Starting phenix.real_space_refine on Tue Aug 26 00:05:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ci1_45607/08_2025/9ci1_45607_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ci1_45607/08_2025/9ci1_45607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ci1_45607/08_2025/9ci1_45607_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ci1_45607/08_2025/9ci1_45607_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ci1_45607/08_2025/9ci1_45607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ci1_45607/08_2025/9ci1_45607.map" } resolution = 2.88 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 216 5.16 5 C 20032 2.51 5 N 5616 2.21 5 O 5916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31780 Number of models: 1 Model: "" Number of chains: 16 Chain: "1" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "2" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "3" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "4" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "5" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "6" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "7" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "8" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 519 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "A" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3461 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 21, 'TRANS': 419} Chain breaks: 1 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: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3446 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 21, 'TRANS': 417} Chain breaks: 1 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: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3461 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 21, 'TRANS': 419} Chain breaks: 1 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: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3446 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 21, 'TRANS': 417} Chain breaks: 1 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: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3461 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 21, 'TRANS': 419} Chain breaks: 1 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: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3446 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 21, 'TRANS': 417} Chain breaks: 1 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: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3461 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 21, 'TRANS': 419} Chain breaks: 1 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: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3446 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 21, 'TRANS': 417} Chain breaks: 1 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 Time building chain proxies: 8.03, per 1000 atoms: 0.25 Number of scatterers: 31780 At special positions: 0 Unit cell: (135.85, 135.85, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 216 16.00 O 5916 8.00 N 5616 7.00 C 20032 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: 3.03 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7296 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 39 sheets defined 39.9% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain '8' and resid 129 through 133 removed outlier: 4.215A pdb=" N THR 8 133 " --> pdb=" O PHE 8 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 61 Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.763A pdb=" N LYS A 81 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.804A pdb=" N LEU A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 108' Processing helix chain 'A' and resid 112 through 121 removed outlier: 4.192A pdb=" N MET A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.616A pdb=" N LYS A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 163 Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.799A pdb=" N GLY A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 removed outlier: 3.971A pdb=" N ARG A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.506A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.569A pdb=" N THR A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.902A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.516A pdb=" N LEU A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.564A pdb=" N GLY A 361 " --> pdb=" O ARG A 358 " (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 395 Processing helix chain 'A' and resid 413 through 432 removed outlier: 3.569A pdb=" N VAL A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 454 through 459 removed outlier: 4.007A pdb=" N ALA A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 removed outlier: 4.018A pdb=" N ALA B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.632A pdb=" N LYS B 81 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.824A pdb=" N LEU B 107 " --> pdb=" O PRO B 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 108' Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.633A pdb=" N LYS B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.687A pdb=" N ALA B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 removed outlier: 3.564A pdb=" N ARG B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 220 " --> pdb=" O ASP B 216 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 224 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 260 removed outlier: 3.603A pdb=" N ALA B 257 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.506A pdb=" N ASN B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.761A pdb=" N LEU B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 316 " --> pdb=" O ARG B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.750A pdb=" N ASP B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 349 " --> pdb=" O PHE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 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 395 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.987A pdb=" N LEU B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 432 removed outlier: 3.834A pdb=" N GLY B 416 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASN B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 449 Processing helix chain 'B' and resid 452 through 462 removed outlier: 3.526A pdb=" N VAL B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 63 Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.716A pdb=" N LYS C 81 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.804A pdb=" N LEU C 107 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.580A 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 112 through 121 removed outlier: 4.192A pdb=" N MET C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.616A pdb=" N LYS C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.800A pdb=" N GLY C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 removed outlier: 3.971A pdb=" N ARG C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 260 removed outlier: 3.506A pdb=" N ARG C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA C 254 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 256 " --> pdb=" O LYS C 252 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.570A pdb=" N THR C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.902A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 351 removed outlier: 3.516A pdb=" N LEU C 343 " --> pdb=" O ARG C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.565A pdb=" N GLY C 361 " --> pdb=" O ARG C 358 " (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 395 removed outlier: 3.516A pdb=" N GLU C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 432 removed outlier: 4.055A pdb=" N ASN C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN C 429 " --> pdb=" O GLU C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 450 Processing helix chain 'C' and resid 454 through 459 removed outlier: 4.010A pdb=" N ALA C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 60 removed outlier: 3.561A pdb=" N ALA D 53 " --> pdb=" O PRO D 49 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 55 " --> pdb=" O GLU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.639A pdb=" N LYS D 81 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.824A pdb=" N LEU D 107 " --> pdb=" O PRO D 104 " (cutoff:3.500A) removed outlier: 3.579A 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 121 Processing helix chain 'D' and resid 141 through 146 removed outlier: 3.633A pdb=" N LYS D 146 " --> pdb=" O PRO D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 163 Processing helix chain 'D' and resid 181 through 196 removed outlier: 3.687A pdb=" N ALA D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 189 " --> pdb=" O TYR D 185 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY D 196 " --> pdb=" O CYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 233 removed outlier: 3.564A pdb=" N