Starting phenix.real_space_refine on Thu Mar 5 21:28:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y75_33652/03_2026/7y75_33652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y75_33652/03_2026/7y75_33652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y75_33652/03_2026/7y75_33652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y75_33652/03_2026/7y75_33652.map" model { file = "/net/cci-nas-00/data/ceres_data/7y75_33652/03_2026/7y75_33652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y75_33652/03_2026/7y75_33652.cif" } resolution = 3.1 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= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 S 146 5.16 5 C 16350 2.51 5 N 4004 2.21 5 O 4678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 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: 25186 Number of models: 1 Model: "" Number of chains: 26 Chain: "B" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4499 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 552} Chain: "A" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6102 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 35, 'TRANS': 714} Chain: "E" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "D" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4499 Classifications: {'peptide': 573} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 552} Chain: "C" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6102 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 35, 'TRANS': 714} Chain: "F" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1581 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PH': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 172 Unusual residues: {'3PH': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.40, per 1000 atoms: 0.21 Number of scatterers: 25186 At special positions: 0 Unit cell: (116.309, 151.093, 217.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 146 16.00 P 6 15.00 O 4678 8.00 N 4004 7.00 C 16350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 139 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.05 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.00 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 358 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.05 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.04 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.04 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 901 " - " ASN A 322 " " NAG B1001 " - " ASN B 131 " " NAG B1002 " - " ASN B 332 " " NAG C 901 " - " ASN C 322 " " NAG D1001 " - " ASN D 131 " " NAG D1002 " - " ASN D 332 " " NAG G 1 " - " ASN B 357 " " NAG H 1 " - " ASN A 53 " " NAG I 1 " - " ASN A 90 " " NAG J 1 " - " ASN A 103 " " NAG K 1 " - " ASN A 432 " " NAG L 1 " - " ASN A 546 " " NAG M 1 " - " ASN A 690 " " NAG N 1 " - " ASN E 343 " " NAG O 1 " - " ASN D 357 " " NAG P 1 " - " ASN C 53 " " NAG Q 1 " - " ASN C 90 " " NAG R 1 " - " ASN C 103 " " NAG S 1 " - " ASN C 432 " " NAG T 1 " - " ASN C 546 " " NAG U 1 " - " ASN C 690 " " NAG V 1 " - " ASN F 343 " Time building additional restraints: 2.31 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 378 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 374 " pdb="ZN ZN C 902 " - pdb=" NE2 HIS C 378 " 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5704 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 14 sheets defined 61.1% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 11 through 23 removed outlier: 4.160A pdb=" N VAL B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.882A pdb=" N TYR B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 55 removed outlier: 3.827A pdb=" N LEU B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 56 through 70 Processing helix chain 'B' and resid 72 through 81 removed outlier: 4.357A pdb=" N TRP B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 85 through 115 removed outlier: 4.132A pdb=" N VAL B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET B 100 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 105 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.741A pdb=" N PHE B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 187 removed outlier: 3.565A pdb=" N ARG B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 201 through 216 removed outlier: 3.857A pdb=" N THR B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.569A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.799A pdb=" N TRP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 253 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 263 removed outlier: 3.613A pdb=" N ALA B 261 " --> pdb=" O GLY B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 321 removed outlier: 4.066A pdb=" N HIS B 275 " --> pdb=" O ASN B 271 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 340 Processing helix chain 'B' and resid 344 through 350 removed outlier: 4.456A pdb=" N GLU B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.750A pdb=" N THR B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 387 through 416 removed outlier: 4.007A pdb=" N TRP B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA B 413 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 445 Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.563A pdb=" N THR B 449 " --> pdb=" O MET B 446 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET B 450 " --> pdb=" O VAL B 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 446 through 450' Processing helix chain 'B' and resid 452 through 483 removed outlier: 3.913A pdb=" N TRP B 456 " --> pdb=" O ALA B 452 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 498 Processing helix chain 'B' and resid 502 through 511 removed outlier: 3.516A pdb=" N ALA B 510 " --> pdb=" O LYS B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 530 removed outlier: 4.028A pdb=" N VAL B 518 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 3.576A pdb=" N LEU B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 558 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 580 removed outlier: 3.767A pdb=" N PHE B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 53 Processing helix chain 'A' and resid 56 through 80 removed outlier: 3.776A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.755A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.669A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.590A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.691A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 231 removed outlier: 4.073A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.721A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.695A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 366 through 385 removed outlier: 3.929A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.663A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.589A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 4.007A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.722A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.606A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.603A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.653A pdb=" N ALA A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 658 removed outlier: 3.634A pdb=" N MET A 640 " --> pdb=" O ASN A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 696 through 715 removed outlier: 3.639A pdb=" N SER A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N SER A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 710 " --> pdb=" O MET A 706 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 715 " --> pdb=" O ILE A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 767 removed outlier: 3.946A pdb=" N VAL A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 removed outlier: 4.134A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.577A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.579A pdb=" N TYR E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.635A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.882A pdb=" N TYR D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 55 removed outlier: 3.827A pdb=" N LEU D 44 " --> pdb=" O GLY D 40 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 56 through 70 Processing helix chain 'D' and resid 72 through 81 removed outlier: 4.356A pdb=" N TRP D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 81 " --> pdb=" O TRP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 84 No H-bonds generated for 'chain 'D' and resid 82 through 84' Processing helix chain 'D' and resid 85 