Starting phenix.real_space_refine on Thu Mar 5 05:29:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o1n_0593/03_2026/6o1n_0593.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o1n_0593/03_2026/6o1n_0593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o1n_0593/03_2026/6o1n_0593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o1n_0593/03_2026/6o1n_0593.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o1n_0593/03_2026/6o1n_0593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o1n_0593/03_2026/6o1n_0593.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.074 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 140 5.16 5 C 12660 2.51 5 N 3320 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19608 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Restraints were copied for chains: B, C, D Time building chain proxies: 4.17, per 1000 atoms: 0.21 Number of scatterers: 19608 At special positions: 0 Unit cell: (134.493, 132.375, 124.962, 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 140 16.00 O 3488 8.00 N 3320 7.00 C 12660 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: 1.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 4 sheets defined 55.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.649A pdb=" N ASP A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.594A pdb=" N ALA A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.608A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.613A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.064A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.547A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 205' Processing helix chain 'A' and resid 208 through 211 removed outlier: 3.802A pdb=" N PHE A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 212 through 222 removed outlier: 3.883A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.645A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.929A pdb=" N GLN A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.814A pdb=" N VAL A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.564A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.643A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.633A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 406 through 411 removed outlier: 4.139A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 removed outlier: 3.616A pdb=" N ALA A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.504A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 removed outlier: 4.275A pdb=" N MET A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 504 through 512 removed outlier: 3.509A pdb=" N HIS A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.024A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 581 removed outlier: 3.562A pdb=" N PHE A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.649A pdb=" N ASP B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.594A pdb=" N ALA B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.608A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.612A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.064A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.548A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 205' Processing helix chain 'B' and resid 208 through 211 removed outlier: 3.802A pdb=" N PHE B 211 " --> pdb=" O ASN B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 211' Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.882A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.646A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.928A pdb=" N GLN B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.814A pdb=" N VAL B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.564A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.643A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.634A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.139A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 removed outlier: 3.616A pdb=" N ALA B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.504A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 4.276A pdb=" N MET B 466 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.510A pdb=" N HIS B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.024A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 removed outlier: 3.561A pdb=" N PHE B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.649A pdb=" N ASP C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 38 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.594A pdb=" N ALA C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.608A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.613A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.064A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.548A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 205' Processing helix chain 'C' and resid 208 through 211 removed outlier: 3.801A pdb=" N PHE C 211 " --> pdb=" O ASN C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 212 through 222 removed outlier: 3.881A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.645A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.929A pdb=" N GLN C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.813A pdb=" N VAL C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.565A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.644A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 removed outlier: 3.633A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 406 through 411 removed outlier: 4.139A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 removed outlier: 3.615A pdb=" N ALA C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 removed outlier: 3.503A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 removed outlier: 4.274A pdb=" N MET C 466 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.510A pdb=" N HIS C 509 " --> pdb=" O ALA C 505 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 533 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.023A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 581 removed outlier: 3.562A pdb=" N PHE C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 47 removed outlier: 3.648A pdb=" N ASP D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 36 " --> pdb=" O TYR D 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.595A pdb=" N ALA D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.609A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.613A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.065A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.547A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 205' Processing helix chain 'D' and resid 208 through 211 removed outlier: 3.802A pdb=" N PHE D 211 " --> pdb=" O ASN D 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 211' Processing helix chain 'D' and resid 212 through 222 removed outlier: 3.883A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.646A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 249 " --> pdb=" O LYS D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 removed outlier: 3.928A pdb=" N GLN D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.814A pdb=" N VAL D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.564A pdb=" N ALA D 304 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.643A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 removed outlier: 3.634A pdb=" N MET D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 406 through 411 removed outlier: 4.140A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 443 removed outlier: 3.616A pdb=" N ALA D 433 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 462 removed outlier: 3.504A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 removed outlier: 4.276A pdb=" N MET D 466 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 504 Processing helix chain 'D' and resid 504 through 512 removed outlier: 3.510A pdb=" N HIS D 509 " --> pdb=" O ALA D 505 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 533 " --> pdb=" O ALA D 529 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.023A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 removed outlier: 3.561A pdb=" N PHE D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.832A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 274 " --> pdb=" O ASN A 635 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 264 through 268 removed outlier: 6.831A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR B 274 " --> pdb=" O ASN B 635 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 264 through 268 removed outlier: 6.831A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 274 " --> pdb=" O ASN C 635 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 264 through 268 removed outlier: 6.832A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR D 274 " --> pdb=" O ASN D 635 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1524 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: 3.16 