Starting phenix.real_space_refine on Mon Jul 6 16:31:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ck5_45641/07_2026/9ck5_45641_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ck5_45641/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ck5_45641/07_2026/9ck5_45641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ck5_45641/07_2026/9ck5_45641.map" model { file = "/net/cci-nas-00/data/ceres_data/9ck5_45641/07_2026/9ck5_45641_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ck5_45641/07_2026/9ck5_45641_neut.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 8.37, per 1000 atoms: 0.23 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: 2.48 Conformation dependent library (CDL) restraints added in 1.2 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: 1.15 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: 7.35 Time building geometry restraints manager: 3.49 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=" O1 CAP C 502 " pdb=" P1 CAP C 502 " ideal model delta sigma weight residual 1.708 1.608 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" O1 CAP A 502 " pdb=" P1 CAP A 502 " ideal model delta sigma weight residual 1.708 1.608 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" O1 CAP H 502 " pdb=" P1 CAP H 502 " ideal model delta sigma weight residual 1.708 1.609 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O1 CAP G 502 " pdb=" P1 CAP G 502 " ideal model delta sigma weight residual 1.708 1.609 0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" O1 CAP D 502 " pdb=" P1 CAP D 502 " ideal model delta sigma weight residual 1.708 1.609 0.099 2.00e-02 2.50e+03 2.45e+01 ... (remaining 38011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 50203 1.93 - 3.86: 1160 3.86 - 5.79: 177 5.79 - 7.72: 39 7.72 - 9.65: 29 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 - 17.86: 19246 17.86 - 35.71: 2389 35.71 - 53.57: 681 53.57 - 71.42: 125 71.42 - 89.28: 55 Dihedral angle restraints: 22496 sinusoidal: 9224 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=" CA ASP B 203 " pdb=" CB ASP B 203 " pdb=" CG ASP B 203 " pdb=" OD1 ASP B 203 " ideal model delta sinusoidal sigma weight residual -30.00 -89.86 59.86 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP A 352 " pdb=" CB ASP A 352 " pdb=" CG ASP A 352 " pdb=" OD1 ASP A 352 " ideal model delta sinusoidal sigma weight residual -30.00 -88.81 58.81 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 22493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4234 0.053 - 0.106: 1064 0.106 - 0.159: 131 0.159 - 0.212: 3 0.212 - 0.265: 8 Chirality restraints: 5440 Sorted by residual: chirality pdb=" C3 CAP E 502 " pdb=" C2 CAP E 502 " pdb=" C4 CAP E 502 " pdb=" O3 CAP E 502 " both_signs ideal model delta sigma weight residual False -2.19 -2.46 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C3 CAP A 502 " pdb=" C2 CAP A 502 " pdb=" C4 CAP A 502 " pdb=" O3 CAP A 502 " both_signs ideal model delta sigma weight residual False -2.19 -2.46 0.26 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C3 CAP F 502 " pdb=" C2 CAP F 502 " pdb=" C4 CAP F 502 " pdb=" O3 CAP F 502 " both_signs ideal model delta sigma weight residual False -2.19 -2.46 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 5437 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: 1.780 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.440 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 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:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 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 : 0.004 0.100 38016 Z= 0.209 Angle : 0.747 9.649 51608 Z= 0.422 Chirality : 0.045 0.265 5440 Planarity : 0.005 0.064 6728 Dihedral : 17.268 89.275 14064 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/Z covalent geometry : bond 0.00412 / 0.21 (38016) covalent geometry : angle 0.74740 / 0.42 (51608) hydrogen bonds : bond 0.32865 / 21.71 ( 901) hydrogen bonds : angle 7.84772 / 5.33 ( 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 : 1.426 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: 0.8107 time to fit residues: 506.5490 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 : 1.481 ------------------------------------------------------------------------------- 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: 8.9990 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... 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 J 107 GLN K 24 ASN K 90 ASN L 24 ASN L 90 ASN 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 = 0.3381 r_free = 0.3381 target = 0.117875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.103840 restraints weight = 46222.245| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.35 r_work: 0.3126 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1751 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= 0.238 Angle : 0.794 10.055 51608 Z= 0.416 Chirality : 0.052 0.228 5440 Planarity : 0.007 0.069 6728 Dihedral : 8.096 88.130 5461 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.87 % Favored : 92.70 % Rotamer: Outliers : 3.10 % Allowed : 22.40 % Favored : 74.51 % 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: -3.32 (0.11), residues: 4600 helix: -1.97 (0.13), residues: 1336 sheet: -1.22 (0.19), residues: 672 loop : -2.69 (0.10), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 258 TYR 0.021 0.002 TYR H 29 PHE 0.035 0.002 PHE C 345 TRP 0.017 0.002 TRP A 214 HIS 0.008 0.002 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (38016) covalent