through 115 removed outlier: 4.131A pdb=" N VAL D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N MET D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL D 104 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN D 106 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 143 through 151 removed outlier: 3.741A pdb=" N PHE D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 187 removed outlier: 3.564A pdb=" N ARG D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.857A pdb=" N THR D 216 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.569A pdb=" N LEU D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.800A pdb=" N TRP D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 253 " --> pdb=" O PHE D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 263 removed outlier: 3.613A pdb=" N ALA D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 321 removed outlier: 4.066A pdb=" N HIS D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE D 292 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 321 " --> pdb=" O LEU D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 340 Processing helix chain 'D' and resid 344 through 350 removed outlier: 4.457A pdb=" N GLU D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.750A pdb=" N THR D 366 " --> pdb=" O SER D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 379 Processing helix chain 'D' and resid 387 through 416 removed outlier: 4.007A pdb=" N TRP D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA D 413 " --> pdb=" O GLY D 409 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 445 Processing helix chain 'D' and resid 446 through 450 removed outlier: 3.563A pdb=" N THR D 449 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET D 450 " --> pdb=" O VAL D 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 446 through 450' Processing helix chain 'D' and resid 452 through 483 removed outlier: 3.913A pdb=" N TRP D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP D 462 " --> pdb=" O ASP D 458 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA D 464 " --> pdb=" O PHE D 460 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU D 469 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 498 Processing helix chain 'D' and resid 502 through 511 removed outlier: 3.517A pdb=" N ALA D 510 " --> pdb=" O LYS D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 530 removed outlier: 4.028A pdb=" N VAL D 518 " --> pdb=" O PRO D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 removed outlier: 3.575A pdb=" N LEU D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA D 557 " --> pdb=" O ALA D 553 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL D 558 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 580 removed outlier: 3.766A pdb=" N PHE D 578 " --> pdb=" O ALA D 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 Processing helix chain 'C' and resid 56 through 80 removed outlier: 3.776A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 65 " --> pdb=" O ASN C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.755A pdb=" N GLN C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.670A pdb=" N ILE C 151 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.591A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 176 through 193 removed outlier: 3.691A pdb=" N GLU C 182 " --> pdb=" O PRO C 178 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 220 through 231 removed outlier: 4.074A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.721A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 294 through 299 Processing helix chain 'C' and resid 303 through 318 removed outlier: 3.694A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 366 through 385 removed outlier: 3.929A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 393 removed outlier: 3.664A pdb=" N ARG C 393 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 412 removed outlier: 3.588A pdb=" N ALA C 403 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 Processing helix chain 'C' and resid 431 through 447 removed outlier: 4.006A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 466 Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.722A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE C 523 " --> pdb=" O THR C 519 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 547 through 559 removed outlier: 3.606A pdb=" N GLY C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.603A pdb=" N LEU C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'C' and resid 623 through 629 removed outlier: 3.653A pdb=" N ALA C 627 " --> pdb=" O SER C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 658 removed outlier: 3.634A pdb=" N MET C 640 " --> pdb=" O ASN C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 696 through 715 removed outlier: 3.640A pdb=" N SER C 707 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N SER C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG C 710 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 715 " --> pdb=" O ILE C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 767 removed outlier: 3.640A pdb=" N VAL C 745 " --> pdb=" O ILE C 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 removed outlier: 4.134A pdb=" N VAL F 341 " --> pdb=" O PRO F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 410 removed outlier: 3.577A pdb=" N GLU F 406 " --> pdb=" O ARG F 403 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.579A pdb=" N TYR F 421 " --> pdb=" O ASN F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.636A pdb=" N SER F 443 " --> pdb=" O ASN F 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.869A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.215A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 670 through 676 removed outlier: 4.035A pdb=" N LEU A 675 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N SER A 680 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS A 619 " --> pdb=" O LEU A 725 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.845A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'C' and resid 132 through 133 Processing sheet with id=AA9, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.869A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.216A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 670 through 676 removed outlier: 4.034A pdb=" N LEU C 675 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER C 680 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS C 619 " --> pdb=" O LEU C 725 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.845A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'F' and resid 473 through 474 1219 hydrogen bonds defined for protein. 3555 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: 4.33 Time building geometry restraints manager: 3.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7722 1.34 - 1.47: 6850 1.47 - 1.59: 11036 1.59 - 1.72: 6 1.72 - 1.84: 232 Bond restraints: 25846 Sorted by residual: bond pdb=" C31 3PH B1003 " pdb=" O31 3PH B1003 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" C31 3PH D1003 " pdb=" O31 3PH D1003 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C31 3PH D1005 " pdb=" O31 3PH D1005 " ideal model delta sigma weight residual 1.325 1.455 -0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" C31 3PH B1005 " pdb=" O31 3PH B1005 " ideal model delta sigma weight residual 1.325 1.454 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C21 3PH D1003 " pdb=" O21 3PH D1003 " ideal model delta sigma weight residual 1.328 1.456 -0.128 2.00e-02 2.50e+03 4.10e+01 ... (remaining 25841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 34311 2.29 - 4.58: 648 4.58 - 6.88: 94 6.88 - 9.17: 22 9.17 - 11.46: 3 Bond angle restraints: 35078 Sorted by residual: angle pdb=" N ARG A 678 " pdb=" CA ARG A 678 " pdb=" C ARG A 678 " ideal model delta sigma weight residual 112.93 105.68 7.25 1.12e+00 7.97e-01 4.19e+01 angle pdb=" N ARG C 678 " pdb=" CA ARG C 678 " pdb=" C ARG C 678 " ideal model delta sigma weight residual 112.93 105.69 7.24 1.12e+00 7.97e-01 4.17e+01 angle pdb=" C LEU C 267 " pdb=" N GLY C 268 " pdb=" CA GLY C 268 " ideal model delta sigma weight residual 123.08 117.67 5.41 1.12e+00 7.97e-01 2.33e+01 angle pdb=" C LEU A 267 " pdb=" N GLY A 268 " pdb=" CA GLY A 268 " ideal model delta sigma weight residual 123.08 117.71 5.37 1.12e+00 7.97e-01 2.30e+01 angle pdb=" CA PRO A 737 " pdb=" N PRO A 737 " pdb=" CD PRO A 737 " ideal model delta sigma weight residual 112.00 106.33 5.67 1.40e+00 5.10e-01 1.64e+01 ... (remaining 35073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 13659 17.87 - 35.74: 1530 35.74 - 53.61: 440 53.61 - 71.48: 87 71.48 - 89.35: 30 Dihedral angle restraints: 15746 sinusoidal: 6842 harmonic: 8904 Sorted by residual: dihedral pdb=" CB CYS F 379 " pdb=" SG CYS F 379 " pdb=" SG CYS F 432 " pdb=" CB CYS F 432 " ideal model delta sinusoidal sigma weight residual 93.00 12.80 80.20 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 15.48 77.52 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS F 391 " pdb=" SG CYS F 391 " pdb=" SG CYS F 525 " pdb=" CB CYS F 525 " ideal model delta sinusoidal sigma weight residual 93.00 25.07 67.93 1 1.00e+01 1.00e-02 5.99e+01 ... (remaining 15743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 3777 0.108 - 0.216: 115 0.216 - 0.324: 8 0.324 - 0.432: 0 0.432 - 0.540: 2 Chirality restraints: 3902 Sorted by residual: chirality pdb=" C1 NAG D1001 " pdb=" ND2 ASN D 131 " pdb=" C2 NAG D1001 " pdb=" O5 NAG D1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.30e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 131 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.24e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3899 not shown) Planarity restraints: 4390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 737 " 0.054 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO A 738 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 733 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO A 734 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 734 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 734 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 522 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C GLN A 522 " 0.032 2.00e-02 2.50e+03 pdb=" O GLN A 522 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE A 523 " -0.011 2.00e-02 2.50e+03 ... (remaining 4387 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 135 2.52 - 3.12: 19062 3.12 - 3.71: 37335 3.71 - 4.31: 53565 4.31 - 4.90: 89817 Nonbonded interactions: 199914 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 902 " model vdw 1.927 2.230 nonbonded pdb=" OE2 GLU C 402 " pdb="ZN ZN C 902 " model vdw 1.928 2.230 nonbonded pdb=" O LEU D 113 " pdb=" OG SER D 116 " model vdw 2.206 3.040 nonbonded pdb=" O LEU B 113 " pdb=" OG SER B 116 " model vdw 2.206 3.040 nonbonded pdb=" O LEU D 121 " pdb=" OG SER D 124 " model vdw 2.212 3.040 ... (remaining 199909 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.680 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 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 : 0.010 0.553 25902 Z= 0.419 Angle : 0.868 27.545 35220 Z= 0.443 Chirality : 0.051 0.540 3902 Planarity : 0.004 0.082 4368 Dihedral : 16.438 89.352 10000 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.10 % Favored : 92.74 % Rotamer: Outliers : 4.43 % Allowed : 14.70 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -2.95 (0.13), residues: 3030 helix: -1.28 (0.11), residues: 1680 sheet: -1.40 (0.44), residues: 142 loop : -2.94 (0.15), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 115 TYR 0.018 0.002 TYR A 385 PHE 0.016 0.002 PHE D 295 TRP 0.015 0.002 TRP B 111 HIS 0.008 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00842 (25846) covalent geometry : angle 0.80457 (35078) SS BOND : bond 0.01221 ( 14) SS BOND : angle 7.56156 ( 28) hydrogen bonds : bond 0.15337 ( 1219) hydrogen bonds : angle 6.04040 ( 3555) metal coordination : bond 0.44064 ( 4) link_BETA1-4 : bond 0.00609 ( 16) link_BETA1-4 : angle 2.63897 ( 48) link_NAG-ASN : bond 0.01000 ( 22) link_NAG-ASN : angle 5.32260 ( 66) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 293 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 135 TYR cc_start: 0.8586 (m-10) cc_final: 0.8371 (m-10) REVERT: B 175 LEU cc_start: 0.7041 (mp) cc_final: 0.6818 (mp) REVERT: B 361 GLU cc_start: 0.8255 (pt0) cc_final: 0.7608 (tm-30) REVERT: B 446 MET cc_start: 0.7585 (tpp) cc_final: 0.7375 (mpp) REVERT: B 534 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.4244 (tp) REVERT: B 545 GLN cc_start: 0.7471 (mt0) cc_final: 0.6946 (mt0) REVERT: A 67 ASP cc_start: 0.7979 (m-30) cc_final: 0.7630 (m-30) REVERT: A 114 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8226 (mtpp) REVERT: A 270 MET cc_start: 0.9104 (tpp) cc_final: 0.8857 (tpp) REVERT: A 564 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8129 (mp0) REVERT: A 719 ASP cc_start: 0.8046 (t0) cc_final: 0.7712 (t0) REVERT: E 369 TYR cc_start: 0.6206 (t80) cc_final: 0.6003 (t80) REVERT: E 406 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7794 (mt-10) REVERT: E 432 CYS cc_start: 0.4689 (OUTLIER) cc_final: 0.4263 (m) REVERT: E 464 PHE cc_start: 0.8156 (m-80) cc_final: 0.7840 (m-80) REVERT: D 100 MET cc_start: 0.6372 (ptm) cc_final: 0.6119 (ptm) REVERT: D 135 TYR cc_start: 0.8620 (m-10) cc_final: 0.8374 (m-10) REVERT: D 361 GLU cc_start: 0.8317 (pt0) cc_final: 0.7664 (tm-30) REVERT: D 534 LEU cc_start: 0.5139 (OUTLIER) cc_final: 0.4226 (tp) REVERT: D 545 GLN cc_start: 0.7397 (mt0) cc_final: 0.6860 (mt0) REVERT: C 67 ASP cc_start: 0.8073 (m-30) cc_final: 0.7742 (m-30) REVERT: C 114 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8222 (mtpp) REVERT: C 270 MET cc_start: 0.9176 (tpp) cc_final: 0.8884 (tpp) REVERT: C 564 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8129 (mp0) REVERT: C 719 ASP cc_start: 0.8067 (t0) cc_final: 0.7699 (t0) REVERT: F 406 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7802 (mt-10) REVERT: F 432 CYS cc_start: 0.4947 (OUTLIER) cc_final: 0.4427 (m) REVERT: F 464 PHE cc_start: 0.8156 (m-80) cc_final: 0.7850 (m-80) outliers start: 117 outliers final: 75 residues processed: 398 average time/residue: 0.1646 time to fit residues: 104.6351 Evaluate side-chains 319 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 240 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 634 GLU Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 679 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 523 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 634 GLU Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain F residue 432 CYS Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 523 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 71 GLN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 58 ASN A 98 GLN A 137 ASN A 139 GLN A 159 ASN A 210 ASN A 239 HIS A 277 ASN A 401 HIS A 437 ASN A 472 GLN A 493 HIS A 505 HIS A 718 ASN A 735 ASN E 422 ASN D 71 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN ** D 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 98 GLN C 137 ASN C 139 GLN C 159 ASN C 210 ASN C 239 HIS C 401 HIS C 437 ASN C 472 GLN C 493 HIS C 505 HIS C 718 ASN F 422 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.171306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093171 restraints weight = 36721.914| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.74 r_work: 0.2809 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25902 Z= 0.194 Angle : 0.681 16.924 35220 Z= 0.332 Chirality : 0.045 0.318 3902 Planarity : 0.005 0.071 4368 Dihedral : 11.108 76.674 4509 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.14 % Favored : 93.73 % Rotamer: Outliers : 4.13 % Allowed : 16.86 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -1.49 (0.15), residues: 3030 helix: 0.07 (0.13), residues: 1656 sheet: -1.12 (0.45), residues: 142 loop : -2.47 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 493 TYR 0.046 0.002 TYR B 21 PHE 0.015 0.001 PHE A 684 TRP 0.014 0.001 TRP B 168 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00463 (25846) covalent geometry : angle 0.65155 (35078) SS BOND : bond 0.00675 ( 14) SS BOND : angle 1.47577 ( 28) hydrogen bonds : bond 0.05266 ( 1219) hydrogen bonds : angle 4.44113 ( 3555) metal coordination : bond 0.02605 ( 4) link_BETA1-4 : bond 0.00519 ( 16) link_BETA1-4 : angle 2.08201 ( 48) link_NAG-ASN : bond 0.00704 ( 22) link_NAG-ASN : angle 4.22357 ( 66) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 253 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6785 (mp) REVERT: B 344 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.6517 (p90) REVERT: B 361 GLU cc_start: 0.8389 (pt0) cc_final: 0.7551 (tm-30) REVERT: B 534 LEU cc_start: 0.5370 (OUTLIER) cc_final: 0.4380 (tp) REVERT: B 537 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.6167 (mt0) REVERT: B 545 GLN cc_start: 0.7173 (mt0) cc_final: 0.6641 (mt0) REVERT: A 67 ASP cc_start: 0.8399 (m-30) cc_final: 0.7986 (m-30) REVERT: A 114 