Starting phenix.real_space_refine on Thu May 29 07:43:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ci1_45607/05_2025/9ci1_45607_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ci1_45607/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ci1_45607/05_2025/9ci1_45607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ci1_45607/05_2025/9ci1_45607.map" model { file = "/net/cci-nas-00/data/ceres_data/9ci1_45607/05_2025/9ci1_45607_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ci1_45607/05_2025/9ci1_45607_neut.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 20.03, per 1000 atoms: 0.63 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: 6.84 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 3.23 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: 9.50 Time building geometry restraints manager: 8.04 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: 0.04 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: 7.530 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: 1.290 Check model and map are aligned: 0.230 Set scattering table: 0.350 Process input model: 64.630 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.160 ------------------------------------------------------------------------------- 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 : 7.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP H 214 HIS 0.003 0.001 HIS C 238 PHE 0.026 0.001 PHE E 345 TYR 0.012 0.001 TYR G 25 ARG 0.004 0.000 ARG G 194 Details of bonding type rmsd hydrogen bonds : bond 0.34270 ( 1022) hydrogen bonds : angle 7.67696 ( 2877) covalent geometry : bond 0.00800 (32516) covalent geometry : angle 0.99121 (43980) *********************** 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 : 3.470 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: 1.3759 time to fit residues: 1030.9671 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 : 3.530 ------------------------------------------------------------------------------- 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 341 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 316 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 366 optimal weight: 7.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 6 92 ASN 6 100 GLN 7 68 ASN A 327 HIS D 327 HIS D 420 ASN E 327 HIS E 429 GLN E 432 ASN F 327 HIS G 327 HIS G 429 GLN H 327 HIS H 420 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.055437 restraints weight = 80099.372| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 3.18 r_work: 0.2709 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32516 Z= 0.145 Angle : 0.610 6.315 43980 Z= 0.330 Chirality : 0.044 0.167 4656 Planarity : 0.004 0.051 5792 Dihedral : 6.808 59.266 4631 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.14 % Favored : 92.01 % Rotamer: Outliers : 4.28 % Allowed : 25.12 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.12), residues: 4032 helix: -0.24 (0.14), residues: 1396 sheet: -0.77 (0.21), residues: 556 loop : -2.31 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 214 HIS 0.004 0.001 HIS A 238 PHE 0.034 0.002 PHE D 345 TYR 0.024 0.001 TYR A 29 ARG 0.004 0.000 ARG D 421 Details of bonding type rmsd hydrogen bonds : bond 0.07465 ( 1022) hydrogen bonds : angle 5.16265 ( 2877) covalent geometry : bond 0.00305 (32516) covalent geometry : angle 0.61016 (43980) *********************** 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 373 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 233 time to evaluate : 3.298 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7440 (t80) cc_final: 0.7121 (t80) REVERT: 2 135 ASP cc_start: 0.8209 (t0) cc_final: 0.7907 (t0) REVERT: 2 136 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5970 (pt0) REVERT: 4 97 PHE cc_start: 0.7964 (t80) cc_final: 0.7706 (t80) REVERT: 4 100 GLN cc_start: 0.8468 (mp-120) cc_final: 0.8206 (mp10) REVERT: 4 101 PHE cc_start: 0.4400 (m-10) cc_final: 0.4181 (m-80) REVERT: 4 115 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8403 (mm-30) REVERT: 6 97 PHE cc_start: 0.6897 (t80) cc_final: 0.6337 (t80) REVERT: 6 101 PHE cc_start: 0.4936 (m-10) cc_final: 0.4455 (m-10) REVERT: 8 101 PHE cc_start: 0.5009 (m-10) cc_final: 0.4759 (m-80) REVERT: 8 115 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8729 (mt-10) outliers start: 140 outliers final: 52 residues processed: 348 average time/residue: 1.3918 time to fit residues: 576.9922 Evaluate side-chains 271 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 3.261 ------------------------------------------------------------------------------- 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 2 residue 136 GLU Chi-restraints excluded: chain 3 residue 65 THR Chi-restraints excluded: chain 3 residue 81 VAL 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 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 76 GLU 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 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 40 PHE 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 40 PHE 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 40 PHE 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 178 LEU Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 40 PHE 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 226 optimal weight: 2.9990 chunk 313 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 299 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 366 optimal weight: 5.9990 chunk 277 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 5 68 ASN 7 68 ASN A 96 GLN C 96 GLN E 96 GLN F 432 ASN G 96 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.068396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.050886 restraints weight = 