Starting phenix.real_space_refine on Fri Jun 27 12:44:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ci1_45607/06_2025/9ci1_45607_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ci1_45607/06_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_45607/06_2025/9ci1_45607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ci1_45607/06_2025/9ci1_45607.map" model { file = "/net/cci-nas-00/data/ceres_data/9ci1_45607/06_2025/9ci1_45607_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ci1_45607/06_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-5710/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: 20.43, per 1000 atoms: 0.64 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: 6.76 Conformation dependent library (CDL) restraints added in 4.0 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: 3.30 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: 10.51 Time building geometry restraints manager: 8.16 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: 0.03 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } ncs_group { reference = (chain 'A' and resid 24 through 466) selection = chain 'B' selection = (chain 'C' and resid 24 through 466) selection = chain 'D' selection = (chain 'E' and resid 24 through 466) selection = chain 'F' selection = (chain 'G' and resid 24 through 466) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.680 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 67.760 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.540 ------------------------------------------------------------------------------- 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 : 3.279 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: 1.4076 time to fit residues: 1054.0459 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 : 3.358 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.055439 restraints weight = 80099.368| |-----------------------------------------------------------------------------| 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 : 4.537 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7441 (t80) cc_final: 0.7123 (t80) REVERT: 2 135 ASP cc_start: 0.8208 (t0) cc_final: 0.7906 (t0) REVERT: 2 136 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.5965 (pt0) REVERT: 4 97 PHE cc_start: 0.7964 (t80) cc_final: 0.7707 (t80) REVERT: 4 100 GLN cc_start: 0.8471 (mp-120) cc_final: 0.8210 (mp10) REVERT: 4 101 PHE cc_start: 0.4406 (m-10) cc_final: 0.4188 (m-80) REVERT: 4 115 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8403 (mm-30) REVERT: 6 97 PHE cc_start: 0.6904 (t80) cc_final: 0.6341 (t80) REVERT: 6 101 PHE cc_start: 0.4946 (m-10) cc_final: 0.4466 (m-10) REVERT: 8 101 PHE cc_start: 0.5013 (m-10) cc_final: 0.4761 (m-80) REVERT: 8 115 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8730 (mt-10) outliers start: 140 outliers final: 52 residues processed: 348 average time/residue: 1.8570 time to fit residues: 768.0767 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 : 3.531 ------------------------------------------------------------------------------- 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: 6.9990 chunk 169 optimal weight: 8.9990 chunk 299 optimal weight: 4.9990 chunk 125 optimal weight: 0.1980 chunk 366 optimal weight: 5.9990 chunk 277 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- 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 = 0.3140 r_free = 0.3140 target = 0.068473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.050914 restraints weight = 81446.534| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.19 r_work: 0.2612 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 32516 Z= 0.194 Angle : 0.629 6.978 43980 Z= 0.338 Chirality : 0.047 0.189 4656 Planarity : 0.005 0.057 5792 Dihedral : 5.647 58.691 4542 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 1.02 % Allowed : 7.42 % Favored : 91.57 % Rotamer: Outliers : 3.61 % Allowed : 24.60 % Favored : 71.79 % 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: -1.56 (0.13), residues: 4032 helix: 0.38 (0.14), residues: 1400 sheet: -0.77 (0.22), residues: 508 loop : -2.16 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 214 HIS 0.005 0.001 HIS F 153 PHE 0.032 0.002 PHE D 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 0.07416 ( 1022) hydrogen bonds : angle 4.64357 ( 2877) covalent geometry : bond 0.00465 (32516) covalent geometry : angle 0.62854 (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: 118 poor density : 221 time to evaluate : 3.476 Fit side-chains REVERT: 2 135 ASP cc_start: 0.8235 (t0) cc_final: 0.8001 (t0) REVERT: 4 87 LYS cc_start: 0.8859 (mmtp) cc_final: 0.8514 (mmmm) REVERT: 4 115 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8482 (mm-30) REVERT: 5 87 LYS cc_start: 0.8464 (mttp) cc_final: 0.8255 (mmmt) REVERT: 6 66 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6646 (mtmp) REVERT: 8 115 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8725 (mt-10) REVERT: C 446 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7403 (mtp180) REVERT: C 465 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8694 (pp) REVERT: D 231 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: H 231 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.7674 (mp0) outliers start: 118 outliers final: 60 residues processed: 315 average time/residue: 1.5313 time to fit residues: 565.6128 Evaluate