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3164 1.31 - 1.44: 5472 1.44 - 1.56: 11197 1.56 - 1.68: 3 1.68 - 1.81: 228 Bond restraints: 20064 Sorted by residual: bond pdb=" N TYR D 623 " pdb=" CA TYR D 623 " ideal model delta sigma weight residual 1.462 1.557 -0.096 1.44e-02 4.82e+03 4.40e+01 bond pdb=" N TYR B 623 " pdb=" CA TYR B 623 " ideal model delta sigma weight residual 1.462 1.557 -0.095 1.44e-02 4.82e+03 4.39e+01 bond pdb=" N TYR C 623 " pdb=" CA TYR C 623 " ideal model delta sigma weight residual 1.462 1.557 -0.095 1.44e-02 4.82e+03 4.36e+01 bond pdb=" N TYR A 623 " pdb=" CA TYR A 623 " ideal model delta sigma weight residual 1.462 1.557 -0.095 1.44e-02 4.82e+03 4.36e+01 bond pdb=" N PRO C 614 " pdb=" CD PRO C 614 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.17e+01 ... (remaining 20059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 26409 3.25 - 6.49: 655 6.49 - 9.74: 140 9.74 - 12.98: 24 12.98 - 16.23: 20 Bond angle restraints: 27248 Sorted by residual: angle pdb=" N GLN C 370 " pdb=" CA GLN C 370 " pdb=" C GLN C 370 " ideal model delta sigma weight residual 110.30 126.53 -16.23 1.50e+00 4.44e-01 1.17e+02 angle pdb=" N GLN A 370 " pdb=" CA GLN A 370 " pdb=" C GLN A 370 " ideal model delta sigma weight residual 110.30 126.53 -16.23 1.50e+00 4.44e-01 1.17e+02 angle pdb=" N GLN B 370 " pdb=" CA GLN B 370 " pdb=" C GLN B 370 " ideal model delta sigma weight residual 110.30 126.51 -16.21 1.50e+00 4.44e-01 1.17e+02 angle pdb=" N GLN D 370 " pdb=" CA GLN D 370 " pdb=" C GLN D 370 " ideal model delta sigma weight residual 110.30 126.49 -16.19 1.50e+00 4.44e-01 1.16e+02 angle pdb=" N LEU C 229 " pdb=" CA LEU C 229 " pdb=" C LEU C 229 " ideal model delta sigma weight residual 110.24 94.65 15.59 1.47e+00 4.63e-01 1.12e+02 ... (remaining 27243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 11047 15.19 - 30.37: 719 30.37 - 45.56: 126 45.56 - 60.74: 36 60.74 - 75.93: 8 Dihedral angle restraints: 11936 sinusoidal: 4780 harmonic: 7156 Sorted by residual: dihedral pdb=" C PHE B 611 " pdb=" N PHE B 611 " pdb=" CA PHE B 611 " pdb=" CB PHE B 611 " ideal model delta harmonic sigma weight residual -122.60 -102.25 -20.35 0 2.50e+00 1.60e-01 6.63e+01 dihedral pdb=" C PHE D 611 " pdb=" N PHE D 611 " pdb=" CA PHE D 611 " pdb=" CB PHE D 611 " ideal model delta harmonic sigma weight residual -122.60 -102.26 -20.34 0 2.50e+00 1.60e-01 6.62e+01 dihedral pdb=" C PHE A 611 " pdb=" N PHE A 611 " pdb=" CA PHE A 611 " pdb=" CB PHE A 611 " ideal model delta harmonic sigma weight residual -122.60 -102.26 -20.34 0 2.50e+00 1.60e-01 6.62e+01 ... (remaining 11933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2639 0.090 - 0.181: 405 0.181 - 0.271: 32 0.271 - 0.361: 18 0.361 - 0.452: 6 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CA PHE C 611 " pdb=" N PHE C 611 " pdb=" C PHE C 611 " pdb=" CB PHE C 611 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CA PHE D 611 " pdb=" N PHE D 611 " pdb=" C PHE D 611 " pdb=" CB PHE D 611 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CA PHE B 611 " pdb=" N PHE B 611 " pdb=" C PHE B 611 " pdb=" CB PHE B 611 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.06e+00 ... (remaining 3097 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 623 " -0.023 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C TYR B 623 " 0.085 2.00e-02 2.50e+03 pdb=" O TYR B 623 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY B 624 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 623 " -0.023 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C TYR A 623 " 0.085 2.00e-02 2.50e+03 pdb=" O TYR A 623 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY A 624 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 623 " -0.023 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C TYR C 623 " 0.084 2.00e-02 2.50e+03 pdb=" O TYR C 623 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY C 624 " -0.027 2.00e-02 2.50e+03 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 52 2.47 - 3.07: 11599 3.07 - 3.68: 27979 3.68 - 4.29: 40943 4.29 - 4.90: 66731 Nonbonded interactions: 147304 Sorted by model distance: nonbonded pdb=" O GLN B 230 " pdb=" O SER B 231 " model vdw 1.856 3.040 nonbonded pdb=" O GLN A 230 " pdb=" O SER A 231 " model vdw 1.857 3.040 nonbonded pdb=" O GLN C 230 " pdb=" O SER C 231 " model vdw 1.857 3.040 nonbonded pdb=" O GLN D 230 " pdb=" O SER D 231 " model vdw 1.857 3.040 nonbonded pdb=" O HIS D 228 " pdb=" C LEU D 229 " model vdw 2.009 3.270 ... (remaining 147299 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 17.200 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 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 : 0.011 0.119 20064 Z= 0.469 Angle : 1.374 16.229 27248 Z= 0.811 Chirality : 0.072 0.452 3100 Planarity : 0.009 0.097 3460 Dihedral : 11.022 75.928 7312 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.39 % Favored : 93.11 % Rotamer: Outliers : 1.51 % Allowed : 1.51 % Favored : 96.98 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.01 (0.12), residues: 2440 helix: -4.73 (0.05), residues: 1272 sheet: -3.48 (0.46), residues: 84 loop : -2.88 (0.16), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 350 TYR 0.012 0.003 TYR A 349 PHE 0.044 0.004 PHE C 508 TRP 0.032 0.004 TRP A 629 HIS 0.015 0.003 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.01065 (20064) covalent geometry : angle 1.37421 (27248) hydrogen bonds : bond 0.34778 ( 536) hydrogen bonds : angle 9.84321 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 552 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8340 (tp) cc_final: 0.8099 (tm) REVERT: A 80 GLU cc_start: 0.7434 (pm20) cc_final: 0.7097 (pm20) REVERT: A 91 ASN cc_start: 0.6288 (m-40) cc_final: 0.5709 (p0) REVERT: A 136 LEU cc_start: 0.7604 (mt) cc_final: 0.7254 (mp) REVERT: A 220 LEU cc_start: 0.7886 (mt) cc_final: 0.7397 (pp) REVERT: A 455 SER cc_start: 0.8724 (m) cc_final: 0.8461 (p) REVERT: A 580 ASP cc_start: 0.7161 (m-30) cc_final: 0.6910 (t70) REVERT: B 44 ILE cc_start: 0.7495 (mt) cc_final: 0.7259 (mt) REVERT: B 111 LEU cc_start: 0.8187 (mt) cc_final: 0.7908 (mt) REVERT: B 311 THR cc_start: 0.8466 (t) cc_final: 0.8171 (m) REVERT: B 368 LEU cc_start: 0.7935 (mp) cc_final: 0.7729 (pp) REVERT: B 381 GLN cc_start: 0.7538 (mt0) cc_final: 0.7300 (tm-30) REVERT: B 406 ASP cc_start: 0.8349 (t0) cc_final: 0.7897 (t0) REVERT: C 80 GLU cc_start: 0.8097 (pm20) cc_final: 0.7374 (pm20) REVERT: C 111 LEU cc_start: 0.8296 (mt) cc_final: 0.8015 (mt) REVERT: C 112 CYS cc_start: 0.7642 (t) cc_final: 0.7259 (t) REVERT: C 303 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7380 (mm-30) REVERT: D 115 PHE cc_start: 0.7779 (m-80) cc_final: 0.7570 (m-80) REVERT: D 215 MET cc_start: 0.8165 (tpp) cc_final: 0.7960 (tpp) REVERT: D 228 HIS cc_start: 0.6322 (OUTLIER) cc_final: 0.5821 (m-70) REVERT: D 233 GLU cc_start: 0.6768 (tt0) cc_final: 0.5945 (tp30) REVERT: D 314 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7579 (ttpp) REVERT: D 381 GLN cc_start: 0.6866 (mt0) cc_final: 0.6493 (tm-30) REVERT: D 442 MET cc_start: 0.7923 (mmm) cc_final: 0.7720 (mmt) REVERT: D 447 MET cc_start: 0.8044 (mmm) cc_final: 0.7760 (mmt) outliers start: 32 outliers final: 15 residues processed: 567 average time/residue: 0.6177 time to fit residues: 392.6591 Evaluate side-chains 305 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 289 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 286 TRP Chi-restraints excluded: chain C residue 623 TYR Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 128 GLN A 208 ASN A 217 ASN A 238 HIS A 252 ASN A 446 ASN A 483 GLN A 519 ASN A 572 ASN A 596 GLN B 51 GLN B 128 GLN B 157 HIS B 238 HIS B 252 ASN B 446 ASN C 51 GLN C 128 GLN C 157 HIS C 238 HIS C 252 ASN C 446 ASN D 51 GLN D 214 GLN D 238 HIS D 257 GLN D 310 GLN D 446 ASN D 519 ASN D 572 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.177053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126416 restraints weight = 26239.393| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.01 r_work: 0.3566 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20064 Z= 0.174 Angle : 0.747 12.029 27248 Z= 0.379 Chirality : 0.044 0.228 3100 Planarity : 0.005 0.047 3460 Dihedral : 7.327 58.332 2705 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.74 % Favored : 94.10 % Rotamer: Outliers : 4.25 % Allowed : 11.70 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.80 (0.14), residues: 2440 helix: -3.43 (0.10), residues: 1292 sheet: -3.32 (0.46), residues: 84 loop : -2.67 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 610 TYR 0.017 0.002 TYR C 415 PHE 0.019 0.002 PHE C 211 TRP 0.030 0.002 TRP D 583 HIS 0.009 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00398 (20064) covalent geometry : angle 0.74650 (27248) hydrogen bonds : bond 0.04382 ( 536) hydrogen bonds : angle 5.09777 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 360 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8316 (tp) cc_final: 0.8078 (tm) REVERT: A 80 GLU