geometry : angle 0.79398 / 0.42 (51608) hydrogen bonds : bond 0.08864 / 5.77 ( 901) hydrogen bonds : angle 4.92613 / 3.40 ( 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 404 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 285 time to evaluate : 1.570 Fit side-chains REVERT: A 249 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7985 (mt-10) REVERT: A 258 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7403 (ttt180) REVERT: A 447 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: B 21 ARG cc_start: 0.8206 (ptm160) cc_final: 0.7827 (ptm160) REVERT: B 204 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: B 466 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7702 (mmtt) REVERT: C 158 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8330 (tt0) REVERT: C 249 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8149 (mt-10) REVERT: C 305 ARG cc_start: 0.8577 (ptm-80) cc_final: 0.8287 (ttt180) REVERT: D 30 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: D 187 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8433 (ptp-170) REVERT: D 249 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8232 (mt-10) REVERT: E 249 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8310 (mt-10) REVERT: F 204 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8370 (pt0) REVERT: F 249 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8298 (mt-10) REVERT: G 249 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8190 (mt-10) REVERT: H 249 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8237 (mt-10) REVERT: H 258 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7545 (ttt180) REVERT: H 338 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: I 37 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7620 (mttp) REVERT: J 21 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7026 (mp) REVERT: J 37 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7626 (mttt) REVERT: K 21 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.7079 (mp) REVERT: K 37 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7595 (mttt) REVERT: L 28 ARG cc_start: 0.7856 (mmm-85) cc_final: 0.7450 (mtm180) REVERT: L 37 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7627 (mttt) REVERT: L 106 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7405 (mtp85) REVERT: M 37 LYS cc_start: 0.8149 (mmmt) cc_final: 0.7623 (mttt) REVERT: N 37 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7561 (mttt) REVERT: O 37 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7602 (mttt) REVERT: O 80 TYR cc_start: 0.8242 (m-80) cc_final: 0.7896 (m-80) REVERT: O 106 ARG cc_start: 0.8188 (mtp180) cc_final: 0.7878 (mtp85) REVERT: P 37 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7684 (mttt) outliers start: 119 outliers final: 36 residues processed: 388 average time/residue: 0.8524 time to fit residues: 389.1696 Evaluate side-chains 316 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 268 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 258 ARG 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 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 H residue 338 GLU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 21 LEU 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 100 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 21 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 51 optimal weight: 6.9990 chunk 272 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 434 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 401 optimal weight: 0.9980 chunk 252 optimal weight: 8.9990 chunk 425 optimal weight: 6.9990 chunk 332 optimal weight: 0.8980 chunk 306 optimal weight: 3.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 325 HIS B 156 GLN D 156 GLN E 156 GLN F 156 GLN H 156 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106017 restraints weight = 46172.482| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.35 r_work: 0.3153 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 38016 Z= 0.166 Angle : 0.655 10.701 51608 Z= 0.344 Chirality : 0.047 0.191 5440 Planarity : 0.006 0.066 6728 Dihedral : 7.418 88.586 5435 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.15 % Favored : 93.41 % Rotamer: Outliers : 2.81 % Allowed : 22.14 % 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: -3.09 (0.11), residues: 4600 helix: -1.60 (0.14), residues: 1336 sheet: -1.37 (0.18), residues: 728 loop : -2.58 (0.10), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 258 TYR 0.013 0.001 TYR G 29 PHE 0.028 0.002 PHE F 345 TRP 0.014 0.001 TRP A 214 HIS 0.006 0.002 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (38016) covalent geometry : angle 0.65501 / 0.34 (51608) hydrogen bonds : bond 0.07111 / 4.63 ( 901) hydrogen bonds : angle 4.58052 / 3.16 ( 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 386 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 278 time to evaluate : 1.531 Fit side-chains REVERT: A 249 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8043 (mt-10) REVERT: A 392 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: A 447 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: A 450 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8382 (mtmt) REVERT: B 21 ARG cc_start: 0.8205 (ptm160) cc_final: 0.7846 (ptm160) REVERT: B 204 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8273 (pt0) REVERT: B 466 LYS cc_start: 0.8111 (mtmm) cc_final: 0.7655 (mmpt) REVERT: C 249 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8145 (mt-10) REVERT: D 30 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: D 249 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8246 (mt-10) REVERT: D 338 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: E 204 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: F 204 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8467 (pt0) REVERT: F 249 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8247 (mt-10) REVERT: F 338 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7371 (tt0) REVERT: G 249 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8191 (mt-10) REVERT: H 21 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7089 (ptp-170) REVERT: H 204 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: H 249 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8251 (mt-10) REVERT: H 258 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7585 (ttt180) REVERT: H 338 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: I 37 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7548 (mttt) REVERT: J 37 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7485 (mtmt) REVERT: K 37 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7577 (mttt) REVERT: L 28 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7611 (mtm180) REVERT: L 37 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7563 (mttt) REVERT: L 106 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7407 (mtp85) REVERT: M 37 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7548 (mttt) REVERT: N 37 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7496 (mttt) REVERT: O 37 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7560 (mttt) REVERT: O 80 TYR cc_start: 0.8260 (m-80) cc_final: 0.7798 (m-80) REVERT: P 37 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7638 (mttt) outliers start: 108 outliers final: 36 residues processed: 370 average time/residue: 0.8808 time to fit residues: 381.0399 Evaluate side-chains 312 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 392 GLU 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 94 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 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 204 GLU Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 384 VAL 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 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 108 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 333 optimal weight: 8.9990 chunk 393 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 267 optimal weight: 5.9990 chunk 309 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 402 optimal weight: 0.0670 chunk 325 optimal weight: 0.0370 chunk 373 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 overall best weight: 1.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 156 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108619 restraints weight = 45877.960| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.35 r_work: 0.3187 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38016 Z= 0.122 Angle : 0.579 10.951 51608 Z= 0.303 Chirality : 0.045 0.247 5440 Planarity : 0.006 0.068 6728 Dihedral : 6.786 87.864 5435 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 1.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.57 % Favored : 93.15 % Rotamer: Outliers : 2.37 % Allowed : 22.55 % Favored : 75.08 % 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: -2.82 (0.11), residues: 4600 helix: -1.30 (0.14), residues: 1336 sheet: -1.26 (0.19), residues: 696 loop : -2.44 (0.10), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 258 TYR 0.010 0.001 TYR E 29 PHE 0.025 0.001 PHE F 345 TRP 0.012 0.001 TRP A 214 HIS 0.006 0.001 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (38016) covalent geometry : angle 0.57880 / 0.30 (51608) hydrogen bonds : bond 0.05287 / 3.44 ( 901) hydrogen bonds : angle 4.30801 / 2.97 ( 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 377 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 286 time to evaluate : 1.521 Fit side-chains REVERT: A 249 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7980 (mt-10) REVERT: A 450 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8327 (mtmt) REVERT: B 21 ARG cc_start: 0.8171 (ptm160) cc_final: 0.7847 (ptm160) REVERT: B 466 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7649 (mmpt) REVERT: C 204 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: C 249 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8169 (mt-10) REVERT: D 249 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8234 (mt-10) REVERT: D 472 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6510 (mp) REVERT: E 204 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7995 (pt0) REVERT: F 30 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: F 204 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8526 (pt0) REVERT: F 249 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8247 (mt-10) REVERT: G 249 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8184 (mt-10) REVERT: H 249 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8265 (mt-10) REVERT: H 258 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7566 (ttt180) REVERT: I 37 LYS cc_start: 0.7972 (mmmt) cc_final: 0.7556 (mttt) REVERT: J 37 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7547 (mttt) REVERT: K 37 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7483 (mttt) REVERT: L 28 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7679 (mtm180) REVERT: L 37 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7543 (mttt) REVERT: M 37 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7519 (mttt) REVERT: N 37 LYS cc_start: 0.7875 (mmmt) cc_final: 0.7431 (mttt) REVERT: O 37 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7553 (mttt) REVERT: O 80 TYR cc_start: 0.8334 (m-80) cc_final: 0.7813 (m-80) REVERT: P 37 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7580 (mttt) outliers start: 91 outliers final: 43 residues processed: 368 average time/residue: 0.8576 time to fit residues: 369.1027 Evaluate side-chains 314 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 265 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 173 THR 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 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 D residue 472 ILE Chi-restraints excluded: chain E residue 94 GLU 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 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 202 ASP Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 384 VAL 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 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 J residue 107 GLN Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain K residue 108 VAL Chi-restraints excluded: chain L residue 21 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 21 LEU Chi-restraints excluded: chain P residue 100 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: 0.5980 chunk 203 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 344 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 361 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.117604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.103686 restraints weight = 46155.313| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.35 r_work: 0.3122 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 38016 Z= 0.218 Angle : 0.732 11.072 51608 Z= 0.383 Chirality : 0.050 0.246 5440 Planarity : 0.007 0.076 6728 Dihedral : 7.192 84.169 5431 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.30 % Favored : 92.41 % Rotamer: Outliers : 2.60 % Allowed : 22.32 % Favored : 75.08 % 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: -3.00 (0.11), residues: 4600 helix: -1.42 (0.14), residues: 1344 sheet: -1.22 (0.19), residues: 728 loop : -2.63 (0.10), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 258 TYR 0.015 0.002 TYR E 29 PHE 0.032 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/Z covalent geometry : bond 0.00510 / 0.22 (38016) covalent geometry : angle 0.73208 / 0.38 (51608) hydrogen bonds : bond 0.08087 / 5.27 ( 901) hydrogen bonds : angle 4.54732 / 3.15 ( 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 375 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 275 time to evaluate : 1.247 Fit side-chains REVERT: A 249 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8002 (mt-10) REVERT: A 338 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: A 447 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: B 30 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: B 466 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7619 (mmtt) REVERT: C 30 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: C 187 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8394 (ptp-170) REVERT: C 204 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: C 249 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8177 (mt-10) REVERT: D 30 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7406 (mm-30) REVERT: D 187 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8300 (ptp-170) REVERT: D 249 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8165 (mt-10) REVERT: D 450 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8482 (ttmt) REVERT: E 30 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7362 (mm-30) REVERT: E 204 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: E 338 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: F 30 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7413 (mm-30) REVERT: F 249 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8282 (mt-10) REVERT: F 450 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8510 (ttmt) REVERT: G 249 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8173 (mt-10) REVERT: G 258 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7533 (ttt180) REVERT: H 249 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8281 (mt-10) REVERT: H 258 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7601 (ttt180) REVERT: I 37 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7646 (mttt) REVERT: J 37 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7664 (mttt) REVERT: K 37 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7626 (mttt) REVERT: L 28 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7753 (mtm180) REVERT: L 37 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7627 (mttt) REVERT: L 80 TYR cc_start: 0.8153 (m-80) cc_final: 0.7913 (m-80) REVERT: M 37 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7632 (mttt) REVERT: N 37 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7567 (mttt) REVERT: O 37 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7655 (mttt) REVERT: P 37 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7737 (mttt) outliers start: 100 outliers final: 59 residues processed: 353 average time/residue: 0.8167 time to fit residues: 334.9403 Evaluate side-chains 343 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 268 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 338 GLU 