side-chains 272 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 207 time to evaluate : 3.712 ------------------------------------------------------------------------------- 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 136 GLU Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 100 GLN Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 8 residue 91 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 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 450 LYS Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 96 GLN 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 231 GLU 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 96 GLN Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain G residue 41 ARG Chi-restraints excluded: chain G residue 96 GLN 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 Chi-restraints excluded: chain H residue 231 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 308 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 385 optimal weight: 10.0000 chunk 269 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 69 optimal weight: 0.0040 overall best weight: 1.5798 ------------------------------------------------------------------------------- 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 = 0.3186 r_free = 0.3186 target = 0.070426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.052967 restraints weight = 80612.900| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.16 r_work: 0.2673 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2646 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= 0.108 Angle : 0.548 6.063 43980 Z= 0.291 Chirality : 0.043 0.162 4656 Planarity : 0.004 0.051 5792 Dihedral : 5.341 55.405 4528 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.30 % Favored : 92.66 % Rotamer: Outliers : 3.24 % Allowed : 24.60 % Favored : 72.16 % 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: -1.21 (0.13), residues: 4032 helix: 0.78 (0.15), residues: 1416 sheet: -0.87 (0.21), residues: 544 loop : -1.98 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 214 HIS 0.003 0.001 HIS E 238 PHE 0.028 0.001 PHE D 345 TYR 0.013 0.001 TYR A 29 ARG 0.002 0.000 ARG C 194 Details of bonding type rmsd hydrogen bonds : bond 0.04944 ( 1022) hydrogen bonds : angle 4.29365 ( 2877) covalent geometry : bond 0.00236 (32516) covalent geometry : angle 0.54770 (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 321 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 215 time to evaluate : 4.093 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7453 (t80) cc_final: 0.7039 (t80) REVERT: 2 135 ASP cc_start: 0.8285 (t0) cc_final: 0.8017 (t0) REVERT: 4 87 LYS cc_start: 0.8906 (mmtp) cc_final: 0.8562 (mmmm) REVERT: 4 115 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8536 (mm-30) REVERT: 5 87 LYS cc_start: 0.8531 (mttp) cc_final: 0.8299 (mmmt) REVERT: 7 87 LYS cc_start: 0.8505 (mttp) cc_final: 0.8272 (mmmt) REVERT: 8 115 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8736 (mt-10) REVERT: B 335 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8027 (pp) REVERT: C 446 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7456 (mtp180) REVERT: H 335 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8045 (pp) outliers start: 106 outliers final: 55 residues processed: 304 average time/residue: 1.6326 time to fit residues: 584.5526 Evaluate side-chains 265 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 207 time to evaluate : 7.967 ------------------------------------------------------------------------------- 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 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 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 335 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 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 96 GLN Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain 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 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 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 96 GLN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 131 ARG Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 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: 0.6980 chunk 154 optimal weight: 7.9990 chunk 318 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 125 optimal weight: 0.0170 chunk 145 optimal weight: 3.9990 chunk 353 optimal weight: 1.9990 chunk 304 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.1424 ------------------------------------------------------------------------------- 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 C 96 GLN E 96 GLN G 96 GLN H 432 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.052630 restraints weight = 80369.470| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.15 r_work: 0.2666 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32516 Z= 0.121 Angle : 0.547 6.614 43980 Z= 0.288 Chirality : 0.044 0.165 4656 Planarity : 0.004 0.050 5792 Dihedral : 5.196 54.312 4526 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.32 % Favored : 92.63 % Rotamer: Outliers : 3.09 % Allowed : 24.33 % Favored : 72.59 % 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: -0.98 (0.13), residues: 4032 helix: 1.02 (0.15), residues: 1408 sheet: -0.65 (0.21), residues: 584 loop : -1.93 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 214 HIS 