81310.487| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.17 r_work: 0.2613 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 32516 Z= 0.189 Angle : 0.627 6.994 43980 Z= 0.336 Chirality : 0.047 0.189 4656 Planarity : 0.005 0.058 5792 Dihedral : 5.636 58.349 4542 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 1.04 % Allowed : 7.19 % Favored : 91.77 % Rotamer: Outliers : 3.67 % Allowed : 24.51 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 4032 helix: 0.46 (0.14), residues: 1404 sheet: -0.90 (0.22), residues: 544 loop : -2.10 (0.12), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 214 HIS 0.005 0.001 HIS C 386 PHE 0.032 0.002 PHE F 345 TYR 0.016 0.001 TYR A 29 ARG 0.003 0.000 ARG A 431 Details of bonding type rmsd hydrogen bonds : bond 0.07273 ( 1022) hydrogen bonds : angle 4.57445 ( 2877) covalent geometry : bond 0.00448 (32516) covalent geometry : angle 0.62746 (43980) *********************** 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 339 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 219 time to evaluate : 3.355 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7590 (t80) cc_final: 0.7086 (t80) REVERT: 2 135 ASP cc_start: 0.8241 (t0) cc_final: 0.8008 (t0) REVERT: 4 87 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8527 (mmmm) REVERT: 4 115 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8482 (mm-30) REVERT: 5 87 LYS cc_start: 0.8448 (mttp) cc_final: 0.8231 (mmmt) REVERT: 6 66 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6661 (mtmp) REVERT: 8 115 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8725 (mt-10) REVERT: C 123 ASN cc_start: 0.8380 (m-40) cc_final: 0.8161 (p0) REVERT: C 446 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7417 (mtp180) REVERT: C 465 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8700 (pp) outliers start: 120 outliers final: 54 residues processed: 317 average time/residue: 1.4891 time to fit residues: 552.2323 Evaluate side-chains 265 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 3.240 ------------------------------------------------------------------------------- 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 136 GLU Chi-restraints excluded: chain 5 residue 65 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 8 residue 91 VAL 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 69 VAL 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 C residue 41 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL 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 112 SER 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 D residue 450 LYS Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 173 THR 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 308 optimal weight: 10.0000 chunk 162 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 11 optimal weight: 7.9990 chunk 385 optimal weight: 10.0000 chunk 269 optimal weight: 0.0010 chunk 277 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 69 optimal weight: 0.0470 overall best weight: 1.4488 ------------------------------------------------------------------------------- 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 96 GLN B 432 ASN C 96 GLN E 96 GLN G 96 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.070880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.053472 restraints weight = 80506.596| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.16 r_work: 0.2685 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32516 Z= 0.102 Angle : 0.539 6.063 43980 Z= 0.285 Chirality : 0.043 0.157 4656 Planarity : 0.004 0.050 5792 Dihedral : 5.259 54.773 4526 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 1.12 % Allowed : 6.13 % Favored : 92.76 % Rotamer: Outliers : 3.24 % Allowed : 24.42 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4032 helix: 0.87 (0.15), residues: 1412 sheet: -0.68 (0.21), residues: 584 loop : -1.96 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 214 HIS 0.003 0.000 HIS A 238 PHE 0.027 0.001 PHE D 345 TYR 0.012 0.001 TYR A 29 ARG 0.001 0.000 ARG G 194 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 1022) hydrogen bonds : angle 4.21355 ( 2877) covalent geometry : bond 0.00221 (32516) covalent geometry : angle 0.53862 (43980) *********************** 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 323 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 217 time to evaluate : 3.473 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7494 (t80) cc_final: 0.7061 (t80) REVERT: 2 135 ASP cc_start: 0.8265 (t0) cc_final: 0.7987 (t0) REVERT: 4 87 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8538 (mmmm) REVERT: 4 97 PHE cc_start: 0.7795 (t80) cc_final: 0.7404 (t80) REVERT: 4 115 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8522 (mm-30) REVERT: 5 87 LYS cc_start: 0.8503 (mttp) cc_final: 0.8278 (mmmt) REVERT: 8 115 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8709 (mt-10) REVERT: B 231 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: B 335 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8007 (pp) REVERT: C 446 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7425 (mtp180) REVERT: D 231 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: F 231 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: G 83 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8735 (ptm160) REVERT: H 231 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: H 335 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8021 (pp) outliers start: 106 outliers final: 50 residues processed: 306 average time/residue: 1.4964 time to fit residues: 539.7115 Evaluate side-chains 263 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 3.801 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain 3 residue 100 GLN Chi-restraints