cc_start: 0.7596 (pm20) cc_final: 0.6926 (pm20) REVERT: A 91 ASN cc_start: 0.6346 (m-40) cc_final: 0.5538 (p0) REVERT: A 220 LEU cc_start: 0.8106 (mt) cc_final: 0.7244 (pp) REVERT: A 233 GLU cc_start: 0.7075 (mp0) cc_final: 0.6790 (mm-30) REVERT: A 381 GLN cc_start: 0.6228 (tm-30) cc_final: 0.5521 (tm-30) REVERT: A 442 MET cc_start: 0.7474 (mmt) cc_final: 0.7212 (mmm) REVERT: A 455 SER cc_start: 0.8939 (m) cc_final: 0.8469 (p) REVERT: A 587 GLN cc_start: 0.7240 (mm-40) cc_final: 0.6825 (tt0) REVERT: B 80 GLU cc_start: 0.8131 (pm20) cc_final: 0.7476 (pm20) REVERT: B 111 LEU cc_start: 0.7876 (mt) cc_final: 0.7587 (mt) REVERT: B 214 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: B 220 LEU cc_start: 0.8075 (mt) cc_final: 0.7601 (mt) REVERT: B 234 LEU cc_start: 0.7382 (mm) cc_final: 0.7157 (mt) REVERT: B 291 SER cc_start: 0.7981 (t) cc_final: 0.7573 (p) REVERT: B 368 LEU cc_start: 0.7457 (mp) cc_final: 0.7142 (pp) REVERT: B 381 GLN cc_start: 0.7575 (mt0) cc_final: 0.6309 (tm-30) REVERT: B 406 ASP cc_start: 0.8216 (t0) cc_final: 0.7917 (t0) REVERT: B 482 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.7105 (mm) REVERT: B 496 LEU cc_start: 0.8352 (tt) cc_final: 0.8098 (mt) REVERT: C 55 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6571 (mt-10) REVERT: C 80 GLU cc_start: 0.7909 (pm20) cc_final: 0.7097 (pm20) REVERT: C 139 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6214 (ttm110) REVERT: C 214 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7554 (mp10) REVERT: C 250 GLU cc_start: 0.7787 (tp30) cc_final: 0.7576 (tp30) REVERT: C 286 TRP cc_start: 0.6580 (OUTLIER) cc_final: 0.6143 (m-90) REVERT: C 303 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7911 (mp0) REVERT: C 367 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6700 (pt) REVERT: C 381 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: C 496 LEU cc_start: 0.8451 (tt) cc_final: 0.8244 (mp) REVERT: C 578 MET cc_start: 0.8270 (mmm) cc_final: 0.7848 (mtt) REVERT: C 591 GLU cc_start: 0.7847 (tt0) cc_final: 0.7411 (tt0) REVERT: D 215 MET cc_start: 0.8012 (tpp) cc_final: 0.7698 (mmm) REVERT: D 233 GLU cc_start: 0.7371 (tt0) cc_final: 0.6422 (tp30) REVERT: D 246 LEU cc_start: 0.6988 (tp) cc_final: 0.6219 (tt) REVERT: D 303 GLU cc_start: 0.7170 (tp30) cc_final: 0.6873 (tp30) REVERT: D 311 THR cc_start: 0.7924 (t) cc_final: 0.6982 (m) REVERT: D 314 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7726 (ttpp) REVERT: D 322 LYS cc_start: 0.7885 (pptt) cc_final: 0.7424 (mmmt) REVERT: D 381 GLN cc_start: 0.7274 (mt0) cc_final: 0.6355 (tm-30) REVERT: D 485 MET cc_start: 0.7653 (mmt) cc_final: 0.7346 (mtt) REVERT: D 515 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6574 (mm-30) REVERT: D 591 GLU cc_start: 0.7381 (tt0) cc_final: 0.7156 (tp30) outliers start: 90 outliers final: 20 residues processed: 411 average time/residue: 0.5470 time to fit residues: 254.7094 Evaluate side-chains 301 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 286 TRP Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 567 THR Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 286 TRP Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 chunk 164 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 159 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 157 HIS A 206 GLN A 310 GLN B 127 ASN B 128 GLN B 157 HIS B 252 ASN C 128 GLN C 157 HIS C 206 GLN C 252 ASN C 267 GLN C 483 GLN D 519 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.176530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.124933 restraints weight = 26342.224| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.05 r_work: 0.3541 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20064 Z= 0.114 Angle : 0.655 11.872 27248 Z= 0.325 Chirality : 0.041 0.245 3100 Planarity : 0.004 0.042 3460 Dihedral : 6.072 56.065 2684 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.43 % Rotamer: Outliers : 3.96 % Allowed : 14.91 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.15), residues: 2440 helix: -2.49 (0.12), residues: 1304 sheet: -2.94 (0.50), residues: 76 loop : -2.55 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 409 TYR 0.016 0.001 TYR C 32 PHE 0.014 0.001 PHE A 537 TRP 0.015 0.001 TRP D 583 HIS 0.006 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00261 (20064) covalent geometry : angle 0.65475 (27248) hydrogen bonds : bond 0.03887 ( 536) hydrogen bonds : angle 4.46368 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 316 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7216 (mmt-90) cc_final: 0.6972 (mmt-90) REVERT: A 39 LEU cc_start: 0.8345 (tp) cc_final: 0.8037 (tm) REVERT: A 43 ARG cc_start: 0.7132 (mmm-85) cc_final: 0.6921 (mmm-85) REVERT: A 57 ASP cc_start: 0.5477 (m-30) cc_final: 0.5047 (t0) REVERT: A 80 GLU cc_start: 0.7589 (pm20) cc_final: 0.6874 (pm20) REVERT: A 91 ASN cc_start: 0.6480 (m-40) cc_final: 0.5568 (p0) REVERT: A 126 MET cc_start: 0.7429 (tpt) cc_final: 0.6859 (ttp) REVERT: A 220 LEU cc_start: 0.8196 (mt) cc_final: 0.7364 (pp) REVERT: A 233 GLU cc_start: 0.6763 (mp0) cc_final: 0.6551 (mm-30) REVERT: A 368 LEU cc_start: 0.7905 (tp) cc_final: 0.7682 (mt) REVERT: A 381 GLN cc_start: 0.6311 (tm-30) cc_final: 0.5339 (tm-30) REVERT: A 455 SER cc_start: 0.8933 (m) cc_final: 0.8490 (p) REVERT: A 470 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7701 (mtt90) REVERT: A 515 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6337 (mm-30) REVERT: A 570 MET cc_start: 0.8512 (mmm) cc_final: 0.7925 (mmm) REVERT: A 587 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7050 (tt0) REVERT: B 80 GLU cc_start: 0.8069 (pm20) cc_final: 0.7418 (pm20) REVERT: B 111 LEU cc_start: 0.7745 (mt) cc_final: 0.7536 (mt) REVERT: B 195 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6086 (tt) REVERT: B 220 LEU cc_start: 0.8001 (mt) cc_final: 0.7574 (mt) REVERT: B 234 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7216 (mm) REVERT: B 291 SER cc_start: 0.8031 (t) cc_final: 0.7652 (p) REVERT: B 368 LEU cc_start: 0.7479 (mp) cc_final: 0.7190 (pp) REVERT: B 381 GLN cc_start: 0.7499 (mt0) cc_final: 0.6226 (tm-30) REVERT: B 406 ASP cc_start: 0.8281 (t0) cc_final: 0.7759 (t0) REVERT: B 482 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7177 (mm) REVERT: B 515 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6798 (mm-30) REVERT: C 55 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6564 (mt-10) REVERT: C 80 GLU cc_start: 0.8054 (pm20) cc_final: 0.7231 (pm20) REVERT: C 104 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7244 (pp20) REVERT: C 111 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7187 (mt) REVERT: C 139 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6346 (ttm110) REVERT: C 220 LEU cc_start: 0.8146 (mt) cc_final: 0.7369 (pp) REVERT: C 303 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8011 (mp0) REVERT: C 371 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7281 (ptpp) REVERT: C 381 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: C 414 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7302 (ttp-110) REVERT: C 591 GLU cc_start: 0.7826 (tt0) cc_final: 0.7353 (tt0) REVERT: C 608 MET cc_start: 0.7774 (mtm) cc_final: 0.7171 (mtm) REVERT: D 99 MET cc_start: 0.6390 (mtp) cc_final: 0.6186 (ttp) REVERT: D 178 ILE cc_start: 0.6908 (mm) cc_final: 0.6700 (mp) REVERT: D 209 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6415 (mmmt) REVERT: D 214 GLN cc_start: 0.8313 (tp-100) cc_final: 0.7976 (mt0) REVERT: D 215 MET cc_start: 0.8116 (tpp) cc_final: 0.7705 (mmm) REVERT: D 233 GLU cc_start: 0.7348 (tt0) cc_final: 0.6226 (tp30) REVERT: D 303 GLU cc_start: 0.7333 (tp30) cc_final: 0.6544 (tp30) REVERT: D 314 LYS cc_start: 0.7824 (ttpp) cc_final: 0.7554 (ttpp) REVERT: D 322 LYS cc_start: 0.7830 (pptt) cc_final: 0.7571 (mmmt) REVERT: D 381 GLN cc_start: 0.7341 (mt0) cc_final: 0.6340 (tm-30) REVERT: D 485 MET cc_start: 0.7713 (mmt) cc_final: 0.7424 (mtt) REVERT: D 515 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7330 (mm-30) REVERT: D 525 ASP cc_start: 0.6936 (t0) cc_final: 0.6014 (p0) REVERT: D 553 PHE cc_start: 0.7002 (t80) cc_final: 0.6605 (p90) REVERT: D 588 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7408 (tt0) REVERT: D 591 GLU cc_start: 0.7627 (tt0) cc_final: 0.7289 (tt0) REVERT: D 608 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6935 (mtm) outliers start: 84 outliers final: 25 residues processed: 370 average time/residue: 0.5225 time to fit residues: 220.6017 Evaluate side-chains 318 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 470 ARG Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 260 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 152 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 0.0570 chunk 18 optimal weight: 0.0470 chunk 33 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS B 157 HIS B 206 GLN C 127 ASN C 157 HIS C 310 GLN D 237 ASN D 519 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.174130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.121980 