ARG D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 220 " --> pdb=" O ASP D 216 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 230 " --> pdb=" O PHE D 226 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 260 removed outlier: 3.604A pdb=" N ALA D 257 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 260 " --> pdb=" O PHE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 288 removed outlier: 3.507A pdb=" N ASN D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.761A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 351 removed outlier: 3.649A pdb=" N ASP D 347 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 349 " --> pdb=" O PHE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 361 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 395 removed outlier: 3.695A pdb=" N GLU D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.988A pdb=" N LEU D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 432 removed outlier: 3.813A pdb=" N GLY D 416 " --> pdb=" O GLY D 412 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 449 removed outlier: 3.586A pdb=" N ALA D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 462 removed outlier: 3.510A pdb=" N GLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 removed outlier: 3.657A pdb=" N ALA E 55 " --> pdb=" O GLU E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 removed outlier: 3.731A pdb=" N LYS E 81 " --> pdb=" O ASP E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.804A pdb=" N LEU E 107 " --> pdb=" O PRO E 104 " (cutoff:3.500A) removed outlier: 3.580A 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 112 through 121 removed outlier: 4.192A pdb=" N MET E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.616A pdb=" N LYS E 146 " --> pdb=" O PRO E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 163 Processing helix chain 'E' and resid 181 through 195 removed outlier: 3.799A pdb=" N GLY E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 233 removed outlier: 3.970A pdb=" N ARG E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS E 227 " --> pdb=" O GLU E 223 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 260 removed outlier: 3.506A pdb=" N ARG E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 254 " --> pdb=" O MET E 250 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA E 257 " --> pdb=" O ARG E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 288 removed outlier: 3.569A pdb=" N THR E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 322 removed outlier: 3.901A pdb=" N LEU E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 351 removed outlier: 3.517A pdb=" N LEU E 343 " --> pdb=" O ARG E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.565A pdb=" N GLY E 361 " --> pdb=" O ARG E 358 " (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 395 Processing helix chain 'E' and resid 413 through 432 removed outlier: 3.570A pdb=" N VAL E 418 " --> pdb=" O ALA E 414 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA E 419 " --> pdb=" O PRO E 415 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 451 removed outlier: 4.460A pdb=" N TRP E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 459 removed outlier: 3.954A pdb=" N ALA E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 60 removed outlier: 3.834A pdb=" N ALA F 55 " --> pdb=" O GLU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.622A pdb=" N LYS F 81 " --> pdb=" O ASP F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.824A pdb=" N LEU F 107 " --> pdb=" O PRO F 104 " (cutoff:3.500A) removed outlier: 3.579A 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 121 Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.633A pdb=" N LYS F 146 " --> pdb=" O PRO F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 163 Processing helix chain 'F' and resid 181 through 196 removed outlier: 3.686A pdb=" N ALA F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL F 189 " --> pdb=" O TYR F 185 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY F 196 " --> pdb=" O CYS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 removed outlier: 3.564A pdb=" N ARG F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE F 220 " --> pdb=" O ASP F 216 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA F 224 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA F 230 " --> pdb=" O PHE F 226 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 260 removed outlier: 3.603A pdb=" N ALA F 257 " --> pdb=" O ARG F 253 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 260 " --> pdb=" O PHE F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 288 removed outlier: 3.506A pdb=" N ASN F 277 " --> pdb=" O GLY F 273 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR F 279 " --> pdb=" O THR F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.761A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 316 " --> pdb=" O ARG F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 351 removed outlier: 3.644A pdb=" N ASP F 347 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU F 348 " --> pdb=" O GLY F 344 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU F 349 " --> pdb=" O PHE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 361 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 395 removed outlier: 3.623A pdb=" N LEU F 390 " --> pdb=" O HIS F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 408 removed outlier: 3.840A pdb=" N LEU F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 432 removed outlier: 3.826A pdb=" N GLY F 416 " --> pdb=" O GLY F 412 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL F 418 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS F 427 " --> pdb=" O ALA F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 449 Processing helix chain 'F' and resid 452 through 462 removed outlier: 3.564A pdb=" N VAL F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 61 removed outlier: 3.966A pdb=" N ALA G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 81 removed outlier: 3.719A pdb=" N LYS G 81 " --> pdb=" O ASP G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.805A pdb=" N LEU G 107 " --> pdb=" O PRO G 104 " (cutoff:3.500A) removed outlier: 3.580A 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: 4.191A pdb=" N MET G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 146 removed outlier: 3.617A pdb=" N LYS G 146 " --> pdb=" O PRO G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 163 Processing helix chain 'G' and resid 181 through 195 removed outlier: 3.800A pdb=" N GLY G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 233 removed outlier: 3.971A pdb=" N ARG G 217 " --> pdb=" O ARG G 213 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS G 227 " --> pdb=" O GLU G 223 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR G 232 " --> pdb=" O SER G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 260 removed outlier: 3.506A pdb=" N ARG G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA G 254 " --> pdb=" O MET G 250 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN G 255 " --> pdb=" O MET G 251 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE G 256 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA G 257 " --> pdb=" O ARG G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 288 removed outlier: 3.570A pdb=" N THR G 279 " --> pdb=" O THR G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.903A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 351 removed outlier: 3.516A pdb=" N LEU G 343 " --> pdb=" O ARG G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 361 removed outlier: 3.565A pdb=" N GLY G 361 " --> pdb=" O ARG G 358 " (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 395 Processing helix chain 'G' and resid 413 through 432 removed outlier: 3.570A pdb=" N VAL G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 419 " --> pdb=" O PRO G 415 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 450 Processing helix chain 'G' and resid 454 through 462 removed outlier: 4.035A pdb=" N ALA G 458 " --> pdb=" O GLU G 454 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS G 459 " --> pdb=" O LEU G 455 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLU G 460 " --> pdb=" O ALA G 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 60 removed outlier: 3.896A pdb=" N ALA H 55 " --> pdb=" O GLU H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 removed outlier: 3.640A pdb=" N LYS H 81 " --> pdb=" O ASP H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.825A pdb=" N LEU H 107 " --> pdb=" O PRO H 104 " (cutoff:3.500A) removed outlier: 3.579A 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 121 Processing helix chain 'H' and resid 141 through 146 removed outlier: 3.633A pdb=" N LYS H 146 " --> pdb=" O PRO H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 163 Processing helix chain 'H' and resid 181 through 196 removed outlier: 3.686A pdb=" N ALA H 188 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL