Starting phenix.real_space_refine on Mon Jun 23 23:35:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zvi_60511/06_2025/8zvi_60511.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zvi_60511/06_2025/8zvi_60511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zvi_60511/06_2025/8zvi_60511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zvi_60511/06_2025/8zvi_60511.map" model { file = "/net/cci-nas-00/data/ceres_data/8zvi_60511/06_2025/8zvi_60511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zvi_60511/06_2025/8zvi_60511.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.014 sd= 2.129 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 60 5.16 5 C 18166 2.51 5 N 4832 2.21 5 O 5570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28628 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "B" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "F" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "G" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2281 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 7, 'TRANS': 286} Chain: "H" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "I" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2305 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain: "J" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2281 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 7, 'TRANS': 286} Chain: "K" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2281 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 7, 'TRANS': 286} Chain: "L" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2281 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 7, 'TRANS': 286} Chain: "a" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 532 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "b" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 532 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Time building chain proxies: 16.30, per 1000 atoms: 0.57 Number of scatterers: 28628 At special positions: 0 Unit cell: (201.5, 292.5, 88.4, 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 60 16.00 O 5570 8.00 N 4832 7.00 C 18166 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: 7.00 Conformation dependent library (CDL) restraints added in 3.6 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6896 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 69 sheets defined 29.0% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.03 Creating SS restraints... Processing helix chain 'A' and resid 191 through 196 removed outlier: 3.790A pdb=" N LEU A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 196' Processing helix chain 'A' and resid 257 through 263 removed outlier: 3.628A pdb=" N GLU A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 289 removed outlier: 3.735A pdb=" N ARG A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS A 273 " --> pdb=" O PRO A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 4.435A pdb=" N SER A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.532A pdb=" N ILE A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.965A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 335' Processing helix chain 'A' and resid 336 through 339 Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.893A pdb=" N THR B 231 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 267 through 289 removed outlier: 3.505A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 323 through 329 Processing helix chain 'B' and resid 330 through 335 removed outlier: 4.112A pdb=" N LEU B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 335 " --> pdb=" O ARG B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 335' Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.577A pdb=" N LEU B 339 " --> pdb=" O ARG B 336 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS B 340 " --> pdb=" O HIS B 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 336 through 340' Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.792A pdb=" N LEU C 195 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 196' Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.948A pdb=" N THR C 231 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 267 through 289 removed outlier: 3.520A pdb=" N ILE C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 removed outlier: 4.030A pdb=" N SER C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 330 removed outlier: 3.534A pdb=" N ILE C 327 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 330 " --> pdb=" O THR C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 341 removed outlier: 6.538A pdb=" N ARG C 336 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS C 337 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 339 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS C 340 " --> pdb=" O HIS C 337 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 341 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'D' and resid 191 through 196 removed outlier: 3.790A pdb=" N LEU D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N PHE D 196 " --> pdb=" O VAL D 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 191 through 196' Processing helix chain 'D' and resid 257 through 263 removed outlier: 3.629A pdb=" N GLU D 261 " --> pdb=" O ASP D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 289 removed outlier: 3.644A pdb=" N ARG D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 removed outlier: 4.158A pdb=" N SER D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 330 removed outlier: 3.537A pdb=" N ILE D 327 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER D 328 " --> pdb=" O ALA D 324 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 330 " --> pdb=" O THR D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 341 removed outlier: 6.600A pdb=" N ARG D 336 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N HIS D 337 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS D 340 " --> pdb=" O HIS D 337 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 341 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 353 Processing helix chain 'D' and resid 372 through 377 Processing helix chain 'D' and resid 407 through 409 No H-bonds generated for 'chain 'D' and resid 407 through 409' Processing helix chain 'E' and resid 171 through 174 Processing helix chain 'E' and resid 227 through 231 removed outlier: 3.678A pdb=" N THR E 231 " --> pdb=" O ASP E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 267 through 290 removed outlier: 3.751A pdb=" N LEU E 271 " --> pdb=" O LEU E 267 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 Processing helix chain 'E' and resid 324 through 329 Processing helix chain 'E' and resid 330 through 339 removed outlier: 6.714A pdb=" N ARG E 336 " --> pdb=" O LYS E 333 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS E 337 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU E 339 " --> pdb=" O ARG E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 353 Processing helix chain 'E' and resid 372 through 377 Processing helix chain 'E' and resid 407 through 409 No H-bonds generated for 'chain 'E' and resid 407 through 409' Processing helix chain 'F' and resid 227 through 231 removed outlier: 3.684A pdb=" N THR F 231 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 263 Processing helix chain 'F' and resid 267 through 289 Processing helix chain 'F' and resid 298 through 305 Processing helix chain 'F' and resid 323 through 330 removed outlier: 3.669A pdb=" N LEU F 330 " --> pdb=" O THR F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 339 removed outlier: 6.606A pdb=" N ARG F 336 " --> pdb=" O LYS F 333 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS F 337 " --> pdb=" O LEU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 358 removed outlier: 3.862A pdb=" N ASP F 355 " --> pdb=" O ASP F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 377 Processing helix chain 'G' and resid 191 through 196 removed outlier: 3.790A pdb=" N LEU G 195 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N PHE G 196 " --> pdb=" O VAL G 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 196' Processing helix chain 'G' and resid 257 through 263 Processing helix chain 'G' and resid 267 through 289 Processing helix chain 'G' and resid 298 through 306 removed outlier: 4.158A pdb=" N SER G 304 " --> pdb=" O LEU G 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 330 removed outlier: 3.536A pdb=" N ILE G 327 " --> pdb=" O THR G 323 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER G 328 " --> pdb=" O ALA G 324 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 330 " --> pdb=" O THR G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 335 removed outlier: 3.825A pdb=" N LEU G 334 " --> pdb=" O LEU G 330 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY G 335 " --> pdb=" O ARG G 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 330 through 335' Processing helix chain 'G' and resid 336 through 339 Processing helix chain 'G' and resid 350 through 353 Processing helix chain 'G' and resid 372 through 377 Processing helix chain 'G' and resid 407 through 409 No H-bonds generated for 'chain 'G' and resid 407 through 409' Processing helix chain 'H' and resid 171 through 174 Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.762A pdb=" N LEU H 195 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE H 196 " --> pdb=" O VAL H 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 191 through 196' Processing helix chain 'H' and resid 227 through 232 Processing helix chain 'H' and resid 257 through 262 Processing helix chain 'H' and resid 267 through 289 removed outlier: 3.560A pdb=" N LEU H 271 " --> pdb=" O LEU H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 306 removed outlier: 3.925A pdb=" N SER H 304 " --> pdb=" O LEU H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 330 removed outlier: 3.629A pdb=" N LEU H 330 " --> pdb=" O THR H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 331 through 333 No H-bonds generated for 'chain 'H' and resid 331 through 333' Processing helix chain 'H' and resid 334 through 341 removed outlier: 4.054A pdb=" N HIS H 337 " --> pdb=" O LEU H 334 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU H 339 " --> pdb=" O ARG H 336 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS H 340 " --> pdb=" O HIS H 337 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU H 341 " --> pdb=" O GLY H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 353 Processing helix chain 'H' and resid 359 through 363 removed outlier: 3.757A pdb=" N GLN H 363 " --> pdb=" O GLU H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 377 Processing helix chain 'H' and resid 407 through 409 No H-bonds generated for 'chain 'H' and resid 407 through 409' Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 191 through 196 removed outlier: 3.887A pdb=" N LEU I 195 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE I 196 " --> pdb=" O VAL I 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 191 through 196' Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.545A pdb=" N THR I 231 " --> pdb=" O ASP I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 263 Processing helix chain 'I' and resid 267 through 289 Processing helix chain 'I' and resid 298 through 306 Processing helix chain 'I' and resid 323 through 335 removed outlier: 3.583A pdb=" N ILE I 327 " --> pdb=" O THR I 323 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU I 330 " --> pdb=" O THR I 326 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG I 331 " --> pdb=" O ILE I 327 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG I 332 " --> pdb=" O SER I 328 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS I 333 " --> pdb=" O LYS I 329 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU I 334 " --> pdb=" O LEU I 330 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY I 335 " --> pdb=" O ARG I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 341 removed outlier: 4.172A pdb=" N LYS I 340 " --> pdb=" O HIS I 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU I 341 " --> pdb=" O GLY I 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 337 through 341' Processing helix chain 'I' and resid 350 through 353 Processing helix chain 'I' and resid 359 through 363 removed outlier: 3.822A pdb=" N GLN I 363 " --> pdb=" O GLU I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 377 Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.865A pdb=" N THR J 231 " --> pdb=" O ASP J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 263 Processing helix chain 'J' and resid 267 through 290 Processing helix chain 'J' and resid 298 through 306 Processing helix chain 'J' and resid 323 through 330 removed outlier: 3.561A pdb=" N ILE J 327 " --> pdb=" O THR J 323 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU J 330 " --> pdb=" O THR J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 330 through 335 removed outlier: 3.923A pdb=" N LEU J 334 " --> pdb=" O LEU J 330 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY J 335 " --> pdb=" O ARG J 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 330 through 335' Processing helix chain 'J' and resid 336 through 341 removed outlier: 3.656A pdb=" N LEU J 339 " --> pdb=" O ARG J 336 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS J 340 " --> pdb=" O HIS J 337 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU J 341 " --> pdb=" O GLY J 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 336 through 341' Processing helix chain 'J' and resid 349 through 353 Processing helix chain 'J' and resid 372 through 377 Processing helix chain 'J' and resid 407 through 409 No H-bonds generated for 'chain 'J' and resid 407 through 409' Processing helix chain 'K' and resid 191 through 196 removed outlier: 3.792A pdb=" N LEU K 195 " --> pdb=" O VAL K 191 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N PHE K 196 " --> pdb=" O VAL K 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 191 through 196' Processing helix chain 'K' and resid 257 through 263 removed outlier: 3.628A pdb=" N GLU K 261 " --> pdb=" O ASP K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 289 removed outlier: 3.562A pdb=" N LEU K 271 " --> pdb=" O LEU K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 306 Processing helix chain 'K' and resid 323 through 329 Processing helix chain 'K' and resid 330 through 335 removed outlier: 4.177A pdb=" N LEU K 334 " --> pdb=" O LEU K 330 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY K 335 " --> pdb=" O ARG K 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 330 through 335' Processing helix chain 'K' and resid 336 through 338 No H-bonds generated for 'chain 'K' and resid 336 through 338' Processing helix chain 'K' and resid 349 through 358 Processing helix chain 'K' and resid 359 through 363 Processing helix chain 'K' and resid 372 through 377 Processing helix chain 'K' and resid 407 through 409 No H-bonds generated for 'chain 'K' and resid 407 through 409' Processing helix chain 'L' and resid 227 through 231 removed outlier: 3.547A pdb=" N