restraints weight = 25621.740| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.98 r_work: 0.3490 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20064 Z= 0.123 Angle : 0.630 11.628 27248 Z= 0.312 Chirality : 0.041 0.295 3100 Planarity : 0.004 0.042 3460 Dihedral : 5.494 55.047 2680 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.78 % Favored : 94.18 % Rotamer: Outliers : 4.86 % Allowed : 15.71 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.15), residues: 2440 helix: -1.95 (0.13), residues: 1340 sheet: -3.08 (0.51), residues: 76 loop : -2.42 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 470 TYR 0.016 0.001 TYR D 32 PHE 0.012 0.001 PHE B 72 TRP 0.012 0.001 TRP D 583 HIS 0.004 0.001 HIS B 582 Details of bonding type rmsd covalent geometry : bond 0.00291 (20064) covalent geometry : angle 0.63034 (27248) hydrogen bonds : bond 0.03453 ( 536) hydrogen bonds : angle 4.22192 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 307 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7381 (mmt-90) cc_final: 0.7150 (mmt-90) REVERT: A 39 LEU cc_start: 0.8371 (tp) cc_final: 0.8079 (tm) REVERT: A 43 ARG cc_start: 0.7157 (mmm-85) cc_final: 0.6873 (mmm-85) REVERT: A 57 ASP cc_start: 0.5457 (m-30) cc_final: 0.5017 (t0) REVERT: A 91 ASN cc_start: 0.6532 (m-40) cc_final: 0.5622 (p0) REVERT: A 220 LEU cc_start: 0.8110 (mt) cc_final: 0.7326 (pp) REVERT: A 311 THR cc_start: 0.8509 (t) cc_final: 0.8274 (m) REVERT: A 381 GLN cc_start: 0.6604 (tm-30) cc_final: 0.5798 (tm-30) REVERT: A 442 MET cc_start: 0.7157 (mmt) cc_final: 0.6893 (mmm) REVERT: A 455 SER cc_start: 0.8923 (m) cc_final: 0.8710 (m) REVERT: A 491 MET cc_start: 0.7965 (ptp) cc_final: 0.7765 (ttt) REVERT: A 554 MET cc_start: 0.6513 (tpp) cc_final: 0.6202 (tpp) REVERT: A 587 GLN cc_start: 0.7513 (mm-40) cc_final: 0.6998 (tt0) REVERT: B 80 GLU cc_start: 0.8162 (pm20) cc_final: 0.7297 (pm20) REVERT: B 111 LEU cc_start: 0.7786 (mt) cc_final: 0.7548 (mt) REVERT: B 195 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6110 (tt) REVERT: B 214 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: B 220 LEU cc_start: 0.7982 (mt) cc_final: 0.7201 (pp) REVERT: B 234 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7173 (mm) REVERT: B 291 SER cc_start: 0.7995 (t) cc_final: 0.7567 (p) REVERT: B 332 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8006 (tm) REVERT: B 368 LEU cc_start: 0.7568 (mp) cc_final: 0.7320 (pp) REVERT: B 381 GLN cc_start: 0.7438 (mt0) cc_final: 0.6169 (tm-30) REVERT: B 406 ASP cc_start: 0.8218 (t0) cc_final: 0.7693 (t0) REVERT: B 455 SER cc_start: 0.8939 (m) cc_final: 0.8703 (m) REVERT: B 482 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6991 (mm) REVERT: B 485 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6887 (mtt) REVERT: B 553 PHE cc_start: 0.6711 (t80) cc_final: 0.6509 (t80) REVERT: B 565 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7222 (mm) REVERT: B 577 MET cc_start: 0.7659 (ttp) cc_final: 0.7306 (ttm) REVERT: C 38 MET cc_start: 0.8002 (mtp) cc_final: 0.7745 (mtm) REVERT: C 80 GLU cc_start: 0.8053 (pm20) cc_final: 0.7213 (pm20) REVERT: C 104 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7120 (pp20) REVERT: C 111 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7344 (mt) REVERT: C 139 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6411 (ttm110) REVERT: C 214 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7658 (mp10) REVERT: C 220 LEU cc_start: 0.8035 (mt) cc_final: 0.7306 (pp) REVERT: C 303 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8016 (mp0) REVERT: C 381 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6444 (tm-30) REVERT: C 414 ARG cc_start: 0.7794 (ttm110) cc_final: 0.7338 (ttp-110) REVERT: C 525 ASP cc_start: 0.6941 (t0) cc_final: 0.6171 (p0) REVERT: C 541 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7310 (tt) REVERT: C 565 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7254 (mm) REVERT: C 572 ASN cc_start: 0.8411 (m-40) cc_final: 0.8197 (m110) REVERT: C 608 MET cc_start: 0.7517 (mtm) cc_final: 0.7150 (mtm) REVERT: D 99 MET cc_start: 0.6365 (mtp) cc_final: 0.6085 (mtm) REVERT: D 123 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.5846 (mp) REVERT: D 209 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6418 (mmmt) REVERT: D 215 MET cc_start: 0.8084 (tpp) cc_final: 0.7720 (mmm) REVERT: D 233 GLU cc_start: 0.7346 (tt0) cc_final: 0.6564 (tp30) REVERT: D 302 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.7061 (mtp-110) REVERT: D 303 GLU cc_start: 0.7682 (tp30) cc_final: 0.6783 (tp30) REVERT: D 314 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7472 (ttpp) REVERT: D 381 GLN cc_start: 0.7532 (mt0) cc_final: 0.6613 (tm-30) REVERT: D 442 MET cc_start: 0.7169 (mmt) cc_final: 0.6923 (mmm) REVERT: D 455 SER cc_start: 0.8949 (m) cc_final: 0.8518 (p) REVERT: D 485 MET cc_start: 0.7804 (mmt) cc_final: 0.7519 (mtt) REVERT: D 515 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: D 525 ASP cc_start: 0.6857 (t0) cc_final: 0.6146 (p0) REVERT: D 553 PHE cc_start: 0.7149 (t80) cc_final: 0.6913 (t80) REVERT: D 590 ASP cc_start: 0.7629 (m-30) cc_final: 0.7259 (m-30) REVERT: D 591 GLU cc_start: 0.7941 (tt0) cc_final: 0.7465 (tt0) REVERT: D 608 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.6862 (mtm) REVERT: D 612 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7328 (mt) outliers start: 103 outliers final: 24 residues processed: 372 average time/residue: 0.5353 time to fit residues: 227.0420 Evaluate side-chains 323 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 280 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 214 GLN Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 587 GLN C 157 HIS C 267 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.173323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.121303 restraints weight = 25523.151| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.97 r_work: 0.3477 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20064 Z= 0.118 Angle : 0.618 10.638 27248 Z= 0.304 Chirality : 0.041 0.232 3100 Planarity : 0.004 0.060 3460 Dihedral : 5.319 55.997 2680 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.10 % Allowed : 18.11 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.16), residues: 2440 helix: -1.60 (0.13), residues: 1344 sheet: -3.44 (0.45), residues: 84 loop : -2.29 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 45 TYR 0.013 0.001 TYR B 415 PHE 0.013 0.001 PHE A 574 TRP 0.012 0.001 TRP D 583 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00282 (20064) covalent geometry : angle 0.61780 (27248) hydrogen bonds : bond 0.03333 ( 536) hydrogen bonds : angle 4.12936 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 296 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8321 (tp) cc_final: 0.8003 (tm) REVERT: A 43 ARG cc_start: 0.7201 (mmm-85) cc_final: 0.6874 (mmm-85) REVERT: A 91 ASN cc_start: 0.6521 (m-40) cc_final: 0.5681 (p0) REVERT: A 126 MET cc_start: 0.7732 (tpt) cc_final: 0.6974 (ttp) REVERT: A 139 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7614 (tmt170) REVERT: A 220 LEU cc_start: 0.7907 (mt) cc_final: 0.7282 (pp) REVERT: A 269 THR cc_start: 0.8239 (p) cc_final: 0.7969 (t) REVERT: A 303 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7437 (mm-30) REVERT: A 381 GLN cc_start: 0.6282 (tm-30) cc_final: 0.5392 (tm-30) REVERT: A 442 MET cc_start: 0.7011 (mmt) cc_final: 0.6753 (mmm) REVERT: A 455 SER cc_start: 0.8839 (m) cc_final: 0.8618 (m) REVERT: A 515 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 554 MET cc_start: 0.6322 (tpp) cc_final: 0.6092 (tpp) REVERT: A 587 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7083 (tt0) REVERT: B 80 GLU cc_start: 0.8177 (pm20) cc_final: 0.7236 (pm20) REVERT: B 111 LEU cc_start: 0.7738 (mt) cc_final: 0.7486 (mt) REVERT: B 195 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6156 (tt) REVERT: B 220 LEU cc_start: 0.8120 (mt) cc_final: 0.7355 (pp) REVERT: B 291 SER cc_start: 0.7919 (t) cc_final: 0.7480 (p) REVERT: B 315 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: B 332 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7971 (tm) REVERT: B 381 GLN cc_start: 0.7343 (mt0) cc_final: 0.6074 (tm-30) REVERT: B 382 ASP cc_start: 0.7538 (m-30) cc_final: 0.6915 (p0) REVERT: B 406 ASP cc_start: 0.8173 (t0) cc_final: 0.7629 (t0) REVERT: B 455 SER cc_start: 0.8958 (m) cc_final: 0.8730 (m) REVERT: B 482 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6840 (mm) REVERT: B 489 ASP cc_start: 0.8302 (t70) cc_final: 0.7589 (t0) REVERT: B 502 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8126 (tt) REVERT: B 518 ASN cc_start: 0.8283 (m-40) cc_final: 0.7995 (m110) REVERT: B 553 PHE cc_start: 0.6882 (t80) cc_final: 0.6682 (t80) REVERT: B 565 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7132 (mm) REVERT: C 38 MET cc_start: 0.7965 (mtp) cc_final: 0.7646 (mtm) REVERT: C 80 GLU cc_start: 0.8064 (pm20) cc_final: 0.7207 (pm20) REVERT: C 104 