excluded: chain 3 residue 133 THR 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 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 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 440 GLU 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 96 GLN 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 393 ILE Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 446 ARG 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 342 THR Chi-restraints excluded: chain D residue 450 LYS 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 112 SER 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 96 GLN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 308 optimal weight: 5.9990 chunk 245 optimal weight: 0.0670 chunk 154 optimal weight: 7.9990 chunk 318 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 353 optimal weight: 0.9990 chunk 304 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- 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 C 96 GLN E 96 GLN G 96 GLN H 432 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.069503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.052176 restraints weight = 80499.658| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.08 r_work: 0.2658 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32516 Z= 0.142 Angle : 0.562 6.415 43980 Z= 0.297 Chirality : 0.044 0.173 4656 Planarity : 0.004 0.051 5792 Dihedral : 5.182 53.386 4525 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.47 % Favored : 92.49 % Rotamer: Outliers : 2.69 % Allowed : 24.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4032 helix: 1.02 (0.15), residues: 1408 sheet: -0.71 (0.22), residues: 544 loop : -1.90 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 214 HIS 0.003 0.001 HIS C 386 PHE 0.029 0.001 PHE D 345 TYR 0.010 0.001 TYR A 29 ARG 0.002 0.000 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.05422 ( 1022) hydrogen bonds : angle 4.17921 ( 2877) covalent geometry : bond 0.00336 (32516) covalent geometry : angle 0.56155 (43980) *********************** 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 297 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 209 time to evaluate : 3.777 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7566 (t80) cc_final: 0.7185 (t80) REVERT: 2 135 ASP cc_start: 0.8298 (t0) cc_final: 0.8058 (t0) REVERT: 4 87 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8582 (mmmm) REVERT: 4 97 PHE cc_start: 0.7814 (t80) cc_final: 0.7389 (t80) REVERT: 4 115 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8564 (mm-30) REVERT: 5 87 LYS cc_start: 0.8530 (mttp) cc_final: 0.8297 (mmmt) REVERT: 6 66 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6654 (mtmp) REVERT: 8 115 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8721 (mt-10) REVERT: B 231 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: B 335 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8018 (pp) REVERT: C 446 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7448 (mtp180) REVERT: D 231 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: D 343 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9187 (mp) REVERT: D 463 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8642 (mtpm) REVERT: F 231 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: G 51 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8346 (pm20) REVERT: G 83 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8743 (ptm160) REVERT: H 231 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: H 335 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8050 (pp) outliers start: 88 outliers final: 44 residues processed: 282 average time/residue: 1.4731 time to fit residues: 488.6912 Evaluate side-chains 264 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 3.322 ------------------------------------------------------------------------------- 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 91 VAL Chi-restraints excluded: chain 4 residue 92 ASN Chi-restraints excluded: chain 4 residue 136 GLU 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 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 71 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 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 331 VAL Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 446 ARG 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 343 LEU 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 112 SER 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 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 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 230 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 328 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 271 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 336 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.068594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.051247 restraints weight = 81088.877| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.06 r_work: 0.2637 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 32516 Z= 0.160 Angle : 0.578 7.303 43980 Z= 0.307 Chirality : 0.045 0.175 4656 Planarity : 0.004 0.053 5792 Dihedral : 5.197 52.255 4522 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.60 % Favored : 92.36 % Rotamer: Outliers : 3.70 % Allowed : 23.59 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4032 helix: 1.11 (0.15), residues: 1400 sheet: -0.67 (0.22), residues: 544 loop : -1.90 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 214 HIS 0.004 0.001 HIS C 386 PHE 0.029 0.001 PHE D 345 TYR 0.010 0.001 TYR C 24 ARG 0.002 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.05895 ( 1022) hydrogen bonds : angle 4.20692 ( 2877) covalent geometry : bond 0.00382 (32516) covalent