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8544 (mtpp) REVERT: A 256 ILE cc_start: 0.9714 (OUTLIER) cc_final: 0.9348 (mm) REVERT: A 270 MET cc_start: 0.9333 (tpp) cc_final: 0.9090 (tpp) REVERT: A 368 ASP cc_start: 0.8823 (m-30) cc_final: 0.8533 (m-30) REVERT: A 564 GLU cc_start: 0.9282 (mm-30) cc_final: 0.9005 (mp0) REVERT: A 596 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8899 (mtpt) REVERT: A 719 ASP cc_start: 0.8426 (t0) cc_final: 0.7956 (t0) REVERT: E 369 TYR cc_start: 0.6160 (t80) cc_final: 0.5887 (t80) REVERT: E 392 PHE cc_start: 0.7522 (p90) cc_final: 0.7210 (p90) REVERT: E 406 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7970 (mt-10) REVERT: E 454 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8026 (ttm170) REVERT: E 464 PHE cc_start: 0.8212 (m-80) cc_final: 0.7823 (m-80) REVERT: D 69 MET cc_start: 0.6164 (tpt) cc_final: 0.5805 (tpt) REVERT: D 281 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6798 (mp) REVERT: D 344 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.6542 (p90) REVERT: D 361 GLU cc_start: 0.8381 (pt0) cc_final: 0.7578 (tm-30) REVERT: D 385 MET cc_start: 0.7580 (mtm) cc_final: 0.7321 (mtm) REVERT: D 390 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6461 (tt) REVERT: D 446 MET cc_start: 0.7265 (tpp) cc_final: 0.7011 (mpp) REVERT: D 534 LEU cc_start: 0.5175 (OUTLIER) cc_final: 0.4226 (tp) REVERT: D 537 GLN cc_start: 0.6395 (OUTLIER) cc_final: 0.6135 (mt0) REVERT: C 67 ASP cc_start: 0.8525 (m-30) cc_final: 0.8120 (m-30) REVERT: C 114 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8531 (mtpp) REVERT: C 256 ILE cc_start: 0.9717 (OUTLIER) cc_final: 0.9349 (mm) REVERT: C 270 MET cc_start: 0.9352 (tpp) cc_final: 0.9071 (tpp) REVERT: C 368 ASP cc_start: 0.8746 (m-30) cc_final: 0.8475 (m-30) REVERT: C 564 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9051 (mp0) REVERT: C 596 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.8886 (mtpt) REVERT: C 719 ASP cc_start: 0.8451 (t0) cc_final: 0.7975 (t0) REVERT: F 369 TYR cc_start: 0.6671 (t80) cc_final: 0.6225 (t80) REVERT: F 392 PHE cc_start: 0.7534 (p90) cc_final: 0.7246 (p90) REVERT: F 406 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8083 (mt-10) REVERT: F 454 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8012 (ttm170) REVERT: F 464 PHE cc_start: 0.8213 (m-80) cc_final: 0.7828 (m-80) outliers start: 109 outliers final: 63 residues processed: 345 average time/residue: 0.1471 time to fit residues: 83.9885 Evaluate side-chains 312 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 236 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 735 ASN Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 488 CYS Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 760 LEU Chi-restraints excluded: chain F residue 379 CYS Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 518 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 279 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 69 optimal weight: 0.0770 chunk 75 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS ** D 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN C 378 HIS C 718 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.170629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.092821 restraints weight = 36667.235| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.64 r_work: 0.2804 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.711 25902 Z= 0.302 Angle : 0.672 15.796 35220 Z= 0.328 Chirality : 0.045 0.253 3902 Planarity : 0.004 0.075 4368 Dihedral : 10.168 76.318 4448 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.34 % Favored : 93.50 % Rotamer: Outliers : 4.55 % Allowed : 17.20 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -1.06 (0.15), residues: 3030 helix: 0.39 (0.13), residues: 1664 sheet: -0.88 (0.46), residues: 142 loop : -2.26 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 493 TYR 0.038 0.001 TYR B 21 PHE 0.015 0.001 PHE A 684 TRP 0.013 0.001 TRP A 478 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00529 (25846) covalent geometry : angle 0.64126 (35078) SS BOND : bond 0.00978 ( 14) SS BOND : angle 1.84437 ( 28) hydrogen bonds : bond 0.05256 ( 1219) hydrogen bonds : angle 4.33278 ( 3555) metal coordination : bond 0.50237 ( 4) link_BETA1-4 : bond 0.00473 ( 16) link_BETA1-4 : angle 2.12731 ( 48) link_NAG-ASN : bond 0.00658 ( 22) link_NAG-ASN : angle 4.23412 ( 66) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 248 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 MET cc_start: 0.6306 (tpt) cc_final: 0.6000 (tpt) REVERT: B 175 LEU cc_start: 0.6849 (mp) cc_final: 0.6606 (mp) REVERT: B 281 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6775 (mp) REVERT: B 344 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.6163 (p90) REVERT: B 361 GLU cc_start: 0.8412 (pt0) cc_final: 0.7533 (tm-30) REVERT: B 534 LEU cc_start: 0.5355 (OUTLIER) cc_final: 0.4448 (tp) REVERT: B 537 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.6150 (mt0) REVERT: B 545 GLN cc_start: 0.7238 (mt0) cc_final: 0.6771 (mt0) REVERT: A 67 ASP cc_start: 0.8486 (m-30) cc_final: 0.8056 (m-30) REVERT: A 114 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8548 (mtpp) REVERT: A 183 TYR cc_start: 0.9543 (OUTLIER) cc_final: 0.9119 (t80) REVERT: A 256 ILE cc_start: 0.9709 (OUTLIER) cc_final: 0.9357 (mm) REVERT: A 368 ASP cc_start: 0.8728 (m-30) cc_final: 0.8477 (m-30) REVERT: A 527 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8928 (tt0) REVERT: A 564 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9052 (mp0) REVERT: A 719 ASP cc_start: 0.8522 (t0) cc_final: 0.8089 (t0) REVERT: E 369 TYR cc_start: 0.6498 (t80) cc_final: 0.6218 (t80) REVERT: E 392 PHE cc_start: 0.7603 (p90) cc_final: 0.7272 (p90) REVERT: E 406 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8053 (mt-10) REVERT: E 414 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8320 (mm-40) REVERT: E 454 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8040 (ttm170) REVERT: E 464 PHE cc_start: 0.8136 (m-80) cc_final: 0.7772 (m-80) REVERT: D 281 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6775 (mp) REVERT: D 344 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.6140 (p90) REVERT: D 361 GLU cc_start: 0.8406 (pt0) cc_final: 0.7561 (tm-30) REVERT: D 380 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7301 (tm-30) REVERT: D 385 MET cc_start: 0.7616 (mtm) cc_final: 0.7369 (mtm) REVERT: D 446 MET cc_start: 0.7357 (tpp) cc_final: 0.7088 (mpp) REVERT: D 503 TRP cc_start: 0.4010 (m100) cc_final: 0.3284 (m-90) REVERT: D 537 GLN cc_start: 0.6186 (OUTLIER) cc_final: 0.5933 (mt0) REVERT: D 545 GLN cc_start: 0.7131 (mt0) cc_final: 0.6660 (mt0) REVERT: C 67 ASP cc_start: 0.8399 (m-30) cc_final: 0.7970 (m-30) REVERT: C 114 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8555 (mtpp) REVERT: C 183 TYR cc_start: 0.9533 (OUTLIER) cc_final: 0.9178 (t80) REVERT: C 256 ILE cc_start: 0.9711 (OUTLIER) cc_final: 0.9363 (mm) REVERT: C 368 ASP cc_start: 0.8722 (m-30) cc_final: 0.8452 (m-30) REVERT: C 527 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8916 (tt0) REVERT: C 564 GLU cc_start: 0.9304 (mm-30) cc_final: 0.9037 (mp0) REVERT: C 719 ASP cc_start: 0.8534 (t0) cc_final: 0.8074 (t0) REVERT: F 369 TYR cc_start: 0.6647 (t80) cc_final: 0.6204 (t80) REVERT: F 392 PHE cc_start: 0.7618 (p90) cc_final: 0.7339 (p90) REVERT: F 406 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8043 (mt-10) REVERT: F 414 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8485 (mm-40) REVERT: F 454 ARG cc_start: 0.8534 (ttm-80) cc_final: 0.8014 (ttm170) REVERT: F 464 PHE cc_start: 0.8194 (m-80) cc_final: 0.7818 (m-80) outliers start: 120 outliers final: 81 residues processed: 348 average time/residue: 0.1418 time to fit residues: 82.0085 Evaluate side-chains 333 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 239 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 558 VAL Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 421 ILE Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 379 CYS Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 488 CYS Chi-restraints excluded: chain F residue 518 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 108 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 301 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 GLN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 139 GLN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.172693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.096990 restraints weight = 