optimal weight: 4.9990 chunk 474 optimal weight: 10.0000 chunk 396 optimal weight: 50.0000 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 GLN F 132 GLN ** c 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.192573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152118 restraints weight = 49308.744| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 3.48 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 38674 Z= 0.205 Angle : 0.649 12.328 52405 Z= 0.327 Chirality : 0.046 0.307 6242 Planarity : 0.004 0.056 6752 Dihedral : 6.030 145.125 5574 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.86 % Favored : 93.04 % Rotamer: Outliers : 3.35 % Allowed : 21.28 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.13 (0.12), residues: 4939 helix: -0.78 (0.11), residues: 2353 sheet: -1.08 (0.24), residues: 519 loop : -2.17 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 164 TYR 0.020 0.002 TYR i 21 PHE 0.027 0.002 PHE a 78 TRP 0.030 0.002 TRP b 176 HIS 0.008 0.001 HIS C 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (38673) covalent geometry : angle 0.64919 / 0.33 (52405) hydrogen bonds : bond 0.03668 / 2.47 ( 1306) hydrogen bonds : angle 4.45336 / 3.03 ( 3753) Misc. bond : bond 0.00267 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 354 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6880 (mt) REVERT: A 54 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6922 (tt0) REVERT: A 446 TYR cc_start: 0.6913 (t80) cc_final: 0.6538 (t80) REVERT: B 146 MET cc_start: 0.6271 (ttm) cc_final: 0.5958 (ttm) REVERT: B 216 LEU cc_start: 0.8514 (tt) cc_final: 0.8218 (tp) REVERT: B 430 GLN cc_start: 0.7200 (tt0) cc_final: 0.6983 (tt0) REVERT: C 50 GLU cc_start: 0.6383 (mm-30) cc_final: 0.6069 (mm-30) REVERT: C 90 ARG cc_start: 0.7527 (mtp-110) cc_final: 0.7241 (mtp85) REVERT: C 373 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6806 (mmt90) REVERT: D 202 MET cc_start: 0.7438 (mtm) cc_final: 0.7048 (mtp) REVERT: E 414 ARG cc_start: 0.7870 (ttm110) cc_final: 0.7456 (ttm110) REVERT: F 28 ASP cc_start: 0.6885 (t0) cc_final: 0.6565 (t0) REVERT: F 371 ASP cc_start: 0.7429 (m-30) cc_final: 0.7107 (m-30) REVERT: H 59 ARG cc_start: 0.5713 (ptm160) cc_final: 0.5472 (ptp-110) REVERT: I 44 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7791 (mp) REVERT: S 89 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8346 (mt) REVERT: b 171 GLU cc_start: 0.7935 (pp20) cc_final: 0.7673 (pp20) REVERT: a 43 ILE cc_start: 0.4723 (OUTLIER) cc_final: 0.3906 (mt) REVERT: a 100 MET cc_start: 0.3868 (ptm) cc_final: 0.3570 (ttt) REVERT: a 187 MET cc_start: -0.0621 (tmm) cc_final: -0.1502 (tpt) REVERT: M 69 PHE cc_start: 0.2526 (OUTLIER) cc_final: 0.0885 (m-10) REVERT: O 32 MET cc_start: 0.5677 (mpp) cc_final: 0.3970 (tpp) REVERT: P 32 MET cc_start: 0.5404 (tmm) cc_final: 0.4805 (tpp) REVERT: R 66 MET cc_start: 0.3102 (ppp) cc_final: 0.2845 (ttp) outliers start: 124 outliers final: 106 residues processed: 456 average time/residue: 0.2360 time to fit residues: 179.0267 Evaluate side-chains 453 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 341 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 373 ARG Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 215 SER Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 407 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 61 LYS Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 155 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 60 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 114 PHE Chi-restraints excluded: chain a residue 133 THR Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain N residue 63 PHE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 27 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 461 optimal weight: 0.0670 chunk 383 optimal weight: 40.0000 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 240 optimal weight: 0.6980 chunk 413 optimal weight: 40.0000 chunk 182 optimal weight: 0.9990 chunk 465 optimal weight: 40.0000 chunk 160 optimal weight: 3.9990 chunk 341 optimal weight: 6.9990 chunk 358 optimal weight: 0.3980 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN ** c 23 GLN ** 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 = 0.4362 r_free = 0.4362 target = 0.195436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.151470 restraints weight = 48614.401| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 4.81 r_work: 0.3331 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 38674 Z= 0.113 Angle : 0.568 12.401 52405 Z= 0.286 Chirality : 0.042 0.280 6242 Planarity : 0.004 0.056 6752 Dihedral : 5.671 132.677 5574 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.98 % Favored : 94.90 % Rotamer: Outliers : 2.70 % Allowed : 21.93 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.83 (0.12), residues: 4939 helix: -0.54 (0.11), residues: 2353 sheet: -1.05 (0.23), residues: 536 loop : -1.99 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 164 TYR 0.033 0.001 TYR S 170 PHE 0.029 0.001 PHE a 78 TRP 0.027 0.002 TRP b 176 HIS 0.008 0.001 HIS C 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (38673) covalent geometry : angle 0.56763 / 0.29 (52405) hydrogen bonds : bond 0.03077 / 2.09 ( 1306) hydrogen bonds : angle 4.17841 / 2.84 ( 3753) Misc. bond : bond 0.00370 / 0.19 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9878 Ramachandran restraints generated. 