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7421 (pp20) REVERT: C 111 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7318 (mt) REVERT: C 139 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6425 (ttm110) REVERT: C 220 LEU cc_start: 0.7951 (mt) cc_final: 0.7274 (pp) REVERT: C 303 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7994 (mp0) REVERT: C 381 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6067 (tm-30) REVERT: C 414 ARG cc_start: 0.7797 (ttm110) cc_final: 0.7314 (ttp-110) REVERT: C 481 MET cc_start: 0.8146 (tpt) cc_final: 0.7709 (tpt) REVERT: C 485 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6708 (mpp) REVERT: C 502 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8145 (tt) REVERT: C 525 ASP cc_start: 0.6858 (t0) cc_final: 0.6101 (p0) REVERT: C 565 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7219 (mm) REVERT: C 572 ASN cc_start: 0.8430 (m-40) cc_final: 0.8142 (m-40) REVERT: C 608 MET cc_start: 0.7593 (mtm) cc_final: 0.7135 (mtm) REVERT: D 123 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6195 (mp) REVERT: D 209 LYS cc_start: 0.6959 (OUTLIER) cc_final: 0.6340 (mmmt) REVERT: D 233 GLU cc_start: 0.7324 (tt0) cc_final: 0.6446 (tm-30) REVERT: D 250 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: D 302 ARG cc_start: 0.7794 (ttp-110) cc_final: 0.7267 (mtp-110) REVERT: D 314 LYS cc_start: 0.7638 (ttpp) cc_final: 0.7339 (ttpt) REVERT: D 322 LYS cc_start: 0.8463 (mmpt) cc_final: 0.8083 (mmtt) REVERT: D 381 GLN cc_start: 0.7559 (mt0) cc_final: 0.6648 (tm-30) REVERT: D 442 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6754 (mmm) REVERT: D 455 SER cc_start: 0.8874 (m) cc_final: 0.8464 (p) REVERT: D 492 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7538 (ptp-170) REVERT: D 515 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7282 (mm-30) REVERT: D 525 ASP cc_start: 0.6834 (t0) cc_final: 0.6114 (p0) REVERT: D 590 ASP cc_start: 0.7697 (m-30) cc_final: 0.7474 (m-30) REVERT: D 591 GLU cc_start: 0.7982 (tt0) cc_final: 0.7536 (tt0) REVERT: D 608 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.6956 (mtm) outliers start: 87 outliers final: 27 residues processed: 351 average time/residue: 0.5386 time to fit residues: 215.2859 Evaluate side-chains 327 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 279 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 554 MET Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 492 ARG Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 515 GLU Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 0.0670 chunk 169 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 211 optimal weight: 0.0170 chunk 62 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 187 optimal weight: 0.5980 chunk 197 optimal weight: 0.7980 chunk 91 optimal weight: 0.0980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 158 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 587 GLN C 157 HIS C 519 ASN D 519 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.176219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124316 restraints weight = 25269.277| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.98 r_work: 0.3519 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 20064 Z= 0.098 Angle : 0.601 11.399 27248 Z= 0.292 Chirality : 0.039 0.187 3100 Planarity : 0.003 0.047 3460 Dihedral : 5.051 57.477 2680 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.68 % Allowed : 19.20 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.16), residues: 2440 helix: -1.22 (0.14), residues: 1332 sheet: -3.47 (0.44), residues: 84 loop : -2.09 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 302 TYR 0.014 0.001 TYR D 32 PHE 0.029 0.001 PHE D 553 TRP 0.010 0.001 TRP D 583 HIS 0.003 0.000 HIS D 238 Details of bonding type rmsd covalent geometry : bond 0.00218 (20064) covalent geometry : angle 0.60101 (27248) hydrogen bonds : bond 0.02938 ( 536) hydrogen bonds : angle 3.98935 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 304 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8297 (tp) cc_final: 0.7987 (tm) REVERT: A 43 ARG cc_start: 0.7211 (mmm-85) cc_final: 0.6901 (mmm-85) REVERT: A 91 ASN cc_start: 0.6540 (m-40) cc_final: 0.5700 (p0) REVERT: A 126 MET cc_start: 0.7699 (tpt) cc_final: 0.6854 (ttm) REVERT: A 127 ASN cc_start: 0.7395 (t0) cc_final: 0.6414 (m110) REVERT: A 139 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7681 (tmt170) REVERT: A 162 TYR cc_start: 0.7869 (m-10) cc_final: 0.7438 (m-10) REVERT: A 220 LEU cc_start: 0.7836 (mt) cc_final: 0.7280 (pp) REVERT: A 269 THR cc_start: 0.8225 (p) cc_final: 0.7965 (t) REVERT: A 303 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7411 (mm-30) REVERT: A 348 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8035 (mp) REVERT: A 381 GLN cc_start: 0.6381 (tm-30) cc_final: 0.5456 (tm-30) REVERT: A 442 MET cc_start: 0.6938 (mmt) cc_final: 0.6679 (mtt) REVERT: A 455 SER cc_start: 0.8757 (m) cc_final: 0.8539 (m) REVERT: A 542 ASP cc_start: 0.7137 (m-30) cc_final: 0.6418 (p0) REVERT: A 554 MET cc_start: 0.6330 (tpp) cc_final: 0.6102 (mmt) REVERT: A 587 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7159 (tt0) REVERT: B 80 GLU cc_start: 0.8179 (pm20) cc_final: 0.7225 (pm20) REVERT: B 111 LEU cc_start: 0.7700 (mt) cc_final: 0.7494 (mt) REVERT: B 195 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6113 (tt) REVERT: B 216 TYR cc_start: 0.7217 (t80) cc_final: 0.6987 (t80) REVERT: B 220 LEU cc_start: 0.8091 (mt) cc_final: 0.7287 (pp) REVERT: B 291 SER cc_start: 0.7840 (t) cc_final: 0.7383 (p) REVERT: B 332 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7848 (tm) REVERT: B 381 GLN cc_start: 0.7265 (mt0) cc_final: 0.5661 (tm-30) REVERT: B 382 ASP cc_start: 0.7381 (m-30) cc_final: 0.6925 (p0) REVERT: B 406 ASP cc_start: 0.8113 (t0) cc_final: 0.7602 (t0) REVERT: B 455 SER cc_start: 0.8919 (m) cc_final: 0.8684 (m) REVERT: B 482 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6979 (mm) REVERT: B 518 ASN cc_start: 0.8288 (m-40) cc_final: 0.7970 (m110) REVERT: B 525 ASP cc_start: 0.6817 (t0) cc_final: 0.6177 (p0) REVERT: B 553 PHE cc_start: 0.6868 (t80) cc_final: 0.6659 (t80) REVERT: B 554 MET cc_start: 0.7486 (mmp) cc_final: 0.7197 (tpp) REVERT: B 565 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.7095 (mm) REVERT: B 577 MET cc_start: 0.7620 (ttp) cc_final: 0.7388 (ttm) REVERT: C 38 MET cc_start: 0.7745 (mtp) cc_final: 0.7447 (mtm) REVERT: C 80 GLU cc_start: 0.8173 (pm20) cc_final: 0.7259 (pm20) REVERT: C 104 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6948 (pp20) REVERT: C 111 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7265 (mt) REVERT: C 139 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6322 (ttm110) REVERT: C 220 LEU cc_start: 0.7956 (mt) cc_final: 0.7271 (pp) REVERT: C 303 GLU cc_start: 0.8229 (mm-30) cc_final: 0.8013 (mp0) REVERT: C 371 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6583 (pmmt) REVERT: C 381 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.5913 (tm-30) REVERT: C 414 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7306 (ttp-110) REVERT: C 489 ASP cc_start: 0.8067 (t70) cc_final: 0.7462 (t0) REVERT: C 525 ASP cc_start: 0.6839 (t0) cc_final: 0.6235 (p0) REVERT: C 542 ASP cc_start: 0.7477 (m-30) cc_final: 0.6812 (p0) REVERT: C 565 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7156 (mm) REVERT: C 572 ASN cc_start: 0.8414 (m-40) cc_final: 0.8119 (m-40) REVERT: C 608 MET cc_start: 0.7374 (mtm) cc_final: 0.6919 (mtm) REVERT: D 134 ARG cc_start: 0.7486 (mmm160) cc_final: 0.7108 (tpp80) REVERT: D 209 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6278 (mmmt) REVERT: D 214 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7973 (tp-100) REVERT: D 233 GLU cc_start: 0.7463 (tt0) cc_final: 0.6519 (tm-30) REVERT: D 250 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: D 260 MET cc_start: 0.6891 (mmt) cc_final: 0.6678 (tpt) REVERT: D 302 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.7272 (mtp-110) REVERT: D 303 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6781 (tp30) REVERT: D 314 LYS cc_start: 0.7445 (ttpp) cc_final: 0.7165 (ttpt) REVERT: D 381 GLN cc_start: 0.7584 (mt0) cc_final: 0.6669 (tm-30) REVERT: D 455 SER cc_start: 0.8780 (m) cc_final: 0.8345 (p) REVERT: D 515 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7161 (mm-30) REVERT: D 525 ASP cc_start: 0.6794 (t0) cc_final: 0.6021 (p0) REVERT: D 570 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7875 (mmt) REVERT: D 590 ASP cc_start: 0.7691 (m-30) cc_final: 0.7490 (m-30) REVERT: D 591 GLU cc_start: 0.7942 (tt0) cc_final: 0.7482 (tt0) REVERT: D 608 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.6767 (mtm) REVERT: D 613 TRP cc_start: 0.7537 (t60) cc_final: 0.7177 (t60) outliers start: 78 outliers final: 21 residues processed: 352 average time/residue: 0.5372 time to fit residues: 215.5310 Evaluate side-chains 315 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 277 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 