geometry : angle 0.57820 (43980) *********************** 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 322 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 201 time to evaluate : 3.569 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7538 (t80) cc_final: 0.7221 (t80) REVERT: 4 87 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8520 (mmmm) REVERT: 4 97 PHE cc_start: 0.7778 (t80) cc_final: 0.7549 (t80) REVERT: 4 113 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8447 (tmmt) REVERT: 4 115 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8456 (mm-30) REVERT: 5 87 LYS cc_start: 0.8488 (mttp) cc_final: 0.8254 (mmmt) REVERT: 6 66 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6519 (mtmp) REVERT: 6 102 LYS cc_start: 0.7764 (tppt) cc_final: 0.7280 (mppt) REVERT: 8 97 PHE cc_start: 0.7576 (t80) cc_final: 0.7291 (t80) REVERT: 8 113 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8438 (tmmt) REVERT: 8 115 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8385 (mm-30) REVERT: B 227 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8427 (mtpp) REVERT: B 231 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: B 335 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7938 (pp) REVERT: B 440 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: C 446 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7436 (mtp180) REVERT: D 227 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8160 (tttm) REVERT: D 231 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: D 335 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7945 (pp) REVERT: D 440 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: D 463 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8614 (mtpm) REVERT: F 227 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8420 (mtpp) REVERT: F 231 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: F 440 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: G 51 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: G 83 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8687 (ptm160) REVERT: H 227 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8163 (tttm) REVERT: H 231 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: H 335 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7958 (pp) REVERT: H 440 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7457 (pt0) outliers start: 121 outliers final: 59 residues processed: 303 average time/residue: 1.4658 time to fit residues: 525.1061 Evaluate side-chains 277 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 196 time to evaluate : 3.556 ------------------------------------------------------------------------------- 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 113 LYS 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 7 residue 65 THR Chi-restraints excluded: chain 7 residue 100 GLN Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 8 residue 113 LYS 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 32 LYS Chi-restraints excluded: chain B residue 41 ARG 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 393 ILE Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 41 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 41 ARG 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 H residue 41 ARG 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 238 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 4 optimal weight: 0.0570 chunk 167 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 255 optimal weight: 8.9990 chunk 93 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 overall best weight: 4.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 98 ASN A 96 GLN B 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.067044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.049620 restraints weight = 81404.186| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.13 r_work: 0.2593 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3002 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= 0.202 Angle : 0.621 7.496 43980 Z= 0.331 Chirality : 0.047 0.249 4656 Planarity : 0.005 0.056 5792 Dihedral : 5.365 52.041 4522 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.94 % Allowed : 6.57 % Favored : 92.49 % Rotamer: Outliers : 3.24 % Allowed : 23.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4032 helix: 1.06 (0.15), residues: 1388 sheet: -0.68 (0.22), residues: 544 loop : -1.94 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 214 HIS 0.004 0.001 HIS B 153 PHE 0.030 0.002 PHE F 345 TYR 0.010 0.001 TYR C 24 ARG 0.003 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.06965 ( 1022) hydrogen bonds : angle 4.35474 ( 2877) covalent geometry : bond 0.00491 (32516) covalent geometry : angle 0.62104 (43980) *********************** 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 300 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 194 time to evaluate : 3.378 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7596 (t80) cc_final: 0.7248 (t80) REVERT: 4 97 PHE cc_start: 0.7791 (t80) cc_final: 0.7242 (t80) REVERT: 4 100 GLN cc_start: 0.8663 (mp10) cc_final: 0.8462 (pm20) REVERT: 4 113 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8498 (tmmt) REVERT: 4 115 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8478 (mm-30) REVERT: 5 87 LYS cc_start: 0.8479 (mttp) cc_final: 0.8226 (mmmt) REVERT: 6 66 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6504 (mtmp) REVERT: 6 102 LYS cc_start: 0.7852 (tppt) cc_final: 0.7646 (mmtp) REVERT: 7 136 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: 8 97 PHE cc_start: 0.7629 (t80) cc_final: 0.7313 (t80) REVERT: 8 113 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8338 (tmmt) REVERT: 8 115 