H 189 " --> pdb=" O TYR H 185 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY H 196 " --> pdb=" O CYS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 233 removed outlier: 3.565A pdb=" N ARG H 217 " --> pdb=" O ARG H 213 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA H 224 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE H 226 " --> pdb=" O ALA H 222 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS H 227 " --> pdb=" O GLU H 223 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA H 230 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 260 removed outlier: 3.604A pdb=" N ALA H 257 " --> pdb=" O ARG H 253 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG H 258 " --> pdb=" O ALA H 254 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU H 260 " --> pdb=" O PHE H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 288 removed outlier: 3.506A pdb=" N ASN H 277 " --> pdb=" O GLY H 273 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR H 279 " --> pdb=" O THR H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 301 Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.760A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS H 316 " --> pdb=" O ARG H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 351 removed outlier: 3.749A pdb=" N ASP H 347 " --> pdb=" O LEU H 343 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU H 348 " --> pdb=" O GLY H 344 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU H 349 " --> pdb=" O PHE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 361 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 395 Processing helix chain 'H' and resid 403 through 408 removed outlier: 3.988A pdb=" N LEU H 407 " --> pdb=" O GLY H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 432 removed outlier: 3.635A pdb=" N VAL H 418 " --> pdb=" O ALA H 414 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA H 419 " --> pdb=" O PRO H 415 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 449 Processing helix chain 'H' and resid 452 through 462 Processing sheet with id=AA1, first strand: chain '1' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain '2' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain '3' and resid 80 through 81 Processing sheet with id=AA4, first strand: chain '4' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain '5' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain '7' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain '8' and resid 80 through 81 Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 89 removed outlier: 6.137A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A 97 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 132 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 308 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 169 through 172 removed outlier: 6.732A pdb=" N LEU A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N PHE A 402 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY A 171 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 326 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 264 through 268 Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.186A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP B 86 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 97 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 40 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU B 37 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 132 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 308 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 201 removed outlier: 7.140A pdb=" N LEU B 170 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N KCX B 201 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N CYS B 172 " --> pdb=" O KCX B 201 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N PHE B 402 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY B 171 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE B 326 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 240 through 241 removed outlier: 6.329A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASP B 268 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'C' and resid 83 through 89 removed outlier: 6.226A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR C 97 " --> pdb=" O MET C 42 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA C 132 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 308 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 172 removed outlier: 6.732A pdb=" N LEU C 169 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE C 402 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY C 171 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 326 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 264 through 268 Processing sheet with id=AC1, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AC2, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.178A pdb=" N CYS D 84 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALA D 102 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP D 86 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR D 97 " --> pdb=" O MET D 42 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 40 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU D 37 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU D 138 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA D 39 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA D 132 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY D 308 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 199 through 201 removed outlier: 7.140A pdb=" N LEU D 170 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N KCX D 201 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS D 172 " --> pdb=" O KCX D 201 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU D 169 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N PHE D 402 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY D 171 " --> pdb=" O PHE D 402 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE D 326 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 240 through 241 removed outlier: 6.329A pdb=" N LEU D 240 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASP D 268 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AC6, first strand: chain 'E' and resid 83 through 89 removed outlier: 6.178A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR E 97 " --> pdb=" O MET E 42 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA E 132 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY E 308 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 169 through 172 removed outlier: 6.732A pdb=" N LEU E 169 " --> pdb=" O LEU E 400 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N PHE E 402 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY E 171 " --> pdb=" O PHE E 402 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLN E 401 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA E 378 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE E 326 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER E 379 " --> pdb=" O ILE E 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 264 through 268 Processing sheet with id=AC9, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AD1, first strand: chain 'F' and resid 83 through 89 removed outlier: 6.172A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP F 86 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR F 97 " --> pdb=" O MET F 42 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE F 40 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU F 37 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA F 132 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY F 308 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 199 through 201 removed outlier: 7.140A pdb=" N LEU F 170 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N KCX F 201 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N CYS F 172 " --> pdb=" O KCX F 201 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N PHE F 402 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY F 171 " --> pdb=" O PHE F 402 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE F 326 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 240 through 241 removed outlier: 6.329A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ASP F 268 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AD5, 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: 7.010A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR G 97 " --> pdb=" O MET G 42 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU G 37 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA G 132 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY G 308 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 169 through 172 removed outlier: 6.732A pdb=" N LEU G 169 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE G 402 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY G 171 " --> pdb=" O