24 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 chunk 172 optimal weight: 0.3980 chunk 10 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 164 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 252 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 587 GLN C 51 GLN C 157 HIS D 127 ASN D 238 HIS D 582 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.174182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.122219 restraints weight = 25464.573| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.99 r_work: 0.3479 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20064 Z= 0.110 Angle : 0.619 10.940 27248 Z= 0.299 Chirality : 0.040 0.175 3100 Planarity : 0.003 0.033 3460 Dihedral : 5.006 57.359 2680 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.40 % Allowed : 19.91 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.16), residues: 2440 helix: -0.96 (0.14), residues: 1340 sheet: -3.36 (0.46), residues: 84 loop : -2.04 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 302 TYR 0.014 0.001 TYR B 415 PHE 0.017 0.001 PHE D 553 TRP 0.009 0.001 TRP D 583 HIS 0.003 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00259 (20064) covalent geometry : angle 0.61875 (27248) hydrogen bonds : bond 0.03172 ( 536) hydrogen bonds : angle 4.00328 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 305 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7586 (mmt-90) cc_final: 0.7353 (mmt-90) REVERT: A 39 LEU cc_start: 0.8332 (tp) cc_final: 0.7993 (tm) REVERT: A 43 ARG cc_start: 0.7227 (mmm-85) cc_final: 0.6925 (mmm-85) REVERT: A 57 ASP cc_start: 0.5583 (m-30) cc_final: 0.5029 (t0) REVERT: A 91 ASN cc_start: 0.6478 (m-40) cc_final: 0.5667 (p0) REVERT: A 126 MET cc_start: 0.7750 (tpt) cc_final: 0.6868 (ttm) REVERT: A 127 ASN cc_start: 0.7499 (t0) cc_final: 0.6588 (m110) REVERT: A 139 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7644 (tmt170) REVERT: A 220 LEU cc_start: 0.7861 (mt) cc_final: 0.7327 (pp) REVERT: A 269 THR cc_start: 0.8219 (p) cc_final: 0.7924 (t) REVERT: A 303 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7402 (mm-30) REVERT: A 381 GLN cc_start: 0.6215 (tm-30) cc_final: 0.5348 (tm-30) REVERT: A 455 SER cc_start: 0.8719 (m) cc_final: 0.8507 (m) REVERT: A 481 MET cc_start: 0.7875 (mmm) cc_final: 0.7653 (mmm) REVERT: A 520 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.7008 (tt) REVERT: A 542 ASP cc_start: 0.7173 (m-30) cc_final: 0.6380 (p0) REVERT: A 554 MET cc_start: 0.6377 (tpp) cc_final: 0.6163 (mmt) REVERT: A 587 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7047 (tt0) REVERT: B 80 GLU cc_start: 0.8163 (pm20) cc_final: 0.6879 (pp20) REVERT: B 88 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5608 (tt) REVERT: B 195 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6229 (tt) REVERT: B 220 LEU cc_start: 0.8032 (mt) cc_final: 0.7614 (mt) REVERT: B 291 SER cc_start: 0.7893 (t) cc_final: 0.7425 (p) REVERT: B 332 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7769 (tm) REVERT: B 381 GLN cc_start: 0.7244 (mt0) cc_final: 0.5747 (tm-30) REVERT: B 382 ASP cc_start: 0.7497 (m-30) cc_final: 0.7167 (p0) REVERT: B 406 ASP cc_start: 0.8151 (t0) cc_final: 0.7655 (t0) REVERT: B 442 MET cc_start: 0.6689 (mtt) cc_final: 0.6472 (mtt) REVERT: B 455 SER cc_start: 0.8898 (m) cc_final: 0.8688 (m) REVERT: B 482 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6880 (mm) REVERT: B 489 ASP cc_start: 0.8156 (t70) cc_final: 0.7531 (t0) REVERT: B 502 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8153 (tt) REVERT: B 518 ASN cc_start: 0.8237 (m-40) cc_final: 0.7964 (m-40) REVERT: B 525 ASP cc_start: 0.6816 (t0) cc_final: 0.6179 (p0) REVERT: B 542 ASP cc_start: 0.7100 (m-30) cc_final: 0.6743 (p0) REVERT: B 565 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6949 (mm) REVERT: C 80 GLU cc_start: 0.8153 (pm20) cc_final: 0.7261 (pm20) REVERT: C 88 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5732 (tt) REVERT: C 104 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6920 (pp20) REVERT: C 111 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7259 (mt) REVERT: C 139 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6282 (ttm110) REVERT: C 220 LEU cc_start: 0.7920 (mt) cc_final: 0.7278 (pp) REVERT: C 303 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7979 (mp0) REVERT: C 340 MET cc_start: 0.7039 (mmm) cc_final: 0.6787 (mmm) REVERT: C 371 LYS cc_start: 0.6830 (OUTLIER) cc_final: 0.6622 (pmmt) REVERT: C 381 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.5876 (tm-30) REVERT: C 489 ASP cc_start: 0.7916 (t70) cc_final: 0.7097 (t0) REVERT: C 502 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8131 (tt) REVERT: C 525 ASP cc_start: 0.6871 (t0) cc_final: 0.6283 (p0) REVERT: C 542 ASP cc_start: 0.7523 (m-30) cc_final: 0.6819 (p0) REVERT: C 565 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7125 (mm) REVERT: C 572 ASN cc_start: 0.8420 (m-40) cc_final: 0.8096 (m-40) REVERT: C 608 MET cc_start: 0.7489 (mtm) cc_final: 0.7049 (mtm) REVERT: D 80 GLU cc_start: 0.7194 (pm20) cc_final: 0.6577 (pp20) REVERT: D 134 ARG cc_start: 0.7493 (mmm160) cc_final: 0.7241 (tpp80) REVERT: D 195 LEU cc_start: 0.6376 (tp) cc_final: 0.6023 (tt) REVERT: D 209 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6306 (mmmt) REVERT: D 214 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7900 (tp-100) REVERT: D 233 GLU cc_start: 0.7495 (tt0) cc_final: 0.6590 (tm-30) REVERT: D 250 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: D 260 MET cc_start: 0.6848 (mmt) cc_final: 0.6589 (tpt) REVERT: D 302 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7190 (mtp-110) REVERT: D 381 GLN cc_start: 0.7507 (mt0) cc_final: 0.6706 (tm-30) REVERT: D 455 SER cc_start: 0.8735 (m) cc_final: 0.8319 (p) REVERT: D 486 ILE cc_start: 0.8362 (tt) cc_final: 0.8159 (tt) REVERT: D 502 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8084 (tt) REVERT: D 515 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6974 (mm-30) REVERT: D 525 ASP cc_start: 0.6846 (t0) cc_final: 0.6344 (p0) REVERT: D 591 GLU cc_start: 0.7946 (tt0) cc_final: 0.7610 (tt0) REVERT: D 608 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.6783 (mtm) outliers start: 72 outliers final: 24 residues processed: 353 average time/residue: 0.5471 time to fit residues: 219.9215 Evaluate side-chains 330 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 155 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 239 optimal weight: 0.0870 chunk 73 optimal weight: 10.0000 chunk 237 optimal weight: 0.8980 chunk 203 optimal weight: 0.0050 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.5572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 572 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 158 ASN B 587 GLN C 157 HIS C 582 HIS D 519 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.175326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.123170 restraints weight = 25417.844| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 3.00 r_work: 0.3502 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20064 Z= 0.102 Angle : 0.616 10.775 27248 Z= 0.296 Chirality : 0.040 0.163 3100 Planarity : 0.003 0.043 3460 Dihedral : 4.882 59.609 2678 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.92 % Allowed : 21.42 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.17), residues: 2440 helix: -0.72 (0.14), residues: 1336 sheet: -3.32 (0.45), residues: 84 loop : -1.91 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 139 TYR 0.016 0.001 TYR B 415 PHE 0.020 0.001 PHE C 553 TRP 0.010 0.001 TRP D 583 HIS 0.003 0.000 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00238 (20064) covalent geometry : angle 0.61563 (27248) hydrogen bonds : bond 0.03102 ( 536) hydrogen bonds : angle 3.95693 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 296 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7601 (mmt-90) cc_final: 0.7370 (mmt-90) REVERT: A 39 LEU cc_start: 0.8348 (tp) cc_final: 0.7997 (tm) REVERT: A 43 ARG cc_start: 0.7266 (mmm-85) cc_final: 0.6973 (mmm-85) REVERT: A 91 ASN cc_start: 0.6512 (m-40) cc_final: 0.5858 (p0) REVERT: A 126 MET cc_start: 0.7806 (tpt) cc_final: 0.6950 (ttm) REVERT: A 127 ASN cc_start: 0.7520 (t0) cc_final: 0.6607 (m110) REVERT: A 139 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7645 (tmt170) REVERT: A 220 LEU cc_start: 0.7867 (mt) cc_final: 0.7336 (pp) REVERT: A 269 THR cc_start: 0.8262 (p) cc_final: 0.7961 (t) REVERT: A 303 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7395 (mm-30) REVERT: A 322 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8176 (mmpt) REVERT: A 381 GLN cc_start: 0.6448 (tm-30) cc_final: 0.5634 (tm-30) REVERT: A 442 MET cc_start: 0.7034 (mtt) cc_final: 0.6624 (mtt) REVERT: A 455 SER cc_start: 0.8724 (m) cc_final: 0.8504 (m) REVERT: A 520 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6933 (tt) REVERT: A 542 ASP cc_start: 0.7137 (m-30) cc_final: 0.6384 (p0) REVERT: A 554 MET cc_start: 0.6348 (tpp) cc_final: 0.6135 (mmt) REVERT: A 572 ASN cc_start: 0.8007 (m-40) cc_final: 0.7702 (m-40) REVERT: A 587 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7100 (tt0) REVERT: B 80 GLU cc_start: 0.8207 (pm20) cc_final: 0.6827 (pp20) REVERT: B 88 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5630 (tt) REVERT: B 195 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.6215 (tt) REVERT: B 220 LEU cc_start: 0.8011 (mt) cc_final: 0.7592 (mt) REVERT: B 291 SER cc_start: 0.7847 (t) cc_final: 0.7380 (p) REVERT: B 332 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7721 (tm) REVERT: B 381 GLN cc_start: 0.7239 (mt0) cc_final: 0.5748 (tm-30) REVERT: B 382 ASP cc_start: 0.7433 (m-30) cc_final: 0.7216 (p0) REVERT: B 406 ASP cc_start: 0.8126 (t0) cc_final: 0.7655 (t0) REVERT: B 482 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6998 (mm) REVERT: B 489 ASP cc_start: 0.8047 (t70) cc_final: 0.7498 (t0) REVERT: B 502 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8203 (tt) REVERT: B 518 ASN cc_start: 0.8198 (m-40) cc_final: 0.7930 (m-40) REVERT: B 525 ASP cc_start: 0.6839 (t0) cc_final: 0.6195 (p0) REVERT: B 542 ASP cc_start: 0.6998 (m-30) cc_final: 0.6636 (p0) REVERT: B 565 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.7038 (mm) REVERT: C 80 GLU cc_start: 0.8186 (pm20) cc_final: 0.7279 (pm20) REVERT: C 104 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6965 (pp20) REVERT: C 111 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7265 (mt) REVERT: C 139 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6300 (ttm110) REVERT: C 220 LEU cc_start: 0.7928 (mt) cc_final: 0.7267 (pp) REVERT: C 340 MET cc_start: 0.7140 (mmm) cc_final: 0.6731 (mmm) REVERT: C 371 LYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6428 (pmmt) REVERT: C 381 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.5940 (tm-30) REVERT: C 382 ASP cc_start: 0.7079 (m-30) cc_final: 0.6508 (p0) REVERT: C 482 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6984 (mm) REVERT: C 489 ASP cc_start: 0.7890 (t70) cc_final: 0.7088 (t0) REVERT: C 497 MET cc_start: 0.6416 (ttt) cc_final: 0.6159 (tmm) REVERT: C 525 ASP cc_start: 0.6818 (t0) cc_final: 0.6210 (p0) REVERT: C 542 ASP cc_start: 0.7451 (m-30) cc_final: 0.6833 (p0) REVERT: C 565 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7180 (mm) REVERT: C 572 ASN cc_start: 0.8514 (m-40) cc_final: 0.8209 (m-40) REVERT: D 80 GLU cc_start: 0.7104 (pm20) cc_final: 0.6565 (pp20) REVERT: D 104 GLU cc_start: 0.7623 (pm20) cc_final: 0.7273 (pp20) REVERT: D 134 ARG cc_start: 0.7507 (mmm160) cc_final: 0.7121 (tpp80) REVERT: D 195 LEU cc_start: 0.6504 (tp) cc_final: 0.6177 (tt) REVERT: D 209 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6301 (mmmt) REVERT: D 214 GLN cc_start: 0.8436 (mt0) cc_final: 0.7812 (tp-100) REVERT: D 220 LEU cc_start: 0.7207 (mm) cc_final: 0.6750 (mm) REVERT: D 233 GLU cc_start: 0.7514 (tt0) cc_final: 0.6895 (tp30) REVERT: D 246 LEU cc_start: 0.6688 (tp) cc_final: 0.5621 (tt) REVERT: D 250 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6080 (mp0) REVERT: D 260 MET cc_start: 0.6913 (mmt) cc_final: 0.6626 (tpt) REVERT: D 302 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7142 (mtp-110) REVERT: D 381 GLN cc_start: 0.7524 (mt0) cc_final: 0.6721 (tm-30) REVERT: D 455 SER cc_start: 0.8711 (m) cc_final: 0.8339 (p) REVERT: D 481 MET cc_start: 0.7435 (mmm) cc_final: 0.7170 (tpt) REVERT: D 502 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8179 (tt) REVERT: D 515 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7179 (mm-30) REVERT: D 525 ASP cc_start: 0.6874 (t0) cc_final: 0.6077 (p0) REVERT: D 591 GLU cc_start: 0.7994 (tt0) cc_final: 0.7697 (tt0) REVERT: D 608 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6742 (mtm) outliers start: 62 outliers final: 24 residues processed: 341 average time/residue: 0.5187 time to fit residues: 202.7581 Evaluate side-chains 323 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 279 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 69 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 63 optimal weight: 0.0000 chunk 121 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 0.0270 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 0.1980 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 587 GLN C 157 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.176694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124819 restraints weight = 25100.033| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.99 r_work: 0.3503 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20064 Z= 0.099 Angle : 0.621 13.756 27248 Z= 0.295 Chirality : 0.040 0.169 3100 Planarity : 0.003 0.040 3460 Dihedral : 4.742 58.845 2678 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.36 % Allowed : 22.55 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.17), residues: 2440 helix: -0.53 (0.14), residues: 1336 sheet: -3.28 (0.45), residues: 84 loop : -1.93 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 302 TYR 0.017 0.001 TYR B 415 PHE 0.024 0.001 PHE A 574 TRP 0.008 0.001 TRP D 583 HIS 0.003 0.000 HIS D 84 Details of bonding type rmsd covalent geometry : bond 0.00223 (20064) covalent geometry : angle 0.62129 (27248) hydrogen bonds : bond 0.02899 ( 536) hydrogen bonds : angle 3.92538 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 309 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8457 (tp) cc_final: 0.8144 (tm) REVERT: A 43 ARG cc_start: 0.7252 (mmm-85) cc_final: 0.6971 (mmm-85) REVERT: A 80 GLU cc_start: 0.7858 (pm20) cc_final: 0.7002 (pm20) REVERT: A 91 ASN cc_start: 0.6503 (m-40) cc_final: 0.5873 (p0) REVERT: A 111 LEU cc_start: 0.8429 (mm) cc_final: 0.8226 (tp) REVERT: A 113 GLU cc_start: 0.7160 (pm20) cc_final: 0.6923 (pm20) REVERT: A 126 MET cc_start: 0.7779 (tpt) cc_final: 0.6903 (ttm) REVERT: A 127 ASN cc_start: 0.7523 (t0) cc_final: 0.6581 (m110) REVERT: A 139 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7630 (tmt170) REVERT: A 162 TYR cc_start: 0.7656 (m-10) cc_final: 0.7117 (m-10) REVERT: A 220 LEU cc_start: 0.7905 (mt) cc_final: 0.7354 (pp) REVERT: A 269 THR cc_start: 0.8242 (p) cc_final: 0.7942 (t) REVERT: A 322 LYS cc_start: 0.8605 (mttt) cc_final: 0.8141 (mmpt) REVERT: A 381 GLN cc_start: 0.6491 (tm-30) cc_final: 0.5742 (tm-30) REVERT: A 455 SER cc_start: 0.8673 (m) cc_final: 0.8260 (p) REVERT: A 515 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 542 ASP cc_start: 0.7121 (m-30) cc_final: 0.6435 (p0) REVERT: A 554 MET cc_start: 0.6305 (tpp) cc_final: 0.6048 (tpp) REVERT: A 572 ASN cc_start: 0.8066 (m-40) cc_final: 0.7839 (m-40) REVERT: A 629 TRP cc_start: 0.8212 (m100) cc_final: 0.7962 (m100) REVERT: B 38 MET cc_start: 0.7763 (mtp) cc_final: 0.7500 (mtm) REVERT: B 49 LEU cc_start: 0.6889 (tp) cc_final: 0.6640 (pt) REVERT: B 195 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6190 (tt) REVERT: B 214 GLN cc_start: 0.8037 (mt0) cc_final: 0.7704 (mp10) REVERT: B 220 LEU cc_start: 0.7925 (mt) cc_final: 0.7517 (mt) REVERT: B 250 GLU cc_start: 0.8014 (tp30) cc_final: 0.7809 (tp30) REVERT: B 291 SER cc_start: 0.7821 (t) cc_final: 0.7341 (p) REVERT: B 332 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7782 (tm) REVERT: B 381 GLN cc_start: 0.7399 (mt0) cc_final: 0.5901 (tm-30) REVERT: B 406 ASP cc_start: 0.8095 (t0) cc_final: 0.7859 (t70) REVERT: B 482 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6926 (mm) REVERT: B 518 ASN cc_start: 0.8122 (m-40) cc_final: 0.7876 (m-40) REVERT: B 525 ASP cc_start: 0.6868 (t0) cc_final: 0.6360 (p0) REVERT: B 565 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.7005 (mm) REVERT: C 104 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7064 (pp20) REVERT: C 111 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7280 (mt) REVERT: C 139 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6322 (ttm110) REVERT: C 220 LEU cc_start: 0.7899 (mt) cc_final: 0.7255 (pp) REVERT: C 371 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6318 (pmmt) REVERT: C 381 GLN cc_start: 0.6821 (OUTLIER) cc_final: 0.5944 (tm-30) REVERT: C 382 ASP cc_start: 0.7030 (m-30) cc_final: 0.6575 (p0) REVERT: C 525 ASP cc_start: 0.6830 (t0) cc_final: 0.6304 (p0) REVERT: C 542 ASP cc_start: 0.7311 (m-30) cc_final: 0.6913 (p0) REVERT: C 565 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7155 (mm) REVERT: C 572 ASN cc_start: 0.8485 (m-40) cc_final: 0.8174 (m-40) REVERT: D 80 GLU cc_start: 0.7033 (pm20) cc_final: 0.6475 (pp20) REVERT: D 134 ARG cc_start: 0.7530 (mmm160) cc_final: 0.7114 (tpp80) REVERT: D 195 LEU cc_start: 0.6548 (tp) cc_final: 0.6222 (tt) REVERT: D 209 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6297 (mmmt) REVERT: D 214 GLN cc_start: 0.8560 (mt0) cc_final: 0.7882 (tp-100) REVERT: D 233 GLU cc_start: 0.7573 (tt0) cc_final: 0.6957 (tp30) REVERT: D 246 LEU cc_start: 0.6479 (tp) cc_final: 0.5387 (tt) REVERT: D 250 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.5978 (mp0) REVERT: D 260 MET cc_start: 0.6755 (mmt) cc_final: 0.6361 (tpt) REVERT: D 302 ARG cc_start: 0.7620 (ttp-110) cc_final: 0.7198 (mtp-110) REVERT: D 381 GLN cc_start: 0.7388 (mt0) cc_final: 0.6601 (tm-30) REVERT: D 455 SER cc_start: 0.8702 (m) cc_final: 0.8353 (p) REVERT: D 502 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8163 (tt) REVERT: D 515 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7025 (mm-30) REVERT: D 525 ASP cc_start: 0.6814 (t0) cc_final: 0.6306 (p0) REVERT: D 608 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6661 (mtm) outliers start: 50 outliers final: 18 residues processed: 347 average time/residue: 0.5220 time to fit residues: 207.4605 Evaluate side-chains 317 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 284 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 64 optimal weight: 0.2980 chunk 217 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.0030 chunk 58 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 587 GLN C 157 HIS C 217 ASN D 519 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.176525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124577 restraints weight = 25479.337| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 3.01 r_work: 0.3519 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.094 20064 Z= 0.106 Angle : 0.649 14.682 27248 Z= 0.309 Chirality : 0.040 0.229 3100 Planarity : 0.003 0.048 3460 Dihedral : 4.710 57.285 2678 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.41 % Allowed : 23.92 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.17), residues: 2440 helix: -0.37 (0.15), residues: 1332 sheet: -3.30 (0.44), residues: 84 loop : -1.80 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 139 TYR 0.018 0.001 TYR B 415 PHE 0.028 0.001 PHE A 574 TRP 0.008 0.001 TRP D 583 HIS 0.003 0.000 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00247 (20064) covalent geometry : angle 0.64945 (27248) hydrogen bonds : bond 0.02974 ( 536) hydrogen bonds : angle 3.98560 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 299 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.8570 (tp) cc_final: 0.8294 (tm) REVERT: A 43 ARG cc_start: 0.7299 (mmm-85) cc_final: 0.7040 (mmm-85) REVERT: A 91 ASN cc_start: 0.6511 (m-40) cc_final: 0.5917 (p0) REVERT: A 111 LEU cc_start: 0.8451 (mm) cc_final: 0.8234 (tp) REVERT: A 113 GLU cc_start: 0.7122 (pm20) cc_final: 0.6908 (pm20) REVERT: A 126 MET cc_start: 0.7831 (tpt) cc_final: 0.6963 (ttm) REVERT: A 127 ASN cc_start: 0.7526 (t0) cc_final: 0.6676 (m110) REVERT: A 139 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7630 (tmt170) REVERT: A 220 LEU cc_start: 0.7928 (mt) cc_final: 0.7393 (pp) REVERT: A 269 THR cc_start: 0.8248 (p) cc_final: 0.7928 (t) REVERT: A 286 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.6353 (m-10) REVERT: A 303 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7646 (mp0) REVERT: A 322 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8152 (mmpt) REVERT: A 381 GLN cc_start: 0.6438 (tm-30) cc_final: 0.5763 (tm-30) REVERT: A 442 MET cc_start: 0.6931 (mtt) cc_final: 0.6510 (mtt) REVERT: A 455 SER cc_start: 0.8697 (m) cc_final: 0.8314 (p) REVERT: A 497 MET cc_start: 0.6348 (ttt) cc_final: 0.6033 (tmm) REVERT: A 515 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7112 (mm-30) REVERT: A 520 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6919 (tt) REVERT: A 542 ASP cc_start: 0.7072 (m-30) cc_final: 0.6531 (p0) REVERT: A 554 MET cc_start: 0.6373 (tpp) cc_final: 0.6153 (mmt) REVERT: A 572 ASN cc_start: 0.8082 (m-40) cc_final: 0.7785 (m-40) REVERT: A 587 GLN cc_start: 0.7947 (mp10) cc_final: 0.7431 (pt0) REVERT: A 629 TRP cc_start: 0.8135 (m100) cc_final: 0.7867 (m100) REVERT: B 38 MET cc_start: 0.7826 (mtp) cc_final: 0.7552 (mtm) REVERT: B 49 LEU cc_start: 0.6916 (tp) cc_final: 0.6677 (pt) REVERT: B 195 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6401 (tp) REVERT: B 214 GLN cc_start: 0.8028 (mt0) cc_final: 0.7703 (mp10) REVERT: B 220 LEU cc_start: 0.7945 (mt) cc_final: 0.7533 (mt) REVERT: B 238 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7321 (m170) REVERT: B 250 GLU cc_start: 0.7752 (tp30) cc_final: 0.7191 (mp0) REVERT: B 291 SER cc_start: 0.7832 (t) cc_final: 0.7354 (p) REVERT: B 332 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7722 (tm) REVERT: B 381 GLN cc_start: 0.7412 (mt0) cc_final: 0.6192 (tm-30) REVERT: B 406 ASP cc_start: 0.8090 (t0) cc_final: 0.7849 (t70) REVERT: B 497 MET cc_start: 0.6986 (tmm) cc_final: 0.6109 (tpt) REVERT: B 518 ASN cc_start: 0.8132 (m-40) cc_final: 0.7853 (m-40) REVERT: B 525 ASP cc_start: 0.6886 (t0) cc_final: 0.6305 (p0) REVERT: B 565 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.7033 (mm) REVERT: B 635 ASN cc_start: 0.7752 (m110) cc_final: 0.7360 (m110) REVERT: C 104 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7041 (pp20) REVERT: C 111 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7294 (mt) REVERT: C 139 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6372 (ttm110) REVERT: C 200 LEU cc_start: 0.8014 (tt) cc_final: 0.7799 (mm) REVERT: C 214 GLN cc_start: 0.7863 (mt0) cc_final: 0.7640 (mp10) REVERT: C 220 LEU cc_start: 0.7828 (mt) cc_final: 0.7222 (pp) REVERT: C 371 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.6355 (pmmt) REVERT: C 381 GLN cc_start: 0.6816 (OUTLIER) cc_final: 0.5564 (tm-30) REVERT: C 382 ASP cc_start: 0.7144 (m-30) cc_final: 0.6812 (p0) REVERT: C 497 MET cc_start: 0.6955 (tmm) cc_final: 0.6192 (tpt) REVERT: C 506 SER cc_start: 0.9015 (t) cc_final: 0.8494 (p) REVERT: C 525 ASP cc_start: 0.6895 (t0) cc_final: 0.6393 (p0) REVERT: C 542 ASP cc_start: 0.7314 (m-30) cc_final: 0.6899 (p0) REVERT: C 565 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.7095 (mm) REVERT: C 572 ASN cc_start: 0.8484 (m-40) cc_final: 0.8139 (m-40) REVERT: D 80 GLU cc_start: 0.7120 (pm20) cc_final: 0.6564 (pp20) REVERT: D 134 ARG cc_start: 0.7502 (mmm160) cc_final: 0.7060 (tpp80) REVERT: D 195 LEU cc_start: 0.6586 (tp) cc_final: 0.6234 (tp) REVERT: D 209 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6433 (mmmt) REVERT: D 233 GLU cc_start: 0.7537 (tt0) cc_final: 0.7041 (tp30) REVERT: D 246 LEU cc_start: 0.6437 (tp) cc_final: 0.5437 (tt) REVERT: D 250 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6087 (mp0) REVERT: D 302 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7253 (mtp-110) REVERT: D 381 GLN cc_start: 0.7363 (mt0) cc_final: 0.6651 (tm-30) REVERT: D 455 SER cc_start: 0.8722 (m) cc_final: 0.8378 (p) REVERT: D 502 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8199 (tt) REVERT: D 515 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7019 (mm-30) REVERT: D 525 ASP cc_start: 0.6875 (t0) cc_final: 0.6244 (p0) REVERT: D 608 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6630 (mtm) outliers start: 51 outliers final: 24 residues processed: 336 average time/residue: 0.5261 time to fit residues: 202.3477 Evaluate side-chains 326 residues out of total 2120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 285 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 286 TRP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain C residue 104 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 139 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 501 ILE Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 570 MET Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 209 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 173 optimal weight: 0.2980 chunk 158 optimal weight: 0.5980 chunk 167 optimal weight: 0.8980 chunk 228 optimal weight: 0.6980 chunk 150 optimal weight: 0.1980 chunk 214 optimal weight: 3.9990 chunk 126 optimal weight: 0.0980 chunk 42 optimal weight: 0.0980 chunk 88 optimal weight: 5.9990 overall best weight: 0.2580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 587 GLN C 129 ASN C 157 HIS C 158 ASN D 572 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.177972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.126208 restraints weight = 25396.254| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.99 r_work: 0.3549 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.6719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 20064 Z= 0.102 Angle : 0.647 14.113 27248 Z= 0.305 Chirality : 0.040 0.215 3100 Planarity : 0.003 0.034 3460 Dihedral : 4.603 57.329 2678 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.45 % Allowed : 23.92 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.17), residues: 2440 helix: -0.13 (0.15), residues: 1304 sheet: -3.30 (0.43), residues: 84 loop : -1.69 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 302 TYR 0.018 0.001 TYR B 415 PHE 0.020 0.001 PHE D 553 TRP 0.009 0.001 TRP C 629 HIS 0.003 0.000 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00233 (20064) covalent geometry : angle 0.64701 (27248) hydrogen bonds : bond 0.02774 ( 536) hydrogen bonds : angle 3.93485 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6216.17 seconds wall clock time: 106 minutes 55.34 seconds (6415.34 seconds total)