4939 Oldfield, 0 Emsley, 4939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 348 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6598 (mt) REVERT: A 54 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7754 (tt0) REVERT: A 446 TYR cc_start: 0.7804 (t80) cc_final: 0.7340 (t80) REVERT: B 146 MET cc_start: 0.6694 (ttm) cc_final: 0.6305 (ttm) REVERT: B 216 LEU cc_start: 0.8245 (tt) cc_final: 0.7883 (tp) REVERT: B 430 GLN cc_start: 0.7539 (tt0) cc_final: 0.7294 (tt0) REVERT: C 50 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6684 (mm-30) REVERT: C 90 ARG cc_start: 0.7034 (mtp-110) cc_final: 0.6752 (mtp85) REVERT: C 392 LEU cc_start: 0.8263 (mt) cc_final: 0.7851 (tp) REVERT: C 426 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: D 202 MET cc_start: 0.7484 (mtm) cc_final: 0.7167 (mtm) REVERT: E 374 ARG cc_start: 0.7268 (tpp-160) cc_final: 0.6813 (tpp80) REVERT: E 414 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7382 (ttm110) REVERT: F 28 ASP cc_start: 0.8059 (t0) cc_final: 0.7672 (t0) REVERT: F 371 ASP cc_start: 0.8203 (m-30) cc_final: 0.7872 (m-30) REVERT: F 429 HIS cc_start: 0.7168 (m170) cc_final: 0.6944 (m170) REVERT: G 193 TYR cc_start: 0.6041 (m-10) cc_final: 0.5792 (m-80) REVERT: H 59 ARG cc_start: 0.5367 (ptm160) cc_final: 0.5000 (ptp-110) REVERT: H 134 ARG cc_start: 0.6691 (mtp180) cc_final: 0.6340 (tpt-90) REVERT: I 44 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7719 (mp) REVERT: S 89 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8118 (mt) REVERT: S 163 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5602 (pt) REVERT: b 171 GLU cc_start: 0.6457 (pp20) cc_final: 0.6171 (pp20) REVERT: a 43 ILE cc_start: 0.3437 (OUTLIER) cc_final: 0.3157 (mt) REVERT: a 100 MET cc_start: 0.3092 (ptm) cc_final: 0.2705 (ttt) REVERT: a 187 MET cc_start: -0.1365 (tmm) cc_final: -0.1784 (tpt) REVERT: K 60 MET cc_start: 0.1909 (tmm) cc_final: 0.0374 (ptp) REVERT: M 32 MET cc_start: 0.5258 (mtt) cc_final: 0.4967 (mtp) REVERT: M 69 PHE cc_start: 0.2851 (OUTLIER) cc_final: 0.1986 (m-10) REVERT: O 32 MET cc_start: 0.6373 (mpp) cc_final: 0.4139 (tpp) REVERT: P 32 MET cc_start: 0.5175 (tmm) cc_final: 0.4258 (tpp) REVERT: R 66 MET cc_start: 0.4865 (ppp) cc_final: 0.4006 (ttp) outliers start: 100 outliers final: 88 residues processed: 433 average time/residue: 0.2333 time to fit residues: 168.4359 Evaluate side-chains 437 residues out of total 4027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 342 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 327 THR Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 407 SER Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 308 SER Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 41 GLN Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 61 LYS Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 155 ASP Chi-restraints excluded: chain S residue 163 ILE Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 204 LEU Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain a residue 19 ILE Chi-restraints excluded: chain a residue 40 ASN Chi-restraints excluded: chain a residue 43 ILE Chi-restraints excluded: chain a residue 60 ILE Chi-restraints excluded: chain a residue 67 THR Chi-restraints excluded: chain a residue 114 PHE Chi-restraints excluded: chain a residue 133 THR Chi-restraints excluded: chain a residue 209 ILE Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain M residue 69 PHE Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 16 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 168 optimal weight: 3.9990 chunk 463 optimal weight: 9.9990 chunk 332 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 400 optimal weight: 40.0000 chunk 14 optimal weight: 3.9990 chunk 315 optimal weight: 3.9990 chunk 465 optimal weight: 0.7980 chunk 455 optimal weight: 10.0000 chunk 407 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.193508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.157120 restraints weight = 49082.221| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.93 r_work: 0.3436 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 38674 Z= 0.160 Angle : 0.614 12.575 52405 Z= 0.308 Chirality : 0.044 0.301 6242 Planarity : 0.004 0.054 6752 Dihedral : 5.868 132.167 5574 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.96 % Favored : 92.93 % Rotamer: Outliers : 2.97 % Allowed : 21.72 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.93 (0.12), residues: 4939 helix: -0.60 (0.11), residues: 2357 sheet: -1.15 (0.24), residues: 515 loop : -2.06 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 184 TYR 0.033 0.002 TYR b 140 PHE 0.031 0.001 PHE a 78 TRP 0.032 0.002 TRP b 176 HIS 0.006 0.001 HIS D 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (38673) covalent geometry : angle 0.61354 / 0.31 (52405) hydrogen bonds : bond 0.03400 / 2.29 ( 1306) hydrogen bonds : angle 4.32178 / 2.94 ( 3753) Misc. bond : bond 0.00333 / 0.18 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8668.63 seconds wall clock time: 149 minutes 22.00 seconds (8962.00 seconds total)