0.003 0.001 HIS A 238 PHE 0.028 0.001 PHE D 345 TYR 0.011 0.001 TYR A 29 ARG 0.002 0.000 ARG G 194 Details of bonding type rmsd hydrogen bonds : bond 0.05000 ( 1022) hydrogen bonds : angle 4.16732 ( 2877) covalent geometry : bond 0.00277 (32516) covalent geometry : angle 0.54663 (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 311 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 210 time to evaluate : 4.874 Fit side-chains REVERT: 2 97 PHE cc_start: 0.7487 (t80) cc_final: 0.7136 (t80) REVERT: 2 135 ASP cc_start: 0.8291 (t0) cc_final: 0.8058 (t0) REVERT: 4 87 LYS cc_start: 0.8915 (mmtp) cc_final: 0.8579 (mmmm) REVERT: 4 97 PHE cc_start: 0.7797 (t80) cc_final: 0.7453 (t80) REVERT: 4 115 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8557 (mm-30) REVERT: 5 87 LYS cc_start: 0.8550 (mttp) cc_final: 0.8310 (mmmt) REVERT: 6 66 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6655 (mtmp) REVERT: 7 87 LYS cc_start: 0.8525 (mttp) cc_final: 0.8284 (mmmt) REVERT: 8 115 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8615 (mt-10) REVERT: B 231 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: B 335 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8031 (pp) REVERT: C 446 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7462 (mtp180) REVERT: D 231 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: D 343 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9191 (mp) REVERT: D 463 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8632 (mtpm) REVERT: F 231 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: G 51 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: G 83 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8781 (ptm160) REVERT: G 96 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8487 (tp40) REVERT: H 231 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: H 335 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8057 (pp) outliers start: 101 outliers final: 51 residues processed: 294 average time/residue: 1.5129 time to fit residues: 523.0664 Evaluate side-chains 270 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 100 GLN Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 2 residue 91 VAL Chi-restraints excluded: chain 3 residue 65 THR Chi-restraints excluded: chain 3 residue 100 GLN Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 4 residue 92 ASN Chi-restraints excluded: chain 4 residue 136 GLU Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 100 GLN Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 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 124 VAL Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 343 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 231 GLU Chi-restraints excluded: chain G residue 51 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 H residue 96 GLN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 335 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 230 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 328 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 271 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 245 optimal weight: 0.4980 chunk 336 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 C 96 GLN E 96 GLN G 96 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.069920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.052608 restraints weight = 80680.629| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.07 r_work: 0.2669 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32516 Z= 0.124 Angle : 0.546 7.126 43980 Z= 0.288 Chirality : 0.044 0.164 4656 Planarity : 0.004 0.050 5792 Dihedral : 5.101 53.557 4524 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.37 % Favored : 92.58 % Rotamer: Outliers : 3.15 % Allowed : 24.27 % Favored : 72.59 % 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: -0.87 (0.13), residues: 4032 helix: 1.14 (0.15), residues: 1408 sheet: -0.57 (0.21), residues: 584 loop : -1.89 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 214 HIS 0.003 0.001 HIS B 238 PHE 0.028 0.001 PHE D 345 TYR 0.010 0.001 TYR G 97 ARG 0.001 0.000 ARG C 194 Details of bonding type rmsd hydrogen bonds : bond 0.04938 ( 1022) hydrogen bonds : angle 4.08963 ( 2877) covalent geometry : bond 0.00288 (32516) covalent geometry : angle 0.54646 (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 307 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 204 time to evaluate : 3.497 Fit side-chains REVERT: 4 87 LYS cc_start: 0.8906 (mmtp) cc_final: 0.8565 (mmmm) REVERT: 4 97 PHE cc_start: 0.7745 (t80) cc_final: 0.7398 (t80) REVERT: 4 115 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8544 (mm-30) REVERT: 5 87 LYS cc_start: 0.8551 (mttp) cc_final: 0.8300 (mmmt) REVERT: 6 66 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6580 (mtmp) REVERT: 6 102 LYS cc_start: 0.7743 (tppt) cc_final: 0.7234 (mppt) REVERT: 7 87 LYS cc_start: 0.8504 (mttp) cc_final: 0.8259 (mmmt) REVERT: 8 81 VAL cc_start: 0.7617 (OUTLIER) cc_final: 0.7111 (m) REVERT: 8 97 PHE cc_start: 0.7587 (t80) cc_final: 0.7294 (t80) REVERT: 8 115 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8508 (mm-30) REVERT: B 231 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: B 335 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8014 (pp) REVERT: C 446 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7427 (mtp180) REVERT: D 231 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: D 463 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8627 (mtpm) REVERT: F 231 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: G 51 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8340 (pm20) REVERT: G 83 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8752 (ptm160) REVERT: H 231 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: H 335 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8035 (pp) REVERT: H 440 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7396 (pt0) outliers start: 103 outliers final: 55 residues processed: 296 average time/residue: 2.1340 time to fit residues: 755.7721 Evaluate side-chains 272 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 204 time to evaluate : 6.681 ------------------------------------------------------------------------------- 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 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 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 8 residue 65 THR Chi-restraints excluded: chain 8 residue 81 VAL 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 178 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 450 LYS 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 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 124 VAL Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 463 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 67 THR Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain 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 96 GLN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 124 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 238 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 4 optimal weight: 0.0770 chunk 167 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 211 optimal weight: 0.0470 chunk 255 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 68 ASN 5 68 ASN 5 98 ASN A 96 GLN C 96 GLN E 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.070337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.052885 restraints weight = 80600.065| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 3.17 r_work: 0.2659 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32516 Z= 0.111 Angle : 0.539 7.869 43980 Z= 0.282 Chirality : 0.043 0.158 4656 Planarity : 0.004 0.049 5792 Dihedral : 5.011 53.415 4522 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.92 % Allowed : 6.55 % Favored : 92.53 % Rotamer: Outliers : 2.78 % Allowed : 24.54 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.75 (0.13), residues: 4032 helix: 1.27 (0.15), residues: 1396 sheet: -0.49 (0.21), residues: 584 loop : -1.83 (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 G 345 TYR 0.008 0.001 TYR A 29 ARG 0.001 0.000 ARG G 194 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 1022) hydrogen bonds : angle 4.00708 ( 2877) covalent geometry : bond 0.00254 (32516) covalent geometry : angle 0.53865 (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 295 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 204 time to evaluate : 4.388 Fit side-chains REVERT: 4 87 LYS cc_start: 0.8904 (mmtp) cc_final: 0.8570 (mmmm) REVERT: 4 97 PHE cc_start: 0.7765 (t80) cc_final: 0.7304 (t80) REVERT: 4 115 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8549 (mm-30) REVERT: 5 87 LYS cc_start: 0.8556 (mttp) cc_final: 0.8300 (mmmt) REVERT: 6 66 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6514 (mtmp) REVERT: 6 102 LYS cc_start: 0.7780 (tppt) cc_final: 0.7566 (mmtp) REVERT: 7 87 LYS cc_start: 0.8513 (mttp) cc_final: 0.8267 (mmmt) REVERT: 8 81 VAL cc_start: 0.7592 (OUTLIER) cc_final: 0.7068 (m) REVERT: 8 115 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8517 (mm-30) REVERT: B 227 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8188 (tttm) REVERT: B 231 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: B 335 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8013 (pp) REVERT: B 440 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: C 446 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7415 (mtp180) REVERT: D 227 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8222 (tttm) REVERT: D 231 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: D 440 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: D 463 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8630 (mtpm) REVERT: F 227 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8207 (tttm) REVERT: F 231 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: F 440 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: F 463 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8622 (mtpm) REVERT: G 51 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: H 227 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8228 (tttm) REVERT: H 231 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: H 335 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8014 (pp) REVERT: H 440 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7436 (pt0) outliers start: 91 outliers final: 46 residues processed: 283 average time/residue: 1.6516 time to fit residues: 547.5801 Evaluate side-chains 263 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 65 THR Chi-restraints excluded: chain 1 residue 133 THR Chi-restraints excluded: chain 2 residue 91 VAL Chi-restraints excluded: chain 3 residue 100 GLN Chi-restraints excluded: chain 3 residue 133 