36495.593| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.54 r_work: 0.2864 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25902 Z= 0.129 Angle : 0.612 14.801 35220 Z= 0.296 Chirality : 0.042 0.273 3902 Planarity : 0.004 0.043 4368 Dihedral : 9.685 76.134 4436 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 3.75 % Allowed : 18.75 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.66 (0.15), residues: 3030 helix: 0.73 (0.13), residues: 1666 sheet: -0.83 (0.45), residues: 142 loop : -2.07 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 493 TYR 0.041 0.001 TYR B 21 PHE 0.011 0.001 PHE C 315 TRP 0.014 0.001 TRP C 478 HIS 0.004 0.001 HIS D 132 Details of bonding type rmsd covalent geometry : bond 0.00291 (25846) covalent geometry : angle 0.58672 (35078) SS BOND : bond 0.00681 ( 14) SS BOND : angle 1.49374 ( 28) hydrogen bonds : bond 0.04388 ( 1219) hydrogen bonds : angle 4.16597 ( 3555) metal coordination : bond 0.00317 ( 4) link_BETA1-4 : bond 0.00433 ( 16) link_BETA1-4 : angle 2.02873 ( 48) link_NAG-ASN : bond 0.00899 ( 22) link_NAG-ASN : angle 3.62389 ( 66) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 256 time to evaluate : 0.999 Fit side-chains revert: symmetry clash REVERT: B 69 MET cc_start: 0.6368 (tpt) cc_final: 0.6073 (tpt) REVERT: B 344 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.5948 (p90) REVERT: B 380 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7328 (tm-30) REVERT: B 385 MET cc_start: 0.7487 (mtm) cc_final: 0.7260 (mtm) REVERT: B 391 TRP cc_start: 0.7289 (m100) cc_final: 0.7075 (m100) REVERT: B 534 LEU cc_start: 0.5200 (OUTLIER) cc_final: 0.4285 (tp) REVERT: B 537 GLN cc_start: 0.6317 (OUTLIER) cc_final: 0.5913 (mt0) REVERT: B 545 GLN cc_start: 0.7269 (mt0) cc_final: 0.6741 (mt0) REVERT: A 67 ASP cc_start: 0.8362 (m-30) cc_final: 0.7923 (m-30) REVERT: A 114 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8507 (mtpp) REVERT: A 142 LEU cc_start: 0.8815 (mt) cc_final: 0.8562 (mt) REVERT: A 256 ILE cc_start: 0.9696 (OUTLIER) cc_final: 0.9358 (mm) REVERT: A 325 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8079 (tp-100) REVERT: A 332 MET cc_start: 0.8924 (ttp) cc_final: 0.8634 (ttp) REVERT: A 368 ASP cc_start: 0.8780 (m-30) cc_final: 0.8520 (m-30) REVERT: A 564 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8977 (mp0) REVERT: A 596 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.8967 (mtpt) REVERT: A 719 ASP cc_start: 0.8426 (t0) cc_final: 0.7964 (t0) REVERT: E 392 PHE cc_start: 0.7626 (p90) cc_final: 0.7303 (p90) REVERT: E 406 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8074 (mt-10) REVERT: E 414 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8527 (mm-40) REVERT: E 454 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.7951 (ttm170) REVERT: E 464 PHE cc_start: 0.8061 (m-80) cc_final: 0.7683 (m-80) REVERT: D 69 MET cc_start: 0.6368 (tpt) cc_final: 0.6015 (tpt) REVERT: D 281 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6786 (mp) REVERT: D 344 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.5959 (p90) REVERT: D 380 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7478 (tm-30) REVERT: D 385 MET cc_start: 0.7620 (mtm) cc_final: 0.7387 (mtm) REVERT: D 503 TRP cc_start: 0.4111 (m100) cc_final: 0.3387 (m-90) REVERT: D 534 LEU cc_start: 0.5206 (OUTLIER) cc_final: 0.4315 (tp) REVERT: D 537 GLN cc_start: 0.6387 (OUTLIER) cc_final: 0.5968 (mt0) REVERT: D 545 GLN cc_start: 0.7164 (mt0) cc_final: 0.6642 (mt0) REVERT: C 34 HIS cc_start: 0.8208 (t-90) cc_final: 0.7818 (m90) REVERT: C 35 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8405 (mt-10) REVERT: C 67 ASP cc_start: 0.8397 (m-30) cc_final: 0.7965 (m-30) REVERT: C 114 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8513 (mtpp) REVERT: C 142 LEU cc_start: 0.8805 (mt) cc_final: 0.8546 (mt) REVERT: C 183 TYR cc_start: 0.9499 (OUTLIER) cc_final: 0.9267 (t80) REVERT: C 256 ILE cc_start: 0.9697 (OUTLIER) cc_final: 0.9360 (mm) REVERT: C 368 ASP cc_start: 0.8792 (m-30) cc_final: 0.8528 (m-30) REVERT: C 564 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8960 (mp0) REVERT: C 596 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.8956 (mtpt) REVERT: C 719 ASP cc_start: 0.8326 (t0) cc_final: 0.7945 (t0) REVERT: F 369 TYR cc_start: 0.6575 (t80) cc_final: 0.6157 (t80) REVERT: F 392 PHE cc_start: 0.7560 (p90) cc_final: 0.7308 (p90) REVERT: F 406 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8073 (mt-10) REVERT: F 454 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.7929 (ttm170) REVERT: F 464 PHE cc_start: 0.8117 (m-80) cc_final: 0.7817 (m-80) outliers start: 99 outliers final: 52 residues processed: 339 average time/residue: 0.1433 time to fit residues: 80.4794 Evaluate side-chains 309 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 245 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain F residue 379 CYS Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 488 CYS Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 110 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 15 optimal weight: 20.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 HIS ** B 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 139 GLN A 674 ASN D 132 HIS ** D 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.172365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.094032 restraints weight = 36072.265| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.51 r_work: 0.2841 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25902 Z= 0.189 Angle : 0.646 14.132 35220 Z= 0.313 Chirality : 0.044 0.267 3902 Planarity : 0.004 0.066 4368 Dihedral : 9.633 75.426 4425 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.04 % Favored : 93.86 % Rotamer: Outliers : 4.28 % Allowed : 18.86 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.59 (0.15), residues: 3030 helix: 0.75 (0.13), residues: 1680 sheet: -0.72 (0.45), residues: 142 loop : -2.03 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 493 TYR 0.036 0.001 TYR B 21 PHE 0.015 0.001 PHE A 684 TRP 0.020 0.001 TRP D 77 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00455 (25846) covalent geometry : angle 0.62021 (35078) SS BOND : bond 0.00755 ( 14) SS BOND : angle 1.79933 ( 28) hydrogen bonds : bond 0.04806 ( 1219) hydrogen bonds : angle 4.18907 ( 3555) metal coordination : bond 0.00561 ( 4) link_BETA1-4 : bond 0.00420 ( 16) link_BETA1-4 : angle 2.05508 ( 48) link_NAG-ASN : bond 0.00578 ( 22) link_NAG-ASN : angle 3.70439 ( 66) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 247 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: B 69 MET cc_start: 0.6325 (tpt) cc_final: 0.6078 (tpt) REVERT: B 202 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6276 (mp) REVERT: B 380 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7515 (tm-30) REVERT: B 385 MET cc_start: 0.7422 (mtm) cc_final: 0.7209 (mtm) REVERT: B 387 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7554 (p) REVERT: B 391 TRP cc_start: 0.7320 (m100) cc_final: 0.7113 (m100) REVERT: B 534 LEU cc_start: 0.5361 (OUTLIER) cc_final: 0.4463 (tp) REVERT: B 537 GLN cc_start: 0.6198 (OUTLIER) cc_final: 0.5936 (mt0) REVERT: B 545 GLN cc_start: 0.7271 (mt0) cc_final: 0.6729 (mt0) REVERT: A 67 ASP cc_start: 0.8368 (m-30) cc_final: 0.7966 (m-30) REVERT: A 114 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8518 (mtpp) REVERT: A 183 TYR cc_start: 0.9604 (OUTLIER) cc_final: 0.9338 (t80) REVERT: A 256 ILE cc_start: 0.9699 (OUTLIER) cc_final: 0.9364 (mm) REVERT: A 325 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8057 (tp-100) REVERT: A 368 ASP cc_start: 0.8775 (m-30) cc_final: 0.8489 (m-30) REVERT: A 401 HIS cc_start: 0.9427 (OUTLIER) cc_final: 0.8764 (t-90) REVERT: A 527 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8867 (tt0) REVERT: A 564 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8946 (mp0) REVERT: A 596 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8956 (mtpt) REVERT: E 392 PHE cc_start: 0.7553 (p90) cc_final: 0.7285 (p90) REVERT: E 406 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8075 (mt-10) REVERT: E 414 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8558 (mm-40) REVERT: E 454 ARG cc_start: 0.8456 (ttm-80) cc_final: 0.7950 (ttm170) REVERT: E 464 PHE cc_start: 0.8026 (m-80) cc_final: 0.7665 (m-80) REVERT: D 69 MET cc_start: 0.6338 (tpt) cc_final: 0.5997 (tpt) REVERT: D 281 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6766 (mp) REVERT: D 451 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6467 (mp0) REVERT: D 476 GLU cc_start: 0.5292 (mm-30) cc_final: 0.4704 (tp30) REVERT: D 503 TRP cc_start: 0.3879 (m100) cc_final: 0.3277 (m-90) REVERT: D 537 GLN cc_start: 0.6310 (OUTLIER) cc_final: 0.6044 (mt0) REVERT: D 545 GLN cc_start: 0.7185 (mt0) cc_final: 0.6652 (mt0) REVERT: C 34 HIS cc_start: 0.8141 (t-90) cc_final: 0.7726 (m90) REVERT: C 67 ASP cc_start: 0.8369 (m-30) cc_final: 0.7947 (m-30) REVERT: C 114 LYS cc_start: 0.8749 (mtmt) cc_final: 0.8514 (mtpp) REVERT: C 183 TYR cc_start: 0.9584 (OUTLIER) cc_final: 0.9318 (t80) REVERT: C 256 ILE cc_start: 0.9697 (OUTLIER) cc_final: 0.9367 (mm) REVERT: C 325 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8049 (tp-100) REVERT: C 368 ASP cc_start: 0.8723 (m-30) cc_final: 0.8448 (m-30) REVERT: C 401 HIS cc_start: 0.9427 (OUTLIER) cc_final: 0.8759 (t-90) REVERT: C 527 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8858 (tt0) REVERT: C 564 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8940 (mp0) REVERT: C 596 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.8976 (mtpt) REVERT: C 719 ASP cc_start: 0.8425 (t0) cc_final: 0.8074 (t0) REVERT: F 369 TYR cc_start: 0.6585 (t80) cc_final: 0.6127 (t80) REVERT: F 392 PHE cc_start: 0.7558 (p90) cc_final: 0.7310 (p90) REVERT: F 406 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8081 (mt-10) REVERT: F 454 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.7918 (ttm170) REVERT: F 464 PHE cc_start: 0.8064 (m-80) cc_final: 0.7794 (m-80) outliers start: 113 outliers final: 74 residues processed: 346 average time/residue: 0.1500 time to fit residues: 84.9800 Evaluate side-chains 332 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 241 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 CYS Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 472 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 183 TYR Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 215 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 270 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 146 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS D 243 ASN ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 ASN C 718 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.173873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095869 restraints weight = 36309.495| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.48 r_work: 0.2874 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25902 Z= 0.135 Angle : 0.610 13.386 35220 Z= 0.293 Chirality : 0.042 0.327 3902 Planarity : 0.004 0.038 4368 Dihedral : 9.315 74.265 4425 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.69 % Rotamer: Outliers : 3.75 % Allowed : 19.36 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.36 (0.15), residues: 3030 helix: 0.94 (0.13), residues: 1678 sheet: -0.66 (0.46), residues: 142 loop : -1.91 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.036 0.001 TYR D 21 PHE 0.012 0.001 PHE C 684 TRP 0.016 0.001 TRP B 77 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00314 (25846) covalent geometry : angle 0.58393 (35078) SS BOND : bond 0.00697 ( 14) SS BOND : angle 1.63719 ( 28) hydrogen bonds : bond 0.04279 ( 1219) hydrogen bonds : angle 4.07558 ( 3555) metal coordination : bond 0.00287 ( 4) link_BETA1-4 : bond 0.00423 ( 16) link_BETA1-4 : angle 2.00746 ( 48) link_NAG-ASN : bond 0.00550 ( 22) link_NAG-ASN : angle 3.60393 ( 66) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 258 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: B 69 MET cc_start: 0.6288 (tpt) cc_final: 0.6057 (tpt) REVERT: B 202 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6120 (mp) REVERT: B 380 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7551 (tm-30) REVERT: B 385 MET cc_start: 0.7493 (mtm) cc_final: 0.7284 (mtm) REVERT: B 387 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7339 (p) REVERT: B 401 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7457 (ppp) REVERT: B 476 GLU cc_start: 0.5392 (OUTLIER) cc_final: 0.4752 (tp30) REVERT: B 534 LEU cc_start: 0.5254 (OUTLIER) cc_final: 0.4325 (tp) REVERT: B 537 GLN cc_start: 0.6300 (OUTLIER) cc_final: 0.6020 (mt0) REVERT: B 545 GLN cc_start: 0.7254 (mt0) cc_final: 0.6701 (mt0) REVERT: A 67 ASP cc_start: 0.8305 (m-30) cc_final: 0.7910 (m-30) REVERT: A 114 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8472 (mtpp) REVERT: A 183 TYR cc_start: 0.9579 (OUTLIER) cc_final: 0.9251 (t80) REVERT: A 256 ILE cc_start: 0.9684 (OUTLIER) cc_final: 0.9364 (mm) REVERT: A 325 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8078 (tp-100) REVERT: A 368 ASP cc_start: 0.8760 (m-30) cc_final: 0.8480 (m-30) REVERT: A 401 HIS cc_start: 0.9402 (OUTLIER) cc_final: 0.8753 (t-90) REVERT: A 564 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8936 (mp0) REVERT: A 596 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.8947 (mtpt) REVERT: E 392 PHE cc_start: 0.7637 (p90) cc_final: 0.7376 (p90) REVERT: E 406 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8057 (mt-10) REVERT: E 454 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.7914 (ttm170) REVERT: E 464 PHE cc_start: 0.7988 (m-80) cc_final: 0.7650 (m-80) REVERT: D 69 MET cc_start: 0.6268 (tpt) cc_final: 0.5942 (tpt) REVERT: D 281 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6772 (mp) REVERT: D 380 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7449 (tm-30) REVERT: D 451 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6508 (mm-30) REVERT: D 476 GLU cc_start: 0.5059 (mm-30) cc_final: 0.4366 (tp30) REVERT: D 503 TRP cc_start: 0.3879 (m100) cc_final: 0.3321 (m-90) REVERT: D 534 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4265 (tp) REVERT: D 537 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.6093 (mt0) REVERT: D 545 GLN cc_start: 0.7242 (mt0) cc_final: 0.6695 (mt0) REVERT: C 34 HIS cc_start: 0.8205 (t-90) cc_final: 0.7780 (m90) REVERT: C 67 ASP cc_start: 0.8384 (m-30) cc_final: 0.7959 (m-30) REVERT: C 114 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8474 (mtpp) REVERT: C 142 LEU cc_start: 0.8727 (mt) cc_final: 0.8455 (mt) REVERT: C 256 ILE cc_start: 0.9683 (OUTLIER) cc_final: 0.9370 (mm) REVERT: C 325 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8081 (tp-100) REVERT: C 368 ASP cc_start: 0.8715 (m-30) cc_final: 0.8496 (m-30) REVERT: C 401 HIS cc_start: 0.9398 (OUTLIER) cc_final: 0.8747 (t-90) REVERT: C 564 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8930 (mp0) REVERT: C 596 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.8965 (mtpt) REVERT: C 719 ASP cc_start: 0.8336 (t0) cc_final: 0.7987 (t0) REVERT: F 369 TYR cc_start: 0.6567 (t80) cc_final: 0.6166 (t80) REVERT: F 380 TYR cc_start: 0.8416 (m-80) cc_final: 0.8097 (m-80) REVERT: F 406 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8108 (mt-10) REVERT: F 454 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.7875 (ttm170) REVERT: F 464 PHE cc_start: 0.8063 (m-80) cc_final: 0.7802 (m-80) outliers start: 99 outliers final: 61 residues processed: 339 average time/residue: 0.1515 time to fit residues: 83.7305 Evaluate side-chains 330 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 252 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 GLN Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 149 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 282 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS D 273 GLN ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.172423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098904 restraints weight = 36376.880| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.59 r_work: 0.2852 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25902 Z= 0.137 Angle : 0.609 12.881 35220 Z= 0.294 Chirality : 0.042 0.270 3902 Planarity : 0.004 0.041 4368 Dihedral : 9.003 72.696 4418 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.09 % Rotamer: Outliers : 3.75 % Allowed : 19.96 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.26 (0.15), residues: 3030 helix: 1.00 (0.13), residues: 1680 sheet: -0.65 (0.46), residues: 140 loop : -1.84 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 493 TYR 0.044 0.001 TYR D 21 PHE 0.014 0.001 PHE F 392 TRP 0.046 0.001 TRP B 391 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00320 (25846) covalent geometry : angle 0.58399 (35078) SS BOND : bond 0.00899 ( 14) SS BOND : angle 1.50772 ( 28) hydrogen bonds : bond 0.04259 ( 1219) hydrogen bonds : angle 4.04055 ( 3555) metal coordination : bond 0.00308 ( 4) link_BETA1-4 : bond 0.00407 ( 16) link_BETA1-4 : angle 1.99749 ( 48) link_NAG-ASN : bond 0.00524 ( 22) link_NAG-ASN : angle 