Starting phenix.real_space_refine on Sat Feb 7 21:14:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ck5_45641/02_2026/9ck5_45641_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ck5_45641/02_2026/9ck5_45641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ck5_45641/02_2026/9ck5_45641_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ck5_45641/02_2026/9ck5_45641_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ck5_45641/02_2026/9ck5_45641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ck5_45641/02_2026/9ck5_45641.map" } resolution = 3.0 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= 0.005 sd= 0.062 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 16 5.49 5 Mg 8 5.21 5 S 224 5.16 5 C 23536 2.51 5 N 6416 2.21 5 O 6856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37056 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "J" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "K" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "L" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "M" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "N" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "O" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "P" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.01, per 1000 atoms: 0.24 Number of scatterers: 37056 At special positions: 0 Unit cell: (130.707, 130.707, 128.853, 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 224 16.00 P 16 15.00 Mg 8 11.99 O 6856 8.00 N 6416 7.00 C 23536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8432 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 41 sheets defined 37.8% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.813A pdb=" N TYR A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 59 removed outlier: 3.704A pdb=" N ALA A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 54 " --> pdb=" O PRO A 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.783A pdb=" N GLY A 73 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 74 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 113 through 119 removed outlier: 3.560A pdb=" N THR A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 4.137A pdb=" N PHE A 127 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.505A pdb=" N SER A 145 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 141 through 146' Processing helix chain 'A' and resid 155 through 163 removed outlier: 3.625A pdb=" N LEU A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 194 removed outlier: 4.222A pdb=" N TYR A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 removed outlier: 3.771A pdb=" N ARG A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE A 218 " --> pdb=" O TRP A 214 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 removed outlier: 3.655A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 removed outlier: 3.638A pdb=" N THR A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 286 " --> pdb=" O HIS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.585A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 316 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.881A pdb=" N ARG A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.607A pdb=" N LEU A 390 " --> pdb=" O HIS A 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 391 " --> pdb=" O MET A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 391' Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.254A pdb=" N LEU A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 408' Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.607A pdb=" N VAL A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 432 removed outlier: 3.542A pdb=" N ALA A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.724A pdb=" N TRP A 451 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.686A pdb=" N ALA A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 457' Processing helix chain 'B' and resid 20 through 25 removed outlier: 3.830A pdb=" N TYR B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 3.803A pdb=" N ALA B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 75 removed outlier: 4.008A pdb=" N ASP B 72 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 73 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 74 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B 75 " --> pdb=" O ASP B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 75' Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.650A pdb=" N ARG B 79 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 123 through 127 removed outlier: 4.131A pdb=" N PHE B 127 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.509A pdb=" N SER B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 141 through 146' Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.503A pdb=" N GLY B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 removed outlier: 3.614A pdb=" N LEU B 219 " --> pdb=" O ARG B 215 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.180A pdb=" N GLN B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA B 257 " --> pdb=" O ARG B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.674A pdb=" N THR B 278 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.703A pdb=" N LEU B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 316 " --> pdb=" O ARG B 312 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 removed outlier: 3.981A pdb=" N ASP B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 349 " --> pdb=" O PHE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 391 Processing helix chain 'B' and resid 413 through 432 removed outlier: 3.747A pdb=" N VAL B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN B 432 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 452 through 457 removed outlier: 3.705A pdb=" N ALA B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 457 " --> pdb=" O PRO B 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 457' Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.794A pdb=" N TYR C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 63 removed outlier: 3.721A pdb=" N ALA C 53 " --> pdb=" O PRO C 49 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 54 " --> pdb=" O PRO C 50 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER C 61 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 75 removed outlier: 3.915A pdb=" N ASP C 72 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 73 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 75 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.959A pdb=" N LEU C 107 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 108' Processing helix chain 'C' and resid 113 through 119 removed outlier: 3.673A pdb=" N SER C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 127 removed outlier: 4.238A pdb=" N PHE C 127 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.705A pdb=" N LYS C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 removed outlier: 3.778A pdb=" N LEU C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.532A pdb=" N TYR C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU C 191 " --> pdb=" O ARG C 187 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 removed outlier: 3.756A pdb=" N LEU C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C 220 " --> pdb=" O ASP C 216 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 261 removed outlier: 3.642A pdb=" N MET C 251 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C 254 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 288 removed outlier: 3.889A pdb=" N THR C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.744A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 351 removed outlier: 4.098A pdb=" N ASP C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU C 348 " --> pdb=" O GLY C 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 349 " --> pdb=" O PHE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 391 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.184A pdb=" N LEU C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 408' Processing helix chain 'C' and resid 413 through 432 removed outlier: 3.830A pdb=" N VAL C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA C 419 " --> pdb=" O PRO C 415 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 449 Processing helix chain 'C' and resid 452 through 462 removed outlier: 3.668A pdb=" N ALA C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 457 " --> pdb=" O PRO C 453 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TRP C 462 " --> pdb=" O ALA C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.829A pdb=" N TYR D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 60 removed outlier: 3.788A pdb=" N VAL D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.988A pdb=" N ASP D 72 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY D 73 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 74 " --> pdb=" O THR D 71 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR D 75 " --> pdb=" O ASP D 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 69 through 75' Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.896A pdb=" N LEU D 107 " --> pdb=" O PRO D 104 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.665A pdb=" N SER D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 removed outlier: 4.239A pdb=" N PHE D 127 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 removed outlier: 3.792A pdb=" N LYS D 146 " --> pdb=" O PRO D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 removed outlier: 3.517A pdb=" N LEU D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.815A pdb=" N VAL D 189 " --> pdb=" O TYR D 185 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR D 190 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 233 removed outlier: 3.751A pdb=" N ARG D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 261 removed outlier: 3.821A pdb=" N MET D 251 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 254 " --> pdb=" O MET D 250 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN D 255 " --> pdb=" O MET D 251 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA D 257 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 260 " --> pdb=" O PHE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.651A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET D 320 " --> pdb=" O LYS D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 351 removed outlier: 3.619A pdb=" N THR D 342 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP D 347 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 349 " --> pdb=" O PHE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 386 through 391 removed outlier: 3.610A pdb=" N LEU D 390 " --> pdb=" O HIS D 386 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 391 " --> pdb=" O MET D 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 391' Processing helix chain 'D' and resid 403 through 408 removed outlier: 4.230A pdb=" N LEU D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 403 through 408' Processing helix chain 'D' and resid 413 through 432 removed outlier: 3.809A pdb=" N VAL D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 449 Processing helix chain 'D' and resid 452 through 457 removed outlier: 3.728A pdb=" N ALA D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA D 457 " --> pdb=" O PRO D 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 