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8565 (mt-10) REVERT: B 227 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8443 (mtpp) REVERT: B 231 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: B 335 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7900 (pp) REVERT: B 440 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: D 227 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8448 (mtpp) REVERT: D 231 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: D 440 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: D 463 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8655 (mtpm) REVERT: F 227 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8422 (mtpp) REVERT: F 231 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: F 440 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7197 (mp0) REVERT: F 463 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8642 (mtpm) REVERT: G 51 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8385 (pm20) REVERT: H 227 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8448 (mtpp) REVERT: H 231 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: H 335 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7902 (pp) REVERT: H 440 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7638 (pt0) outliers start: 106 outliers final: 56 residues processed: 282 average time/residue: 1.5475 time to fit residues: 510.2060 Evaluate side-chains 267 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 190 time to evaluate : 3.487 ------------------------------------------------------------------------------- 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 100 GLN Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 4 residue 113 LYS 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 7 residue 65 THR 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 8 residue 113 LYS Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 96 GLN 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 41 ARG 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 331 VAL 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 41 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 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 41 ARG 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 173 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 331 VAL Chi-restraints excluded: chain H residue 41 ARG 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 102 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 341 optimal weight: 10.0000 chunk 384 optimal weight: 3.9990 chunk 342 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 98 optimal weight: 0.4980 chunk 109 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.069423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.051979 restraints weight = 80806.335| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.09 r_work: 0.2645 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 32516 Z= 0.113 Angle : 0.548 8.228 43980 Z= 0.288 Chirality : 0.044 0.341 4656 Planarity : 0.004 0.049 5792 Dihedral : 5.132 51.833 4519 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.92 % Allowed : 6.40 % Favored : 92.68 % Rotamer: Outliers : 2.38 % Allowed : 24.57 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4032 helix: 1.24 (0.15), residues: 1400 sheet: -0.40 (0.21), residues: 584 loop : -1.88 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 214 HIS 0.003 0.000 HIS A 238 PHE 0.026 0.001 PHE C 345 TYR 0.016 0.001 TYR A 97 ARG 0.002 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 1022) hydrogen bonds : angle 4.06449 ( 2877) covalent geometry : bond 0.00260 (32516) covalent geometry : angle 0.54811 (43980) *********************** 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 273 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 195 time to evaluate : 3.381 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7429 (t80) cc_final: 0.7213 (t80) REVERT: 4 97 PHE cc_start: 0.7668 (t80) cc_final: 0.7079 (t80) REVERT: 4 100 GLN cc_start: 0.8620 (mp10) cc_final: 0.8419 (pm20) REVERT: 4 115 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8522 (mm-30) REVERT: 5 87 LYS cc_start: 0.8456 (mttp) cc_final: 0.8197 (mmmt) REVERT: 6 66 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6328 (mtmp) REVERT: 8 97 PHE cc_start: 0.7308 (t80) cc_final: 0.6955 (t80) REVERT: 8 115 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8482 (mm-30) REVERT: B 227 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8091 (tttm) REVERT: B 231 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: B 335 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7940 (pp) REVERT: B 440 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: C 446 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7447 (mtp180) REVERT: D 227 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8102 (tttm) REVERT: D 231 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: D 335 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7977 (pp) REVERT: D 440 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: D 463 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8613 (mtpm) REVERT: F 227 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8100 (tttm) REVERT: F 231 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: F 440 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: F 463 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8599 (mtpm) REVERT: G 51 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: G 83 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8677 (ptm160) REVERT: G 262 MET cc_start: 0.9470 (mmp) cc_final: 0.9143 (mmp) REVERT: H 227 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8103 (tttm) REVERT: H 231 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7568 (mp0) REVERT: H 335 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7929 (pp) REVERT: H 440 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7460 (pt0) outliers start: 78 outliers final: 42 residues processed: 269 average time/residue: 1.5992 time to fit residues: 503.7026 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 : 3.463 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain 4 residue 136 GLU 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 133 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 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 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 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 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 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 87 optimal weight: 9.9990 chunk 60 optimal weight: 0.3980 chunk 23 optimal weight: 0.0030 chunk 114 optimal weight: 0.3980 chunk 348 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 355 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 overall best weight: 2.3594 ------------------------------------------------------------------------------- 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 7 68 ASN A 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.069030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.051533 restraints weight = 80780.269| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 3.12 r_work: 0.2638 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32516 Z= 0.126 Angle : 0.559 8.870 43980 Z= 0.293 Chirality : 0.044 0.186 4656 Planarity : 0.004 0.050 5792 Dihedral : 5.057 51.821 4519 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.92 % Allowed : 6.25 % Favored : 92.83 % Rotamer: Outliers : 2.26 % Allowed : 24.76 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4032 helix: 1.32 (0.15), residues: 1400 sheet: -0.38 (0.21), residues: 584 loop : -1.83 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 214 HIS 0.003 0.001 HIS 5 96 PHE 0.027 0.001 PHE G 345 TYR 0.008 0.001 TYR C 185 ARG 0.002 0.000 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.04982 ( 1022) hydrogen bonds : angle 4.03326 ( 2877) covalent geometry : bond 0.00292 (32516) covalent geometry : angle 0.55948 (43980) *********************** 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 266 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 192 time to evaluate : 3.244 Fit side-chains REVERT: 4 97 PHE cc_start: 0.7691 (t80) cc_final: 0.7080 (t80) REVERT: 4 113 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8395 (tmmt) REVERT: 4 115 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8448 (mm-30) REVERT: 5 87 LYS cc_start: 0.8474 (mttp) cc_final: 0.8201 (mmmt) REVERT: 6 66 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6315 (mtmp) REVERT: 8 97 PHE cc_start: 0.7439 (t80) cc_final: 0.6905 (t80) REVERT: 8 115 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8465 (mm-30) REVERT: A 262 MET cc_start: 0.9465 (mmp) cc_final: 0.9173 (mmp) REVERT: A 440 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8329 (pt0) REVERT: B 227 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8097 (tttm) REVERT: B 231 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: B 335 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7955 (pp) REVERT: B 440 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7107 (mp0) REVERT: C 262 MET cc_start: 0.9470 (mmp) cc_final: 0.9180 (mmp) REVERT: C 446 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7429 (mtp180) REVERT: D 227 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8107 (tttm) REVERT: D 231 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: D 335 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8005 (pp) REVERT: D 440 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7548 (pt0) REVERT: D 463 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8598 (mtpm) REVERT: E 262 MET cc_start: 0.9464 (mmp) cc_final: 0.9163 (mmp) REVERT: F 227 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8105 (tttm) REVERT: F 231 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: F 440 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: F 463 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8608 (mtpm) REVERT: G 51 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: G 83 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8689 (ptm160) REVERT: G 262 MET cc_start: 0.9485 (mmp) cc_final: 0.9175 (mmp) REVERT: H 227 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8109 (tttm) REVERT: H 231 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: H 335 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7923 (pp) REVERT: H 440 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7562 (pt0) outliers start: 74 outliers final: 42 residues processed: 260 average time/residue: 1.5221 time to fit residues: 462.8236 Evaluate side-chains 255 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 3.392 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain 4 residue 113 LYS 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 133 THR Chi-restraints excluded: chain A residue 96 GLN 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 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 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 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 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 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 35 optimal weight: 10.0000 chunk 345 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 370 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 247 optimal weight: 0.0370 chunk 63 optimal weight: 7.9990 chunk 292 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- 