THR Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 6 residue 65 THR Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 6 residue 91 VAL Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 8 residue 65 THR Chi-restraints excluded: chain 8 residue 81 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 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 446 ARG Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 231 GLU Chi-restraints excluded: chain D residue 440 GLU Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 463 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 102 optimal weight: 0.0570 chunk 89 optimal weight: 0.8980 chunk 341 optimal weight: 4.9990 chunk 384 optimal weight: 0.9990 chunk 342 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 68 ASN 5 98 ASN C 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.070798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.053290 restraints weight = 80398.915| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.13 r_work: 0.2684 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32516 Z= 0.103 Angle : 0.529 7.848 43980 Z= 0.274 Chirality : 0.043 0.150 4656 Planarity : 0.004 0.048 5792 Dihedral : 4.863 52.892 4521 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.94 % Allowed : 6.50 % Favored : 92.56 % Rotamer: Outliers : 2.54 % Allowed : 24.85 % Favored : 72.62 % 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: -0.57 (0.13), residues: 4032 helix: 1.41 (0.15), residues: 1400 sheet: -0.39 (0.21), residues: 584 loop : -1.72 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 214 HIS 0.003 0.000 HIS A 238 PHE 0.025 0.001 PHE C 345 TYR 0.008 0.001 TYR A 29 ARG 0.002 0.000 ARG C 339 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 1022) hydrogen bonds : angle 3.88008 ( 2877) covalent geometry : bond 0.00236 (32516) covalent geometry : angle 0.52933 (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 282 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 199 time to evaluate : 3.627 Fit side-chains REVERT: 4 87 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8501 (mmmm) REVERT: 4 97 PHE cc_start: 0.7672 (t80) cc_final: 0.7197 (t80) REVERT: 4 115 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8514 (mm-30) REVERT: 5 87 LYS cc_start: 0.8509 (mttp) cc_final: 0.8259 (mmmt) REVERT: 6 66 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.6339 (mtmp) REVERT: 7 87 LYS cc_start: 0.8465 (mttp) cc_final: 0.8225 (mmmt) REVERT: 8 81 VAL cc_start: 0.7414 (OUTLIER) cc_final: 0.6873 (m) REVERT: 8 87 LYS cc_start: 0.8830 (mmtp) cc_final: 0.8473 (mmmm) REVERT: 8 97 PHE cc_start: 0.7434 (t80) cc_final: 0.6902 (t80) REVERT: 8 115 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8487 (mm-30) REVERT: A 440 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8274 (pt0) REVERT: B 227 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8067 (tttm) REVERT: B 231 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: B 335 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7982 (pp) REVERT: B 440 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: C 440 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8311 (pt0) REVERT: C 446 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7328 (mtp180) REVERT: D 227 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8080 (tttm) REVERT: D 231 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: D 335 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7982 (pp) REVERT: D 440 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: D 463 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8591 (mtpm) REVERT: F 227 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8086 (tttm) REVERT: F 231 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: F 440 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: F 463 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8586 (mtpm) REVERT: G 51 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8333 (pm20) REVERT: G 262 MET cc_start: 0.9402 (mmp) cc_final: 0.9172 (mmp) REVERT: H 227 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8084 (tttm) REVERT: H 231 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: H 335 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7985 (pp) REVERT: H 440 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7417 (pt0) outliers start: 83 outliers final: 39 residues processed: 275 average time/residue: 1.5621 time to fit residues: 506.1258 Evaluate side-chains 254 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 192 time to evaluate : 3.933 ------------------------------------------------------------------------------- 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 5 residue 65 THR Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 65 THR Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 6 residue 76 GLU Chi-restraints excluded: chain 6 residue 91 VAL Chi-restraints excluded: chain 6 residue 93 LEU Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 8 residue 65 THR Chi-restraints excluded: chain 8 residue 81 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL 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 67 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 124 VAL 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 F residue 67 THR Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 124 VAL 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 