452 through 457' Processing helix chain 'D' and resid 457 through 462 removed outlier: 3.937A pdb=" N VAL D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TRP D 462 " --> pdb=" O ALA D 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 457 through 462' Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.884A pdb=" N TYR E 25 " --> pdb=" O ARG E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 60 removed outlier: 3.707A pdb=" N ALA E 53 " --> pdb=" O PRO E 49 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 75 removed outlier: 3.917A pdb=" N ASP E 72 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY E 73 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR E 75 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.901A pdb=" N LEU E 107 " --> pdb=" O PRO E 104 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE E 108 " --> pdb=" O LEU E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 104 through 108' Processing helix chain 'E' and resid 113 through 119 removed outlier: 3.692A pdb=" N SER E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 4.204A pdb=" N PHE E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.524A pdb=" N SER E 145 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS E 146 " --> pdb=" O PRO E 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 141 through 146' Processing helix chain 'E' and resid 155 through 163 removed outlier: 3.718A pdb=" N LEU E 162 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.533A pdb=" N TYR E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA E 188 " --> pdb=" O ASN E 184 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL E 189 " --> pdb=" O TYR E 185 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 233 removed outlier: 3.811A pdb=" N ARG E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 227 " --> pdb=" O GLU E 223 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 261 removed outlier: 3.782A pdb=" N MET E 251 " --> pdb=" O CYS E 247 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS E 252 " --> pdb=" O GLU E 248 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 254 " --> pdb=" O MET E 250 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA E 257 " --> pdb=" O ARG E 253 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG E 258 " --> pdb=" O ALA E 254 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 removed outlier: 3.676A pdb=" N ASN E 277 " --> pdb=" O GLY E 273 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 322 removed outlier: 3.757A pdb=" N LEU E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS E 316 " --> pdb=" O ARG E 312 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA E 317 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 319 " --> pdb=" O ALA E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 351 removed outlier: 4.096A pdb=" N ASP E 347 " --> pdb=" O LEU E 343 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU E 348 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 349 " --> pdb=" O PHE E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 386 through 391 Processing helix chain 'E' and resid 403 through 408 removed outlier: 4.234A pdb=" N LEU E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 403 through 408' Processing helix chain 'E' and resid 413 through 432 removed outlier: 3.774A pdb=" N VAL E 418 " --> pdb=" O ALA E 414 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA E 419 " --> pdb=" O PRO E 415 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU E 424 " --> pdb=" O ASN E 420 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN E 429 " --> pdb=" O GLU E 425 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN E 432 " --> pdb=" O VAL E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 449 removed outlier: 4.029A pdb=" N ILE E 445 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 448 " --> pdb=" O ILE E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 462 removed outlier: 3.689A pdb=" N ALA E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA E 457 " --> pdb=" O PRO E 453 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU E 460 " --> pdb=" O ALA E 456 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TRP E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.838A pdb=" N TYR F 25 " --> pdb=" O ARG F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 60 removed outlier: 3.538A pdb=" N ALA F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 55 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA F 58 " --> pdb=" O GLY F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 75 removed outlier: 4.029A pdb=" N ASP F 72 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY F 73 " --> pdb=" O TRP F 70 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU F 74 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 75 " --> pdb=" O ASP F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 69 through 75' Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.914A pdb=" N LEU F 107 " --> pdb=" O PRO F 104 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 104 through 108' Processing helix chain 'F' and resid 113 through 119 removed outlier: 3.668A pdb=" N SER F 119 " --> pdb=" O ASN F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 removed outlier: 4.237A pdb=" N PHE F 127 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.530A pdb=" N SER F 145 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS F 146 " --> pdb=" O PRO F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'F' and resid 155 through 163 Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.783A pdb=" N VAL F 189 " --> pdb=" O TYR F 185 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 removed outlier: 3.753A pdb=" N ARG F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU F 219 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 261 removed outlier: 3.790A pdb=" N MET F 251 " --> pdb=" O CYS F 247 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS F 252 " --> pdb=" O GLU F 248 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA F 254 " --> pdb=" O MET F 250 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN F 255 " --> pdb=" O MET F 251 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE F 256 " --> pdb=" O LYS F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 288 removed outlier: 3.702A pdb=" N THR F 279 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU F 280 " --> pdb=" O ALA F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.837A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS F 316 " --> pdb=" O ARG F 312 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 317 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET F 320 " --> pdb=" O LYS F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 351 removed outlier: 3.504A pdb=" N THR F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP F 347 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU F 348 " --> pdb=" O GLY F 344 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 349 " --> pdb=" O PHE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 386 through 391 Processing helix chain 'F' and resid 403 through 408 removed outlier: 4.228A pdb=" N LEU F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY F 408 " --> pdb=" O GLY F 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 403 through 408' Processing helix chain 'F' and resid 413 through 432 removed outlier: 3.854A pdb=" N VAL F 418 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA F 419 " --> pdb=" O PRO F 415 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASN F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS F 427 " --> pdb=" O ALA F 423 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN F 429 " --> pdb=" O GLU F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 449 Processing helix chain 'F' and resid 452 through 457 removed outlier: 3.725A pdb=" N ALA F 456 " --> pdb=" O SER F 452 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 452 through 457' Processing helix chain 'F' and resid 457 through 462 removed outlier: 3.954A pdb=" N VAL F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP F 462 " --> pdb=" O ALA F 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 457 through 462' Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.669A pdb=" N TYR G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 60 removed outlier: 3.724A pdb=" N ALA G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 75 removed outlier: 3.939A pdb=" N ASP G 72 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY G 73 " --> pdb=" O TRP G 70 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU G 74 " --> pdb=" O THR G 71 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR G 75 " --> pdb=" O ASP G 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 69 through 75' Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.901A pdb=" N LEU G 107 " --> pdb=" O PRO G 104 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE G 108 " --> pdb=" O LEU G 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 104 through 108' Processing helix chain 'G' and resid 112 through 121 removed outlier: 4.111A pdb=" N MET G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 127 removed outlier: 4.068A pdb=" N PHE G 127 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 146 removed outlier: 3.525A pdb=" N SER G 145 " --> pdb=" O PRO G 141 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS G 146 " --> pdb=" O PRO G 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 141 through 146' Processing helix chain 'G' and resid 155 through 163 removed outlier: 3.604A pdb=" N LEU G 162 " --> pdb=" O GLU G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.511A pdb=" N TYR G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY G 186 " --> pdb=" O ALA G 182 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL G 189 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR G 190 " --> pdb=" O GLY G 186 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS G 192 " --> pdb=" O ALA G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 233 removed outlier: 3.807A pdb=" N ARG G 217 " --> pdb=" O ARG G 213 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE G 226 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS G 227 " --> pdb=" O GLU G 223 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR G 232 " --> pdb=" O SER G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 260 removed outlier: 3.703A pdb=" N MET G 251 " --> pdb=" O CYS G 247 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS G 252 " --> pdb=" O GLU G 248 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA G 254 " --> pdb=" O MET G 250 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN G 255 " --> pdb=" O MET G 251 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N PHE G 256 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA G 257 " --> pdb=" O ARG G 253 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG G 258 " --> pdb=" O ALA G 254 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 260 " --> pdb=" O PHE G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 288 removed outlier: 3.870A pdb=" N THR G 279 " --> pdb=" O THR G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.853A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS G 316 " --> pdb=" O ARG G 312 