PHE G 402 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE G 326 " --> pdb=" O VAL G 377 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 264 through 268 Processing sheet with id=AD8, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AD9, first strand: chain 'H' and resid 83 through 89 removed outlier: 6.187A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR H 97 " --> pdb=" O MET H 42 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE H 40 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU H 37 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU H 138 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA H 39 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA H 132 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY H 308 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 199 through 201 removed outlier: 7.140A pdb=" N LEU H 170 " --> pdb=" O PHE H 199 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N KCX H 201 " --> pdb=" O LEU H 170 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS H 172 " --> pdb=" O KCX H 201 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N PHE H 402 " --> pdb=" O LEU H 169 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLY H 171 " --> pdb=" O PHE H 402 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE H 326 " --> pdb=" O VAL H 377 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 240 through 241 removed outlier: 6.329A pdb=" N LEU H 240 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASP H 268 " --> pdb=" O LEU H 240 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 353 through 354 1022 hydrogen bonds defined for protein. 2877 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: 6.41 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6970 1.33 - 1.45: 7507 1.45 - 1.57: 17735 1.57 - 1.69: 0 1.69 - 1.81: 304 Bond restraints: 32516 Sorted by residual: bond pdb=" NZ KCX D 201 " pdb=" CX KCX D 201 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" NZ KCX H 201 " pdb=" CX KCX H 201 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" NZ KCX B 201 " pdb=" CX KCX B 201 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ KCX F 201 " pdb=" CX KCX F 201 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ KCX E 201 " pdb=" CX KCX E 201 " ideal model delta sigma weight residual 1.411 1.330 0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 32511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 39869 1.77 - 3.55: 3695 3.55 - 5.32: 380 5.32 - 7.10: 24 7.10 - 8.87: 12 Bond angle restraints: 43980 Sorted by residual: angle pdb=" N LYS 3 113 " pdb=" CA LYS 3 113 " pdb=" C LYS 3 113 " ideal model delta sigma weight residual 114.62 107.43 7.19 1.14e+00 7.69e-01 3.98e+01 angle pdb=" N LYS 1 113 " pdb=" CA LYS 1 113 " pdb=" C LYS 1 113 " ideal model delta sigma weight residual 114.62 107.85 6.77 1.14e+00 7.69e-01 3.53e+01 angle pdb=" N LYS 7 113 " pdb=" CA LYS 7 113 " pdb=" C LYS 7 113 " ideal model delta sigma weight residual 114.62 108.18 6.44 1.14e+00 7.69e-01 3.19e+01 angle pdb=" CA GLY H 329 " pdb=" C GLY H 329 " pdb=" O GLY H 329 " ideal model delta sigma weight residual 122.29 118.15 4.14 8.10e-01 1.52e+00 2.61e+01 angle pdb=" N VAL C 461 " pdb=" CA VAL C 461 " pdb=" C VAL C 461 " ideal model delta sigma weight residual 111.90 107.89 4.01 8.10e-01 1.52e+00 2.46e+01 ... (remaining 43975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 15998 17.91 - 35.81: 2055 35.81 - 53.72: 762 53.72 - 71.62: 225 71.62 - 89.53: 44 Dihedral angle restraints: 19084 sinusoidal: 7572 harmonic: 11512 Sorted by residual: dihedral pdb=" CA LEU 2 70 " pdb=" C LEU 2 70 " pdb=" N VAL 2 71 " pdb=" CA VAL 2 71 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASP 8 135 " pdb=" CB ASP 8 135 " pdb=" CG ASP 8 135 " pdb=" OD1 ASP 8 135 " ideal model delta sinusoidal sigma weight residual -30.00 -89.33 59.33 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASN 2 98 " pdb=" CB ASN 2 98 " pdb=" CG ASN 2 98 " pdb=" OD1 ASN 2 98 " ideal model delta sinusoidal sigma weight residual -90.00 -163.69 73.69 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 19081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3121 0.054 - 0.107: 994 0.107 - 0.161: 417 0.161 - 0.214: 119 0.214 - 0.268: 5 Chirality restraints: 4656 Sorted by residual: chirality pdb=" CA ILE A 174 " pdb=" N ILE A 174 " pdb=" C ILE A 174 " pdb=" CB ILE A 174 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE A 465 " pdb=" N ILE A 465 " pdb=" C ILE A 465 " pdb=" CB ILE A 465 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE E 465 " pdb=" N ILE E 465 " pdb=" C ILE E 465 " pdb=" CB ILE E 465 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 4653 not shown) Planarity restraints: 5792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 121 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C VAL B 121 " -0.062 2.00e-02 2.50e+03 pdb=" O VAL B 121 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY B 122 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA 4 124 " 0.012 2.00e-02 2.50e+03 2.52e-02 6.37e+00 pdb=" C ALA 4 124 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA 4 124 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY 4 125 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET E 262 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO E 263 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO E 263 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 263 " -0.029 5.00e-02 4.00e+02 ... (remaining 5789 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 10889 2.84 - 3.35: 26887 3.35 - 3.87: 48835 3.87 - 4.38: 57322 4.38 - 4.90: 99690 Nonbonded interactions: 243623 Sorted by model distance: nonbonded pdb=" O THR C 68 " pdb=" OG1 THR C 68 " model vdw 2.324 3.040 nonbonded pdb=" O ASN E 95 " pdb=" NE2 GLN E 96 " model vdw 2.328 3.120 nonbonded pdb=" O ASN A 95 " pdb=" NE2 GLN A 96 " model vdw 2.328 3.120 nonbonded pdb=" O ASN G 95 " pdb=" NE2 GLN G 96 " model vdw 2.328 3.120 nonbonded pdb=" O ASN C 95 " pdb=" NE2 GLN C 96 " model vdw 2.328 3.120 ... (remaining 243618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } ncs_group { reference = (chain 'A' and resid 24 through 466) selection = chain 'B' selection = (chain 'C' and resid 24 through 466) selection = chain 'D' selection = (chain 'E' and resid 24 through 466) selection = chain 'F' selection = (chain 'G' and resid 24 through 466) selection = chain 'H' } 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: 12.230 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: 0.040 Extract box with map and model: 0.840 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 31.300 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 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 : 0.008 0.082 32516 Z= 0.586 Angle : 0.991 8.874 43980 Z= 0.707 Chirality : 0.064 0.268 4656 Planarity : 0.004 0.052 5792 Dihedral : 19.100 89.526 11788 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 1.93 % Allowed : 10.07 % Favored : 88.00 % Rotamer: Outliers : 11.89 % Allowed : 21.49 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -2.92 (0.12), residues: 4032 helix: -1.72 (0.12), residues: 1356 sheet: -0.26 (0.23), residues: 532 loop : -2.60 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 194 TYR 0.012 0.001 TYR G 25 PHE 0.026 0.001 PHE E 345 TRP 0.009 0.001 TRP H 214 HIS 0.003 0.001 HIS C 238 Details of bonding type rmsd covalent geometry : bond 0.00800 (32516) covalent geometry : angle 0.99121 (43980) hydrogen bonds : bond 0.34270 ( 1022) hydrogen bonds : angle 7.67696 ( 2877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 389 poor density : 375 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: 2 67 PRO cc_start: 0.7927 (Cg_exo) cc_final: 0.7684 (Cg_endo) REVERT: 2 98 ASN cc_start: 0.7943 (t0) cc_final: 0.7392 (t160) REVERT: 2 101 PHE cc_start: 0.2494 (m-10) cc_final: 0.2136 (m-10) REVERT: 4 67 PRO cc_start: 0.8045 (Cg_exo) cc_final: 0.7805 (Cg_endo) REVERT: 8 115 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8495 (mt-10) outliers start: 389 outliers final: 79 residues processed: 635 average time/residue: 0.7502 time to fit residues: 558.4810 Evaluate side-chains 327 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 247 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 67 PRO Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 2 residue 75 CYS Chi-restraints excluded: chain 2 residue 91 VAL Chi-restraints excluded: chain 3 residue 65 THR Chi-restraints excluded: chain 3 residue 67 PRO Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 5 residue 67 PRO Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 75 CYS Chi-restraints excluded: chain 6 residue 91 VAL Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 67 PRO Chi-restraints excluded: chain 7 residue 97 PHE Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 8 residue 75 CYS Chi-restraints excluded: chain 8 residue 91 VAL Chi-restraints excluded: chain 8 residue 115 GLU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 