THR L 230 " --> pdb=" O THR L 227 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR L 231 " --> pdb=" O ASP L 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 227 through 231' Processing helix chain 'L' and resid 256 through 263 Processing helix chain 'L' and resid 267 through 289 Processing helix chain 'L' and resid 298 through 306 Processing helix chain 'L' and resid 323 through 330 removed outlier: 3.535A pdb=" N ILE L 327 " --> pdb=" O THR L 323 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER L 328 " --> pdb=" O ALA L 324 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU L 330 " --> pdb=" O THR L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 331 through 341 removed outlier: 6.536A pdb=" N ARG L 336 " --> pdb=" O LYS L 333 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS L 337 " --> pdb=" O LEU L 334 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU L 339 " --> pdb=" O ARG L 336 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS L 340 " --> pdb=" O HIS L 337 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU L 341 " --> pdb=" O GLY L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 353 Processing helix chain 'L' and resid 372 through 377 Processing helix chain 'L' and resid 407 through 409 No H-bonds generated for 'chain 'L' and resid 407 through 409' Processing helix chain 'a' and resid 3 through 11 removed outlier: 4.088A pdb=" N THR a 9 " --> pdb=" O SER a 5 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE a 10 " --> pdb=" O GLY a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 22 removed outlier: 3.613A pdb=" N PHE a 22 " --> pdb=" O SER a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 23 through 25 No H-bonds generated for 'chain 'a' and resid 23 through 25' Processing helix chain 'a' and resid 26 through 31 removed outlier: 4.595A pdb=" N TYR a 30 " --> pdb=" O ALA a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 32 through 42 removed outlier: 4.056A pdb=" N PHE a 36 " --> pdb=" O PRO a 32 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU a 37 " --> pdb=" O SER a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 48 through 64 removed outlier: 3.655A pdb=" N ILE a 64 " --> pdb=" O TYR a 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 11 removed outlier: 3.840A pdb=" N THR b 9 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE b 10 " --> pdb=" O GLY b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 24 Processing helix chain 'b' and resid 24 through 31 removed outlier: 4.085A pdb=" N LYS b 29 " --> pdb=" O VAL b 25 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR b 30 " --> pdb=" O ALA b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 32 through 42 removed outlier: 3.724A pdb=" N PHE b 36 " --> pdb=" O PRO b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 199 removed outlier: 6.648A pdb=" N GLU A 197 " --> pdb=" O MET A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241 removed outlier: 5.843A pdb=" N THR A 207 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ARG F 181 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE F 183 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 218 through 220 removed outlier: 4.349A pdb=" N LYS F 248 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 248 through 256 removed outlier: 3.512A pdb=" N ALA A 433 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 437 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 420 " --> pdb=" O THR A 437 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG A 439 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA A 418 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.055A pdb=" N SER A 452 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY A 453 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU A 401 " --> pdb=" O GLY A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 381 through 382 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 177 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 177 Processing sheet with id=AB2, first strand: chain 'B' and resid 197 through 200 removed outlier: 6.638A pdb=" N GLU B 197 " --> pdb=" O MET B 413 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG B 415 " --> pdb=" O GLU B 197 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU B 199 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ARG B 417 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ALA B 418 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG B 439 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 443 through 444 removed outlier: 5.267A pdb=" N ALA B 418 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ARG B 439 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU C 233 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B 252 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 309 through 315 removed outlier: 6.949A pdb=" N ALA B 314 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B 403 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR B 455 " --> pdb=" O GLU B 401 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU B 401 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE B 402 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N LEU B 344 " --> pdb=" O PRO B 386 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N VAL B 388 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 346 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER B 390 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL B 348 " --> pdb=" O SER B 390 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 182 through 183 Processing sheet with id=AB6, first strand: chain 'C' and resid 197 through 199 removed outlier: 4.161A pdb=" N GLU C 197 " --> pdb=" O PHE C 411 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 417 through 426 removed outlier: 6.039A pdb=" N ALA C 418 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG C 439 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 420 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 437 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 433 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 432 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS C 248 " --> pdb=" O VAL D 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 417 through 426 removed outlier: 6.039A pdb=" N ALA C 418 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG C 439 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 420 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 437 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA C 433 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 432 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU D 233 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C 252 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.056A pdb=" N SER C 452 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLY C 453 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU C 401 " --> pdb=" O GLY C 453 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE C 402 " --> pdb=" O SER C 349 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL C 348 " --> pdb=" O SER C 390 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 381 through 382 Processing sheet with id=AC2, first strand: chain 'D' and resid 176 through 177 Processing sheet with id=AC3, first strand: chain 'D' and resid 182 through 183 Processing sheet with id=AC4, first strand: chain 'D' and resid 197 through 199 removed outlier: 6.648A pdb=" N GLU D 197 " --> pdb=" O MET D 413 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 248 through 256 removed outlier: 3.512A pdb=" N ALA D 433 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 437 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 420 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG D 439 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ALA D 418 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 310 through 311 removed outlier: 6.755A pdb=" N VAL D 310 " --> pdb=" O THR D 454 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 403 " --> pdb=" O GLY D 453 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 381 through 382 Processing sheet with id=AC8, first strand: chain 'E' and resid 176 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 182 through 183 Processing sheet with id=AD1, first strand: chain 'E' and resid 197 through 199 removed outlier: 6.818A pdb=" N GLU E 197 " --> pdb=" O MET E 413 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 247 through 256 removed outlier: 3.582A pdb=" N TYR E 247 " --> pdb=" O VAL E 440 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ARG E 439 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ALA E 418 " --> pdb=" O ARG E 439 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 309 through 315 removed outlier: 3.505A pdb=" N ALA E 456 " --> pdb=" O THR E 312 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA E 314 " --> pdb=" O ALA E 456 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 388 through 389 Processing sheet with id=AD5, first strand: chain 'E' and resid 381 through 382 Processing sheet with id=AD6, first strand: chain 'F' and resid 197 through 199 removed outlier: 6.732A pdb=" N GLU F 197 " --> pdb=" O MET F 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'F' and resid 309 through 315 removed outlier: 3.653A pdb=" N ALA F 456 " --> pdb=" O THR F 312 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA F 314 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA F 403 " --> pdb=" O GLY F 453 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU F 346 " --> pdb=" O VAL F 388 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N SER F 390 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL F 348 " --> pdb=" O SER F 390 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 177 through 183 removed outlier: 3.723A pdb=" N THR H 207 " --> pdb=" O ILE G 177 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU H 209 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ARG G 181 " --> pdb=" O LEU H 209 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 197 through 199 removed outlier: 6.648A pdb=" N GLU G 197 " --> pdb=" O MET G 413 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 209 through 210 Processing sheet with id=AE2, first strand: chain 'G' and resid 218 through 220 removed outlier: 4.288A pdb=" N LYS L 248 " --> pdb=" O VAL G 220 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU G 233 " --> pdb=" O LYS L 252 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N PHE L 254 " --> pdb=" O GLU G 233 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 218 through 220 removed outlier: 4.288A pdb=" N LYS L 248 " --> pdb=" O VAL G 220 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN L 438 " --> pdb=" O LEU L 249 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA L 433 " --> pdb=" O GLU L 424 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR L 437 " --> pdb=" O THR L 420 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR L 420 " --> pdb=" O THR L 437 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG L 439 " --> pdb=" O ALA L 418 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA L 418 " --> pdb=" O ARG L 439 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 417 through 426 removed outlier: 5.937A pdb=" N ALA G 418 " --> pdb=" O ARG G 439 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG G 439 " --> pdb=" O ALA G 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 420 " --> pdb=" O THR G 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR G 437 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA G 433 " --> pdb=" O GLU G 424 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS G 248 " --> pdb=" O VAL H 220 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 309 through 311 removed outlier: 6.054A pdb=" N SER G 452 " --> pdb=" O VAL G 310 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY G 453 " --> pdb=" O GLU G 401 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU G 401 " --> pdb=" O GLY G 453 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 381 through 382 Processing sheet with id=AE7, first strand: chain 'H' and resid 176 through 183 removed outlier: 4.362A pdb=" N LEU I 209 " --> pdb=" O SER H 179 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ARG H 181 " --> pdb=" O LEU I 209 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 197 through 199 removed outlier: 6.647A pdb=" N GLU H 197 " --> pdb=" O MET H 413 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 417 through 426 removed outlier: 5.938A pdb=" N ALA H 418 " --> pdb=" O ARG H 439 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG H 439 " --> pdb=" O ALA H 418 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR H 420 " --> pdb=" O THR H 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR H 437 " --> pdb=" O THR H 420 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA H 433 " --> pdb=" O GLU H 424 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP H 432 " --> pdb=" O ILE H 255 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE H 255 " --> pdb=" O ASP H 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR H 434 " --> pdb=" O SER H 253 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER H 253 " --> pdb=" O TYR H 434 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL H 436 " --> pdb=" O ALA H 251 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 251 " --> pdb=" O VAL H 436 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS H 248 " --> pdb=" O VAL I 220 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 417 through 426 removed outlier: 5.938A pdb=" N ALA H 418 " --> pdb=" O ARG H 439 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG H 439 " --> pdb=" O ALA H 418 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR H 420 " --> pdb=" O THR H 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR H 437 " --> pdb=" O THR H 420 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA H 433 " --> pdb=" O GLU H 424 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP H 432 " --> pdb=" O ILE H 255 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE H 255 " --> pdb=" O ASP H 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR H 434 " --> pdb=" O SER H 253 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER H 253 " --> pdb=" O TYR H 434 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL H 436 " --> pdb=" O ALA H 251 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 251 " --> pdb=" O VAL H 436 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU I 233 " --> pdb=" O ALA H 250 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS H 252 " --> pdb=" O GLU I 233 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 309 through 315 removed outlier: 3.509A pdb=" N ALA H 456 " --> pdb=" O THR H 312 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA H 314 " --> pdb=" O ALA H 456 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA H 403 " --> pdb=" O GLY H 453 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 381 through 382 Processing sheet with id=AF4, first