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA G 317 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU G 318 " --> pdb=" O LEU G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 351 removed outlier: 4.111A pdb=" N ASP G 347 " --> pdb=" O LEU G 343 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU G 348 " --> pdb=" O GLY G 344 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU G 349 " --> pdb=" O PHE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 385 No H-bonds generated for 'chain 'G' and resid 383 through 385' Processing helix chain 'G' and resid 386 through 391 Processing helix chain 'G' and resid 403 through 408 removed outlier: 4.219A pdb=" N LEU G 407 " --> pdb=" O GLY G 403 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY G 408 " --> pdb=" O GLY G 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 403 through 408' Processing helix chain 'G' and resid 413 through 432 removed outlier: 3.814A pdb=" N VAL G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA G 419 " --> pdb=" O PRO G 415 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU G 424 " --> pdb=" O ASN G 420 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN G 429 " --> pdb=" O GLU G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 442 through 449 Processing helix chain 'G' and resid 452 through 462 removed outlier: 3.666A pdb=" N ALA G 456 " --> pdb=" O SER G 452 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA G 457 " --> pdb=" O PRO G 453 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA G 458 " --> pdb=" O GLU G 454 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU G 460 " --> pdb=" O ALA G 456 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL G 461 " --> pdb=" O ALA G 457 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP G 462 " --> pdb=" O ALA G 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 25 removed outlier: 3.612A pdb=" N TYR H 25 " --> pdb=" O ARG H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 60 removed outlier: 3.537A pdb=" N ALA H 53 " --> pdb=" O PRO H 49 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA H 58 " --> pdb=" O GLY H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 75 removed outlier: 3.979A pdb=" N ASP H 72 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY H 73 " --> pdb=" O TRP H 70 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU H 74 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR H 75 " --> pdb=" O ASP H 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 69 through 75' Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.890A pdb=" N LEU H 107 " --> pdb=" O PRO H 104 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 104 through 108' Processing helix chain 'H' and resid 113 through 119 removed outlier: 3.661A pdb=" N SER H 119 " --> pdb=" O ASN H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 127 removed outlier: 4.187A pdb=" N PHE H 127 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 146 removed outlier: 3.530A pdb=" N SER H 145 " --> pdb=" O PRO H 141 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS H 146 " --> pdb=" O PRO H 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 141 through 146' Processing helix chain 'H' and resid 155 through 163 removed outlier: 3.591A pdb=" N LEU H 162 " --> pdb=" O GLU H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 194 removed outlier: 3.989A pdb=" N VAL H 189 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR H 190 " --> pdb=" O GLY H 186 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU H 191 " --> pdb=" O ARG H 187 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS H 192 " --> pdb=" O ALA H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 230 removed outlier: 3.755A pdb=" N ARG H 217 " --> pdb=" O ARG H 213 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU H 219 " --> pdb=" O ARG H 215 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS H 227 " --> pdb=" O GLU H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 261 removed outlier: 3.725A pdb=" N MET H 251 " --> pdb=" O CYS H 247 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS H 252 " --> pdb=" O GLU H 248 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA H 254 " --> pdb=" O MET H 250 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN H 255 " --> pdb=" O MET H 251 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE H 256 " --> pdb=" O LYS H 252 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA H 257 " --> pdb=" O ARG H 253 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG H 258 " --> pdb=" O ALA H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 288 removed outlier: 3.664A pdb=" N ASN H 277 " --> pdb=" O GLY H 273 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR H 279 " --> pdb=" O THR H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.730A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS H 316 " --> pdb=" O ARG H 312 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA H 317 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU H 318 " --> pdb=" O LEU H 314 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET H 320 " --> pdb=" O LYS H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 351 removed outlier: 3.603A pdb=" N THR H 342 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU H 343 " --> pdb=" O ARG H 339 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP H 347 " --> pdb=" O LEU H 343 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU H 348 " --> pdb=" O GLY H 344 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU H 349 " --> pdb=" O PHE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 385 No H-bonds generated for 'chain 'H' and resid 383 through 385' Processing helix chain 'H' and resid 386 through 391 removed outlier: 3.620A pdb=" N LEU H 390 " --> pdb=" O HIS H 386 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 391 " --> pdb=" O MET H 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 386 through 391' Processing helix chain 'H' and resid 403 through 408 removed outlier: 4.281A pdb=" N LEU H 407 " --> pdb=" O GLY H 403 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY H 408 " --> pdb=" O GLY H 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 403 through 408' Processing helix chain 'H' and resid 413 through 432 removed outlier: 3.837A pdb=" N VAL H 418 " --> pdb=" O ALA H 414 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA H 419 " --> pdb=" O PRO H 415 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASN H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS H 427 " --> pdb=" O ALA H 423 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN H 429 " --> pdb=" O GLU H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 449 Processing helix chain 'H' and resid 452 through 457 removed outlier: 3.802A pdb=" N ALA H 456 " --> pdb=" O SER H 452 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA H 457 " --> pdb=" O PRO H 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 452 through 457' Processing helix chain 'H' and resid 457 through 462 removed outlier: 3.832A pdb=" N VAL H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TRP H 462 " --> pdb=" O ALA H 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 457 through 462' Processing helix chain 'I' and resid 26 through 35 removed outlier: 3.572A pdb=" N ILE I 30 " --> pdb=" O ILE I 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 92 removed outlier: 4.306A pdb=" N HIS I 87 " --> pdb=" O ARG I 83 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS I 88 " --> pdb=" O GLU I 84 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS I 89 " --> pdb=" O ILE I 85 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA I 91 " --> pdb=" O HIS I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 35 removed outlier: 3.759A pdb=" N MET J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 92 removed outlier: 4.303A pdb=" N HIS J 87 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS J 88 " --> pdb=" O GLU J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 35 removed outlier: 3.603A pdb=" N ILE K 30 " --> pdb=" O ILE K 26 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR K 32 " --> pdb=" O ARG K 28 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 92 removed outlier: 4.283A pdb=" N HIS K 87 " --> pdb=" O ARG K 83 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS K 89 " --> pdb=" O ILE K 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 35 removed outlier: 3.623A pdb=" N ILE L 30 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP L 31 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET L 33 " --> pdb=" O GLU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 92 removed outlier: 3.693A pdb=" N CYS L 88 " --> pdb=" O GLU L 84 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA L 91 " --> pdb=" O HIS L 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 35 removed outlier: 3.571A pdb=" N ILE M 30 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP M 31 " --> pdb=" O ALA M 27 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET M 33 " --> pdb=" O GLU M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 92 removed outlier: 4.285A pdb=" N HIS M 87 " --> pdb=" O ARG M 83 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N CYS M 88 " --> pdb=" O GLU M 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 35 removed outlier: 3.764A pdb=" N MET N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 92 removed outlier: 3.729A pdb=" N CYS N 88 " --> pdb=" O GLU N 84 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS N 89 " --> pdb=" O ILE N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 35 removed outlier: 3.626A pdb=" N ILE O 30 " --> pdb=" O ILE O 26 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP O 31 " --> pdb=" O ALA O 27 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 92 removed outlier: 4.316A pdb=" N HIS O 87 " --> pdb=" O ARG O 83 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS O 88 " --> pdb=" O GLU O 84 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS O 89 " --> pdb=" O ILE O 85 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA O 91 " --> pdb=" O HIS O 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 35 removed outlier: 3.608A pdb=" N ILE P 30 " --> pdb=" O ILE P 26 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP P 31 " --> pdb=" O ALA P 27 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET P 33 " --> pdb=" O GLU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 92 removed outlier: 4.341A pdb=" N HIS P 87 " --> pdb=" O ARG P 83 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 6.117A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 43 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 132 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 172 removed outlier: 6.607A pdb=" N LEU A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N PHE A 402 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY A 171 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 293 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS A 327 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.110A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP B 86 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 37 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR B 43 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA B 132 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 172 removed outlier: 6.403A pdb=" N LEU B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N PHE B 402 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY B 171 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 240 through 241 removed outlier: 6.499A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ASP B 268 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AA8, first strand: chain 'C' and resid 83 through 89 removed outlier: 6.156A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR C 43 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA C 132 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 169 through 172 removed outlier: 6.445A pdb=" N LEU C 169 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE C 402 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY C 171 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU C 291 " --> pdb=" O HIS C 325 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N HIS C 327 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ILE C 293 " --> pdb=" O HIS C 327 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU C 240 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ASP C 268 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AB2, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.141A pdb=" N CYS D 84 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ALA D 102 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP D 86 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU D 37 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU D 138 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA D 39 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR D 43 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA D 132 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 169 through 171 removed outlier: 6.418A pdb=" N LEU D 169 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU D 291 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS D 327 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ILE D 293 " --> pdb=" O HIS D 327 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU D 240 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ASP D 268 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB5, first strand: chain 'E' and resid 83 through 89 removed outlier: 6.149A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR E 43 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA E 132 " --> pdb=" O THR E 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 171 removed outlier: 6.438A pdb=" N LEU E 169 " --> pdb=" O LEU E 400 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU E 291 " --> pdb=" O HIS E 325 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N HIS E 327 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ILE E 293 " --> pdb=" O HIS E 327 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AB8, first strand: chain 'F' and resid 83 through 89 removed outlier: 6.131A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP F 86 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET F 42 " --> pdb=" O TYR F 97 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU F 37 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 43 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA F 132 " --> pdb=" O THR F 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 169 through 171 removed outlier: 6.418A pdb=" N LEU F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 240 through 241 removed outlier: 6.482A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N ASP F 268 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AC3, first strand: chain 'G' and resid 83 through 89 removed outlier: 6.156A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU G 37 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR G 43 " --> pdb=" O ALA G 132 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA G 132 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 169 through 171 removed outlier: 6.441A pdb=" N LEU G 169 " --> pdb=" O LEU G 400 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 240 through 241 removed outlier: 6.211A pdb=" N LEU G 240 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ASP G 268 " --> pdb=" O LEU G 240 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AC7, first strand: chain 'H' and resid 83 through 89 removed outlier: 6.157A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ASP H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU H 37 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU H 138 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ALA H 39 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR H 43 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA H 132 " --> pdb=" O THR H 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 169 through 172 removed outlier: 6.395A pdb=" N LEU H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N PHE H 402 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY H 171 " --> pdb=" O PHE H 402 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU H 291 " --> pdb=" O HIS H 325 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N HIS H 327 " --> pdb=" O LEU H 291 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N ILE H 293 " --> pdb=" O HIS H 327 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AD1, first strand: chain 'I' and resid 66 through 67 removed outlier: 3.754A pdb=" N CYS I 41 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP I 45 " --> pdb=" O PHE I 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 66 through 67 removed outlier: 3.754A pdb=" N CYS I 41 " --> pdb=" O LEU I 100 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP I 45 " --> pdb=" O PHE I 96 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE I 97 " --> pdb=" O VAL I 115 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE I 113 " --> pdb=" O VAL I 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 66 through 67 removed outlier: 3.783A pdb=" N CYS J 41 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP J 45 " --> pdb=" O PHE J 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 66 through 67 removed outlier: 3.783A pdb=" N CYS J 41 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP J 45 " --> pdb=" O PHE J 96 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE J 97 " --> pdb=" O VAL J 115 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE J 113 " --> pdb=" O VAL J 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 66 through 67 removed outlier: 3.800A pdb=" N CYS K 41 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP K 45 " --> pdb=" O PHE K 96 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 66 through 67 removed outlier: 3.800A pdb=" N CYS K 41 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP K 45 " --> pdb=" O PHE K 96 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE K 97 " --> pdb=" O VAL K 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE K 113 " --> pdb=" O VAL K 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 66 through 67 removed outlier: 3.687A pdb=" N CYS L 41 " --> pdb=" O LEU L 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP L 45 " --> pdb=" O PHE L 96 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE L 97 " --> pdb=" O VAL L 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE L 113 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY L 101 " --> pdb=" O CYS L 111 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS L 111 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASP L 103 " --> pdb=" O GLN L 109 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLN L 109 " --> pdb=" O ASP L 103 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 66 through 67 removed outlier: 3.752A pdb=" N CYS M 41 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP M 45 " --> pdb=" O PHE M 96 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL M 108 " --> pdb=" O ASP M 103 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 66 through 67 removed outlier: 3.752A pdb=" N CYS M 41 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP M 45 " --> pdb=" O PHE M 96 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE M 97 " --> pdb=" O VAL M 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE M 113 " --> pdb=" O VAL M 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 66 through 67 removed outlier: 3.777A pdb=" N CYS N 41 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP N 45 " --> pdb=" O PHE N 96 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 66 through 67 removed outlier: 3.777A pdb=" N CYS N 41 " --> pdb=" O LEU N 100 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP N 45 " --> pdb=" O PHE N 96 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE N 97 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE N 113 " --> pdb=" O VAL N 99 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 66 through 67 removed outlier: 3.623A pdb=" N CYS O 41 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU O 100 " --> pdb=" O CYS O 41 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP O 45 " --> pdb=" O PHE O 96 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE O 97 " --> pdb=" O VAL O 115 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE O 113 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY O 101 " --> pdb=" O CYS O 111 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS O 111 " --> pdb=" O GLY O 101 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ASP O 103 " --> pdb=" O GLN O 109 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN O 109 " --> pdb=" O ASP O 103 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 66 through 67 removed outlier: 3.831A pdb=" N CYS P 41 " --> pdb=" O LEU P 100 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP P 45 " --> pdb=" O PHE P 96 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 66 through 67 removed outlier: 3.831A pdb=" N CYS P 41 " --> pdb=" O LEU P 100 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP P 45 " --> pdb=" O PHE P 96 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE P 97 " --> pdb=" O VAL P 115 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE P 113 " --> pdb=" O VAL P 99 " (cutoff:3.500A) 949 hydrogen bonds defined for protein. 