330 THR Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 422 VAL Chi-restraints excluded: chain H residue 40 PHE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 178 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 68 ASN 2 68 ASN 2 92 ASN ** 2 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 68 ASN 4 68 ASN 5 68 ASN 5 98 ASN 6 92 ASN 6 100 GLN 7 68 ASN A 327 HIS D 420 ASN E 327 HIS E 429 GLN E 432 ASN G 327 HIS G 429 GLN H 420 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054320 restraints weight = 80240.350| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.12 r_work: 0.2697 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32516 Z= 0.156 Angle : 0.624 6.260 43980 Z= 0.336 Chirality : 0.045 0.174 4656 Planarity : 0.005 0.053 5792 Dihedral : 6.855 58.964 4631 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.87 % Allowed : 7.12 % Favored : 92.01 % Rotamer: Outliers : 4.43 % Allowed : 24.91 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -2.09 (0.12), residues: 4032 helix: -0.31 (0.14), residues: 1396 sheet: -0.98 (0.22), residues: 516 loop : -2.30 (0.12), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 421 TYR 0.024 0.001 TYR A 29 PHE 0.037 0.002 PHE D 345 TRP 0.017 0.001 TRP H 214 HIS 0.005 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00348 (32516) covalent geometry : angle 0.62382 (43980) hydrogen bonds : bond 0.07231 ( 1022) hydrogen bonds : angle 5.12689 ( 2877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 229 time to evaluate : 1.364 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7510 (t80) cc_final: 0.7133 (t80) REVERT: 2 135 ASP cc_start: 0.8226 (t0) cc_final: 0.7926 (t0) REVERT: 4 81 VAL cc_start: 0.7691 (OUTLIER) cc_final: 0.7082 (m) REVERT: 4 101 PHE cc_start: 0.4662 (m-10) cc_final: 0.4372 (m-80) REVERT: 4 115 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8431 (mm-30) REVERT: 6 97 PHE cc_start: 0.6971 (t80) cc_final: 0.6372 (t80) REVERT: 6 101 PHE cc_start: 0.5122 (m-10) cc_final: 0.4612 (m-10) REVERT: 8 101 PHE cc_start: 0.5205 (m-10) cc_final: 0.4841 (m-80) REVERT: 8 115 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8732 (mt-10) outliers start: 145 outliers final: 51 residues processed: 347 average time/residue: 0.7209 time to fit residues: 296.3938 Evaluate side-chains 266 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 97 PHE Chi-restraints excluded: chain 1 residue 100 GLN Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 3 residue 65 THR Chi-restraints excluded: chain 3 residue 97 PHE Chi-restraints excluded: chain 3 residue 100 GLN Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 4 residue 81 VAL Chi-restraints excluded: chain 4 residue 136 GLU Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 5 residue 102 LYS Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 80 CYS Chi-restraints excluded: chain 7 residue 100 GLN Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 173 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 21 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 231 optimal weight: 0.8980 chunk 258 optimal weight: 0.0010 chunk 219 optimal weight: 7.9990 chunk 347 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 349 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 overall best weight: 4.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 68 ASN 2 98 ASN 3 68 ASN 4 74 ASN 4 92 ASN 5 68 ASN 7 68 ASN A 96 GLN B 327 HIS C 96 GLN E 96 GLN F 327 HIS G 96 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.050082 restraints weight = 81678.481| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.13 r_work: 0.2601 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32516 Z= 0.217 Angle : 0.653 7.489 43980 Z= 0.352 Chirality : 0.048 0.198 4656 Planarity : 0.005 0.060 5792 Dihedral : 5.761 59.026 4532 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 1.12 % Allowed : 7.37 % Favored : 91.52 % Rotamer: Outliers : 3.85 % Allowed : 24.11 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -1.59 (0.13), residues: 4032 helix: 0.34 (0.14), residues: 1400 sheet: -0.76 (0.22), residues: 508 loop : -2.18 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 134 TYR 0.017 0.001 TYR A 29 PHE 0.033 0.002 PHE D 345 TRP 0.016 0.001 TRP B 214 HIS 0.006 0.002 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00521 (32516) covalent geometry : angle 0.65302 (43980) hydrogen bonds : bond 0.08044 ( 1022) hydrogen bonds : angle 4.67388 ( 2877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 223 time to evaluate : 1.342 Fit side-chains REVERT: 2 135 ASP cc_start: 0.8288 (t0) cc_final: 0.8040 (t0) REVERT: 3 131 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8391 (mp) REVERT: 4 87 LYS cc_start: 0.8879 (mmtp) cc_final: 0.8540 (mmmm) REVERT: 4 115 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8521 (mm-30) REVERT: 5 87 LYS cc_start: 0.8490 (mttp) cc_final: 0.8260 (mmmt) REVERT: 6 66 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6771 (mtmp) REVERT: 8 115 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8756 (mt-10) REVERT: C 178 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7704 (tm) REVERT: C 465 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8733 (pp) REVERT: F 335 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7887 (pp) outliers start: 126 outliers final: 59 residues processed: 326 average time/residue: 0.7931 time to fit residues: 300.9274 Evaluate side-chains 270 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 100 GLN Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 2 residue 91 VAL Chi-restraints excluded: chain 3 residue 65 THR Chi-restraints excluded: chain 3 residue 100 GLN Chi-restraints excluded: chain 3 residue 131 LEU Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 4 residue 91 VAL Chi-restraints excluded: chain 4 residue 93 LEU Chi-restraints excluded: chain 4 residue 136 GLU Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 100 GLN Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 177 LYS Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 440 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 386 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 400 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 402 optimal weight: 5.9990 chunk 220 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 68 ASN 3 68 ASN 4 74 ASN 4 92 ASN 5 68 ASN 5 98 ASN 7 68 ASN A 123 ASN C 123 ASN F 432 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.068569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.051165 restraints weight = 80910.585| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.09 r_work: 0.2631 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 32516 Z= 0.153 Angle : 0.588 6.116 43980 Z= 0.314 Chirality : 0.045 0.179 4656 Planarity : 0.004 0.054 5792 Dihedral : 5.538 56.287 4530 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.52 % Favored : 92.44 % Rotamer: Outliers : 3.00 % Allowed : 24.33 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.13), residues: 4032 helix: 0.69 (0.14), residues: 1408 sheet: -0.65 (0.22), residues: 508 loop : -2.07 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 134 TYR 0.013 0.001 TYR A 29 PHE 0.030 0.001 PHE D 345 TRP 0.014 0.001 TRP H 214 HIS 0.003 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00359 (32516) covalent geometry : angle 0.58814 (43980) hydrogen bonds : bond 0.06154 ( 1022) hydrogen bonds : angle 4.41733 ( 2877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 213 time to evaluate : 1.640 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7559 (t80) cc_final: 0.7149 (t80) REVERT: 4 115 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8523 (mm-30) REVERT: 5 87 LYS cc_start: 0.8520 (mttp) cc_final: 0.8286 (mmmt) REVERT: 6 113 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8464 (tmmt) REVERT: 8 115 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8729 (mt-10) REVERT: B 231 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: B 335 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7978 (pp) REVERT: C 334 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6451 (mtmt) REVERT: C 446 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7495 (mtp180) REVERT: C 465 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8759 (pp) REVERT: D 231 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: F 231 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: H 231 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: H 335 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8028 (pp) outliers start: 98 outliers final: 61 residues processed: 295 average time/residue: 0.7395 time to fit residues: 256.3665 Evaluate side-chains 276 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 205 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 100 GLN Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 2 residue 91 VAL Chi-restraints excluded: chain 3 residue 65 THR Chi-restraints excluded: chain 3 residue 100 