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 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.069060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.051553 restraints weight = 80909.043| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.12 r_work: 0.2639 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3114 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= 0.126 Angle : 0.553 8.360 43980 Z= 0.290 Chirality : 0.044 0.182 4656 Planarity : 0.004 0.050 5792 Dihedral : 5.040 51.791 4519 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.84 % Allowed : 6.42 % Favored : 92.73 % Rotamer: Outliers : 2.23 % Allowed : 24.79 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4032 helix: 1.34 (0.15), residues: 1396 sheet: -0.35 (0.21), residues: 584 loop : -1.79 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 214 HIS 0.003 0.001 HIS A 238 PHE 0.026 0.001 PHE A 345 TYR 0.018 0.001 TYR A 97 ARG 0.002 0.000 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 1022) hydrogen bonds : angle 4.01753 ( 2877) covalent geometry : bond 0.00294 (32516) covalent geometry : angle 0.55327 (43980) ********************** 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 265 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 192 time to evaluate : 3.484 Fit side-chains REVERT: 4 87 LYS cc_start: 0.8850 (mmtp) cc_final: 0.8514 (mmmm) REVERT: 4 97 PHE cc_start: 0.7536 (t80) cc_final: 0.7158 (t80) REVERT: 4 113 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8389 (tmmt) REVERT: 4 115 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8462 (mm-30) REVERT: 5 87 LYS cc_start: 0.8476 (mttp) cc_final: 0.8202 (mmmt) REVERT: 6 66 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6282 (mtmp) REVERT: 8 97 PHE cc_start: 0.7355 (t80) cc_final: 0.6911 (t80) REVERT: 8 115 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8466 (mm-30) REVERT: A 262 MET cc_start: 0.9470 (mmp) cc_final: 0.9172 (mmp) REVERT: A 440 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8338 (pt0) REVERT: B 227 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8097 (tttm) REVERT: B 231 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: B 335 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7947 (pp) REVERT: B 440 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: C 262 MET cc_start: 0.9475 (mmp) cc_final: 0.9181 (mmp) REVERT: C 446 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7430 (mtp180) REVERT: D 227 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8099 (tttm) REVERT: D 231 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: D 335 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8005 (pp) REVERT: D 440 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: D 463 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8600 (mtpm) REVERT: E 262 MET cc_start: 0.9470 (mmp) cc_final: 0.9163 (mmp) REVERT: F 227 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8093 (tttm) REVERT: F 231 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: F 440 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7083 (mp0) REVERT: F 463 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8606 (mtpm) REVERT: G 51 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8377 (pm20) REVERT: G 83 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8619 (ptm160) REVERT: H 227 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8101 (tttm) REVERT: H 231 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: H 335 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7918 (pp) REVERT: H 440 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7586 (pt0) outliers start: 73 outliers final: 43 residues processed: 257 average time/residue: 1.5925 time to fit residues: 484.0739 Evaluate side-chains 254 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 188 time to evaluate : 3.645 ------------------------------------------------------------------------------- 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 113 LYS 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 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 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 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 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 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 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 101 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 234 optimal weight: 0.0980 chunk 218 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 357 optimal weight: 8.9990 chunk 184 optimal weight: 10.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.068018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.050555 restraints weight = 80989.060| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.07 r_work: 0.2612 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32516 Z= 0.160 Angle : 0.588 8.771 43980 Z= 0.309 Chirality : 0.045 0.175 4656 Planarity : 0.004 0.052 5792 Dihedral : 5.123 51.491 4519 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.60 % Favored : 92.53 % Rotamer: Outliers : 2.11 % Allowed : 25.18 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4032 helix: 1.28 (0.15), residues: 1404 sheet: -0.35 (0.21), residues: 584 loop : -1.78 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 214 HIS 0.003 0.001 HIS 5 96 PHE 0.027 0.001 PHE B 345 TYR 0.009 0.001 TYR E 185 ARG 0.002 0.000 ARG H 41 Details of bonding type rmsd hydrogen bonds : bond 0.05839 ( 1022) hydrogen bonds : angle 4.12450 ( 2877) covalent geometry : bond 0.00383 (32516) covalent geometry : angle 0.58756 (43980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16289.25 seconds wall clock time: 282 minutes 29.93 seconds (16949.93 seconds total)