2571 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: 7.18 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12195 1.34 - 1.46: 8221 1.46 - 1.57: 17240 1.57 - 1.69: 16 1.69 - 1.81: 344 Bond restraints: 38016 Sorted by residual: bond pdb=" NZ KCX H 201 " pdb=" CX KCX H 201 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX E 201 " pdb=" CX KCX E 201 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" NZ KCX A 201 " pdb=" CX KCX A 201 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" NZ KCX G 201 " pdb=" CX KCX G 201 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" NZ KCX D 201 " pdb=" CX KCX D 201 " ideal model delta sigma weight residual 1.411 1.328 0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 38011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 50384 1.93 - 3.86: 1075 3.86 - 5.79: 121 5.79 - 7.72: 25 7.72 - 9.65: 3 Bond angle restraints: 51608 Sorted by residual: angle pdb=" C PRO B 44 " pdb=" N GLN B 45 " pdb=" CA GLN B 45 " ideal model delta sigma weight residual 120.49 128.47 -7.98 1.42e+00 4.96e-01 3.16e+01 angle pdb=" C PRO D 44 " pdb=" N GLN D 45 " pdb=" CA GLN D 45 " ideal model delta sigma weight residual 120.49 128.23 -7.74 1.42e+00 4.96e-01 2.97e+01 angle pdb=" C PRO F 44 " pdb=" N GLN F 45 " pdb=" CA GLN F 45 " ideal model delta sigma weight residual 120.49 128.15 -7.66 1.42e+00 4.96e-01 2.91e+01 angle pdb=" C PRO H 44 " pdb=" N GLN H 45 " pdb=" CA GLN H 45 " ideal model delta sigma weight residual 120.49 127.64 -7.15 1.42e+00 4.96e-01 2.54e+01 angle pdb=" N ALA A 389 " pdb=" CA ALA A 389 " pdb=" C ALA A 389 " ideal model delta sigma weight residual 114.75 108.89 5.86 1.26e+00 6.30e-01 2.16e+01 ... (remaining 51603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.22: 20240 24.22 - 48.43: 1809 48.43 - 72.65: 234 72.65 - 96.87: 51 96.87 - 121.08: 2 Dihedral angle restraints: 22336 sinusoidal: 9064 harmonic: 13272 Sorted by residual: dihedral pdb=" CA LYS H 175 " pdb=" C LYS H 175 " pdb=" N PRO H 176 " pdb=" CA PRO H 176 " ideal model delta harmonic sigma weight residual 180.00 134.91 45.09 0 5.00e+00 4.00e-02 8.13e+01 dihedral pdb=" C3 CAP B 502 " pdb=" C CAP B 502 " pdb=" C2 CAP B 502 " pdb=" O6 CAP B 502 " ideal model delta sinusoidal sigma weight residual 81.86 -157.05 -121.08 1 2.00e+01 2.50e-03 3.64e+01 dihedral pdb=" C3 CAP C 502 " pdb=" C CAP C 502 " pdb=" C2 CAP C 502 " pdb=" O6 CAP C 502 " ideal model delta sinusoidal sigma weight residual 81.86 -165.34 -112.80 1 2.00e+01 2.50e-03 3.33e+01 ... (remaining 22333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3383 0.038 - 0.075: 1548 0.075 - 0.113: 430 0.113 - 0.151: 68 0.151 - 0.188: 3 Chirality restraints: 5432 Sorted by residual: chirality pdb=" CA LYS H 175 " pdb=" N LYS H 175 " pdb=" C LYS H 175 " pdb=" CB LYS H 175 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CB THR H 474 " pdb=" CA THR H 474 " pdb=" OG1 THR H 474 " pdb=" CG2 THR H 474 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CB THR F 474 " pdb=" CA THR F 474 " pdb=" OG1 THR F 474 " pdb=" CG2 THR F 474 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 5429 not shown) Planarity restraints: 6728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 262 " 0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO D 263 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 263 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 263 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP N 45 " -0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO N 46 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO N 46 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO N 46 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET H 262 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO H 263 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO H 263 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 263 " -0.029 5.00e-02 4.00e+02 ... (remaining 6725 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 134 2.52 - 3.11: 23425 3.11 - 3.71: 48462 3.71 - 4.30: 67847 4.30 - 4.90: 126090 Nonbonded interactions: 265958 Sorted by model distance: nonbonded pdb="MG MG H 501 " pdb=" O6 CAP H 502 " model vdw 1.920 2.170 nonbonded pdb="MG MG G 501 " pdb=" O6 CAP G 502 " model vdw 1.922 2.170 nonbonded pdb="MG MG E 501 " pdb=" O6 CAP E 502 " model vdw 1.926 2.170 nonbonded pdb=" OQ2 KCX G 201 " pdb="MG MG G 501 " model vdw 1.929 2.170 nonbonded pdb=" OQ2 KCX H 201 " pdb="MG MG H 501 " model vdw 1.930 2.170 ... (remaining 265953 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 33.700 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 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 : 0.003 0.084 38016 Z= 0.174 Angle : 0.684 9.649 51608 Z= 0.410 Chirality : 0.044 0.188 5432 Planarity : 0.005 0.064 6728 Dihedral : 17.189 121.083 13904 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.24 % Favored : 94.35 % Rotamer: Outliers : 1.64 % Allowed : 23.02 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % 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: -3.35 (0.11), residues: 4600 helix: -2.11 (0.13), residues: 1336 sheet: -1.51 (0.18), residues: 800 loop : -2.57 (0.11), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 439 TYR 0.013 0.001 TYR O 80 PHE 0.023 0.001 PHE D 345 TRP 0.008 0.001 TRP B 214 HIS 0.006 0.001 HIS D 238 Details of bonding type rmsd covalent geometry : bond 0.00341 (38016) covalent geometry : angle 0.68432 (51608) hydrogen bonds : bond 0.32865 ( 901) hydrogen bonds : angle 7.84772 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 467 time to evaluate : 1.582 Fit side-chains REVERT: A 249 GLU cc_start: 0.5918 (mm-30) cc_final: 0.5252 (mt-10) REVERT: A 336 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.5976 (tp30) REVERT: B 21 ARG cc_start: 0.6231 (ptm160) cc_final: 0.5875 (ptm160) REVERT: B 371 MET cc_start: 0.6442 (ttp) cc_final: 0.6150 (ttm) REVERT: B 464 GLU cc_start: 0.7234 (pm20) cc_final: 0.6724 (mt-10) REVERT: B 466 LYS cc_start: 0.6679 (mtmm) cc_final: 0.6041 (mmtt) REVERT: C 249 GLU cc_start: 0.5680 (mm-30) cc_final: 0.5168 (mt-10) REVERT: C 305 ARG cc_start: 0.7147 (ptm-80) cc_final: 0.6857 (ttt-90) REVERT: C 371 MET cc_start: 0.6489 (ttp) cc_final: 0.6119 (ttm) REVERT: D 249 GLU cc_start: 0.5779 (mm-30) cc_final: 0.5329 (mt-10) REVERT: D 251 MET cc_start: 0.6458 (mmm) cc_final: 0.6162 (mmp) REVERT: D 305 ARG cc_start: 0.6896 (ptm-80) cc_final: 0.6603 (ttt180) REVERT: D 371 MET cc_start: 0.6595 (ttp) cc_final: 0.6255 (ttm) REVERT: D 464 GLU cc_start: 0.7097 (pm20) cc_final: 0.6897 (mp0) REVERT: D 466 LYS cc_start: 0.5890 (mmtt) cc_final: 0.5680 (mmtt) REVERT: D 473 ASP cc_start: 0.5712 (t0) cc_final: 0.5496 (t70) REVERT: E 249 GLU cc_start: 0.5732 (mm-30) cc_final: 0.5494 (mt-10) REVERT: E 251 MET cc_start: 0.6624 (mmm) cc_final: 0.6374 (mmt) REVERT: E 371 MET cc_start: 0.6620 (ttp) cc_final: 0.6386 (ttm) REVERT: E 464 GLU cc_start: 0.7143 (pm20) cc_final: 0.6736 (mp0) REVERT: F 18 LYS cc_start: 0.6858 (ptpp) cc_final: 0.6609 (ptpt) REVERT: F 249 GLU cc_start: 0.5962 (mm-30) cc_final: 0.5505 (mt-10) REVERT: F 251 MET cc_start: 0.6496 (mmm) cc_final: 0.6270 (mmp) REVERT: F 259 GLU cc_start: 0.5109 (tp30) cc_final: 0.4832 (tt0) REVERT: F 371 MET cc_start: 0.6908 (ttp) cc_final: 0.6635 (ttm) REVERT: F 464 GLU cc_start: 0.6922 (pm20) cc_final: 0.6460 (mt-10) REVERT: F 466 LYS cc_start: 0.5945 (mmtt) cc_final: 0.5736 (mmtt) REVERT: G 249 GLU cc_start: 0.5543 (mm-30) cc_final: 0.5162 (mt-10) REVERT: G 251 MET cc_start: 0.6547 (mmm) cc_final: 0.6338 (mmt) REVERT: G 371 MET cc_start: 0.6918 (ttp) cc_final: 0.6592 (ttm) REVERT: H 249 GLU cc_start: 0.5869 (mm-30) cc_final: 0.5528 (mt-10) REVERT: H 251 MET cc_start: 0.6665 (mmm) cc_final: 0.6407 (mmt) REVERT: H 466 LYS cc_start: 0.6276 (mmtt) cc_final: 0.6029 (mmtt) REVERT: I 37 LYS cc_start: 0.5600 (mmmt) cc_final: 0.5307 (mttp) REVERT: I 104 ASN cc_start: 0.5694 (p0) cc_final: 0.5431 (p0) REVERT: J 37 LYS cc_start: 0.5523 (mmmt) cc_final: 0.5287 (mttt) REVERT: J 104 ASN cc_start: 0.5877 (p0) cc_final: 0.5621 (p0) REVERT: K 28 ARG cc_start: 0.5121 (mmm-85) cc_final: 0.4863 (mtm180) REVERT: K 37 LYS cc_start: 0.5706 (mmmt) cc_final: 0.5371 (mttt) REVERT: K 104 ASN cc_start: 0.5845 (p0) cc_final: 0.5571 (p0) REVERT: L 37 LYS cc_start: 0.5730 (mmmt) cc_final: 0.5461 (mttt) REVERT: L 104 ASN cc_start: 0.6020 (p0) cc_final: 0.5729 (p0) REVERT: M 16 SER cc_start: 0.6458 (t) cc_final: 0.5865 (p) REVERT: M 37 LYS cc_start: 0.5836 (mmmt) cc_final: 0.5369 (mttt) REVERT: N 16 SER cc_start: 0.6730 (t) cc_final: 0.6253 (p) REVERT: N 37 LYS cc_start: 0.5519 (mmmt) cc_final: 0.5193 (mttt) REVERT: N 104 ASN cc_start: 0.5839 (p0) cc_final: 0.5537 (p0) REVERT: O 37 LYS cc_start: 0.5803 (mmmt) cc_final: 0.5384 (mttp) REVERT: P 16 SER cc_start: 0.6686 (t) cc_final: 0.6186 (p) REVERT: P 37 LYS cc_start: 0.5648 (mmmt) cc_final: 0.5350 (mttt) outliers start: 63 outliers final: 36 residues processed: 529 average time/residue: 0.8741 time to fit residues: 541.7061 Evaluate side-chains 350 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 247 CYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 247 CYS Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 45 GLN Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain P residue 108 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 0.4980 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 325 HIS B 156 GLN C 115 ASN D 115 ASN D 156 GLN E 115 ASN E 156 GLN F 115 ASN F 156 GLN F 255 GLN G 156 GLN H 115 ASN I 24 ASN I 90 ASN J 24 ASN J 90 ASN K 24 ASN K 90 ASN L 24 ASN L 90 ASN L 107 GLN M 24 ASN M 90 ASN N 24 ASN N 90 ASN O 24 ASN O 90 ASN P 24 ASN P 90 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104286 restraints weight = 46190.613| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.34 r_work: 0.3130 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 38016 Z= 0.239 Angle : 0.780 9.637 51608 Z= 0.410 Chirality : 0.052 0.213 5432 Planarity : 0.007 0.069 6728 Dihedral : 7.411 119.937 5301 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.87 % Favored : 92.72 % Rotamer: Outliers : 2.89 % Allowed : 22.55 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % 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: -3.24 (0.11), residues: 4600 helix: -1.89 (0.14), residues: 1336 sheet: -1.16 (0.19), residues: 672 loop : -2.66 (0.10), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 258 TYR 0.020 0.002 TYR G 29 PHE 0.035 0.002 PHE C 345 TRP 0.016 0.002 TRP A 214 HIS 0.008 0.002 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00563 (38016) covalent geometry : angle 0.78015 (51608) hydrogen bonds : bond 0.08892 ( 901) hydrogen bonds : angle 4.91679 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 283 time to evaluate : 1.382 Fit side-chains REVERT: A 249 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8037 (mt-10) REVERT: A 447 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: B 21 ARG cc_start: 0.8207 (ptm160) cc_final: 0.7825 (ptm160) REVERT: B 204 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: B 466 LYS cc_start: 0.8095 (mtmm) cc_final: 0.7700 (mmtt) REVERT: C 158 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: C 249 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8180 (mt-10) REVERT: C 305 ARG cc_start: 0.8557 (ptm-80) cc_final: 0.8303 (ttt180) REVERT: D 30 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: D 187 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8436 (ptp-170) REVERT: D 204 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8299 (pt0) REVERT: D 249 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8245 (mt-10) REVERT: D 466 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7822 (mmtt) REVERT: E 249 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8299 (mt-10) REVERT: F 204 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: F 249 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8273 (mt-10) REVERT: G 249 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8180 (mt-10) REVERT: H 249 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8224 (mt-10) REVERT: H 258 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7522 (ttt180) REVERT: H 473 ASP cc_start: 0.7326 (t0) cc_final: 0.7103 (t70) REVERT: I 37 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7608 (mttt) REVERT: J 21 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.7002 (mp) REVERT: J 37 