GLN Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 4 residue 92 ASN Chi-restraints excluded: chain 4 residue 136 GLU Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 91 VAL Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 6 residue 113 LYS Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 450 LYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 393 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 212 MET Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 393 ILE Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 131 ARG Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 387 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 322 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 358 optimal weight: 0.0570 chunk 176 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 366 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 68 ASN 3 68 ASN 4 92 ASN 5 68 ASN 5 98 ASN 7 68 ASN A 123 ASN C 123 ASN E 123 ASN G 123 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.070015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.052680 restraints weight = 80657.852| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.09 r_work: 0.2670 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32516 Z= 0.107 Angle : 0.543 6.460 43980 Z= 0.287 Chirality : 0.043 0.160 4656 Planarity : 0.004 0.051 5792 Dihedral : 5.291 53.232 4529 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.57 % Favored : 92.39 % Rotamer: Outliers : 3.06 % Allowed : 23.99 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.97 (0.13), residues: 4032 helix: 1.00 (0.15), residues: 1400 sheet: -0.52 (0.21), residues: 584 loop : -1.93 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 194 TYR 0.010 0.001 TYR A 29 PHE 0.027 0.001 PHE D 345 TRP 0.012 0.001 TRP H 214 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00237 (32516) covalent geometry : angle 0.54257 (43980) hydrogen bonds : bond 0.04637 ( 1022) hydrogen bonds : angle 4.13348 ( 2877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 210 time to evaluate : 1.362 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7566 (t80) cc_final: 0.7280 (t80) REVERT: 4 87 LYS cc_start: 0.8913 (mmtp) cc_final: 0.8576 (mmmm) REVERT: 4 97 PHE cc_start: 0.7812 (t80) cc_final: 0.7420 (t80) REVERT: 4 115 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8535 (mm-30) REVERT: 5 87 LYS cc_start: 0.8541 (mttp) cc_final: 0.8289 (mmmt) REVERT: 6 66 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6690 (mtmp) REVERT: 6 102 LYS cc_start: 0.7766 (tppt) cc_final: 0.7456 (mptt) REVERT: 8 87 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8525 (mmmm) REVERT: 8 115 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8595 (mt-10) REVERT: B 231 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: B 335 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8027 (pp) REVERT: C 446 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7498 (mtp180) REVERT: D 231 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: D 463 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8642 (mtpm) REVERT: F 231 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: G 83 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8767 (ptm160) REVERT: H 231 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: H 335 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8048 (pp) outliers start: 100 outliers final: 47 residues processed: 293 average time/residue: 0.7671 time to fit residues: 262.3131 Evaluate side-chains 263 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 206 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 100 GLN Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 2 residue 91 VAL Chi-restraints excluded: chain 3 residue 65 THR Chi-restraints excluded: chain 3 residue 100 GLN Chi-restraints excluded: chain 4 residue 91 VAL Chi-restraints excluded: chain 4 residue 136 GLU Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 8 residue 91 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 440 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 221 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 chunk 233 optimal weight: 10.0000 chunk 346 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 310 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 170 optimal weight: 0.0870 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 68 ASN 3 68 ASN 5 68 ASN 5 98 ASN 7 68 ASN A 123 ASN C 123 ASN E 123 ASN G 123 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.068284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.050863 restraints weight = 80696.280| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.13 r_work: 0.2611 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 32516 Z= 0.154 Angle : 0.576 7.144 43980 Z= 0.306 Chirality : 0.045 0.176 4656 Planarity : 0.004 0.054 5792 Dihedral : 5.244 51.706 4525 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.42 % Favored : 92.53 % Rotamer: Outliers : 3.51 % Allowed : 23.84 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.92 (0.13), residues: 4032 helix: 1.13 (0.15), residues: 1396 sheet: -0.62 (0.22), residues: 544 loop : -1.91 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 194 TYR 0.010 0.001 TYR A 29 PHE 0.029 0.001 PHE D 345 TRP 0.011 0.001 TRP H 214 HIS 0.003 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00367 (32516) covalent geometry : angle 0.57641 (43980) hydrogen bonds : bond 0.05954 ( 1022) hydrogen bonds : angle 4.18821 ( 2877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 199 time to evaluate : 1.124 Fit side-chains REVERT: 4 97 PHE cc_start: 0.7824 (t80) cc_final: 0.7245 (t80) REVERT: 4 115 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8556 (mm-30) REVERT: 5 87 LYS cc_start: 0.8524 (mttp) cc_final: 0.8270 (mmmt) REVERT: 6 66 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6586 (mtmp) REVERT: 7 136 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8316 (tm-30) REVERT: 8 87 LYS cc_start: 0.8859 (mmtp) cc_final: 0.8529 (mmmm) REVERT: 8 97 PHE cc_start: 0.7671 (t80) cc_final: 0.7447 (t80) REVERT: 8 115 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8725 (mt-10) REVERT: B 227 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8494 (mtpp) REVERT: B 231 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: B 335 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7967 (pp) REVERT: B 440 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: C 334 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6476 (mtmt) REVERT: D 227 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8229 (tttm) REVERT: D 231 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: D 335 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7977 (pp) REVERT: D 440 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7512 (pt0) REVERT: D 463 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8657 (mtpm) REVERT: F 227 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8479 (mtpp) REVERT: F 231 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: F 440 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: G 51 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8372 (pm20) REVERT: G 83 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8813 (ptm160) REVERT: H 227 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8229 (tttm) REVERT: H 231 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: H 335 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7994 (pp) REVERT: H 440 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7532 (pt0) outliers start: 115 outliers final: 54 residues processed: 295 average time/residue: 0.6301 time to fit residues: 218.0285 Evaluate side-chains 270 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 195 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 2 residue 91 VAL Chi-restraints excluded: chain 2 residue 113 LYS Chi-restraints excluded: chain 3 residue 65 THR Chi-restraints excluded: chain 3 residue 100 GLN Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 4 residue 91 VAL Chi-restraints excluded: chain 4 residue 136 GLU Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 6 residue 91 VAL Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 6 residue 113 LYS Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 8 residue 91 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 393 ILE Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 440 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 77 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 385 optimal weight: 10.0000 chunk 388 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 310 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 340 optimal weight: 0.0670 chunk 128 optimal weight: 5.