strand: chain 'I' and resid 176 through 177 Processing sheet with id=AF5, first strand: chain 'I' and resid 182 through 183 Processing sheet with id=AF6, first strand: chain 'I' and resid 197 through 199 removed outlier: 4.002A pdb=" N GLU I 197 " --> pdb=" O PHE I 411 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 417 through 426 removed outlier: 6.145A pdb=" N ALA I 418 " --> pdb=" O ARG I 439 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ARG I 439 " --> pdb=" O ALA I 418 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR I 420 " --> pdb=" O THR I 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR I 437 " --> pdb=" O THR I 420 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA I 433 " --> pdb=" O GLU I 424 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL I 440 " --> pdb=" O TYR I 247 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU J 233 " --> pdb=" O ALA I 250 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS I 252 " --> pdb=" O GLU J 233 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 309 through 311 removed outlier: 3.847A pdb=" N ALA I 403 " --> pdb=" O GLY I 453 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL I 345 " --> pdb=" O VAL I 406 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 381 through 382 Processing sheet with id=AG1, first strand: chain 'J' and resid 182 through 183 Processing sheet with id=AG2, first strand: chain 'J' and resid 197 through 199 removed outlier: 6.649A pdb=" N GLU J 197 " --> pdb=" O MET J 413 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 412 " --> pdb=" O GLN J 443 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 417 through 426 removed outlier: 5.936A pdb=" N ALA J 418 " --> pdb=" O ARG J 439 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG J 439 " --> pdb=" O ALA J 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR J 420 " --> pdb=" O THR J 437 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR J 437 " --> pdb=" O THR J 420 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA J 433 " --> pdb=" O GLU J 424 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS J 248 " --> pdb=" O VAL K 220 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 417 through 426 removed outlier: 5.936A pdb=" N ALA J 418 " --> pdb=" O ARG J 439 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG J 439 " --> pdb=" O ALA J 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR J 420 " --> pdb=" O THR J 437 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR J 437 " --> pdb=" O THR J 420 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA J 433 " --> pdb=" O GLU J 424 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N GLU K 233 " --> pdb=" O LYS J 248 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA J 250 " --> pdb=" O GLU K 233 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 309 through 315 removed outlier: 6.918A pdb=" N ALA J 314 " --> pdb=" O ALA J 456 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLY J 453 " --> pdb=" O PHE J 402 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR J 455 " --> pdb=" O ALA J 400 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA J 400 " --> pdb=" O TYR J 455 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 347 through 348 Processing sheet with id=AG7, first strand: chain 'J' and resid 381 through 382 Processing sheet with id=AG8, first strand: chain 'K' and resid 178 through 183 removed outlier: 5.798A pdb=" N THR L 207 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG K 181 " --> pdb=" O THR L 207 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 197 through 199 removed outlier: 6.649A pdb=" N GLU K 197 " --> pdb=" O MET K 413 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 248 through 256 removed outlier: 3.512A pdb=" N ALA K 433 " --> pdb=" O GLU K 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR K 437 " --> pdb=" O THR K 420 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR K 420 " --> pdb=" O THR K 437 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG K 439 " --> pdb=" O ALA K 418 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ALA K 418 " --> pdb=" O ARG K 439 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 309 through 315 removed outlier: 7.051A pdb=" N ALA K 314 " --> pdb=" O ALA K 456 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA K 403 " --> pdb=" O GLY K 453 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR K 455 " --> pdb=" O GLU K 401 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU K 401 " --> pdb=" O TYR K 455 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 381 through 382 Processing sheet with id=AH4, first strand: chain 'L' and resid 197 through 199 removed outlier: 6.648A pdb=" N GLU L 197 " --> pdb=" O MET L 413 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 309 through 311 removed outlier: 6.055A pdb=" N SER L 452 " --> pdb=" O VAL L 310 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY L 453 " --> pdb=" O GLU L 401 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU L 401 " --> pdb=" O GLY L 453 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 381 through 382 885 hydrogen bonds defined for protein. 2268 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: 10.40 Time building geometry restraints manager: 8.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4892 1.28 - 1.41: 7105 1.41 - 1.54: 16905 1.54 - 1.67: 60 1.67 - 1.80: 120 Bond restraints: 29082 Sorted by residual: bond pdb=" CA LYS F 325 " pdb=" C LYS F 325 " ideal model delta sigma weight residual 1.524 1.396 0.128 1.29e-02 6.01e+03 9.82e+01 bond pdb=" CA SER C 179 " pdb=" C SER C 179 " ideal model delta sigma weight residual 1.524 1.410 0.114 1.27e-02 6.20e+03 8.12e+01 bond pdb=" CA ALA F 366 " pdb=" C ALA F 366 " ideal model delta sigma weight residual 1.523 1.409 0.115 1.28e-02 6.10e+03 8.01e+01 bond pdb=" CA ALA E 366 " pdb=" C ALA E 366 " ideal model delta sigma weight residual 1.521 1.433 0.088 9.90e-03 1.02e+04 7.89e+01 bond pdb=" CA TYR F 353 " pdb=" C TYR F 353 " ideal model delta sigma weight residual 1.524 1.411 0.112 1.27e-02 6.20e+03 7.81e+01 ... (remaining 29077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 34201 3.27 - 6.54: 4011 6.54 - 9.82: 891 9.82 - 13.09: 183 13.09 - 16.36: 22 Bond angle restraints: 39308 Sorted by residual: angle pdb=" N LYS B 340 " pdb=" CA LYS B 340 " pdb=" C LYS B 340 " ideal model delta sigma weight residual 111.07 124.32 -13.25 1.07e+00 8.73e-01 1.53e+02 angle pdb=" N LEU G 356 " pdb=" CA LEU G 356 " pdb=" C LEU G 356 " ideal model delta sigma weight residual 113.41 98.44 14.97 1.22e+00 6.72e-01 1.51e+02 angle pdb=" N LEU I 356 " pdb=" CA LEU I 356 " pdb=" C LEU I 356 " ideal model delta sigma weight residual 113.41 98.45 14.96 1.22e+00 6.72e-01 1.50e+02 angle pdb=" N LEU B 356 " pdb=" CA LEU B 356 " pdb=" C LEU B 356 " ideal model delta sigma weight residual 113.41 98.49 14.92 1.22e+00 6.72e-01 1.50e+02 angle pdb=" N LEU D 356 " pdb=" CA LEU D 356 " pdb=" C LEU D 356 " ideal model delta sigma weight residual 113.41 98.52 14.89 1.22e+00 6.72e-01 1.49e+02 ... (remaining 39303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 15009 17.17 - 34.34: 1719 34.34 - 51.51: 666 51.51 - 68.68: 252 68.68 - 85.85: 12 Dihedral angle restraints: 17658 sinusoidal: 6940 harmonic: 10718 Sorted by residual: dihedral pdb=" C SER K 173 " pdb=" N SER K 173 " pdb=" CA SER K 173 " pdb=" CB SER K 173 " ideal model delta harmonic sigma weight residual -122.60 -143.96 21.36 0 2.50e+00 1.60e-01 7.30e+01 dihedral pdb=" C SER G 173 " pdb=" N SER G 173 " pdb=" CA SER G 173 " pdb=" CB SER G 173 " ideal model delta harmonic sigma weight residual -122.60 -143.92 21.32 0 2.50e+00 1.60e-01 7.28e+01 dihedral pdb=" N SER K 173 " pdb=" C SER K 173 " pdb=" CA SER K 173 " pdb=" CB SER K 173 " ideal model delta harmonic sigma weight residual 122.80 143.42 -20.62 0 2.50e+00 1.60e-01 6.80e+01 ... (remaining 17655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 3489 0.175 - 0.349: 848 0.349 - 0.524: 193 0.524 - 0.698: 29 0.698 - 0.873: 9 Chirality restraints: 4568 Sorted by residual: chirality pdb=" CA SER K 173 " pdb=" N SER K 173 " pdb=" C SER K 173 " pdb=" CB SER K 173 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.90e+01 chirality pdb=" CA SER G 173 " pdb=" N SER G 173 " pdb=" C SER G 173 " pdb=" CB SER G 173 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.89e+01 chirality pdb=" CA GLU I 258 " pdb=" N GLU I 258 " pdb=" C GLU I 258 " pdb=" CB GLU I 258 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.81e+01 ... (remaining 4565 not shown) Planarity restraints: 5000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA K 263 " -0.027 2.00e-02 2.50e+03 5.35e-02 2.86e+01 pdb=" C ALA K 263 " 0.093 2.00e-02 2.50e+03 pdb=" O ALA K 263 " -0.035 2.00e-02 2.50e+03 pdb=" N ILE K 264 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 284 " 0.025 2.00e-02 2.50e+03 5.13e-02 2.64e+01 pdb=" CD GLU E 284 " -0.089 2.00e-02 2.50e+03 pdb=" OE1 GLU E 284 " 0.032 2.00e-02 2.50e+03 pdb=" OE2 GLU E 284 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 415 " 0.025 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C ARG E 415 " -0.087 2.00e-02 2.50e+03 pdb=" O ARG E 415 " 0.032 2.00e-02 2.50e+03 pdb=" N GLN E 416 " 0.030 2.00e-02 2.50e+03 ... (remaining 4997 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7826 2.74 - 3.28: 25691 3.28 - 3.82: 47479 3.82 - 4.36: 59433 4.36 - 4.90: 98964 Nonbonded interactions: 239393 Sorted by model distance: nonbonded pdb=" O GLN K 376 " pdb=" CA GLY L 384 " model vdw 2.203 3.440 nonbonded pdb=" N ALA F 366 " pdb=" N GLN F 367 " model vdw 2.238 2.560 nonbonded pdb=" N PHE C 446 " pdb=" O PHE C 446 " model vdw 2.240 2.496 nonbonded pdb=" CG TYR C 354 " pdb=" CG ARG D 332 " model vdw 2.248 3.660 nonbonded pdb=" NE2 GLN D 378 " pdb=" CD1 LEU E 341 " model vdw 2.255 3.540 ... (remaining 239388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 164 through 457) selection = (chain 'B' and resid 164 through 457) selection = (chain 'C' and resid 164 through 457) selection = (chain 'D' and resid 164 through 457) selection = (chain 'E' and resid 164 through 457) selection = (chain 'F' and resid 164 through 457) selection = chain 'G' selection = (chain 'H' and resid 164 through 457) selection = (chain 'I' and resid 164 through 457) selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 1.090 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 62.510 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.025 0.128 29082 Z= 1.802 Angle : 2.404 16.361 39308 Z= 1.620 Chirality : 0.167 0.873 4568 Planarity : 0.011 0.106 5000 Dihedral : 18.104 85.854 10762 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 2.11 % Allowed : 7.85 % Favored : 90.04 % Rotamer: Outliers : 21.79 % Allowed : 11.87 % Favored : 66.34 % Cbeta Deviations : 5.08 % 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: 3656 helix: -0.13 (0.18), residues: 823 sheet: -1.02 (0.18), residues: 849 loop : -1.41 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP I 219 HIS 0.015 0.003 HIS I 243 PHE 0.033 0.004 PHE a 36 TYR 0.039 0.004 TYR J 445 ARG 0.012 0.002 ARG B 415 Details of bonding type rmsd hydrogen bonds : bond 0.25126 ( 830) hydrogen bonds : angle 9.26576 ( 2268) covalent geometry : bond 0.02458 (29082) covalent geometry : angle 2.40379 (39308) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1778 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 672 poor density : 1106 time to evaluate : 3.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8288 (t) REVERT: A 229 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8331 (p) REVERT: A 236 LYS cc_start: 0.7306 (pttt) cc_final: 0.7005 (tptt) REVERT: A 295 LYS cc_start: 0.8832 (mttt) cc_final: 0.8617 (mttm) REVERT: A 333 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8193 (tptt) REVERT: A 346 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8125 (tt) REVERT: A 363 GLN cc_start: 0.8547 (mt0) cc_final: 0.7900 (mt0) REVERT: A 413 MET cc_start: 0.9060 (mtp) cc_final: 0.8795 (mtm) REVERT: A 422 GLU cc_start: 0.6320 (tt0) cc_final: 0.6021 (tt0) REVERT: A 429 LYS cc_start: 0.7252 (mtmt) cc_final: 0.6982 (tptp) REVERT: A 450 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8699 (t) REVERT: B 205 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8340 (mt) REVERT: B 264 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6367 (mp) REVERT: B 288 MET cc_start: 0.8652 (mmt) cc_final: 0.7609 (mmt) REVERT: B 289 THR cc_start: 0.8987 (p) cc_final: 0.8748 (p) REVERT: B 317 ASP cc_start: 0.6292 (p0) cc_final: 0.5914 (p0) REVERT: B 383 TYR cc_start: 0.8199 (m-80) cc_final: 0.7429 (m-80) REVERT: B 405 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8308 (mt) REVERT: B 430 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7615 (mt0) REVERT: B 446 PHE cc_start: 0.7491 (m-80) cc_final: 0.7268 (m-80) REVERT: C 165 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8556 (m) REVERT: C 175 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7301 (mt-10) REVERT: C 177 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7953 (pt) REVERT: C 180 GLN cc_start: 0.7526 (mt0) cc_final: 0.7151 (mt0) REVERT: C 210 VAL cc_start: 0.9356 (t) cc_final: 0.9145 (t) REVERT: C 213 ASP cc_start: 0.7273 (m-30) cc_final: 0.7070 (m-30) REVERT: C 258 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: C 288 MET cc_start: 0.8215 (mmt) cc_final: 0.7761 (mmt) REVERT: D 269 PRO cc_start: 0.7602 (Cg_exo) cc_final: 0.7342 (Cg_endo) REVERT: D 359 ASP cc_start: 0.7663 (t0) cc_final: 0.7370 (t0) REVERT: D 362 TRP cc_start: 0.8762 (OUTLIER) cc_final: 0.7512 (m-90) REVERT: D 398 ASN cc_start: 0.7805 (m-40) cc_final: 0.7443 (m-40) REVERT: D 430 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7229 (mt0) REVERT: E 167 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8308 (p) REVERT: E 192 VAL cc_start: 0.9144 (OUTLIER) cc_final: 0.8821 (m) REVERT: E 203 SER cc_start: 0.9005 (t) cc_final: 0.8746 (t) REVERT: E 430 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8512 (mm110) REVERT: F 168 GLU cc_start: 0.7258 (pt0) cc_final: 0.7043 (pt0) REVERT: F 187 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6692 (mm-40) REVERT: F 218 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8825 (p) REVERT: F 269 PRO cc_start: 0.9248 (OUTLIER) cc_final: 0.8765 (Cg_endo) REVERT: F 289 THR cc_start: 0.9057 (m) cc_final: 0.8845 (p) REVERT: F 346 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8854 (tp) REVERT: F 362 TRP cc_start: 0.8981 (OUTLIER) cc_final: 0.8312 (m-90) REVERT: F 372 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7360 (p) REVERT: F 382 ILE cc_start: 0.8957 (mm) cc_final: 0.8632 (pt) REVERT: F 420 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8574 (p) REVERT: F 426 GLN cc_start: 0.8076 (mt0) cc_final: 0.7721 (mt0) REVERT: F 450 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8677 (m) REVERT: G 167 VAL cc_start: 0.6864 (OUTLIER) cc_final: 0.6317 (t) REVERT: G 182 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8709 (mt) REVERT: G 255 ILE cc_start: 0.8403 (tt) cc_final: 0.8057 (tt) REVERT: G 312 THR cc_start: 0.7671 (p) cc_final: 0.7171 (t) REVERT: G 364 ASP cc_start: 0.7949 (m-30) cc_final: 0.7662 (m-30) REVERT: G 412 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8074 (m) REVERT: G 430 GLN cc_start: 0.6402 (OUTLIER) cc_final: 0.5273 (mp10) REVERT: H 310 VAL cc_start: 0.8756 (t) cc_final: 0.8393 (t) REVERT: H 311 VAL cc_start: 0.8793 (t) cc_final: 0.8585 (t) REVERT: H 351 ASP cc_start: 0.7169 (t0) cc_final: 0.6902 (t0) REVERT: H 363 GLN cc_start: 0.7892 (mt0) cc_final: 0.7448 (mt0) REVERT: H 399 SER cc_start: 0.8472 (m) cc_final: 0.8003 (t) REVERT: H 413 MET cc_start: 0.8487 (mtp) cc_final: 0.8183 (mtp) REVERT: H 441 ASN cc_start: 0.8149 (t0) cc_final: 0.7764 (t0) REVERT: H 442 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7926 (tt) REVERT: I 227 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8168 (p) REVERT: I 231 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8358 (p) REVERT: I 242 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8682 (pt) REVERT: I 252 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8320 (ptmt) REVERT: I 362 TRP cc_start: 0.8532 (OUTLIER) cc_final: 0.7391 (m-90) REVERT: I 398 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8744 (m-40) REVERT: I 410 ASN cc_start: 0.8605 (t0) cc_final: 0.8281 (t0) REVERT: I 430 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: J 208 MET cc_start: 0.8656 (mtp) cc_final: 0.8421 (mtt) REVERT: J 213 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6699 (p0) REVERT: J 229 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8764 (p) REVERT: J 240 LYS cc_start: 0.8627 (mttt) cc_final: 0.8420 (mtpp) REVERT: J 311 VAL cc_start: 0.8894 (t) cc_final: 0.8649 (p) REVERT: J 399 SER cc_start: 0.7801 (m) cc_final: 0.7213 (t) REVERT: J 444 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6988 (ptp-170) REVERT: K 172 GLU cc_start: -0.0205 (OUTLIER) cc_final: -0.0679 (tt0) REVERT: K 186 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6142 (tm) REVERT: K 270 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7444 (tm) REVERT: K 272 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6392 (tpp-160) REVERT: K 289 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.7937 (p) REVERT: L 168 GLU cc_start: 0.5458 (mt-10) cc_final: 0.5217 (mt-10) REVERT: L 175 GLU cc_start: 0.5601 (OUTLIER) cc_final: 0.2457 (mt-10) REVERT: L 183 ILE cc_start: 0.5801 (OUTLIER) cc_final: 0.5378 (pt) REVERT: L 209 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5604 (mt) REVERT: L 236 LYS cc_start: 0.7202 (pttt) cc_final: 0.5934 (tppt) REVERT: L 273 LYS cc_start: 0.7468 (mtpt) cc_final: 0.7225 (mmtt) REVERT: L 372 SER cc_start: 0.8322 (OUTLIER) cc_final: 0.7827 (p) REVERT: a 60 TYR cc_start: 0.8185 (t80) cc_final: 0.7480 (t80) outliers start: 672 outliers final: 193 residues processed: 1511 average time/residue: 0.4278 time to fit residues: 998.2478 Evaluate side-chains 949 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 708 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 425 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 444 ARG Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 257 ASP Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 269 PRO Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 296 PRO Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 296 PRO Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 430 GLN Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 188 LYS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 269 PRO Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 378 GLN Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 430 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 269 PRO Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 296 PRO Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 362 TRP Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain F residue 389 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 306 ASP Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 448 ASN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 253 SER Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 296 PRO Chi-restraints excluded: chain H residue 348 VAL Chi-restraints excluded: chain H residue 349 SER Chi-restraints excluded: chain H residue 375 LEU Chi-restraints excluded: chain H residue 404 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain H residue 442 LEU Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 188 LYS Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain I residue 227 THR Chi-restraints excluded: chain I residue 229 THR Chi-restraints excluded: chain I residue 231 THR Chi-restraints excluded: chain I residue 242 ILE Chi-restraints excluded: chain I residue 252 LYS Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 269 PRO Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 398 ASN Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain I residue 448 ASN Chi-restraints excluded: chain I residue 450 VAL Chi-restraints excluded: chain I residue 454 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 177 ILE Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 269 PRO Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 296 PRO Chi-restraints excluded: chain J residue 304 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 375 LEU Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain J residue 444 ARG Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 172 GLU Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 231 THR Chi-restraints excluded: chain K residue 239 LEU Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 262 ASP Chi-restraints excluded: chain K residue 270 LEU Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 289 THR Chi-restraints excluded: chain K residue 300 LEU Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 327 ILE Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 412 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 444 ARG Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 209 LEU Chi-restraints excluded: chain L residue 372 SER Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 378 GLN Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 20 ILE Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 45 SER Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 64 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 326 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 180 GLN ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 187 GLN B 279 HIS B 426 GLN B 438 GLN B 443 GLN B 448 ASN C 337 HIS ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS D 363 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 GLN E 367 GLN E 378 GLN E 438 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 GLN F 416 GLN ** F 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 HIS ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 ASN H 162 ASN H 416 GLN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 ASN I 163 GLN I 243 HIS I 367 GLN I 438 GLN I 448 ASN J 367 GLN ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 GLN L 367 GLN L 378 GLN a 47 HIS ** b 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119882 restraints weight = 40975.413| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.04 r_work: 0.3186 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 29082 Z= 0.237 Angle : 0.777 10.490 39308 Z= 0.423 Chirality : 0.049 0.358 4568 Planarity : 0.006 0.078 5000 Dihedral : 11.305 86.383 4425 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.21 % Favored : 93.03 % Rotamer: Outliers : 9.60 % Allowed : 19.36 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 3656 helix: -0.26 (0.18), residues: 785 sheet: -0.97 (0.17), residues: 916 loop : -1.43 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 219 HIS 0.012 0.002 HIS D 279 PHE 0.019 0.002 PHE F 244 TYR 0.033 0.002 TYR E 392 ARG 0.008 0.001 ARG L 336 Details of bonding type rmsd hydrogen bonds : bond 0.04811 ( 830) hydrogen bonds : angle 6.64032 ( 2268) covalent geometry : bond 0.00527 (29082) covalent geometry : angle 0.77699 (39308) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 776 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 175 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7851 (mt-10) REVERT: A 322 VAL cc_start: 0.8957 (t) cc_final: 0.8750 (t) REVERT: A 363 GLN cc_start: 0.8316 (mt0) cc_final: 0.8072 (mt0) REVERT: A 382 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8741 (pt) REVERT: A 410 ASN cc_start: 0.8866 (t0) cc_final: 0.8666 (t0) REVERT: A 413 MET cc_start: 0.9056 (mtp) cc_final: 0.8715 (mtm) REVERT: A 422 GLU cc_start: 0.6679 (tt0) cc_final: 0.6357 (tt0) REVERT: A 429 LYS cc_start: 0.7681 (mtmt) cc_final: 0.6927 (tptt) REVERT: B 186 LEU cc_start: 0.8257 (mt) cc_final: 0.7926 (mt) REVERT: B 204 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7278 (mptt) REVERT: B 240 LYS cc_start: 0.8638 (mttt) cc_final: 0.8293 (mttt) REVERT: B 266 SER cc_start: 0.8423 (m) cc_final: 0.8010 (t) REVERT: B 267 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7713 (tp) REVERT: B 289 THR cc_start: 0.8685 (p) cc_final: 0.8401 (p) REVERT: B 346 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8609 (tp) REVERT: B 364 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6514 (t0) REVERT: B 413 MET cc_start: 0.8127 (mtp) cc_final: 0.7885 (mtp) REVERT: B 430 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.6519 (mp10) REVERT: C 213 ASP cc_start: 0.7645 (m-30) cc_final: 0.7425 (m-30) REVERT: C 277 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: D 197 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7712 (mt-10) REVERT: D 284 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8081 (tm-30) REVERT: D 288 MET cc_start: 0.9205 (mmm) cc_final: 0.8746 (mmt) REVERT: D 351 ASP cc_start: 0.8111 (t70) cc_final: 0.7800 (t0) REVERT: D 358 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7519 (mt-10) REVERT: D 362 TRP cc_start: 0.9066 (OUTLIER) cc_final: 0.7906 (m-90) REVERT: D 392 TYR cc_start: 0.8191 (m-80) cc_final: 0.7860 (m-80) REVERT: D 420 THR cc_start: 0.8586 (p) cc_final: 0.8284 (p) REVERT: D 450 VAL cc_start: 0.8727 (OUTLIER) cc_final: 0.8518 (t) REVERT: E 197 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7434 (mm-30) REVERT: F 181 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7920 (mtp85) REVERT: F 185 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6260 (t0) REVERT: F 311 VAL cc_start: 0.9177 (t) cc_final: 0.8944 (m) REVERT: F 346 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8303 (tp) REVERT: F 372 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8438 (p) REVERT: F 375 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6951 (tm) REVERT: G 175 GLU cc_start: 0.6976 (pt0) cc_final: 0.6612 (pt0) REVERT: G 204 LYS cc_start: 0.6666 (ttpt) cc_final: 0.6459 (tttp) REVERT: G 289 THR cc_start: 0.7667 (t) cc_final: 0.7161 (p) REVERT: G 423 ARG cc_start: 0.7123 (mtp-110) cc_final: 0.6443 (mtp-110) REVERT: G 424 GLU cc_start: 0.7246 (tt0) cc_final: 0.6568 (mm-30) REVERT: G 430 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.5750 (mp10) REVERT: H 182 ILE cc_start: 0.8188 (mt) cc_final: 0.7756 (mm) REVERT: H 186 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7528 (tm) REVERT: H 282 SER cc_start: 0.9145 (p) cc_final: 0.8811 (m) REVERT: H 332 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7469 (mtp85) REVERT: H 351 ASP cc_start: 0.7438 (t0) cc_final: 0.7052 (t0) REVERT: H 399 SER cc_start: 0.8420 (m) cc_final: 0.7966 (t) REVERT: H 413 MET cc_start: 0.8510 (mtp) cc_final: 0.8224 (mtp) REVERT: H 444 ARG cc_start: 0.7854 (mtm180) cc_final: 0.7617 (mtm180) REVERT: I 163 GLN cc_start: 0.8415 (pt0) cc_final: 0.8182 (pt0) REVERT: I 173 SER cc_start: 0.7757 (t) cc_final: 0.7518 (p) REVERT: I 253 SER cc_start: 0.9226 (m) cc_final: 0.8947 (m) REVERT: I 410 ASN cc_start: 0.9165 (t0) cc_final: 0.8696 (t0) REVERT: I 430 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7652 (mt0) REVERT: J 211 GLU cc_start: 0.8588 (tt0) cc_final: 0.8288 (tt0) REVERT: J 257 ASP cc_start: 0.7189 (m-30) cc_final: 0.6973 (m-30) REVERT: J 261 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: J 311 VAL cc_start: 0.8626 (t) cc_final: 0.8344 (p) REVERT: J 358 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7824 (mt-10) REVERT: J 375 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6360 (tm) REVERT: J 382 ILE cc_start: 0.8496 (mm) cc_final: 0.8248 (tt) REVERT: J 392 TYR cc_start: 0.7300 (m-80) cc_final: 0.6654 (m-80) REVERT: J 422 GLU cc_start: 0.6824 (tt0) cc_final: 0.6548 (tt0) REVERT: J 438 GLN cc_start: 0.8416 (tt0) cc_final: 0.8205 (tt0) REVERT: K 172 GLU cc_start: 0.0081 (OUTLIER) cc_final: -0.0571 (tt0) REVERT: K 186 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7022 (tm) REVERT: K 272 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.6746 (mmm160) REVERT: K 325 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8082 (ttmt) REVERT: K 329 LYS cc_start: 0.7688 (mttt) cc_final: 0.7386 (mtpt) REVERT: K 358 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6463 (mp0) REVERT: K 399 SER cc_start: 0.7851 (m) cc_final: 0.7489 (m) REVERT: K 402 PHE cc_start: 0.7908 (p90) cc_final: 0.7704 (p90) REVERT: L 169 VAL cc_start: 0.6907 (OUTLIER) cc_final: 0.6683 (m) REVERT: L 175 GLU cc_start: 0.5160 (OUTLIER) cc_final: 0.1816 (tt0) REVERT: L 181 ARG cc_start: 0.5771 (ttp-170) cc_final: 0.5339 (ttp-170) REVERT: L 230 THR cc_start: 0.6795 (p) cc_final: 0.6555 (p) REVERT: L 273 LYS cc_start: 0.7400 (mtpt) cc_final: 0.6533 (mmtt) REVERT: L 375 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5828 (tm) REVERT: L 381 ARG cc_start: 0.8141 (mtp180) cc_final: 0.7915 (mmm160) REVERT: L 430 GLN cc_start: 0.1509 (OUTLIER) cc_final: 0.1147 (tt0) REVERT: a 38 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7386 (ptp-170) REVERT: a 60 TYR cc_start: 0.8172 (t80) cc_final: 0.7613 (t80) outliers start: 296 outliers final: 151 residues processed: 976 average time/residue: 0.4031 time to fit residues: 613.5918 Evaluate side-chains 747 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 571 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 295 LYS Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 452 SER Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 295 LYS Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 349 SER Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 229 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 375 LEU Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 454 THR Chi-restraints excluded: chain K residue 172 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 203 SER Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 229 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 216 LYS Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 267 LEU Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 405 ILE Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain L residue 430 GLN Chi-restraints excluded: chain a residue 20 ILE Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 48 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 