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7623 (mttt) REVERT: K 37 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7598 (mttt) REVERT: L 21 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7069 (mp) REVERT: L 28 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7411 (mtm180) REVERT: L 37 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7613 (mttt) REVERT: L 106 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7384 (mtp85) REVERT: M 37 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7616 (mttt) REVERT: N 37 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7553 (mttt) REVERT: O 37 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7603 (mttt) REVERT: O 80 TYR cc_start: 0.8238 (m-80) cc_final: 0.7892 (m-80) REVERT: O 106 ARG cc_start: 0.8176 (mtp180) cc_final: 0.7866 (mtp85) REVERT: P 37 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7694 (mttt) outliers start: 111 outliers final: 35 residues processed: 378 average time/residue: 0.8995 time to fit residues: 397.3403 Evaluate side-chains 310 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 258 ARG Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 106 ARG Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain P residue 108 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 51 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 434 optimal weight: 0.7980 chunk 278 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 401 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 425 optimal weight: 8.9990 chunk 332 optimal weight: 0.7980 chunk 306 optimal weight: 0.2980 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 HIS B 156 GLN D 156 GLN H 156 GLN H 325 HIS I 24 ASN J 24 ASN J 107 GLN K 24 ASN L 24 ASN M 24 ASN N 24 ASN O 24 ASN P 24 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.119445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.105486 restraints weight = 46053.888| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.35 r_work: 0.3148 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 38016 Z= 0.175 Angle : 0.673 10.366 51608 Z= 0.353 Chirality : 0.048 0.195 5432 Planarity : 0.006 0.068 6728 Dihedral : 7.105 117.961 5275 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 1.19 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.15 % Favored : 93.39 % Rotamer: Outliers : 2.92 % Allowed : 22.14 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % 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: -3.11 (0.11), residues: 4600 helix: -1.61 (0.14), residues: 1336 sheet: -1.37 (0.18), residues: 728 loop : -2.60 (0.10), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 258 TYR 0.014 0.001 TYR G 29 PHE 0.029 0.002 PHE F 345 TRP 0.014 0.001 TRP A 214 HIS 0.007 0.002 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00397 (38016) covalent geometry : angle 0.67338 (51608) hydrogen bonds : bond 0.07422 ( 901) hydrogen bonds : angle 4.62233 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 271 time to evaluate : 1.475 Fit side-chains REVERT: A 249 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8077 (mt-10) REVERT: A 258 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7481 (ttt180) REVERT: A 447 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: A 450 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8383 (mtmt) REVERT: B 21 ARG cc_start: 0.8235 (ptm160) cc_final: 0.7873 (ptm160) REVERT: B 204 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8270 (pt0) REVERT: B 466 LYS cc_start: 0.8139 (mtmm) cc_final: 0.7738 (mmtt) REVERT: C 249 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8175 (mt-10) REVERT: D 30 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: D 249 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8271 (mt-10) REVERT: D 338 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: E 204 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: F 204 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8428 (pt0) REVERT: F 249 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8315 (mt-10) REVERT: F 338 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: G 249 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8225 (mt-10) REVERT: H 204 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: H 249 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8270 (mt-10) REVERT: H 258 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7570 (ttt180) REVERT: H 338 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: I 37 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7597 (mttt) REVERT: J 37 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7549 (mttt) REVERT: K 37 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7599 (mttt) REVERT: L 28 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7653 (mtm180) REVERT: L 37 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7599 (mttt) REVERT: L 106 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7404 (mtp85) REVERT: M 21 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7239 (mp) REVERT: M 37 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7599 (mttt) REVERT: N 37 LYS cc_start: 0.8083 (mmmt) cc_final: 0.7546 (mttt) REVERT: O 37 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7608 (mttt) REVERT: O 80 TYR cc_start: 0.8289 (m-80) cc_final: 0.7836 (m-80) REVERT: P 37 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7650 (mttt) outliers start: 112 outliers final: 37 residues processed: 368 average time/residue: 0.9468 time to fit residues: 404.6972 Evaluate side-chains 312 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 258 ARG Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 202 ASP Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 258 ARG Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 106 ARG Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain P residue 108 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 333 optimal weight: 9.9990 chunk 393 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 267 optimal weight: 5.9990 chunk 309 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 402 optimal weight: 1.9990 chunk 325 optimal weight: 0.8980 chunk 373 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN H 325 HIS I 24 ASN J 24 ASN K 24 ASN L 24 ASN M 24 ASN N 24 ASN N 107 GLN O 24 ASN P 24 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.123265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109343 restraints weight = 45673.226| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.35 r_work: 0.3204 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 38016 Z= 0.112 Angle : 0.564 10.985 51608 Z= 0.295 Chirality : 0.044 0.255 5432 Planarity : 0.005 0.067 6728 Dihedral : 6.592 109.832 5275 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.09 % Favored : 93.63 % Rotamer: Outliers : 2.24 % Allowed : 22.71 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % 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: -2.78 (0.11), residues: 4600 helix: -1.27 (0.14), residues: 1336 sheet: -1.24 (0.19), residues: 696 loop : -2.41 (0.10), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 258 TYR 0.009 0.001 TYR E 29 PHE 0.025 0.001 PHE F 345 TRP 0.011 0.001 TRP A 214 HIS 0.006 0.001 HIS F 238 Details of bonding type rmsd covalent geometry : bond 0.00241 (38016) covalent geometry : angle 0.56357 (51608) hydrogen bonds : bond 0.04987 ( 901) hydrogen bonds : angle 4.31475 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 289 time to evaluate : 1.359 Fit side-chains REVERT: A 249 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8040 (mt-10) REVERT: A 338 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7172 (tt0) REVERT: A 450 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8252 (mttt) REVERT: B 21 ARG cc_start: 0.8175 (ptm160) cc_final: 0.7845 (ptm160) REVERT: B 466 LYS cc_start: 0.8120 (mtmm) cc_final: 0.7674 (mmpt) REVERT: C 204 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7616 (pt0) REVERT: C 249 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8157 (mt-10) REVERT: D 249 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8230 (mt-10) REVERT: D 472 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6509 (mp) REVERT: F 249 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8243 (mt-10) REVERT: G 249 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8198 (mt-10) REVERT: H 249 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8261 (mt-10) REVERT: H 258 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7573 (ttt180) REVERT: H 338 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: I 37 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7528 (mttt) REVERT: J 37 LYS cc_start: 0.7953 (mmmt) cc_final: 0.7519 (mttt) REVERT: K 37 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7511 (mttt) REVERT: L 28 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7684 (mtm180) REVERT: L 37 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7542 (mttt) REVERT: M 37 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7497 (mttt) REVERT: N 37 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7416 (mttt) REVERT: O 37 LYS cc_start: 0.7961 (mmmt) cc_final: 0.7546 (mttt) REVERT: O 80 TYR cc_start: 0.8313 (m-80) cc_final: 0.7838 (m-80) REVERT: P 37 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7556 (mttt) outliers start: 86 outliers final: 37 residues processed: 370 average time/residue: 0.9225 time to fit residues: 396.4247 Evaluate side-chains 305 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 258 ARG Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 107 GLN Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 331 optimal weight: 10.0000 chunk 366 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 361 optimal weight: 5.9990 chunk 278 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 432 ASN H 325 HIS I 24 ASN J 24 ASN J 107 GLN K 24 ASN L 24 ASN M 24 ASN N 24 ASN O 24 ASN P 24 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103332 restraints weight = 46176.561| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.34 r_work: 0.3111 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 38016 Z= 0.249 Angle : 0.766 10.936 51608 Z= 0.401 Chirality : 0.052 0.258 5432 Planarity : 0.007 0.079 6728 Dihedral : 7.124 110.090 5271 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.52 % Favored : 92.20 % Rotamer: Outliers : 2.89 % Allowed : 22.32 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % 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: -3.01 (0.11), residues: 4600 helix: -1.47 (0.14), residues: 1344 sheet: -0.94 (0.20), residues: 680 loop : -2.68 (0.10), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 258 TYR 0.016 0.002 TYR E 29 PHE 0.033 0.002 PHE B 345 TRP 0.015 0.002 TRP A 214 HIS 0.008 0.002 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00596 (38016) covalent geometry : angle 0.76636 (51608) hydrogen bonds : bond 0.08619 ( 901) hydrogen bonds : angle 4.60144 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 269 time to evaluate : 1.705 Fit side-chains REVERT: A 249 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8021 (mt-10) REVERT: A 447 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: B 30 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7374 (mm-30) REVERT: B 466 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7633 (mmtt) REVERT: C 187 