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 98 ASN A 123 ASN C 123 ASN E 123 ASN G 123 ASN H 327 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.067060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.049496 restraints weight = 81428.987| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.15 r_work: 0.2590 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 32516 Z= 0.207 Angle : 0.621 7.881 43980 Z= 0.331 Chirality : 0.047 0.248 4656 Planarity : 0.005 0.055 5792 Dihedral : 5.371 51.061 4522 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.94 % Allowed : 6.92 % Favored : 92.14 % Rotamer: Outliers : 3.09 % Allowed : 23.96 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -1.00 (0.13), residues: 4032 helix: 1.04 (0.15), residues: 1388 sheet: -0.63 (0.22), residues: 544 loop : -1.93 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 134 TYR 0.010 0.001 TYR G 185 PHE 0.031 0.002 PHE H 345 TRP 0.011 0.001 TRP D 214 HIS 0.004 0.001 HIS C 386 Details of bonding type rmsd covalent geometry : bond 0.00505 (32516) covalent geometry : angle 0.62058 (43980) hydrogen bonds : bond 0.06932 ( 1022) hydrogen bonds : angle 4.33893 ( 2877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 196 time to evaluate : 0.926 Fit side-chains REVERT: 4 97 PHE cc_start: 0.7797 (t80) cc_final: 0.7294 (t80) REVERT: 4 113 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8426 (tmmt) REVERT: 4 115 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8493 (mm-30) REVERT: 5 87 LYS cc_start: 0.8514 (mttp) cc_final: 0.8247 (mmmt) REVERT: 6 66 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6544 (mtmp) REVERT: 6 113 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8457 (tmmt) REVERT: 8 97 PHE cc_start: 0.7621 (t80) cc_final: 0.7305 (t80) REVERT: 8 115 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8748 (mt-10) REVERT: B 227 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8480 (mtpp) REVERT: B 231 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: B 335 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7923 (pp) REVERT: B 440 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: C 334 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6556 (mtmt) REVERT: C 465 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8811 (pp) REVERT: D 227 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8476 (mtpp) REVERT: D 231 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: D 440 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7660 (pt0) REVERT: D 463 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8671 (mtpm) REVERT: F 227 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8465 (mtpp) REVERT: F 231 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: F 440 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: G 51 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: H 227 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8478 (mtpp) REVERT: H 231 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: H 335 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7929 (pp) REVERT: H 440 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7634 (pt0) outliers start: 101 outliers final: 52 residues processed: 284 average time/residue: 0.6515 time to fit residues: 216.7409 Evaluate side-chains 267 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 194 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 2 residue 91 VAL Chi-restraints excluded: chain 2 residue 113 LYS Chi-restraints excluded: chain 3 residue 65 THR Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 4 residue 91 VAL Chi-restraints excluded: chain 4 residue 113 LYS Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 6 residue 91 VAL Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 6 residue 113 LYS Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 8 residue 91 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 440 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 353 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 328 optimal weight: 0.5980 chunk 214 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 307 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 98 ASN A 123 ASN C 123 ASN E 123 ASN G 123 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.069201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.051654 restraints weight = 80525.904| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.13 r_work: 0.2639 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32516 Z= 0.117 Angle : 0.553 7.853 43980 Z= 0.290 Chirality : 0.043 0.208 4656 Planarity : 0.004 0.050 5792 Dihedral : 5.170 51.596 4522 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.30 % Favored : 92.81 % Rotamer: Outliers : 2.38 % Allowed : 24.85 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.78 (0.13), residues: 4032 helix: 1.21 (0.15), residues: 1400 sheet: -0.40 (0.21), residues: 584 loop : -1.87 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 41 TYR 0.008 0.001 TYR E 185 PHE 0.027 0.001 PHE G 345 TRP 0.012 0.001 TRP D 214 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00271 (32516) covalent geometry : angle 0.55326 (43980) hydrogen bonds : bond 0.04647 ( 1022) hydrogen bonds : angle 4.05903 ( 2877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 199 time to evaluate : 0.912 Fit side-chains REVERT: 4 97 PHE cc_start: 0.7705 (t80) cc_final: 0.7170 (t80) REVERT: 4 115 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8531 (mm-30) REVERT: 5 87 LYS cc_start: 0.8477 (mttp) cc_final: 0.8197 (mmmt) REVERT: 6 66 LYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6361 (mtmp) REVERT: 8 97 PHE cc_start: 0.7332 (t80) cc_final: 0.6850 (t80) REVERT: 8 115 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8580 (mt-10) REVERT: A 123 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8393 (p0) REVERT: B 227 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8114 (tttm) REVERT: B 231 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: B 335 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7933 (pp) REVERT: B 440 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: C 123 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8410 (p0) REVERT: C 262 MET cc_start: 0.9477 (mmp) cc_final: 0.9184 (mmp) REVERT: C 334 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6577 (mtmt) REVERT: C 465 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8789 (pp) REVERT: D 227 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8125 (tttm) REVERT: D 231 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: D 335 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7953 (pp) REVERT: D 440 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7455 (pt0) REVERT: D 463 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8612 (mtpm) REVERT: E 123 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8371 (p0) REVERT: F 227 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8116 (tttm) REVERT: F 231 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: F 440 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: F 463 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8608 (mtpm) REVERT: G 51 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: G 83 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8702 (ptm160) REVERT: G 123 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8339 (p0) REVERT: G 262 MET cc_start: 0.9485 (mmp) cc_final: 0.9169 (mmp) REVERT: H 227 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8119 (tttm) REVERT: H 231 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: H 335 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7924 (pp) REVERT: H 440 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7484 (pt0) outliers start: 78 outliers final: 44 residues processed: 268 average time/residue: 0.6745 time to fit residues: 211.5283 Evaluate side-chains 263 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 193 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 2 residue 91 VAL Chi-restraints excluded: chain 3 residue 100 GLN Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 4 residue 91 VAL Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 6 residue 91 VAL Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 123 ASN Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain G residue 393 ILE Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 440 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 140 optimal weight: 0.0870 chunk 349 optimal weight: 7.9990 chunk 318 optimal weight: 4.9990 chunk 295 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 192 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 228 optimal weight: 2.