8 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 335 optimal weight: 9.9990 chunk 280 optimal weight: 0.9990 chunk 291 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN C 363 GLN C 376 GLN D 363 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 HIS ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 ASN F 438 GLN F 448 ASN G 180 GLN ** G 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 GLN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN I 398 ASN I 426 GLN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN L 438 GLN b 47 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.133906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.108099 restraints weight = 41080.010| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.03 r_work: 0.3017 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 29082 Z= 0.306 Angle : 0.753 8.409 39308 Z= 0.404 Chirality : 0.049 0.217 4568 Planarity : 0.005 0.051 5000 Dihedral : 9.310 78.913 4171 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.49 % Favored : 91.82 % Rotamer: Outliers : 8.72 % Allowed : 20.14 % Favored : 71.14 % 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: -1.57 (0.13), residues: 3656 helix: -0.62 (0.18), residues: 796 sheet: -0.78 (0.17), residues: 885 loop : -1.31 (0.13), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 362 HIS 0.012 0.002 HIS A 279 PHE 0.022 0.003 PHE C 244 TYR 0.030 0.002 TYR E 392 ARG 0.010 0.001 ARG K 274 Details of bonding type rmsd hydrogen bonds : bond 0.04541 ( 830) hydrogen bonds : angle 6.28784 ( 2268) covalent geometry : bond 0.00705 (29082) covalent geometry : angle 0.75335 (39308) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 578 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7814 (mt-10) REVERT: A 363 GLN cc_start: 0.8285 (mt0) cc_final: 0.8045 (mt0) REVERT: A 378 GLN cc_start: 0.8247 (pm20) cc_final: 0.7729 (pp30) REVERT: A 413 MET cc_start: 0.9076 (mtp) cc_final: 0.8728 (mtm) REVERT: A 422 GLU cc_start: 0.7581 (tt0) cc_final: 0.7361 (tt0) REVERT: B 204 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7370 (mptt) REVERT: B 240 LYS cc_start: 0.8708 (mttt) cc_final: 0.8377 (mttt) REVERT: B 267 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7449 (tp) REVERT: B 289 THR cc_start: 0.8787 (p) cc_final: 0.8530 (p) REVERT: B 336 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7609 (ptt-90) REVERT: B 346 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8647 (tp) REVERT: B 364 ASP cc_start: 0.6875 (OUTLIER) cc_final: 0.6639 (t0) REVERT: C 279 HIS cc_start: 0.8904 (OUTLIER) cc_final: 0.8413 (m-70) REVERT: C 375 LEU cc_start: 0.9193 (mm) cc_final: 0.8941 (mt) REVERT: D 211 GLU cc_start: 0.8161 (tt0) cc_final: 0.7955 (mt-10) REVERT: D 362 TRP cc_start: 0.9239 (OUTLIER) cc_final: 0.7796 (m-90) REVERT: E 197 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7553 (mm-30) REVERT: E 372 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8514 (p) REVERT: F 181 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7731 (mtp85) REVERT: F 182 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8672 (mm) REVERT: F 185 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7168 (t0) REVERT: F 233 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: F 267 LEU cc_start: 0.8444 (tp) cc_final: 0.8234 (mt) REVERT: F 346 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8565 (tp) REVERT: G 204 LYS cc_start: 0.7063 (ttpt) cc_final: 0.5861 (mmtm) REVERT: G 240 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7349 (tppt) REVERT: G 305 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7259 (mt-10) REVERT: G 364 ASP cc_start: 0.8368 (m-30) cc_final: 0.8133 (m-30) REVERT: G 382 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8026 (pt) REVERT: G 392 TYR cc_start: 0.7585 (m-80) cc_final: 0.7255 (m-80) REVERT: G 430 GLN cc_start: 0.5964 (OUTLIER) cc_final: 0.4707 (mp10) REVERT: H 186 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7679 (tm) REVERT: H 198 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: H 285 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: H 363 GLN cc_start: 0.8043 (mt0) cc_final: 0.7819 (mt0) REVERT: H 399 SER cc_start: 0.8511 (m) cc_final: 0.7969 (t) REVERT: I 253 SER cc_start: 0.9297 (m) cc_final: 0.9052 (m) REVERT: I 430 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7494 (mp10) REVERT: I 437 THR cc_start: 0.8684 (p) cc_final: 0.8479 (p) REVERT: J 261 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: J 311 VAL cc_start: 0.8816 (t) cc_final: 0.8471 (p) REVERT: J 358 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7453 (mt-10) REVERT: J 422 GLU cc_start: 0.7513 (tt0) cc_final: 0.7240 (tt0) REVERT: J 430 GLN cc_start: 0.7074 (mm-40) cc_final: 0.6740 (mm110) REVERT: J 438 GLN cc_start: 0.8527 (tt0) cc_final: 0.8127 (tt0) REVERT: K 172 GLU cc_start: 0.1005 (OUTLIER) cc_final: 0.0588 (mp0) REVERT: K 186 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6912 (tm) REVERT: K 272 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7288 (ttm-80) REVERT: K 358 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6627 (mp0) REVERT: K 359 ASP cc_start: 0.8367 (t0) cc_final: 0.8161 (t70) REVERT: K 422 GLU cc_start: 0.6547 (tt0) cc_final: 0.6139 (tt0) REVERT: K 425 ARG cc_start: 0.8168 (tpt170) cc_final: 0.7819 (tpt170) REVERT: L 175 GLU cc_start: 0.5400 (OUTLIER) cc_final: 0.2064 (tt0) REVERT: L 273 LYS cc_start: 0.7453 (mtpt) cc_final: 0.6474 (mmtt) REVERT: L 444 ARG cc_start: 0.6577 (ttp-110) cc_final: 0.6179 (ttp-110) outliers start: 269 outliers final: 168 residues processed: 766 average time/residue: 0.4078 time to fit residues: 488.7275 Evaluate side-chains 702 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 510 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 421 VAL Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 448 ASN Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 166 SER Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 452 SER Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 203 SER Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 279 HIS Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 289 THR Chi-restraints excluded: chain H residue 295 LYS Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 195 LEU Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 277 GLU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain K residue 172 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 205 ILE Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 208 MET Chi-restraints excluded: chain K residue 227 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 276 ILE Chi-restraints excluded: chain K residue 283 ILE Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 183 ILE Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 219 TRP Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 312 THR Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 48 THR Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 48 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 284 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 303 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 315 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN C 376 GLN ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 426 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 GLN F 376 GLN G 180 GLN G 438 GLN G 443 GLN H 410 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 180 GLN I 367 GLN I 398 ASN ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 376 GLN ** K 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 28 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.112151 restraints weight = 41527.932| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.11 r_work: 0.3093 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29082 Z= 0.158 Angle : 0.594 7.814 39308 Z= 0.321 Chirality : 0.044 0.206 4568 Planarity : 0.004 0.041 5000 Dihedral : 8.261 83.913 4134 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.06 % Favored : 92.34 % Rotamer: Outliers : 7.13 % Allowed : 22.08 % Favored : 70.78 % 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: -1.35 (0.13), residues: 3656 helix: -0.48 (0.18), residues: 786 sheet: -0.65 (0.18), residues: 886 loop : -1.14 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 219 HIS 0.009 0.001 HIS J 279 PHE 0.014 0.001 PHE L 254 TYR 0.017 0.001 TYR E 392 ARG 0.006 0.001 ARG J 181 Details of bonding type rmsd hydrogen bonds : bond 0.03658 ( 830) hydrogen bonds : angle 5.87214 ( 2268) covalent geometry : bond 0.00352 (29082) covalent geometry : angle 0.59387 (39308) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 566 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 THR cc_start: 0.8904 (p) cc_final: 0.8674 (p) REVERT: A 336 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8100 (mtm180) REVERT: A 351 ASP cc_start: 0.7793 (t0) cc_final: 0.7383 (t0) REVERT: A 363 GLN cc_start: 0.8282 (mt0) cc_final: 0.7946 (mt0) REVERT: A 378 GLN cc_start: 0.8138 (pm20) cc_final: 0.7814 (pp30) REVERT: A 413 MET cc_start: 0.8980 (mtp) cc_final: 0.8703 (mtm) REVERT: A 422 GLU cc_start: 0.7613 (tt0) cc_final: 0.7313 (tt0) REVERT: B 204 LYS cc_start: 0.7811 (OUTLIER) cc_final: 0.7169 (mptt) REVERT: B 240 LYS cc_start: 0.8662 (mttt) cc_final: 0.8311 (mttt) REVERT: B 267 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7526 (tp) REVERT: B 289 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8310 (p) REVERT: C 279 HIS cc_start: 0.8797 (OUTLIER) cc_final: 0.8383 (m-70) REVERT: D 266 SER cc_start: 0.7973 (t) cc_final: 0.7648 (p) REVERT: D 288 MET cc_start: 0.9089 (mmm) cc_final: 0.8555 (mmt) REVERT: D 362 TRP cc_start: 0.9188 (OUTLIER) cc_final: 0.7851 (m-90) REVERT: E 197 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7249 (mm-30) REVERT: E 239 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8825 (mt) REVERT: E 426 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.6529 (mp10) REVERT: E 448 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8960 (p0) REVERT: F 181 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7749 (mtp85) REVERT: F 185 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7192 (t0) REVERT: F 346 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8280 (tp) REVERT: F 378 GLN cc_start: 0.8320 (pm20) cc_final: 0.8078 (pm20) REVERT: F 426 GLN cc_start: 0.8408 (mt0) cc_final: 0.8011 (mt0) REVERT: G 204 LYS cc_start: 0.7114 (ttpt) cc_final: 0.5523 (mmtm) REVERT: G 224 THR cc_start: 0.6641 (OUTLIER) cc_final: 0.6400 (p) REVERT: G 240 LYS cc_start: 0.7671 (tttp) cc_final: 0.7309 (tppt) REVERT: G 287 PHE cc_start: 0.8342 (m-10) cc_final: 0.8084 (m-80) REVERT: G 297 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7106 (tttm) REVERT: G 305 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7046 (mm-30) REVERT: G 357 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8091 (mt) REVERT: G 417 ARG cc_start: 0.8052 (ttm170) cc_final: 0.7741 (mtm110) REVERT: G 430 GLN cc_start: 0.5934 (OUTLIER) cc_final: 0.4689 (mp10) REVERT: H 186 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7493 (tm) REVERT: H 285 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7582 (mt-10) REVERT: H 289 THR cc_start: 0.8566 (m) cc_final: 0.8185 (t) REVERT: H 332 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7810 (ttm-80) REVERT: H 359 ASP cc_start: 0.8370 (t0) cc_final: 0.7794 (t0) REVERT: H 363 GLN cc_start: 0.7956 (mt0) cc_final: 0.7693 (mp10) REVERT: H 399 SER cc_start: 0.8370 (m) cc_final: 0.7983 (t) REVERT: H 417 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7922 (ttm170) REVERT: I 253 SER cc_start: 0.9292 (m) cc_final: 0.9001 (m) REVERT: I 410 ASN cc_start: 0.9255 (t0) cc_final: 0.8899 (t0) REVERT: I 430 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: J 167 VAL cc_start: 0.6834 (OUTLIER) cc_final: 0.6576 (m) REVERT: J 247 TYR cc_start: 0.7738 (m-10) cc_final: 0.7531 (m-10) REVERT: J 311 VAL cc_start: 0.8592 (t) cc_final: 0.8346 (p) REVERT: J 358 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7303 (mt-10) REVERT: J 372 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.8763 (p) REVERT: J 422 GLU cc_start: 0.7111 (tt0) cc_final: 0.6697 (tt0) REVERT: J 430 GLN cc_start: 0.6899 (mm-40) cc_final: 0.6682 (mm-40) REVERT: K 186 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7182 (tm) REVERT: K 272 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7210 (ttm-80) REVERT: K 358 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6594 (mp0) REVERT: K 419 VAL cc_start: 0.6431 (OUTLIER) cc_final: 0.6178 (t) REVERT: L 169 VAL cc_start: 0.6588 (OUTLIER) cc_final: 0.6335 (m) REVERT: L 175 GLU cc_start: 0.4706 (OUTLIER) cc_final: 0.1968 (tt0) REVERT: L 189 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6342 (mm-30) REVERT: L 273 LYS cc_start: 0.7184 (mtpt) cc_final: 0.6410 (mmtt) REVERT: L 330 LEU cc_start: 0.8556 (mt) cc_final: 0.8179 (mt) REVERT: L 351 ASP cc_start: 0.8354 (p0) cc_final: 0.7474 (t70) REVERT: L 417 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.5882 (mtm110) REVERT: L 430 GLN cc_start: 0.1482 (OUTLIER) cc_final: 0.0861 (tt0) REVERT: L 444 ARG cc_start: 0.6637 (ttp-110) cc_final: 0.6395 (ptm-80) REVERT: a 58 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7237 (tt0) outliers start: 220 outliers final: 130 residues processed: 724 average time/residue: 0.4396 time to fit residues: 499.9546 Evaluate side-chains 656 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 499 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 283 ILE Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 417 ARG Chi-restraints excluded: chain H residue 429 LYS Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 205 ILE Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 208 MET Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 276 ILE Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 283 ILE Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 417 ARG Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain L residue 430 GLN Chi-restraints excluded: chain L residue 436 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 311 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 316 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 264 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 HIS ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** D 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 GLN F 376 GLN G 180 GLN G 443 GLN H 410 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 378 GLN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 GLN L 367 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.110031 restraints weight = 40694.610| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.04 r_work: 0.3034 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29082 Z= 0.212 Angle : 0.624 9.216 39308 Z= 0.332 Chirality : 0.045 0.190 4568 Planarity : 0.004 0.047 5000 Dihedral : 7.887 81.774 4102 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.47 % Favored : 92.10 % Rotamer: Outliers : 7.68 % Allowed : 22.28 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3656 helix: -0.50 (0.18), residues: 784 sheet: -0.64 (0.18), residues: 884 loop : -1.09 (0.14), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 362 HIS 0.008 0.001 HIS J 279 PHE 0.017 0.002 PHE F 244 TYR 0.016 0.001 TYR I 392 ARG 0.006 0.001 ARG H 444 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 830) hydrogen bonds : angle 5.81228 ( 2268) covalent geometry : bond 0.00489 (29082) covalent geometry : angle 0.62407 (39308) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 503 time to evaluate : 3.