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 202 ASP 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 30 GLU 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 187 ARG Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 297 MET 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 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 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 202 ASP Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 374 VAL 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 297 MET 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 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 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 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: 8.9990 chunk 317 optimal weight: 3.9990 chunk 306 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 402 optimal weight: 0.4980 chunk 106 optimal weight: 9.9990 chunk 410 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.120214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106190 restraints weight = 45944.614| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.38 r_work: 0.3156 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2207 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= 0.149 Angle : 0.627 11.624 51608 Z= 0.329 Chirality : 0.046 0.211 5440 Planarity : 0.006 0.069 6728 Dihedral : 6.827 86.764 5431 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.46 % Favored : 93.26 % Rotamer: Outliers : 2.34 % Allowed : 22.71 % 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: -2.86 (0.11), residues: 4600 helix: -1.31 (0.14), residues: 1352 sheet: -1.26 (0.19), residues: 696 loop : -2.49 (0.10), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 258 TYR 0.012 0.001 TYR P 80 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/Z covalent geometry : bond 0.00333 / 0.15 (38016) covalent geometry : angle 0.62706 / 0.33 (51608) hydrogen bonds : bond 0.06171 / 4.02 ( 901) hydrogen bonds : angle 4.36763 / 3.02 ( 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 363 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 273 time to evaluate : 0.962 Fit side-chains REVERT: A 249 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7977 (mt-10) REVERT: A 338 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: B 466 LYS cc_start: 0.8065 (mtmm) cc_final: 0.7554 (mmtt) REVERT: C 204 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7843 (pt0) REVERT: C 249 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8072 (mt-10) REVERT: D 249 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8097 (mt-10) REVERT: D 338 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7373 (tt0) REVERT: D 450 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8430 (ttmt) REVERT: E 30 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: E 204 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8043 (pt0) REVERT: F 30 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7342 (mm-30) REVERT: F 249 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8213 (mt-10) REVERT: F 338 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: F 450 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8459 (ttmt) REVERT: G 249 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8078 (mt-10) REVERT: G 258 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7435 (ttt180) REVERT: H 204 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.7775 (pt0) REVERT: H 249 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8175 (mt-10) REVERT: I 37 LYS cc_start: 0.7961 (mmmt) cc_final: 0.7505 (mttt) REVERT: J 37 LYS cc_start: 0.7963 (mmmt) cc_final: 0.7477 (mttt) REVERT: K 37 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7496 (mttt) REVERT: L 28 ARG cc_start: 0.8029 (mmm-85) cc_final: 0.7527 (mtm180) REVERT: L 37 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7448 (mttt) REVERT: M 37 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7481 (mttt) REVERT: N 37 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7440 (mttt) REVERT: N 80 TYR cc_start: 0.8097 (m-80) cc_final: 0.7863 (m-80) REVERT: O 37 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7488 (mttt) REVERT: P 31 ASP cc_start: 0.8398 (m-30) cc_final: 0.8188 (m-30) REVERT: P 37 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7610 (mttt) outliers start: 90 outliers final: 44 residues processed: 354 average time/residue: 0.8276 time to fit residues: 340.7672 Evaluate side-chains 317 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 1.293 ------------------------------------------------------------------------------- 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 338 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 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 D residue 173 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 450 LYS 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 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 202 ASP Chi-restraints excluded: chain F residue 338 GLU 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 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 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 100 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: 3.9990 chunk 278 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 231 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 293 optimal weight: 0.9980 chunk 243 optimal weight: 8.9990 chunk 425 optimal weight: 0.4980 chunk 447 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 