3.58543 ( 66) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 263 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: B 69 MET cc_start: 0.6326 (tpt) cc_final: 0.6089 (tpt) REVERT: B 351 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7485 (ttt) REVERT: B 380 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7592 (tm-30) REVERT: B 385 MET cc_start: 0.7373 (mtm) cc_final: 0.7148 (mtm) REVERT: B 401 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7391 (ppp) REVERT: B 451 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: B 476 GLU cc_start: 0.4891 (mm-30) cc_final: 0.4277 (tp30) REVERT: B 503 TRP cc_start: 0.3886 (m100) cc_final: 0.3235 (m-90) REVERT: B 534 LEU cc_start: 0.5322 (OUTLIER) cc_final: 0.4336 (tp) REVERT: B 545 GLN cc_start: 0.7239 (mt0) cc_final: 0.6688 (mt0) REVERT: A 67 ASP cc_start: 0.8358 (m-30) cc_final: 0.7965 (m-30) REVERT: A 114 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8473 (mtpp) REVERT: A 256 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9367 (mm) REVERT: A 325 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8102 (tp-100) REVERT: A 368 ASP cc_start: 0.8763 (m-30) cc_final: 0.8501 (m-30) REVERT: A 401 HIS cc_start: 0.9430 (OUTLIER) cc_final: 0.8809 (t-90) REVERT: A 527 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8848 (tt0) REVERT: A 564 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8927 (mp0) REVERT: A 596 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.8976 (mtpt) REVERT: E 392 PHE cc_start: 0.7657 (p90) cc_final: 0.7450 (p90) REVERT: E 406 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8123 (mt-10) REVERT: E 454 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.7931 (ttm170) REVERT: E 464 PHE cc_start: 0.8037 (m-80) cc_final: 0.7732 (m-80) REVERT: D 69 MET cc_start: 0.6314 (tpt) cc_final: 0.5982 (tpt) REVERT: D 281 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6775 (mp) REVERT: D 380 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7368 (tm-30) REVERT: D 401 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7474 (ppp) REVERT: D 451 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6538 (mm-30) REVERT: D 476 GLU cc_start: 0.5087 (mm-30) cc_final: 0.4533 (tp30) REVERT: D 503 TRP cc_start: 0.3825 (m100) cc_final: 0.3233 (m-90) REVERT: D 534 LEU cc_start: 0.5134 (OUTLIER) cc_final: 0.4242 (tp) REVERT: D 545 GLN cc_start: 0.7254 (mt0) cc_final: 0.6670 (mt0) REVERT: C 34 HIS cc_start: 0.8214 (t-90) cc_final: 0.7792 (m90) REVERT: C 67 ASP cc_start: 0.8343 (m-30) cc_final: 0.7956 (m-30) REVERT: C 114 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8487 (mtpp) REVERT: C 142 LEU cc_start: 0.8662 (mt) cc_final: 0.8405 (mt) REVERT: C 256 ILE cc_start: 0.9686 (OUTLIER) cc_final: 0.9367 (mm) REVERT: C 325 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8089 (tp-100) REVERT: C 368 ASP cc_start: 0.8731 (m-30) cc_final: 0.8509 (m-30) REVERT: C 401 HIS cc_start: 0.9427 (OUTLIER) cc_final: 0.8807 (t-90) REVERT: C 527 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8841 (tt0) REVERT: C 564 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8932 (mp0) REVERT: C 596 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8974 (mtpt) REVERT: C 719 ASP cc_start: 0.8299 (t0) cc_final: 0.7964 (t0) REVERT: F 369 TYR cc_start: 0.6838 (t80) cc_final: 0.6354 (t80) REVERT: F 406 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8145 (mt-10) REVERT: F 454 ARG cc_start: 0.8456 (ttm-80) cc_final: 0.7883 (ttm170) REVERT: F 464 PHE cc_start: 0.8045 (m-80) cc_final: 0.7803 (m-80) outliers start: 99 outliers final: 70 residues processed: 346 average time/residue: 0.1525 time to fit residues: 86.6049 Evaluate side-chains 342 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 256 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 21 TYR Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 472 ILE Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 277 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 289 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 255 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 243 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 96 GLN ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 718 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.173313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.095961 restraints weight = 36434.037| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.47 r_work: 0.2908 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25902 Z= 0.115 Angle : 0.604 12.314 35220 Z= 0.288 Chirality : 0.042 0.385 3902 Planarity : 0.003 0.034 4368 Dihedral : 8.576 69.834 4410 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.62 % Rotamer: Outliers : 3.45 % Allowed : 20.72 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.14 (0.16), residues: 3030 helix: 1.10 (0.13), residues: 1670 sheet: 0.09 (0.49), residues: 120 loop : -1.84 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 493 TYR 0.042 0.001 TYR D 21 PHE 0.010 0.001 PHE C 684 TRP 0.017 0.001 TRP D 505 HIS 0.005 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00260 (25846) covalent geometry : angle 0.57995 (35078) SS BOND : bond 0.00706 ( 14) SS BOND : angle 1.37019 ( 28) hydrogen bonds : bond 0.03942 ( 1219) hydrogen bonds : angle 3.99542 ( 3555) metal coordination : bond 0.00191 ( 4) link_BETA1-4 : bond 0.00432 ( 16) link_BETA1-4 : angle 1.93837 ( 48) link_NAG-ASN : bond 0.00507 ( 22) link_NAG-ASN : angle 3.48447 ( 66) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 265 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: B 69 MET cc_start: 0.6294 (tpt) cc_final: 0.6071 (tpt) REVERT: B 380 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7602 (tm-30) REVERT: B 385 MET cc_start: 0.7515 (mtm) cc_final: 0.7254 (mtm) REVERT: B 401 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7374 (ppp) REVERT: B 451 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: B 476 GLU cc_start: 0.5094 (mm-30) cc_final: 0.4577 (tp30) REVERT: B 503 TRP cc_start: 0.3724 (m100) cc_final: 0.3084 (m-90) REVERT: B 534 LEU cc_start: 0.5238 (OUTLIER) cc_final: 0.4234 (tp) REVERT: B 545 GLN cc_start: 0.7204 (mt0) cc_final: 0.6600 (mt0) REVERT: A 67 ASP cc_start: 0.8315 (m-30) cc_final: 0.7917 (m-30) REVERT: A 114 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8411 (mtpp) REVERT: A 183 TYR cc_start: 0.9555 (OUTLIER) cc_final: 0.9318 (t80) REVERT: A 256 ILE cc_start: 0.9670 (OUTLIER) cc_final: 0.9355 (mm) REVERT: A 325 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8058 (tp-100) REVERT: A 368 ASP cc_start: 0.8691 (m-30) cc_final: 0.8488 (m-30) REVERT: A 527 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8809 (tt0) REVERT: A 564 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8890 (mp0) REVERT: A 596 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.8962 (mtpt) REVERT: E 406 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8020 (mt-10) REVERT: E 454 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.7891 (ttm170) REVERT: E 464 PHE cc_start: 0.8046 (m-80) cc_final: 0.7736 (m-80) REVERT: D 69 MET cc_start: 0.6175 (tpt) cc_final: 0.5910 (tpt) REVERT: D 281 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6904 (mp) REVERT: D 380 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7429 (tm-30) REVERT: D 401 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7429 (ppp) REVERT: D 451 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6512 (mm-30) REVERT: D 476 GLU cc_start: 0.4943 (mm-30) cc_final: 0.4438 (tp30) REVERT: D 503 TRP cc_start: 0.4066 (m100) cc_final: 0.3350 (m-90) REVERT: D 534 LEU cc_start: 0.5023 (OUTLIER) cc_final: 0.4098 (tp) REVERT: D 545 GLN cc_start: 0.7205 (mt0) cc_final: 0.6633 (mt0) REVERT: C 34 HIS cc_start: 0.8174 (t-90) cc_final: 0.7779 (m-70) REVERT: C 67 ASP cc_start: 0.8332 (m-30) cc_final: 0.7903 (m-30) REVERT: C 114 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8412 (mtpp) REVERT: C 256 ILE cc_start: 0.9671 (OUTLIER) cc_final: 0.9354 (mm) REVERT: C 325 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8067 (tp-100) REVERT: C 368 ASP cc_start: 0.8699 (m-30) cc_final: 0.8473 (m-30) REVERT: C 527 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.8796 (tt0) REVERT: C 564 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8890 (mp0) REVERT: C 596 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.8958 (mtpt) REVERT: C 719 ASP cc_start: 0.8227 (t0) cc_final: 0.7950 (t0) REVERT: F 369 TYR cc_start: 0.6915 (t80) cc_final: 0.6570 (t80) REVERT: F 406 