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.8541 (tp) cc_final: 0.8193 (tp) REVERT: A 281 VAL cc_start: 0.9070 (t) cc_final: 0.8839 (t) REVERT: A 304 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8524 (p) REVERT: A 363 GLN cc_start: 0.8262 (mt0) cc_final: 0.7912 (mt0) REVERT: A 378 GLN cc_start: 0.8179 (pm20) cc_final: 0.7878 (pp30) REVERT: A 413 MET cc_start: 0.8915 (mtp) cc_final: 0.8663 (mtm) REVERT: A 422 GLU cc_start: 0.7676 (tt0) cc_final: 0.7043 (tt0) REVERT: B 204 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7263 (mptt) REVERT: B 240 LYS cc_start: 0.8663 (mttt) cc_final: 0.8389 (mttt) REVERT: B 267 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7697 (tp) REVERT: B 289 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8292 (p) REVERT: B 364 ASP cc_start: 0.6333 (OUTLIER) cc_final: 0.6054 (t70) REVERT: C 175 GLU cc_start: 0.6189 (mm-30) cc_final: 0.5417 (pt0) REVERT: C 211 GLU cc_start: 0.8218 (tt0) cc_final: 0.7837 (tt0) REVERT: C 279 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.8349 (m-70) REVERT: C 284 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: C 429 LYS cc_start: 0.5911 (tptp) cc_final: 0.5285 (tptt) REVERT: D 288 MET cc_start: 0.9125 (mmm) cc_final: 0.8776 (mmt) REVERT: D 362 TRP cc_start: 0.9230 (OUTLIER) cc_final: 0.7800 (m-90) REVERT: E 175 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8047 (mt-10) REVERT: E 197 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7431 (mm-30) REVERT: E 239 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9086 (mt) REVERT: E 426 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.6433 (mp10) REVERT: E 448 ASN cc_start: 0.9369 (OUTLIER) cc_final: 0.9092 (p0) REVERT: F 181 ARG cc_start: 0.8100 (mtp180) cc_final: 0.7702 (mtp85) REVERT: F 185 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7265 (t0) REVERT: F 233 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: F 265 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6976 (p90) REVERT: F 267 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8517 (mt) REVERT: F 425 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7789 (tpt90) REVERT: G 172 GLU cc_start: 0.4059 (OUTLIER) cc_final: 0.3105 (pt0) REVERT: G 183 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8221 (pt) REVERT: G 224 THR cc_start: 0.6533 (OUTLIER) cc_final: 0.6256 (p) REVERT: G 240 LYS cc_start: 0.7693 (tttp) cc_final: 0.7354 (tppt) REVERT: G 297 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.6985 (tttm) REVERT: G 305 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7161 (mm-30) REVERT: G 364 ASP cc_start: 0.8100 (m-30) cc_final: 0.7732 (m-30) REVERT: G 382 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.7987 (mm) REVERT: G 392 TYR cc_start: 0.7562 (m-80) cc_final: 0.7354 (m-80) REVERT: G 430 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.4968 (mp10) REVERT: H 186 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7459 (tm) REVERT: H 198 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: H 285 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7739 (mt-10) REVERT: H 359 ASP cc_start: 0.8269 (t0) cc_final: 0.7586 (t0) REVERT: H 363 GLN cc_start: 0.7878 (mt0) cc_final: 0.7662 (mp10) REVERT: H 399 SER cc_start: 0.8398 (m) cc_final: 0.7966 (t) REVERT: H 417 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8114 (ttm170) REVERT: I 253 SER cc_start: 0.9408 (m) cc_final: 0.9124 (m) REVERT: I 358 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7122 (mt-10) REVERT: I 430 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: J 167 VAL cc_start: 0.6830 (OUTLIER) cc_final: 0.6557 (m) REVERT: J 311 VAL cc_start: 0.8655 (t) cc_final: 0.8445 (p) REVERT: J 358 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7402 (mt-10) REVERT: J 422 GLU cc_start: 0.7487 (tt0) cc_final: 0.7158 (tt0) REVERT: K 186 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.6996 (tm) REVERT: K 358 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6783 (mp0) REVERT: K 376 GLN cc_start: 0.8160 (mt0) cc_final: 0.7934 (mt0) REVERT: K 415 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7555 (mtt-85) REVERT: K 425 ARG cc_start: 0.8123 (tpt170) cc_final: 0.7835 (tpt170) REVERT: L 175 GLU cc_start: 0.4893 (OUTLIER) cc_final: 0.2050 (tt0) REVERT: L 189 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6432 (mm-30) REVERT: L 273 LYS cc_start: 0.7258 (mtpt) cc_final: 0.6433 (mmtt) REVERT: L 330 LEU cc_start: 0.8676 (mt) cc_final: 0.8358 (mt) REVERT: L 351 ASP cc_start: 0.8236 (p0) cc_final: 0.7589 (t70) REVERT: L 417 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.6130 (mtm110) REVERT: L 444 ARG cc_start: 0.6528 (ttp-110) cc_final: 0.6235 (ttp80) REVERT: a 58 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7446 (tt0) outliers start: 237 outliers final: 169 residues processed: 672 average time/residue: 0.4081 time to fit residues: 428.0955 Evaluate side-chains 669 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 469 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 282 SER Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 425 ARG Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 293 SER Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 279 HIS Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 417 ARG Chi-restraints excluded: chain H residue 429 LYS Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 170 SER Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 285 GLU Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 378 GLN Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 186 LEU Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain J residue 270 LEU Chi-restraints excluded: chain J residue 277 GLU Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 347 ILE Chi-restraints excluded: chain J residue 349 SER Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain K residue 176 THR Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 207 THR Chi-restraints excluded: chain K residue 208 MET Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 231 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 293 SER Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 432 ASP Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 182 ILE Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 199 LEU Chi-restraints excluded: chain L residue 219 TRP Chi-restraints excluded: chain L residue 255 ILE Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 417 ARG Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 48 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.0970 chunk 331 optimal weight: 30.0000 chunk 180 optimal weight: 50.0000 chunk 199 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 247 optimal weight: 9.9990 chunk 10 optimal weight: 0.0770 chunk 4 optimal weight: 0.2980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 GLN ** H 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 410 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 438 GLN K 416 GLN K 438 GLN K 443 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 49 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.117130 restraints weight = 40520.753| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.14 r_work: 0.3141 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29082 Z= 0.106 Angle : 0.540 7.385 39308 Z= 0.289 Chirality : 0.042 0.164 4568 Planarity : 0.004 0.043 5000 Dihedral : 7.273 87.402 4098 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.70 % Favored : 93.00 % Rotamer: Outliers : 5.90 % Allowed : 24.58 % Favored : 69.52 % 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: -1.15 (0.14), residues: 3656 helix: -0.43 (0.18), residues: 788 sheet: -0.57 (0.17), residues: 875 loop : -0.93 (0.14), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 362 HIS 0.007 0.001 HIS L 279 PHE 0.011 0.001 PHE G 287 TYR 0.014 0.001 TYR E 392 ARG 0.007 0.001 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 830) hydrogen bonds : angle 5.51985 ( 2268) covalent geometry : bond 0.00221 (29082) covalent geometry : angle 0.53954 (39308) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 582 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 VAL cc_start: 0.8960 (t) cc_final: 0.8683 (m) REVERT: A 304 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8482 (p) REVERT: A 351 ASP cc_start: 0.7958 (t0) cc_final: 0.7626 (t0) REVERT: A 363 GLN cc_start: 0.8233 (mt0) cc_final: 0.7889 (mt0) REVERT: A 378 GLN cc_start: 0.8155 (pm20) cc_final: 0.7872 (pp30) REVERT: A 422 GLU cc_start: 0.7671 (tt0) cc_final: 0.6974 (tt0) REVERT: B 175 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 204 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6911 (mptt) REVERT: B 240 LYS cc_start: 0.8699 (mttt) cc_final: 0.8412 (mttt) REVERT: B 267 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7498 (tp) REVERT: B 351 ASP cc_start: 0.8231 (t0) cc_final: 0.7548 (t0) REVERT: C 175 GLU cc_start: 0.6217 (mm-30) cc_final: 0.5724 (pt0) REVERT: C 211 GLU cc_start: 0.8178 (tt0) cc_final: 0.7775 (mt-10) REVERT: C 279 HIS cc_start: 0.8684 (OUTLIER) cc_final: 0.8285 (m-70) REVERT: D 288 MET cc_start: 0.9010 (mmm) cc_final: 0.8459 (mmt) REVERT: D 311 VAL cc_start: 0.8906 (t) cc_final: 0.8530 (p) REVERT: E 197 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7302 (mm-30) REVERT: E 426 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.6502 (mp10) REVERT: E 448 ASN cc_start: 0.9160 (OUTLIER) cc_final: 0.8839 (p0) REVERT: F 185 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.6974 (t0) REVERT: F 265 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6948 (p90) REVERT: F 267 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8472 (mt) REVERT: G 172 GLU cc_start: 0.3865 (OUTLIER) cc_final: 0.3093 (pt0) REVERT: G 202 SER cc_start: 0.8850 (t) cc_final: 0.8586 (t) REVERT: G 240 LYS cc_start: 0.7725 (tttp) cc_final: 0.7362 (tppt) REVERT: G 261 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6385 (pt0) REVERT: G 273 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7180 (mtmt) REVERT: G 297 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7172 (tttm) REVERT: G 305 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7165 (mm-30) REVERT: G 319 SER cc_start: 0.7584 (t) cc_final: 0.7348 (m) REVERT: G 417 ARG cc_start: 0.7797 (ttm170) cc_final: 0.7211 (ttp-170) REVERT: G 430 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.5031 (mp10) REVERT: H 186 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7231 (tm) REVERT: H 236 LYS cc_start: 0.8236 (ptmt) cc_final: 0.6032 (mmmt) REVERT: H 285 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: H 359 ASP cc_start: 0.8205 (t0) cc_final: 0.7507 (t0) REVERT: H 363 GLN cc_start: 0.7964 (mt0) cc_final: 0.7618 (mp10) REVERT: I 253 SER cc_start: 0.9272 (m) cc_final: 0.8972 (m) REVERT: I 359 ASP cc_start: 0.8291 (t0) cc_final: 0.8056 (t0) REVERT: I 410 ASN cc_start: 0.9190 (t0) cc_final: 0.8777 (t0) REVERT: I 430 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: I 448 ASN cc_start: 0.8501 (p0) cc_final: 0.8215 (p0) REVERT: J 167 VAL cc_start: 0.6719 (OUTLIER) cc_final: 0.6415 (m) REVERT: J 184 ARG cc_start: 0.7376 (ptm160) cc_final: 0.6505 (ttp-110) REVERT: J 247 TYR cc_start: 0.7738 (m-10) cc_final: 0.7294 (m-80) REVERT: J 311 VAL cc_start: 0.8488 (t) cc_final: 0.8228 (p) REVERT: J 358 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7307 (mt-10) REVERT: J 359 ASP cc_start: 0.8287 (t0) cc_final: 0.7974 (t0) REVERT: J 422 GLU cc_start: 0.7205 (tt0) cc_final: 0.6915 (tt0) REVERT: K 186 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7124 (tm) REVERT: K 279 HIS cc_start: 0.7609 (OUTLIER) cc_final: 0.7077 (t-90) REVERT: K 287 PHE cc_start: 0.8114 (m-10) cc_final: 0.7875 (m-10) REVERT: K 358 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6655 (mp0) REVERT: K 399 SER cc_start: 0.7459 (m) cc_final: 0.7188 (m) REVERT: K 413 MET cc_start: 0.8271 (mtp) cc_final: 0.8064 (mtm) REVERT: K 422 GLU cc_start: 0.6222 (tt0) cc_final: 0.5941 (tt0) REVERT: K 425 ARG cc_start: 0.8046 (tpt170) cc_final: 0.7740 (tpt170) REVERT: L 169 VAL cc_start: 0.6521 (OUTLIER) cc_final: 0.6277 (m) REVERT: L 175 GLU cc_start: 0.4861 (OUTLIER) cc_final: 0.2069 (tt0) REVERT: L 186 LEU cc_start: 0.7871 (tp) cc_final: 0.7021 (mp) REVERT: L 249 LEU cc_start: 0.7144 (tp) cc_final: 0.6844 (tp) REVERT: L 273 LYS cc_start: 0.7288 (mtpt) cc_final: 0.6523 (mmtt) REVERT: L 315 LYS cc_start: 0.7630 (ttpp) cc_final: 0.7402 (ptmm) REVERT: L 330 LEU cc_start: 0.8566 (mt) cc_final: 0.8243 (mt) REVERT: L 351 ASP cc_start: 0.8222 (p0) cc_final: 0.7527 (t70) REVERT: L 444 ARG cc_start: 0.6705 (ttp-110) cc_final: 0.6385 (ptm-80) REVERT: a 58 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7344 (tt0) outliers start: 182 outliers final: 110 residues processed: 712 average time/residue: 0.5303 time to fit residues: 596.0755 Evaluate side-chains 643 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 511 time to evaluate : 4.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 285 GLU Chi-restraints excluded: chain H residue 429 LYS Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 279 HIS Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 283 ILE Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 20 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 10 optimal weight: 3.9990 chunk 283 optimal weight: 8.9990 chunk 311 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 319 optimal weight: 0.0070 chunk 34 optimal weight: 4.9990 overall best weight: 2.