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8395 (ptp-170) REVERT: C 204 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: C 249 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8175 (mt-10) REVERT: C 338 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: D 30 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: D 187 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8244 (ptp-170) REVERT: D 249 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8191 (mt-10) REVERT: D 472 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.6774 (mp) REVERT: E 30 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7375 (mm-30) REVERT: E 204 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8526 (pt0) REVERT: E 338 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7019 (tt0) REVERT: F 30 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7410 (mm-30) REVERT: F 249 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8292 (mt-10) REVERT: F 338 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: G 249 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8245 (mt-10) REVERT: G 258 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7540 (ttt180) REVERT: H 21 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7482 (ptp-170) REVERT: H 249 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8269 (mt-10) REVERT: H 258 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7617 (ttt180) REVERT: H 338 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: I 37 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7633 (mttt) REVERT: J 37 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7677 (mttt) REVERT: K 37 LYS cc_start: 0.8116 (mmmt) cc_final: 0.7621 (mttt) REVERT: L 28 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7714 (mtm180) REVERT: L 37 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7638 (mttt) REVERT: L 80 TYR cc_start: 0.8172 (m-80) cc_final: 0.7931 (m-80) REVERT: M 37 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7653 (mttt) REVERT: N 37 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7588 (mttt) REVERT: O 37 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7674 (mttt) REVERT: P 37 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7770 (mttt) outliers start: 111 outliers final: 59 residues processed: 364 average time/residue: 0.9003 time to fit residues: 378.4854 Evaluate side-chains 339 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 263 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 374 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 258 ARG Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain H residue 21 ARG Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 258 ARG Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 374 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 246 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 402 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 410 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 432 ASN H 325 HIS I 24 ASN J 24 ASN K 24 ASN L 24 ASN M 24 ASN N 24 ASN O 24 ASN P 24 ASN P 107 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106259 restraints weight = 45934.826| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.34 r_work: 0.3153 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38016 Z= 0.153 Angle : 0.638 11.527 51608 Z= 0.335 Chirality : 0.047 0.211 5432 Planarity : 0.006 0.069 6728 Dihedral : 6.759 106.402 5271 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.54 % Favored : 93.17 % Rotamer: Outliers : 2.40 % Allowed : 22.86 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % 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: -2.90 (0.11), residues: 4600 helix: -1.33 (0.14), residues: 1352 sheet: -1.26 (0.19), residues: 696 loop : -2.52 (0.10), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 258 TYR 0.012 0.001 TYR E 29 PHE 0.027 0.002 PHE E 345 TRP 0.012 0.001 TRP A 214 HIS 0.006 0.001 HIS F 238 Details of bonding type rmsd covalent geometry : bond 0.00340 (38016) covalent geometry : angle 0.63809 (51608) hydrogen bonds : bond 0.06342 ( 901) hydrogen bonds : angle 4.41188 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 272 time to evaluate : 1.349 Fit side-chains REVERT: A 249 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7978 (mt-10) REVERT: A 447 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: B 466 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7634 (mmtt) REVERT: C 30 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: C 204 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7815 (pt0) REVERT: C 249 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8147 (mt-10) REVERT: D 187 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8296 (ptp-170) REVERT: D 249 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8162 (mt-10) REVERT: D 450 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8477 (ttmt) REVERT: E 30 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: E 204 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8543 (pt0) REVERT: F 30 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7371 (mm-30) REVERT: F 249 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8252 (mt-10) REVERT: F 450 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8491 (ttmt) REVERT: G 249 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8141 (mt-10) REVERT: G 258 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7487 (ttt180) REVERT: H 204 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7753 (pt0) REVERT: H 249 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8232 (mt-10) REVERT: H 258 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7561 (ttt180) REVERT: H 338 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: I 37 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7575 (mttt) REVERT: J 37 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7580 (mttt) REVERT: K 37 LYS cc_start: 0.8025 (mmmt) cc_final: 0.7551 (mttt) REVERT: L 28 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7629 (mtm180) REVERT: L 37 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7540 (mttt) REVERT: M 37 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7560 (mttt) REVERT: N 37 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7511 (mttt) REVERT: N 80 TYR cc_start: 0.8127 (m-80) cc_final: 0.7898 (m-80) REVERT: O 37 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7568 (mttt) REVERT: P 37 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7681 (mttt) outliers start: 92 outliers final: 44 residues processed: 352 average time/residue: 0.8874 time to fit residues: 362.1171 Evaluate side-chains 319 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 262 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 30 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 258 ARG Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 258 ARG Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 433 optimal weight: 0.0010 chunk 278 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 231 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 293 optimal weight: 0.9980 chunk 243 optimal weight: 8.9990 chunk 425 optimal weight: 10.0000 chunk 447 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 369 optimal weight: 0.0970 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 432 ASN F 45 GLN H 325 HIS I 24 ASN J 24 ASN K 24 ASN L 24 ASN M 24 ASN N 24 ASN O 24 ASN P 24 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114731 restraints weight = 45354.177| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.28 r_work: 0.3268 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 38016 Z= 0.087 Angle : 0.502 11.678 51608 Z= 0.261 Chirality : 0.042 0.188 5432 Planarity : 0.005 0.064 6728 Dihedral : 5.722 86.258 5271 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.98 % Favored : 94.76 % Rotamer: Outliers : 1.25 % Allowed : 23.59 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % 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: -2.37 (0.11), residues: 4600 helix: -0.98 (0.15), residues: 1312 sheet: -0.75 (0.18), residues: 776 loop : -2.23 (0.10), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 258 TYR 0.014 0.001 TYR P 80 PHE 0.022 0.001 PHE C 345 TRP 0.010 0.001 TRP A 70 HIS 0.006 0.001 HIS F 238 Details of bonding type rmsd covalent geometry : bond 0.00193 (38016) covalent geometry : angle 0.50188 (51608) hydrogen bonds : bond 0.03142 ( 901) hydrogen bonds : angle 4.08887 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 293 time to evaluate : 1.552 Fit side-chains REVERT: A 249 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7961 (mt-10) REVERT: A 447 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: B 466 LYS cc_start: 0.8160 (mtmm) cc_final: 0.7767 (mmpt) REVERT: C 204 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7804 (pt0) REVERT: C 249 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8174 (mt-10) REVERT: D 249 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8228 (mt-10) REVERT: D 450 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8455 (ttmt) REVERT: D 472 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6586 (mp) REVERT: F 249 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8285 (mt-10) REVERT: F 450 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8478 (ttmt) REVERT: H 249 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8203 (mt-10) REVERT: I 37 LYS cc_start: 0.7669 (mmmt) cc_final: 0.7311 (mttt) REVERT: J 37 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7358 (mttt) REVERT: K 29 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7341 (mt-10) REVERT: K 37 LYS cc_start: 0.7762 (mmmt) cc_final: 0.7424 (mttt) REVERT: L 28 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7642 (mtm180) REVERT: L 37 LYS cc_start: 0.7815 (mmmt) cc_final: 0.7447 (mttt) REVERT: M 37 LYS cc_start: 0.7731 (mmmt) cc_final: 0.7409 (mttt) REVERT: N 37 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7391 (mttt) REVERT: O 37 LYS cc_start: 0.7749 (mmmt) cc_final: 0.7422 (mttt) REVERT: P 37 LYS cc_start: 0.7881 (mmmt) cc_final: 0.7538 (mttt) outliers start: 48 outliers final: 26 residues processed: 337 average time/residue: 0.8887 time to fit residues: 348.0100 Evaluate side-chains 308 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain P residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 350 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 427 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 167 optimal weight: 0.0870 chunk 277 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 422 optimal weight: 6.9990 chunk 367 optimal weight: 10.