331 VAL Chi-restraints excluded: chain G residue 393 ILE Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 440 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 87 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 348 optimal weight: 0.6980 chunk 214 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 200 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 355 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.068592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.051065 restraints weight = 80951.435| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.12 r_work: 0.2627 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32516 Z= 0.157 Angle : 0.586 8.422 43980 Z= 0.307 Chirality : 0.045 0.170 4656 Planarity : 0.004 0.053 5792 Dihedral : 4.987 51.845 4516 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.60 % Favored : 92.53 % Rotamer: Outliers : 2.66 % Allowed : 25.21 % Favored : 72.13 % 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: -0.61 (0.13), residues: 4032 helix: 1.34 (0.15), residues: 1404 sheet: -0.36 (0.21), residues: 584 loop : -1.74 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 214 HIS 0.004 0.001 HIS 5 96 PHE 0.028 0.002 PHE E 345 TYR 0.009 0.001 TYR G 185 ARG 0.006 0.000 ARG H 187 Details of bonding type rmsd hydrogen bonds : bond 0.05845 ( 1022) hydrogen bonds : angle 4.07629 ( 2877) covalent geometry : bond 0.00376 (32516) covalent geometry : angle 0.58590 (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 282 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 195 time to evaluate : 3.213 Fit side-chains REVERT: 4 87 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8504 (mmmm) REVERT: 4 97 PHE cc_start: 0.7529 (t80) cc_final: 0.7017 (t80) REVERT: 4 115 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8548 (mm-30) REVERT: 5 87 LYS cc_start: 0.8470 (mttp) cc_final: 0.8215 (mmmt) REVERT: 6 66 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6334 (mtmp) REVERT: 7 87 LYS cc_start: 0.8460 (mttp) cc_final: 0.8213 (mmmt) REVERT: 8 81 VAL cc_start: 0.7458 (OUTLIER) cc_final: 0.6671 (m) REVERT: 8 97 PHE cc_start: 0.7235 (t80) cc_final: 0.6816 (t80) REVERT: 8 115 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8455 (mm-30) REVERT: A 440 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8378 (pt0) REVERT: B 227 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8085 (tttm) REVERT: B 231 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: B 440 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: C 440 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8353 (pt0) REVERT: C 446 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7406 (mtp180) REVERT: D 227 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8092 (tttm) REVERT: D 231 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: D 335 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7976 (pp) REVERT: D 440 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: D 463 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8623 (mtpm) REVERT: F 227 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8094 (tttm) REVERT: F 231 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: F 440 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: F 463 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8612 (mtpm) REVERT: G 51 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8325 (pm20) REVERT: H 227 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8094 (tttm) REVERT: H 231 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: H 335 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7939 (pp) REVERT: H 440 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7602 (pt0) outliers start: 87 outliers final: 39 residues processed: 272 average time/residue: 1.5119 time to fit residues: 483.3264 Evaluate side-chains 253 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 3.331 ------------------------------------------------------------------------------- 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 133 THR Chi-restraints excluded: chain 5 residue 65 THR Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 65 THR Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 8 residue 65 THR Chi-restraints excluded: chain 8 residue 81 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 124 VAL 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 F residue 67 THR Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain 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 331 VAL Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 440 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 35 optimal weight: 10.0000 chunk 345 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 325 optimal weight: 1.9990 chunk 370 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 247 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 292 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 7 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.068748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.051332 restraints weight = 81023.320| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.07 r_work: 0.2630 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32516 Z= 0.146 Angle : 0.578 9.858 43980 Z= 0.302 Chirality : 0.044 0.167 4656 Planarity : 0.004 0.049 5792 Dihedral : 5.000 51.733 4514 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.87 % Allowed : 6.50 % Favored : 92.63 % Rotamer: Outliers : 2.14 % Allowed : 25.55 % Favored : 72.31 % 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: -0.61 (0.13), residues: 4032 helix: 1.36 (0.15), residues: 1400 sheet: -0.35 (0.21), residues: 584 loop : -1.76 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 214 HIS 0.003 0.001 HIS 5 96 PHE 0.027 0.001 PHE F 345 TYR 0.009 0.001 TYR G 185 ARG 0.006 0.000 ARG H 187 Details of bonding type rmsd hydrogen bonds : bond 0.05369 ( 1022) hydrogen bonds : angle 4.06320 ( 2877) covalent geometry : bond 0.00347 (32516) covalent geometry : angle 0.57771 (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 264 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 194 time to evaluate : 3.342 Fit side-chains REVERT: 4 87 LYS cc_start: 0.8837 (mmtp) cc_final: 0.8507 (mmmm) REVERT: 4 97 PHE cc_start: 0.7540 (t80) cc_final: 0.7104 (t80) REVERT: 4 115 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8549 (mm-30) REVERT: 5 87 LYS cc_start: 0.8482 (mttp) cc_final: 0.8213 (mmmt) REVERT: 6 66 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6293 (mtmp) REVERT: 7 87 LYS cc_start: 0.8438 (mttp) cc_final: 0.8192 (mmmt) REVERT: 8 81 VAL cc_start: 0.7426 (OUTLIER) cc_final: 0.6637 (m) REVERT: 8 97 PHE cc_start: 0.7240 (t80) cc_final: 0.6859 (t80) REVERT: 8 115 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8439 (mm-30) REVERT: A 440 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8351 (pt0) REVERT: B 227 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8075 (tttm) REVERT: B 231 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: B 440 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: C 446 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7423 (mtp180) REVERT: D 227 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8080 (tttm) REVERT: D 231 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: D 440 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: D 463 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8614 (mtpm) REVERT: F 227 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8086 (tttm) REVERT: F 231 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: F 440 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: F 463 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8610 (mtpm) REVERT: G 51 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8366 (pm20) REVERT: H 227 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8082 (tttm) REVERT: H 231 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: H 335 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7939 (pp) REVERT: H 440 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7618 (pt0) outliers start: 70 outliers final: 38 residues processed: 259 average time/residue: 1.5499 time to fit residues: 473.5095 Evaluate side-chains 247 residues out of total 3272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 3.570 ------------------------------------------------------------------------------- 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 5 residue 65 THR Chi-restraints excluded: chain 5 residue 133 THR Chi-restraints excluded: chain 6 residue 65 THR Chi-restraints excluded: chain 6 residue 66 LYS Chi-restraints excluded: chain 7 residue 65 THR Chi-restraints excluded: chain 7 residue 133 THR Chi-restraints excluded: chain 8 residue 65 THR Chi-restraints excluded: chain 8 residue 81 VAL Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 LYS Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 440 GLU Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 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 331 VAL Chi-restraints excluded: chain F residue 67 THR 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 331 VAL Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 173 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 440 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 101 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 158 optimal weight: 0.0570 chunk 138 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 chunk 218 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 357 optimal weight: 0.6980 chunk 184 optimal weight: 0.2980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.072013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.054517 restraints weight = 79878.132| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.13 r_work: 0.2712 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 32516 Z= 0.093 Angle : 0.535 9.374 43980 Z= 0.275 Chirality : 0.041 0.147 4656 Planarity : 0.004 0.048 5792 Dihedral : 4.756 52.545 4514 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.27 % Favored : 92.91 % Rotamer: Outliers : 1.80 % Allowed : 26.13 % Favored : 72.07 % 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: -0.41 (0.13), residues: 4032 helix: 1.54 (0.15), residues: 1396 sheet: -0.32 (0.21), residues: 584 loop : -1.62 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 214 HIS 0.003 0.000 HIS A 238 PHE 0.027 0.001 PHE E 345 TYR 0.008 0.001 TYR A 29 ARG 0.006 0.000 ARG H 187 Details of bonding type rmsd hydrogen bonds : bond 0.03106 ( 1022) hydrogen bonds : angle 3.79481 ( 2877) covalent geometry : bond 0.00198 (32516) covalent geometry : angle 0.53515 (43980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18500.00 seconds wall clock time: 325 minutes 43.81 seconds (19543.81 seconds total)