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 68 ASN 4 98 ASN 5 98 ASN A 123 ASN C 123 ASN E 123 ASN G 123 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.069412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.051835 restraints weight = 80400.424| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.13 r_work: 0.2644 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32516 Z= 0.112 Angle : 0.547 9.028 43980 Z= 0.287 Chirality : 0.043 0.187 4656 Planarity : 0.004 0.050 5792 Dihedral : 5.062 52.151 4521 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.25 % Favored : 92.93 % Rotamer: Outliers : 2.20 % Allowed : 25.06 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.64 (0.13), residues: 4032 helix: 1.35 (0.15), residues: 1392 sheet: -0.33 (0.21), residues: 584 loop : -1.78 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 41 TYR 0.007 0.001 TYR A 29 PHE 0.026 0.001 PHE G 345 TRP 0.011 0.001 TRP B 214 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00253 (32516) covalent geometry : angle 0.54697 (43980) hydrogen bonds : bond 0.04545 ( 1022) hydrogen bonds : angle 3.98184 ( 2877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 196 time to evaluate : 1.207 Fit side-chains REVERT: 4 97 PHE cc_start: 0.7530 (t80) cc_final: 0.7087 (t80) REVERT: 4 115 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8529 (mm-30) REVERT: 5 87 LYS cc_start: 0.8471 (mttp) cc_final: 0.8192 (mmmt) REVERT: 6 66 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6323 (mtmp) REVERT: 8 97 PHE cc_start: 0.7241 (t80) cc_final: 0.6830 (t80) REVERT: 8 115 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8438 (mm-30) REVERT: A 262 MET cc_start: 0.9463 (mmp) cc_final: 0.9157 (mmp) REVERT: A 440 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: B 227 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8097 (tttm) REVERT: B 231 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: B 335 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7952 (pp) REVERT: B 440 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: C 262 MET cc_start: 0.9471 (mmp) cc_final: 0.9197 (mmp) REVERT: C 465 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8798 (pp) REVERT: D 227 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8118 (tttm) REVERT: D 231 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: D 335 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7977 (pp) REVERT: D 440 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: D 463 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8587 (mtpm) REVERT: E 262 MET cc_start: 0.9460 (mmp) cc_final: 0.9143 (mmp) REVERT: F 227 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8105 (tttm) REVERT: F 231 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: F 440 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: F 463 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8594 (mtpm) REVERT: G 51 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8387 (pm20) REVERT: G 83 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8684 (ptm160) REVERT: G 262 MET cc_start: 0.9472 (mmp) cc_final: 0.9189 (mmp) REVERT: H 227 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8110 (tttm) REVERT: H 231 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: H 335 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7962 (pp) REVERT: H 440 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7544 (pt0) outliers start: 72 outliers final: 40 residues processed: 261 average time/residue: 0.6812 time to fit residues: 207.7309 Evaluate side-chains 254 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 192 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 100 GLN Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 3 residue 100 GLN Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 4 residue 91 VAL Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 440 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 123 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 354 optimal weight: 0.8980 chunk 383 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 319 optimal weight: 0.0050 chunk 54 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 overall best weight: 2.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 98 ASN 5 98 ASN A 123 ASN C 123 ASN E 123 ASN G 123 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.068561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.050976 restraints weight = 80958.525| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.14 r_work: 0.2626 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32516 Z= 0.137 Angle : 0.567 9.315 43980 Z= 0.298 Chirality : 0.044 0.177 4656 Planarity : 0.004 0.051 5792 Dihedral : 5.077 51.731 4521 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.60 % Favored : 92.53 % Rotamer: Outliers : 2.26 % Allowed : 24.94 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -0.62 (0.13), residues: 4032 helix: 1.33 (0.15), residues: 1404 sheet: -0.32 (0.22), residues: 584 loop : -1.77 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 41 TYR 0.008 0.001 TYR E 185 PHE 0.027 0.001 PHE G 345 TRP 0.010 0.001 TRP B 214 HIS 0.003 0.001 HIS C 386 Details of bonding type rmsd covalent geometry : bond 0.00325 (32516) covalent geometry : angle 0.56670 (43980) hydrogen bonds : bond 0.05250 ( 1022) hydrogen bonds : angle 4.03584 ( 2877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8064 Ramachandran restraints generated. 4032 Oldfield, 0 Emsley, 4032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 194 time to evaluate : 1.340 Fit side-chains REVERT: 4 97 PHE cc_start: 0.7549 (t80) cc_final: 0.7118 (t80) REVERT: 4 115 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8556 (mm-30) REVERT: 5 87 LYS cc_start: 0.8485 (mttp) cc_final: 0.8198 (mmmt) REVERT: 6 66 LYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6294 (mtmp) REVERT: 8 87 LYS cc_start: 0.8792 (mmtp) cc_final: 0.8506 (mmmm) REVERT: 8 97 PHE cc_start: 0.7366 (t80) cc_final: 0.6909 (t80) REVERT: 8 115 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8434 (mm-30) REVERT: A 440 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8395 (pt0) REVERT: B 227 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8095 (tttm) REVERT: B 231 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: B 440 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: D 227 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8108 (tttm) REVERT: D 231 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: D 440 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7591 (pt0) REVERT: D 463 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8601 (mtpm) REVERT: F 227 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8097 (tttm) REVERT: F 231 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: F 440 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: F 463 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8609 (mtpm) REVERT: G 51 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8401 (pm20) REVERT: G 83 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8738 (ptm160) REVERT: H 227 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8103 (tttm) REVERT: H 231 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: H 335 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7936 (pp) REVERT: H 440 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7645 (pt0) outliers start: 74 outliers final: 44 residues processed: 262 average time/residue: 0.7982 time to fit residues: 243.5941 Evaluate side-chains 253 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 190 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 100 GLN Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 2 residue 91 VAL Chi-restraints excluded: chain 3 residue 100 GLN Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 4 residue 91 VAL Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 227 LYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 440 GLU Chi-restraints excluded: chain F residue 463 LYS Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 83 ARG Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 440 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 115 optimal weight: 1.9990 chunk 397 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 355 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 chunk 321 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 84 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 98 ASN 5 98 ASN A 123 ASN C 123 ASN E 123 ASN G 123 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.052526 restraints weight = 80661.412| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.11 r_work: 0.2660 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32516 Z= 0.107 Angle : 0.540 9.163 43980 Z= 0.281 Chirality : 0.043 0.176 4656 Planarity : 0.004 0.049 5792 Dihedral : 4.956 51.942 4521 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.37 % Favored : 92.78 % Rotamer: Outliers : 2.11 % Allowed : 25.21 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.13), residues: 4032 helix: 1.45 (0.15), residues: 1396 sheet: -0.29 (0.21), residues: 584 loop : -1.66 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 41 TYR 0.007 0.001 TYR A 29 PHE 0.027 0.001 PHE A 345 TRP 0.011 0.001 TRP F 214 HIS 0.003 0.001 HIS E 238 Details of bonding type rmsd covalent geometry : bond 0.00244 (32516) covalent geometry : angle 0.53961 (43980) hydrogen bonds : bond 0.04109 ( 1022) hydrogen bonds : angle 3.89325 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8088.70 seconds wall clock time: 139 minutes 13.99 seconds (8353.99 seconds total)