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 432 ASN H 325 HIS I 24 ASN J 24 ASN K 24 ASN L 24 ASN M 24 ASN N 24 ASN O 24 ASN P 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106356 restraints weight = 45454.965| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.35 r_work: 0.3161 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 38016 Z= 0.166 Angle : 0.644 10.728 51608 Z= 0.336 Chirality : 0.047 0.191 5432 Planarity : 0.006 0.071 6728 Dihedral : 6.152 74.399 5271 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.09 % Favored : 92.65 % Rotamer: Outliers : 1.35 % Allowed : 23.59 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % 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: -2.56 (0.11), residues: 4600 helix: -1.03 (0.15), residues: 1344 sheet: -1.07 (0.20), residues: 696 loop : -2.32 (0.10), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 258 TYR 0.015 0.001 TYR P 80 PHE 0.028 0.002 PHE E 345 TRP 0.010 0.001 TRP A 214 HIS 0.006 0.002 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00379 (38016) covalent geometry : angle 0.64361 (51608) hydrogen bonds : bond 0.06445 ( 901) hydrogen bonds : angle 4.27629 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 1.328 Fit side-chains REVERT: A 249 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7882 (mt-10) REVERT: B 466 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7621 (mmpt) REVERT: C 204 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: C 249 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8060 (mt-10) REVERT: D 249 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8126 (mt-10) REVERT: D 450 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8433 (ttmt) REVERT: D 472 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6595 (mp) REVERT: F 249 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8188 (mt-10) REVERT: F 450 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8461 (ttmt) REVERT: H 249 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8158 (mt-10) REVERT: H 338 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: I 37 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7573 (mttt) REVERT: J 37 LYS cc_start: 0.7998 (mmmt) cc_final: 0.7548 (mttt) REVERT: K 29 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7247 (mt-10) REVERT: K 37 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7546 (mttt) REVERT: L 28 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7559 (mtm180) REVERT: L 37 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7577 (mttt) REVERT: M 37 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7558 (mttt) REVERT: N 37 LYS cc_start: 0.7929 (mmmt) cc_final: 0.7507 (mttt) REVERT: O 37 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7549 (mtmt) REVERT: O 80 TYR cc_start: 0.8167 (m-80) cc_final: 0.7930 (m-80) REVERT: P 37 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7735 (mttt) outliers start: 52 outliers final: 31 residues processed: 323 average time/residue: 0.9488 time to fit residues: 355.5567 Evaluate side-chains 300 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain P residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 10.0000 chunk 443 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 333 optimal weight: 5.9990 chunk 417 optimal weight: 4.9990 chunk 439 optimal weight: 0.0010 chunk 361 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 376 optimal weight: 2.9990 overall best weight: 1.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 432 ASN H 325 HIS I 24 ASN J 24 ASN K 24 ASN L 24 ASN M 24 ASN N 24 ASN O 24 ASN P 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.123907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110459 restraints weight = 45813.200| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.27 r_work: 0.3215 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 38016 Z= 0.110 Angle : 0.554 11.219 51608 Z= 0.289 Chirality : 0.044 0.165 5432 Planarity : 0.005 0.066 6728 Dihedral : 5.747 73.650 5271 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.09 % Favored : 93.65 % Rotamer: Outliers : 1.09 % Allowed : 23.98 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % 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: -2.37 (0.11), residues: 4600 helix: -0.84 (0.15), residues: 1344 sheet: -1.00 (0.20), residues: 696 loop : -2.20 (0.10), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 258 TYR 0.016 0.001 TYR P 80 PHE 0.026 0.001 PHE C 345 TRP 0.010 0.001 TRP A 214 HIS 0.006 0.001 HIS D 238 Details of bonding type rmsd covalent geometry : bond 0.00241 (38016) covalent geometry : angle 0.55386 (51608) hydrogen bonds : bond 0.04553 ( 901) hydrogen bonds : angle 4.13121 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 275 time to evaluate : 1.428 Fit side-chains REVERT: A 249 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7993 (mt-10) REVERT: B 466 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7710 (mmpt) REVERT: C 204 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7756 (pt0) REVERT: C 249 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8107 (mt-10) REVERT: D 249 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8236 (mt-10) REVERT: D 450 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8468 (ttmt) REVERT: F 30 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7408 (mt-10) REVERT: F 249 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8249 (mt-10) REVERT: F 450 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8476 (ttmt) REVERT: H 249 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8215 (mt-10) REVERT: I 37 LYS cc_start: 0.7793 (mmmt) cc_final: 0.7511 (mttt) REVERT: J 37 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7448 (mttt) REVERT: K 29 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7326 (mt-10) REVERT: K 37 LYS cc_start: 0.7865 (mmmt) cc_final: 0.7525 (mttt) REVERT: L 28 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7655 (mtm180) REVERT: L 37 LYS cc_start: 0.7952 (mmmt) cc_final: 0.7549 (mttt) REVERT: M 37 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7491 (mttt) REVERT: N 37 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7423 (mttt) REVERT: O 37 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7510 (mttt) REVERT: O 80 TYR cc_start: 0.8184 (m-80) cc_final: 0.7948 (m-80) REVERT: P 37 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7732 (mttt) outliers start: 42 outliers final: 32 residues processed: 312 average time/residue: 0.8824 time to fit residues: 319.5356 Evaluate side-chains 305 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 187 ARG Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain P residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 71 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 281 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 403 optimal weight: 0.1980 chunk 352 optimal weight: 8.9990 chunk 275 optimal weight: 7.9990 chunk 384 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 432 ASN H 325 HIS I 24 ASN J 24 ASN K 24 ASN L 24 ASN M 24 ASN N 24 ASN O 24 ASN P 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106923 restraints weight = 45707.797| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.35 r_work: 0.3169 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38016 Z= 0.153 Angle : 0.623 11.070 51608 Z= 0.325 Chirality : 0.047 0.186 5432 Planarity : 0.006 0.071 6728 Dihedral : 5.965 71.550 5271 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.80 % Favored : 92.93 % Rotamer: Outliers : 1.07 % Allowed : 24.09 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % 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: -2.49 (0.11), residues: 4600 helix: -0.97 (0.15), residues: 1360 sheet: -1.03 (0.20), residues: 696 loop : -2.29 (0.10), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 258 TYR 0.018 0.001 TYR P 80 PHE 0.028 0.002 PHE E 345 TRP 0.010 0.001 TRP A 214 HIS 0.006 0.002 HIS G 292 Details of bonding type rmsd covalent geometry : bond 0.00348 (38016) covalent geometry : angle 0.62275 (51608) hydrogen bonds : bond 0.06032 ( 901) hydrogen bonds : angle 4.22867 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 273 time to evaluate : 1.102 Fit side-chains REVERT: A 249 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7977 (mt-10) REVERT: B 466 LYS cc_start: 0.8068 (mtmm) cc_final: 0.7640 (mmpt) REVERT: C 204 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7740 (pt0) REVERT: C 249 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8248 (mt-10) REVERT: D 30 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: D 249 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8195 (mt-10) REVERT: D 450 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8429 (ttmt) REVERT: F 30 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7433 (mt-10) REVERT: F 249 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8205 (mt-10) REVERT: F 450 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8454 (ttmt) REVERT: H 249 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8177 (mt-10) REVERT: I 37 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7569 (mttt) REVERT: J 37 LYS cc_start: 0.7952 (mmmt) cc_final: 0.7521 (mttt) REVERT: K 29 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7283 (mt-10) REVERT: K 37 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7605 (mttt) REVERT: L 28 ARG cc_start: 0.8056 (mmm-85) cc_final: 0.7577 (mtm180) REVERT: L 37 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7598 (mttt) REVERT: M 37 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7586 (mttt) REVERT: N 37 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7554 (mttt) REVERT: O 37 LYS cc_start: 0.7977 (mmmt) cc_final: 0.7612 (mttt) REVERT: O 80 TYR cc_start: 0.8157 (m-80) cc_final: 0.7935 (m-80) REVERT: P 37 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7751 (mttt) outliers start: 41 outliers final: 31 residues processed: 309 average time/residue: 0.8626 time to fit residues: 308.4562 Evaluate side-chains 303 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 267 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 432 ASN Chi-restraints excluded: chain F residue 30 GLU Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain F residue 475 LEU Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 328 SER Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain P residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 378 optimal weight: 7.9990 chunk 414 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 279 optimal weight: 0.6980 chunk 178 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 232 optimal weight: 4.9990 chunk 408 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 432 ASN H 325 HIS I 24 ASN J 24 ASN K 24 ASN L 24 ASN M 24 ASN N 24 ASN O 24 ASN P 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.121266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107368 restraints weight = 45405.738| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.35 r_work: 0.3180 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38016 Z= 0.142 Angle : 0.610 11.188 51608 Z= 0.319 Chirality : 0.046 0.200 5432 Planarity : 0.006 0.068 6728 Dihedral : 5.926 70.619 5270 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.52 % Favored : 93.22 % Rotamer: Outliers : 1.02 % Allowed : 24.24 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.73 % Cis-general : 0.00 % Twisted Proline : 0.39 % Twisted General : 0.00 % 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: -2.48 (0.11), residues: 4600 helix: -0.94 (0.15), residues: 1360 sheet: -1.05 (0.20), residues: 696 loop : -2.28 (0.10), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 258 TYR 0.020 0.001 TYR P 80 PHE 0.027 0.002 PHE E 345 TRP 0.010 0.001 TRP A 214 HIS 0.006 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00319 (38016) covalent geometry : angle 0.60976 (51608) hydrogen bonds : bond 0.05736 ( 901) hydrogen bonds : angle 4.21744 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9310.63 seconds wall clock time: 159 minutes 39.59 seconds (9579.59 seconds total)