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN A 438 GLN B 443 GLN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 GLN G 180 GLN G 416 GLN G 443 GLN H 243 HIS H 410 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.135620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109753 restraints weight = 41016.661| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.01 r_work: 0.3061 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29082 Z= 0.200 Angle : 0.594 6.776 39308 Z= 0.314 Chirality : 0.045 0.210 4568 Planarity : 0.004 0.039 5000 Dihedral : 7.112 84.313 4079 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.03 % Favored : 92.70 % Rotamer: Outliers : 5.90 % Allowed : 24.64 % Favored : 69.46 % 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: -1.17 (0.14), residues: 3656 helix: -0.27 (0.18), residues: 763 sheet: -0.60 (0.17), residues: 890 loop : -1.01 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 219 HIS 0.010 0.001 HIS D 279 PHE 0.016 0.002 PHE E 265 TYR 0.013 0.001 TYR F 392 ARG 0.006 0.001 ARG F 423 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 830) hydrogen bonds : angle 5.61438 ( 2268) covalent geometry : bond 0.00465 (29082) covalent geometry : angle 0.59362 (39308) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 507 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.8608 (tp) cc_final: 0.8302 (tp) REVERT: A 351 ASP cc_start: 0.7937 (t0) cc_final: 0.7732 (t0) REVERT: A 363 GLN cc_start: 0.8225 (mt0) cc_final: 0.7875 (mt0) REVERT: A 378 GLN cc_start: 0.8156 (pm20) cc_final: 0.7900 (pp30) REVERT: A 422 GLU cc_start: 0.7841 (tt0) cc_final: 0.7169 (tt0) REVERT: B 204 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7321 (mptt) REVERT: B 240 LYS cc_start: 0.8668 (mttt) cc_final: 0.8402 (mttt) REVERT: B 264 ILE cc_start: 0.6936 (mp) cc_final: 0.6729 (mp) REVERT: B 267 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7689 (tp) REVERT: B 350 MET cc_start: 0.8155 (ttt) cc_final: 0.7856 (ttt) REVERT: B 431 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8054 (ptp-170) REVERT: C 175 GLU cc_start: 0.6263 (mm-30) cc_final: 0.5308 (pt0) REVERT: C 211 GLU cc_start: 0.8255 (tt0) cc_final: 0.7826 (tt0) REVERT: C 279 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.8362 (m-70) REVERT: C 284 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: C 391 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7166 (mt-10) REVERT: C 429 LYS cc_start: 0.5627 (tptp) cc_final: 0.5072 (tptt) REVERT: D 288 MET cc_start: 0.9016 (mmm) cc_final: 0.8715 (mmt) REVERT: D 362 TRP cc_start: 0.9211 (OUTLIER) cc_final: 0.7833 (m-90) REVERT: E 197 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7305 (mm-30) REVERT: E 426 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.6519 (mp10) REVERT: E 448 ASN cc_start: 0.9364 (OUTLIER) cc_final: 0.9081 (p0) REVERT: F 185 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7181 (t0) REVERT: F 265 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6514 (p90) REVERT: G 172 GLU cc_start: 0.3983 (OUTLIER) cc_final: 0.3122 (pt0) REVERT: G 177 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8392 (pt) REVERT: G 224 THR cc_start: 0.6439 (OUTLIER) cc_final: 0.6190 (p) REVERT: G 240 LYS cc_start: 0.7715 (tttp) cc_final: 0.7347 (tppt) REVERT: G 297 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6760 (tttm) REVERT: G 305 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7065 (mm-30) REVERT: G 319 SER cc_start: 0.7700 (t) cc_final: 0.7418 (m) REVERT: G 364 ASP cc_start: 0.8127 (m-30) cc_final: 0.7741 (m-30) REVERT: G 392 TYR cc_start: 0.7469 (m-80) cc_final: 0.7215 (m-80) REVERT: G 417 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7756 (ttp-170) REVERT: G 430 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.4844 (mp10) REVERT: G 435 TYR cc_start: 0.6657 (m-80) cc_final: 0.5718 (m-80) REVERT: H 186 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7217 (tm) REVERT: H 291 ASP cc_start: 0.8204 (p0) cc_final: 0.7528 (p0) REVERT: H 359 ASP cc_start: 0.8147 (t0) cc_final: 0.7276 (t0) REVERT: H 363 GLN cc_start: 0.7947 (mt0) cc_final: 0.7647 (mp10) REVERT: H 399 SER cc_start: 0.8251 (m) cc_final: 0.7898 (t) REVERT: H 429 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8059 (mtmt) REVERT: I 208 MET cc_start: 0.9025 (ptp) cc_final: 0.8753 (ptm) REVERT: I 253 SER cc_start: 0.9397 (m) cc_final: 0.9106 (m) REVERT: I 410 ASN cc_start: 0.9296 (t0) cc_final: 0.8933 (t0) REVERT: I 430 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7645 (mp10) REVERT: J 167 VAL cc_start: 0.6854 (OUTLIER) cc_final: 0.6561 (m) REVERT: J 247 TYR cc_start: 0.7807 (m-10) cc_final: 0.7359 (m-80) REVERT: J 311 VAL cc_start: 0.8635 (t) cc_final: 0.8402 (p) REVERT: J 358 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7352 (mt-10) REVERT: K 186 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7131 (tm) REVERT: K 358 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6935 (mp0) REVERT: K 359 ASP cc_start: 0.8384 (t0) cc_final: 0.7936 (t70) REVERT: K 399 SER cc_start: 0.8109 (m) cc_final: 0.7903 (m) REVERT: K 425 ARG cc_start: 0.8090 (tpt170) cc_final: 0.7773 (tpt170) REVERT: L 175 GLU cc_start: 0.5103 (OUTLIER) cc_final: 0.2274 (tt0) REVERT: L 208 MET cc_start: 0.7103 (mtp) cc_final: 0.6469 (mtp) REVERT: L 249 LEU cc_start: 0.7202 (tp) cc_final: 0.6841 (tp) REVERT: L 273 LYS cc_start: 0.7277 (mtpt) cc_final: 0.6506 (mmtt) REVERT: L 295 LYS cc_start: 0.7795 (mptt) cc_final: 0.7269 (ptpp) REVERT: L 330 LEU cc_start: 0.8658 (mt) cc_final: 0.8357 (mt) REVERT: L 351 ASP cc_start: 0.8213 (p0) cc_final: 0.7584 (t70) REVERT: L 444 ARG cc_start: 0.6767 (ttp-110) cc_final: 0.6076 (ptm160) REVERT: a 58 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7493 (tt0) outliers start: 182 outliers final: 141 residues processed: 638 average time/residue: 0.4205 time to fit residues: 422.4695 Evaluate side-chains 658 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 495 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 188 LYS Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 362 TRP Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 429 LYS Chi-restraints excluded: chain H residue 437 THR Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain H residue 454 THR Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 285 GLU Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain I residue 375 LEU Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 430 GLN Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 208 MET Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 277 GLU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 219 TRP Chi-restraints excluded: chain L residue 283 ILE Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 20 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 203 optimal weight: 0.8980 chunk 211 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 253 optimal weight: 0.6980 chunk 258 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 347 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN ** L 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114545 restraints weight = 40857.294| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.02 r_work: 0.3118 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29082 Z= 0.122 Angle : 0.536 7.433 39308 Z= 0.285 Chirality : 0.042 0.194 4568 Planarity : 0.003 0.036 5000 Dihedral : 6.822 87.829 4077 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.81 % Favored : 92.97 % Rotamer: Outliers : 5.51 % Allowed : 25.62 % Favored : 68.87 % 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: -1.11 (0.14), residues: 3656 helix: -0.42 (0.18), residues: 799 sheet: -0.56 (0.18), residues: 858 loop : -0.89 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 219 HIS 0.007 0.001 HIS D 279 PHE 0.015 0.001 PHE G 244 TYR 0.014 0.001 TYR F 392 ARG 0.007 0.001 ARG J 272 Details of bonding type rmsd hydrogen bonds : bond 0.03218 ( 830) hydrogen bonds : angle 5.45097 ( 2268) covalent geometry : bond 0.00268 (29082) covalent geometry : angle 0.53564 (39308) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 548 time to evaluate : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 VAL cc_start: 0.8979 (t) cc_final: 0.8707 (m) REVERT: A 304 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8519 (p) REVERT: A 363 GLN cc_start: 0.8205 (mt0) cc_final: 0.7912 (mt0) REVERT: A 422 GLU cc_start: 0.8113 (tt0) cc_final: 0.7418 (tt0) REVERT: B 204 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7041 (mptt) REVERT: B 240 LYS cc_start: 0.8737 (mttt) cc_final: 0.8438 (mttt) REVERT: B 267 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8062 (tp) REVERT: B 277 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8026 (tm-30) REVERT: B 351 ASP cc_start: 0.8193 (t0) cc_final: 0.7615 (t0) REVERT: C 175 GLU cc_start: 0.6312 (mm-30) cc_final: 0.5389 (pt0) REVERT: C 279 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8345 (m-70) REVERT: C 284 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: C 444 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8351 (ptt180) REVERT: D 288 MET cc_start: 0.9016 (mmm) cc_final: 0.8616 (mmt) REVERT: D 311 VAL cc_start: 0.9067 (t) cc_final: 0.8729 (p) REVERT: D 443 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8217 (mm-40) REVERT: E 350 MET cc_start: 0.8382 (tpp) cc_final: 0.7837 (tpp) REVERT: E 426 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.6384 (mp10) REVERT: E 448 ASN cc_start: 0.9273 (OUTLIER) cc_final: 0.8945 (p0) REVERT: F 185 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7010 (t0) REVERT: F 233 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: F 265 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6413 (p90) REVERT: G 172 GLU cc_start: 0.3836 (OUTLIER) cc_final: 0.3065 (pt0) REVERT: G 189 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6787 (mm-30) REVERT: G 204 LYS cc_start: 0.7214 (ttpt) cc_final: 0.5752 (mmtt) REVERT: G 240 LYS cc_start: 0.7700 (tttp) cc_final: 0.7385 (tppt) REVERT: G 273 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7182 (mtmt) REVERT: G 297 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.6800 (tttm) REVERT: G 305 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7078 (mm-30) REVERT: G 319 SER cc_start: 0.7700 (t) cc_final: 0.7394 (m) REVERT: G 392 TYR cc_start: 0.7263 (m-80) cc_final: 0.7021 (m-80) REVERT: G 430 GLN cc_start: 0.6031 (OUTLIER) cc_final: 0.4880 (mp10) REVERT: G 435 TYR cc_start: 0.6802 (m-80) cc_final: 0.5892 (m-80) REVERT: H 186 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7000 (tm) REVERT: H 291 ASP cc_start: 0.8185 (p0) cc_final: 0.7616 (p0) REVERT: H 306 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: H 359 ASP cc_start: 0.8040 (t0) cc_final: 0.7221 (t0) REVERT: H 399 SER cc_start: 0.8098 (m) cc_final: 0.7747 (t) REVERT: H 429 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8101 (mtmt) REVERT: I 208 MET cc_start: 0.9037 (ptp) cc_final: 0.8697 (ptm) REVERT: I 253 SER cc_start: 0.9307 (m) cc_final: 0.9003 (m) REVERT: I 329 LYS cc_start: 0.8509 (mmtp) cc_final: 0.8309 (mmtp) REVERT: I 358 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7366 (mt-10) REVERT: I 410 ASN cc_start: 0.9245 (t0) cc_final: 0.8825 (t0) REVERT: I 448 ASN cc_start: 0.8553 (p0) cc_final: 0.8248 (p0) REVERT: J 167 VAL cc_start: 0.6794 (OUTLIER) cc_final: 0.6512 (m) REVERT: J 181 ARG cc_start: 0.8258 (ttp80) cc_final: 0.8025 (ttp80) REVERT: J 184 ARG cc_start: 0.7223 (ptm160) cc_final: 0.6558 (ttp-170) REVERT: J 197 GLU cc_start: 0.8065 (mp0) cc_final: 0.7490 (mp0) REVERT: J 247 TYR cc_start: 0.7765 (m-10) cc_final: 0.7336 (m-80) REVERT: J 311 VAL cc_start: 0.8526 (t) cc_final: 0.8266 (p) REVERT: J 358 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7229 (mt-10) REVERT: J 359 ASP cc_start: 0.8413 (t0) cc_final: 0.8034 (t0) REVERT: K 186 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7037 (tm) REVERT: K 201 MET cc_start: 0.8021 (mtm) cc_final: 0.7447 (ptp) REVERT: K 342 SER cc_start: 0.8209 (p) cc_final: 0.7994 (t) REVERT: K 358 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6788 (mp0) REVERT: K 359 ASP cc_start: 0.8278 (t0) cc_final: 0.7803 (t70) REVERT: K 390 SER cc_start: 0.8786 (t) cc_final: 0.8054 (p) REVERT: K 425 ARG cc_start: 0.8062 (tpt170) cc_final: 0.7742 (tpt170) REVERT: L 175 GLU cc_start: 0.5076 (OUTLIER) cc_final: 0.2212 (tt0) REVERT: L 208 MET cc_start: 0.7433 (mtp) cc_final: 0.6642 (mtp) REVERT: L 273 LYS cc_start: 0.7226 (mtpt) cc_final: 0.6484 (mmtt) REVERT: L 295 LYS cc_start: 0.7730 (mptt) cc_final: 0.7258 (ptpp) REVERT: L 306 ASP cc_start: 0.6514 (m-30) cc_final: 0.5816 (m-30) REVERT: L 330 LEU cc_start: 0.8641 (mt) cc_final: 0.8351 (mt) REVERT: L 351 ASP cc_start: 0.8185 (p0) cc_final: 0.7523 (t70) REVERT: L 444 ARG cc_start: 0.6670 (ttp-110) cc_final: 0.6453 (ptm-80) REVERT: a 58 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7504 (tt0) outliers start: 170 outliers final: 120 residues processed: 671 average time/residue: 0.3995 time to fit residues: 424.9552 Evaluate side-chains 654 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 511 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 443 GLN Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 429 LYS Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 257 ASP Chi-restraints excluded: chain J residue 265 PHE Chi-restraints excluded: chain J residue 277 GLU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 375 LEU Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 20 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 94 optimal weight: 2.9990 chunk 275 optimal weight: 8.9990 chunk 304 optimal weight: 20.0000 chunk 101 optimal weight: 0.3980 chunk 116 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 180 optimal weight: 30.0000 chunk 77 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 300 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN E 416 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 ASN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 GLN ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 363 GLN L 438 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.114045 restraints weight = 40810.458| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.04 r_work: 0.3117 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29082 Z= 0.136 Angle : 0.549 8.131 39308 Z= 0.292 Chirality : 0.043 0.210 4568 Planarity : 0.004 0.035 5000 Dihedral : 6.698 86.307 4074 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.11 % Favored : 92.70 % Rotamer: Outliers : 5.25 % Allowed : 26.23 % Favored : 68.51 % 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: -1.08 (0.14), residues: 3656 helix: -0.39 (0.18), residues: 799 sheet: -0.51 (0.17), residues: 894 loop : -0.88 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 362 HIS 0.010 0.001 HIS A 279 PHE 0.019 0.001 PHE K 287 TYR 0.044 0.001 TYR C 392 ARG 0.007 0.001 ARG J 272 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 830) hydrogen bonds : angle 5.43225 ( 2268) covalent geometry : bond 0.00307 (29082) covalent geometry : angle 0.54863 (39308) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 518 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.8506 (tp) cc_final: 0.8234 (tp) REVERT: A 304 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8661 (p) REVERT: A 363 GLN cc_start: 0.8216 (mt0) cc_final: 0.7913 (mt0) REVERT: A 422 GLU cc_start: 0.7974 (tt0) cc_final: 0.7276 (tt0) REVERT: B 204 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7082 (mptt) REVERT: B 240 LYS cc_start: 0.8715 (mttt) cc_final: 0.8438 (mttt) REVERT: B 267 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8052 (tp) REVERT: B 277 GLU cc_start: 0.8238 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 351 ASP cc_start: 0.8167 (t0) cc_final: 0.7619 (t0) REVERT: B 431 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8080 (ptp-170) REVERT: C 175 GLU cc_start: 0.6425 (mm-30) cc_final: 0.5345 (pt0) REVERT: C 211 GLU cc_start: 0.8184 (tt0) cc_final: 0.7946 (tt0) REVERT: C 279 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8304 (m-70) REVERT: C 444 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8337 (ptt90) REVERT: D 288 MET cc_start: 0.8967 (mmm) cc_final: 0.8634 (tpp) REVERT: D 311 VAL cc_start: 0.9111 (t) cc_final: 0.8792 (p) REVERT: E 239 LEU cc_start: 0.8990 (mp) cc_final: 0.8789 (mt) REVERT: E 350 MET cc_start: 0.8455 (tpp) cc_final: 0.7886 (tpp) REVERT: E 426 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.6482 (mp10) REVERT: E 448 ASN cc_start: 0.9328 (OUTLIER) cc_final: 0.8998 (p0) REVERT: F 181 ARG cc_start: 0.7946 (mtp85) cc_final: 0.7693 (ttt-90) REVERT: F 185 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7037 (t0) REVERT: F 233 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: F 265 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6470 (p90) REVERT: G 172 GLU cc_start: 0.3913 (OUTLIER) cc_final: 0.3132 (pt0) REVERT: G 189 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6794 (mm-30) REVERT: G 204 LYS cc_start: 0.7146 (ttpt) cc_final: 0.5761 (mmtt) REVERT: G 224 THR cc_start: 0.6380 (OUTLIER) cc_final: 0.6137 (p) REVERT: G 240 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7485 (tppt) REVERT: G 273 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7225 (mtmt) REVERT: G 297 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.6836 (tttm) REVERT: G 305 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7148 (mm-30) REVERT: G 319 SER cc_start: 0.7723 (t) cc_final: 0.7399 (m) REVERT: G 392 TYR cc_start: 0.7275 (m-80) cc_final: 0.7044 (m-80) REVERT: G 430 GLN cc_start: 0.5927 (OUTLIER) cc_final: 0.4836 (mp10) REVERT: G 435 TYR cc_start: 0.6867 (m-80) cc_final: 0.5912 (m-80) REVERT: G 445 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.6529 (m-10) REVERT: H 186 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6989 (tm) REVERT: H 291 ASP cc_start: 0.8176 (p0) cc_final: 0.7625 (p0) REVERT: H 306 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7535 (m-30) REVERT: H 336 ARG cc_start: 0.8354 (ptp-170) cc_final: 0.7948 (ptp90) REVERT: H 359 ASP cc_start: 0.7652 (t0) cc_final: 0.7416 (t0) REVERT: H 399 SER cc_start: 0.8106 (m) cc_final: 0.7758 (t) REVERT: H 429 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8164 (mtmt) REVERT: I 208 MET cc_start: 0.9035 (ptp) cc_final: 0.8741 (ptm) REVERT: I 253 SER cc_start: 0.9371 (m) cc_final: 0.9071 (m) REVERT: I 410 ASN cc_start: 0.9256 (t0) cc_final: 0.8836 (t0) REVERT: I 448 ASN cc_start: 0.8410 (p0) cc_final: 0.8080 (p0) REVERT: J 167 VAL cc_start: 0.6666 (OUTLIER) cc_final: 0.6378 (m) REVERT: J 197 GLU cc_start: 0.8032 (mp0) cc_final: 0.7441 (mp0) REVERT: J 247 TYR cc_start: 0.7795 (m-10) cc_final: 0.7355 (m-80) REVERT: J 277 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: J 311 VAL cc_start: 0.8529 (t) cc_final: 0.8282 (p) REVERT: J 359 ASP cc_start: 0.8440 (t0) cc_final: 0.8092 (t0) REVERT: K 186 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6835 (tm) REVERT: K 201 MET cc_start: 0.7995 (mtm) cc_final: 0.7564 (ptp) REVERT: K 358 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6634 (mp0) REVERT: K 359 ASP cc_start: 0.8245 (t0) cc_final: 0.7835 (t70) REVERT: K 390 SER cc_start: 0.8869 (t) cc_final: 0.8162 (p) REVERT: K 417 ARG cc_start: 0.7637 (ttm170) cc_final: 0.7425 (ttp80) REVERT: K 425 ARG cc_start: 0.8054 (tpt170) cc_final: 0.7713 (tpt170) REVERT: L 175 GLU cc_start: 0.5052 (OUTLIER) cc_final: 0.2210 (tt0) REVERT: L 181 ARG cc_start: 0.6283 (ttp-170) cc_final: 0.5955 (ttp80) REVERT: L 273 LYS cc_start: 0.7240 (mtpt) cc_final: 0.6591 (mmtt) REVERT: L 295 LYS cc_start: 0.7700 (mptt) cc_final: 0.7208 (ptpp) REVERT: L 306 ASP cc_start: 0.6687 (m-30) cc_final: 0.6045 (m-30) REVERT: L 330 LEU cc_start: 0.8648 (mt) cc_final: 0.8387 (mt) REVERT: L 351 ASP cc_start: 0.8094 (p0) cc_final: 0.7496 (t70) REVERT: L 444 ARG cc_start: 0.6580 (ttp-110) cc_final: 0.6164 (ptm-80) REVERT: a 58 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7516 (tt0) outliers start: 162 outliers final: 117 residues processed: 627 average time/residue: 0.4399 time to fit residues: 440.1591 Evaluate side-chains 642 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 499 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 443 GLN Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 445 TYR Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 429 LYS Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 257 ASP Chi-restraints excluded: chain J residue 277 GLU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 20 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 302 optimal weight: 7.9990 chunk 326 optimal weight: 7.9990 chunk 324 optimal weight: 0.4980 chunk 40 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 352 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 256 optimal weight: 8.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 GLN B 443 GLN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 GLN H 367 GLN ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.109397 restraints weight = 41224.211| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.03 r_work: 0.3032 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29082 Z= 0.215 Angle : 0.617 8.574 39308 Z= 0.325 Chirality : 0.045 0.244 4568 Planarity : 0.004 0.037 5000 Dihedral : 6.950 85.317 4074 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.88 % Favored : 91.93 % Rotamer: Outliers : 5.03 % Allowed : 26.65 % Favored : 68.32 % 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: -1.12 (0.14), residues: 3656 helix: -0.24 (0.18), residues: 769 sheet: -0.54 (0.18), residues: 862 loop : -0.99 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 362 HIS 0.010 0.001 HIS D 279 PHE 0.032 0.002 PHE K 287 TYR 0.027 0.002 TYR C 392 ARG 0.007 0.001 ARG G 272 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 830) hydrogen bonds : angle 5.61678 ( 2268) covalent geometry : bond 0.00503 (29082) covalent geometry : angle 0.61674 (39308) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 500 time to evaluate : 3.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8554 (p) REVERT: A 363 GLN cc_start: 0.8264 (mt0) cc_final: 0.7965 (mt0) REVERT: A 422 GLU cc_start: 0.8078 (tt0) cc_final: 0.7524 (tt0) REVERT: A 429 LYS cc_start: 0.7748 (mtmt) cc_final: 0.6505 (tptt) REVERT: B 204 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7344 (mptt) REVERT: B 240 LYS cc_start: 0.8724 (mttt) cc_final: 0.8451 (mttt) REVERT: B 267 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8107 (tp) REVERT: B 277 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8088 (tm-30) REVERT: B 351 ASP cc_start: 0.7967 (t0) cc_final: 0.7489 (t0) REVERT: B 431 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8027 (ptp-170) REVERT: C 175 GLU cc_start: 0.6468 (mm-30) cc_final: 0.5118 (pt0) REVERT: C 211 GLU cc_start: 0.8214 (tt0) cc_final: 0.7965 (tt0) REVERT: C 279 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8319 (m-70) REVERT: C 429 LYS cc_start: 0.5950 (tptp) cc_final: 0.5429 (tptt) REVERT: C 444 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7941 (ptt90) REVERT: D 288 MET cc_start: 0.8917 (mmm) cc_final: 0.8532 (tpp) REVERT: E 426 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.6582 (mp10) REVERT: E 448 ASN cc_start: 0.9432 (OUTLIER) cc_final: 0.9100 (p0) REVERT: F 185 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7173 (t0) REVERT: F 233 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: F 265 PHE cc_start: 0.7433 (OUTLIER) cc_final: 0.6745 (p90) REVERT: G 172 GLU cc_start: 0.3873 (OUTLIER) cc_final: 0.3049 (pt0) REVERT: G 189 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6862 (mm-30) REVERT: G 204 LYS cc_start: 0.7208 (ttpt) cc_final: 0.5751 (mmtt) REVERT: G 240 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7428 (tppt) REVERT: G 271 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7741 (tt) REVERT: G 297 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.6797 (tttm) REVERT: G 305 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7246 (mm-30) REVERT: G 392 TYR cc_start: 0.7679 (m-80) cc_final: 0.7237 (m-80) REVERT: G 430 GLN cc_start: 0.5991 (OUTLIER) cc_final: 0.4884 (mp10) REVERT: G 435 TYR cc_start: 0.6914 (m-80) cc_final: 0.5912 (m-80) REVERT: H 186 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7155 (tm) REVERT: H 198 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: H 291 ASP cc_start: 0.8169 (p0) cc_final: 0.7598 (p0) REVERT: H 306 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: H 359 ASP cc_start: 0.7642 (t0) cc_final: 0.7371 (t70) REVERT: H 399 SER cc_start: 0.8205 (m) cc_final: 0.7853 (t) REVERT: H 429 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8262 (mtmt) REVERT: I 253 SER cc_start: 0.9393 (m) cc_final: 0.9097 (m) REVERT: I 329 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8328 (mmtp) REVERT: I 410 ASN cc_start: 0.9307 (t0) cc_final: 0.8910 (t0) REVERT: J 167 VAL cc_start: 0.6695 (OUTLIER) cc_final: 0.6389 (m) REVERT: J 184 ARG cc_start: 0.7390 (ptm160) cc_final: 0.6735 (ttp-170) REVERT: J 211 GLU cc_start: 0.8594 (tt0) cc_final: 0.8308 (mt-10) REVERT: J 233 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8102 (mt-10) REVERT: J 247 TYR cc_start: 0.7868 (m-10) cc_final: 0.7452 (m-10) REVERT: J 311 VAL cc_start: 0.8570 (t) cc_final: 0.8338 (p) REVERT: K 186 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.6943 (tm) REVERT: K 201 MET cc_start: 0.8000 (mtm) cc_final: 0.7526 (ptp) REVERT: K 277 GLU cc_start: 0.6668 (pt0) cc_final: 0.6435 (pt0) REVERT: K 358 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6793 (mp0) REVERT: K 359 ASP cc_start: 0.8276 (t0) cc_final: 0.7882 (t70) REVERT: K 422 GLU cc_start: 0.5388 (tt0) cc_final: 0.5160 (tt0) REVERT: K 425 ARG cc_start: 0.8055 (tpt170) cc_final: 0.7696 (tpt170) REVERT: L 175 GLU cc_start: 0.5106 (OUTLIER) cc_final: 0.2259 (tt0) REVERT: L 209 LEU cc_start: 0.6579 (mt) cc_final: 0.6246 (mp) REVERT: L 249 LEU cc_start: 0.7453 (tp) cc_final: 0.7209 (tp) REVERT: L 273 LYS cc_start: 0.7225 (mtpt) cc_final: 0.6469 (mmtt) REVERT: L 295 LYS cc_start: 0.7757 (mptt) cc_final: 0.7242 (ptpp) REVERT: L 297 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7780 (ttpt) REVERT: L 306 ASP cc_start: 0.6852 (m-30) cc_final: 0.6229 (m-30) REVERT: L 313 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: L 330 LEU cc_start: 0.8657 (mt) cc_final: 0.8423 (mt) REVERT: L 351 ASP cc_start: 0.8169 (p0) cc_final: 0.7467 (t70) REVERT: L 353 TYR cc_start: 0.8122 (t80) cc_final: 0.7921 (t80) REVERT: L 444 ARG cc_start: 0.6590 (ttp-110) cc_final: 0.6233 (ptm-80) REVERT: a 58 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7505 (tt0) outliers start: 155 outliers final: 124 residues processed: 613 average time/residue: 0.4033 time to fit residues: 390.1535 Evaluate side-chains 632 residues out of total 3084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 483 time to evaluate : 3.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 304 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 430 GLN Chi-restraints excluded: chain B residue 431 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 279 HIS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 228 ASP Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 295 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 367 GLN Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 426 GLN Chi-restraints excluded: chain E residue 438 GLN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain F residue 265 PHE Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 GLN Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 197 GLU Chi-restraints excluded: chain G residue 211 GLU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 240 LYS Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 273 LYS Chi-restraints excluded: chain G residue 297 LYS Chi-restraints excluded: chain G residue 304 SER Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain G residue 406 VAL Chi-restraints excluded: chain G residue 409 ASP Chi-restraints excluded: chain G residue 419 VAL Chi-restraints excluded: chain G residue 430 GLN Chi-restraints excluded: chain G residue 440 VAL Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain H residue 163 GLN Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 182 ILE Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 229 THR Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain H residue 270 LEU Chi-restraints excluded: chain H residue 273 LYS Chi-restraints excluded: chain H residue 283 ILE Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 429 LYS Chi-restraints excluded: chain H residue 450 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 283 ILE Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 362 TRP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 191 VAL Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 229 THR Chi-restraints excluded: chain J residue 277 GLU Chi-restraints excluded: chain J residue 283 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 368 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 391 GLU Chi-restraints excluded: chain J residue 419 VAL Chi-restraints excluded: chain K residue 186 LEU Chi-restraints excluded: chain K residue 191 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 256 THR Chi-restraints excluded: chain K residue 272 ARG Chi-restraints excluded: chain K residue 356 LEU Chi-restraints excluded: chain K residue 388 VAL Chi-restraints excluded: chain L residue 175 GLU Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 309 LYS Chi-restraints excluded: chain L residue 313 GLU Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 350 MET Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 VAL Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain b residue 20 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 172 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 255 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 283 optimal weight: 2.9990 chunk 354 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 376 GLN ** K 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.132816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.107423 restraints weight = 41077.882| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.05 r_work: 0.3010 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 29082 Z= 0.237 Angle : 0.633 8.547 39308 Z= 0.333 Chirality : 0.046 0.271 4568 Planarity : 0.004 0.046 5000 Dihedral : 7.061 83.714 4073 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.93 % Favored : 91.88 % Rotamer: Outliers : 5.51 % Allowed : 26.17 % Favored : 68.32 % 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: -1.28 (0.13), residues: 3656 helix: -0.41 (0.18), residues: 820 sheet: -0.58 (0.18), residues: 863 loop : -1.12 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 362 HIS 0.009 0.002 HIS D 279 PHE 0.029 0.002 PHE K 287 TYR 0.022 0.002 TYR C 392 ARG 0.007 0.001 ARG G 272 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 830) hydrogen bonds : angle 5.73478 ( 2268) covalent geometry : bond 0.00554 (29082) covalent geometry : angle 0.63258 (39308) =============================================================================== Job complete usr+sys time: 18957.66 seconds wall clock time: 326 minutes 37.02 seconds (19597.02 seconds total)