369 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111133 restraints weight = 45560.087| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.28 r_work: 0.3224 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 38016 Z= 0.100 Angle : 0.532 11.643 51608 Z= 0.277 Chirality : 0.043 0.199 5440 Planarity : 0.005 0.067 6728 Dihedral : 6.115 74.813 5431 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.74 % Favored : 93.98 % Rotamer: Outliers : 1.38 % Allowed : 23.59 % Favored : 75.03 % 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: -2.45 (0.11), residues: 4600 helix: -0.98 (0.15), residues: 1344 sheet: -0.83 (0.18), residues: 776 loop : -2.32 (0.11), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 258 TYR 0.014 0.001 TYR P 80 PHE 0.024 0.001 PHE E 345 TRP 0.010 0.001 TRP A 214 HIS 0.005 0.001 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (38016) covalent geometry : angle 0.53170 / 0.28 (51608) hydrogen bonds : bond 0.04007 / 2.61 ( 901) hydrogen bonds : angle 4.13082 / 2.85 ( 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 345 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 292 time to evaluate : 1.291 Fit side-chains REVERT: A 249 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8025 (mt-10) REVERT: A 338 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7089 (tt0) REVERT: B 466 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7733 (mmpt) REVERT: C 204 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7778 (pt0) REVERT: C 249 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8183 (mt-10) REVERT: D 249 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8245 (mt-10) REVERT: D 450 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8431 (ttmt) REVERT: F 249 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8250 (mt-10) REVERT: F 338 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: F 450 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8450 (ttmt) REVERT: G 249 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8203 (mt-10) REVERT: G 338 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6793 (tt0) REVERT: H 249 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8239 (mt-10) REVERT: I 37 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7536 (mttt) REVERT: J 37 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7440 (mttt) REVERT: K 37 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7536 (mttt) REVERT: L 28 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7658 (mtm180) REVERT: L 37 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7535 (mttt) REVERT: M 37 LYS cc_start: 0.7823 (mmmt) cc_final: 0.7471 (mttt) REVERT: N 37 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7462 (mttt) REVERT: O 37 LYS cc_start: 0.7868 (mmmt) cc_final: 0.7527 (mttt) REVERT: P 37 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7660 (mttt) outliers start: 53 outliers final: 30 residues processed: 337 average time/residue: 0.8528 time to fit residues: 335.6521 Evaluate side-chains 311 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 338 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 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 450 LYS 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 338 GLU Chi-restraints excluded: chain F residue 384 VAL 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 338 GLU 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 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: 0.0050 chunk 96 optimal weight: 9.9990 chunk 427 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 167 optimal weight: 0.0470 chunk 277 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 422 optimal weight: 7.9990 chunk 367 optimal weight: 9.9990 overall best weight: 1.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110861 restraints weight = 45422.285| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.28 r_work: 0.3219 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2246 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= 0.107 Angle : 0.544 10.889 51608 Z= 0.283 Chirality : 0.044 0.172 5440 Planarity : 0.005 0.068 6728 Dihedral : 5.947 74.065 5431 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.85 % Favored : 93.89 % Rotamer: Outliers : 1.35 % Allowed : 23.72 % 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: -2.39 (0.11), residues: 4600 helix: -0.86 (0.15), residues: 1344 sheet: -1.02 (0.20), residues: 696 loop : -2.21 (0.10), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 258 TYR 0.017 0.001 TYR P 80 PHE 0.025 0.001 PHE E 345 TRP 0.009 0.001 TRP A 214 HIS 0.006 0.001 HIS D 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (38016) covalent geometry : angle 0.54369 / 0.28 (51608) hydrogen bonds : bond 0.04457 / 2.90 ( 901) hydrogen bonds : angle 4.07536 / 2.81 ( 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 328 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 1.377 Fit side-chains REVERT: A 249 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8018 (mt-10) REVERT: A 447 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: B 466 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7729 (mmpt) REVERT: C 204 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7669 (pt0) REVERT: C 249 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8213 (mt-10) REVERT: D 249 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8202 (mt-10) REVERT: D 450 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8440 (ttmt) REVERT: F 249 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8288 (mt-10) REVERT: F 450 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8466 (ttmt) REVERT: G 249 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8258 (mt-10) REVERT: G 338 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6740 (tt0) REVERT: H 249 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8225 (mt-10) REVERT: I 37 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7567 (mttt) REVERT: J 37 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7491 (mttt) REVERT: K 37 LYS cc_start: 0.7894 (mmmt) cc_final: 0.7538 (mttt) REVERT: L 28 ARG cc_start: 0.8081 (mmm-85) cc_final: 0.7651 (mtm180) REVERT: L 37 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7576 (mttt) REVERT: M 37 LYS cc_start: 0.7860 (mmmt) cc_final: 0.7547 (mttt) REVERT: N 37 LYS cc_start: 0.7818 (mmmt) cc_final: 0.7488 (mttt) REVERT: O 37 LYS cc_start: 0.7914 (mmmt) cc_final: 0.7594 (mttt) REVERT: O 80 TYR cc_start: 0.8180 (m-80) cc_final: 0.7896 (m-80) REVERT: P 37 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7706 (mttt) outliers start: 52 outliers final: 32 residues processed: 323 average time/residue: 0.8174 time to fit residues: 309.1537 Evaluate side-chains 307 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 127 PHE 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 248 GLU Chi-restraints excluded: chain B residue 384 VAL 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 450 LYS 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 384 VAL 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 338 GLU 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 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 100 LEU 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: 9.9990 chunk 41 optimal weight: 2.9990 chunk 333 optimal weight: 9.9990 chunk 417 optimal weight: 0.0670 chunk 439 optimal weight: 3.9990 chunk 361 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 376 optimal weight: 3.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.125258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110798 restraints weight = 47080.805| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.46 r_work: 0.3174 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 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 : 0.003 0.036 38016 Z= 0.136 Angle : 0.590 10.992 51608 Z= 0.307 Chirality : 0.045 0.176 5440 Planarity : 0.005 0.069 6728 Dihedral : 6.132 72.495 5431 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.28 % Favored : 93.46 % Rotamer: Outliers : 1.28 % Allowed : 23.78 % 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: -2.43 (0.11), residues: 4600 helix: -0.89 (0.15), residues: 1344 sheet: -1.02 (0.20), residues: 696 loop : -2.25 (0.10), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 258 TYR 0.017 0.001 TYR P 80 PHE 0.027 0.002 PHE E 345 TRP 0.010 0.001 TRP A 214 HIS 0.005 0.001 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (38016) covalent geometry : angle 0.58971 / 0.31 (51608) hydrogen bonds : bond 0.05423 / 3.53 ( 901) hydrogen bonds : angle 4.14167 / 2.86 ( 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 321 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 272 time to evaluate : 1.411 Fit side-chains REVERT: A 249 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7896 (mt-10) REVERT: A 447 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7510 (mm-30) REVERT: B 21 ARG cc_start: 0.7859 (ptm160) cc_final: 0.7630 (ptm160) REVERT: B 466 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7514 (mmpt) REVERT: C 204 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: C 249 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8027 (mt-10) REVERT: D 30 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: D 249 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8085 (mt-10) REVERT: D 450 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8366 (ttmt) REVERT: F 249 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8107 (mt-10) REVERT: F 450 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8389 (ttmt) REVERT: G 249 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8094 (mt-10) REVERT: G 338 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6740 (tt0) REVERT: G 466 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7578 (mmpt) REVERT: H 249 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8059 (mt-10) REVERT: I 37 LYS cc_start: 0.7789 (mmmt) cc_final: 0.7410 (mttt) REVERT: J 37 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7350 (mttt) REVERT: K 29 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7171 (mt-10) REVERT: K 37 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7397 (mttt) REVERT: L 28 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7385 (mtm180) REVERT: L 37 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7393 (mttt) REVERT: M 37 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7389 (mttt) REVERT: N 37 LYS cc_start: 0.7764 (mmmt) cc_final: 0.7332 (mttt) REVERT: O 37 LYS cc_start: 0.7857 (mmmt) cc_final: 0.7425 (mttt) REVERT: O 80 TYR cc_start: 0.8118 (m-80) cc_final: 0.7852 (m-80) REVERT: P 37 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7525 (mttt) outliers start: 49 outliers final: 34 residues processed: 314 average time/residue: 0.8209 time to fit residues: 300.3807 Evaluate side-chains 307 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 127 PHE 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 127 PHE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 384 VAL 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 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 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 127 PHE Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 466 LYS Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain I residue 108 VAL 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 100 LEU 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: 0.9980 chunk 255 optimal weight: 0.6980 chunk 281 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 256 optimal weight: 0.5980 chunk 403 optimal weight: 8.9990 chunk 352 optimal weight: 0.4980 chunk 275 optimal weight: 8.9990 chunk 384 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113587 restraints weight = 45518.131| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.28 r_work: 0.3262 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 38016 Z= 0.091 Angle : 0.506 11.213 51608 Z= 0.262 Chirality : 0.042 0.148 5440 Planarity : 0.005 0.065 6728 Dihedral : 5.574 73.131 5431 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.33 % Favored : 94.41 % Rotamer: Outliers : 1.04 % Allowed : 23.85 % Favored : 75.10 % 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: -2.11 (0.12), residues: 4600 helix: -0.72 (0.15), residues: 1320 sheet: -0.58 (0.19), residues: 776 loop : -2.11 (0.11), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 258 TYR 0.017 0.001 TYR P 80 PHE 0.025 0.001 PHE E 345 TRP 0.009 0.001 TRP D 214 HIS 0.005 0.001 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (38016) covalent geometry : angle 0.50585 / 0.26 (51608) hydrogen bonds : bond 0.03475 / 2.26 ( 901) hydrogen bonds : angle 3.98037 / 2.75 ( 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 331 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 291 time to evaluate : 1.100 Fit side-chains REVERT: A 249 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7956 (mt-10) REVERT: A 338 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: B 187 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7696 (ttp-170) REVERT: B 466 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7756 (mmpt) REVERT: C 204 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: C 249 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8201 (mt-10) REVERT: D 249 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8229 (mt-10) REVERT: D 450 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8411 (ttmt) REVERT: F 249 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8266 (mt-10) REVERT: F 450 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8422 (ttmt) REVERT: G 249 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8149 (mt-10) REVERT: H 249 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8169 (mt-10) REVERT: I 37 LYS cc_start: 0.7729 (mmmt) cc_final: 0.7422 (mttt) REVERT: J 37 LYS cc_start: 0.7680 (mmmt) cc_final: 0.7331 (mttt) REVERT: K 37 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7448 (mttt) REVERT: L 28 ARG cc_start: 0.8053 (mmm-85) cc_final: 0.7595 (mtm180) REVERT: L 37 LYS cc_start: 0.7792 (mmmt) cc_final: 0.7439 (mttt) REVERT: M 37 LYS cc_start: 0.7690 (mmmt) cc_final: 0.7384 (mttt) REVERT: N 37 LYS cc_start: 0.7694 (mmmt) cc_final: 0.7356 (mttt) REVERT: O 37 LYS cc_start: 0.7706 (mmmt) cc_final: 0.7419 (mttt) REVERT: O 80 TYR cc_start: 0.8157 (m-80) cc_final: 0.7887 (m-80) REVERT: P 37 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7639 (mttt) outliers start: 40 outliers final: 29 residues processed: 326 average time/residue: 0.7716 time to fit residues: 294.7743 Evaluate side-chains 305 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 338 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 187 ARG Chi-restraints excluded: chain B residue 248 GLU Chi-restraints excluded: chain B residue 384 VAL 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 450 LYS 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 H residue 127 PHE 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 108 VAL Chi-restraints excluded: chain N residue 108 VAL Chi-restraints excluded: chain O residue 103 ASP 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: 5.9990 chunk 414 optimal weight: 0.3980 chunk 297 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 279 optimal weight: 0.0000 chunk 178 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 408 optimal weight: 9.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110853 restraints weight = 45301.266| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.26 r_work: 0.3223 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38016 Z= 0.118 Angle : 0.554 10.825 51608 Z= 0.288 Chirality : 0.044 0.174 5440 Planarity : 0.005 0.068 6728 Dihedral : 5.697 72.418 5430 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.76 % Favored : 93.98 % Rotamer: Outliers : 1.02 % Allowed : 23.96 % Favored : 75.03 % 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: -2.16 (0.12), residues: 4600 helix: -0.72 (0.15), residues: 1320 sheet: -0.81 (0.20), residues: 696 loop : -2.06 (0.10), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 258 TYR 0.017 0.001 TYR L 80 PHE 0.026 0.001 PHE E 345 TRP 0.009 0.001 TRP A 214 HIS 0.005 0.001 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (38016) covalent geometry : angle 0.55405 / 0.29 (51608) hydrogen bonds : bond 0.04588 / 2.99 ( 901) hydrogen bonds : angle 4.00008 / 2.76 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9165.78 seconds wall clock time: 157 minutes 7.49 seconds (9427.49 seconds total)