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8030 (mt-10) REVERT: F 454 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.7855 (ttm170) REVERT: F 464 PHE cc_start: 0.7998 (m-80) cc_final: 0.7767 (m-80) outliers start: 91 outliers final: 64 residues processed: 342 average time/residue: 0.1515 time to fit residues: 84.7305 Evaluate side-chains 333 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 255 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 250 optimal weight: 0.4980 chunk 284 optimal weight: 20.0000 chunk 7 optimal weight: 0.3980 chunk 206 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 281 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.172612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097534 restraints weight = 36659.042| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.53 r_work: 0.2860 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25902 Z= 0.146 Angle : 0.620 11.910 35220 Z= 0.299 Chirality : 0.043 0.360 3902 Planarity : 0.004 0.049 4368 Dihedral : 8.479 66.682 4410 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 3.14 % Allowed : 20.98 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.12 (0.15), residues: 3030 helix: 1.10 (0.13), residues: 1672 sheet: 0.09 (0.49), residues: 120 loop : -1.80 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 716 TYR 0.033 0.001 TYR D 21 PHE 0.013 0.001 PHE C 684 TRP 0.043 0.001 TRP D 505 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00345 (25846) covalent geometry : angle 0.59679 (35078) SS BOND : bond 0.00713 ( 14) SS BOND : angle 1.42861 ( 28) hydrogen bonds : bond 0.04223 ( 1219) hydrogen bonds : angle 4.00597 ( 3555) metal coordination : bond 0.00352 ( 4) link_BETA1-4 : bond 0.00411 ( 16) link_BETA1-4 : angle 1.95805 ( 48) link_NAG-ASN : bond 0.00471 ( 22) link_NAG-ASN : angle 3.44963 ( 66) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 260 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: B 69 MET cc_start: 0.6307 (tpt) cc_final: 0.6083 (tpt) REVERT: B 202 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6300 (mp) REVERT: B 322 ASP cc_start: 0.7779 (m-30) cc_final: 0.7499 (m-30) REVERT: B 380 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7595 (tm-30) REVERT: B 385 MET cc_start: 0.7411 (mtm) cc_final: 0.7208 (mtm) REVERT: B 451 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6426 (mp0) REVERT: B 476 GLU cc_start: 0.5203 (mm-30) cc_final: 0.4749 (tp30) REVERT: B 503 TRP cc_start: 0.3748 (m100) cc_final: 0.3092 (m-90) REVERT: B 534 LEU cc_start: 0.5148 (OUTLIER) cc_final: 0.4172 (tp) REVERT: B 545 GLN cc_start: 0.7152 (mt0) cc_final: 0.6581 (mt0) REVERT: A 67 ASP cc_start: 0.8350 (m-30) cc_final: 0.7949 (m-30) REVERT: A 114 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8458 (mtpp) REVERT: A 256 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9367 (mm) REVERT: A 325 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8089 (tp-100) REVERT: A 368 ASP cc_start: 0.8721 (m-30) cc_final: 0.8459 (m-30) REVERT: A 401 HIS cc_start: 0.9438 (OUTLIER) cc_final: 0.8742 (t-90) REVERT: A 527 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8845 (tt0) REVERT: A 564 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8927 (mp0) REVERT: A 596 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.8968 (mtpt) REVERT: E 406 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8015 (mt-10) REVERT: E 454 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.7912 (ttm170) REVERT: E 464 PHE cc_start: 0.8030 (m-80) cc_final: 0.7763 (m-80) REVERT: D 69 MET cc_start: 0.6192 (tpt) cc_final: 0.5926 (tpt) REVERT: D 100 MET cc_start: 0.7171 (ptt) cc_final: 0.6834 (ptp) REVERT: D 380 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7468 (tm-30) REVERT: D 451 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: D 476 GLU cc_start: 0.5056 (mm-30) cc_final: 0.4557 (tp30) REVERT: D 503 TRP cc_start: 0.4040 (m100) cc_final: 0.3371 (m-90) REVERT: D 534 LEU cc_start: 0.5110 (OUTLIER) cc_final: 0.4208 (tp) REVERT: D 545 GLN cc_start: 0.7155 (mt0) cc_final: 0.6583 (mt0) REVERT: C 34 HIS cc_start: 0.8186 (t-90) cc_final: 0.7789 (m90) REVERT: C 67 ASP cc_start: 0.8338 (m-30) cc_final: 0.7940 (m-30) REVERT: C 114 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8458 (mtpp) REVERT: C 256 ILE cc_start: 0.9680 (OUTLIER) cc_final: 0.9369 (mm) REVERT: C 325 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8062 (tp-100) REVERT: C 368 ASP cc_start: 0.8707 (m-30) cc_final: 0.8446 (m-30) REVERT: C 401 HIS cc_start: 0.9436 (OUTLIER) cc_final: 0.8827 (t-90) REVERT: C 527 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8864 (tt0) REVERT: C 564 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8919 (mp0) REVERT: C 596 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8985 (mtpt) REVERT: C 719 ASP cc_start: 0.8142 (t0) cc_final: 0.7901 (t0) REVERT: F 369 TYR cc_start: 0.6904 (t80) cc_final: 0.6536 (t80) REVERT: F 406 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8035 (mt-10) REVERT: F 454 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.7863 (ttm170) REVERT: F 464 PHE cc_start: 0.7982 (m-80) cc_final: 0.7758 (m-80) outliers start: 83 outliers final: 66 residues processed: 334 average time/residue: 0.1507 time to fit residues: 82.7234 Evaluate side-chains 335 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 256 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 536 TYR Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 536 TYR Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 229 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 154 optimal weight: 0.1980 chunk 205 optimal weight: 8.9990 chunk 273 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 188 optimal weight: 0.0570 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 139 GLN ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.174023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.098650 restraints weight = 36481.024| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.53 r_work: 0.2900 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25902 Z= 0.111 Angle : 0.599 14.130 35220 Z= 0.287 Chirality : 0.042 0.470 3902 Planarity : 0.003 0.034 4368 Dihedral : 8.265 61.208 4410 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 2.99 % Allowed : 21.10 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.03 (0.16), residues: 3030 helix: 1.23 (0.13), residues: 1676 sheet: 0.08 (0.49), residues: 122 loop : -1.75 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 493 TYR 0.031 0.001 TYR D 21 PHE 0.009 0.001 PHE F 515 TRP 0.035 0.001 TRP D 505 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00248 (25846) covalent geometry : angle 0.57801 (35078) SS BOND : bond 0.00858 ( 14) SS BOND : angle 1.34243 ( 28) hydrogen bonds : bond 0.03799 ( 1219) hydrogen bonds : angle 3.94301 ( 3555) metal coordination : bond 0.00131 ( 4) link_BETA1-4 : bond 0.00434 ( 16) link_BETA1-4 : angle 1.91838 ( 48) link_NAG-ASN : bond 0.00467 ( 22) link_NAG-ASN : angle 3.24585 ( 66) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 264 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: B 69 MET cc_start: 0.6293 (tpt) cc_final: 0.6061 (tpt) REVERT: B 202 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6271 (mp) REVERT: B 322 ASP cc_start: 0.7532 (m-30) cc_final: 0.7270 (m-30) REVERT: B 380 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7653 (tm-30) REVERT: B 451 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: B 476 GLU cc_start: 0.5261 (mm-30) cc_final: 0.4691 (tp30) REVERT: B 503 TRP cc_start: 0.3746 (m100) cc_final: 0.3097 (m-90) REVERT: B 534 LEU cc_start: 0.5058 (OUTLIER) cc_final: 0.4018 (tp) REVERT: B 545 GLN cc_start: 0.7152 (mt0) cc_final: 0.6556 (mt0) REVERT: A 67 ASP cc_start: 0.8335 (m-30) cc_final: 0.7929 (m-30) REVERT: A 114 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8450 (mtpp) REVERT: A 183 TYR cc_start: 0.9553 (OUTLIER) cc_final: 0.9316 (t80) REVERT: A 325 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8093 (tp-100) REVERT: A 368 ASP cc_start: 0.8682 (m-30) cc_final: 0.8477 (m-30) REVERT: A 527 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8818 (tt0) REVERT: A 564 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8906 (mp0) REVERT: A 596 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.8981 (mtpt) REVERT: E 406 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8028 (mt-10) REVERT: E 454 ARG cc_start: 0.8378 (ttm-80) cc_final: 0.7862 (ttm170) REVERT: E 464 PHE cc_start: 0.7989 (m-80) cc_final: 0.7743 (m-80) REVERT: D 69 MET cc_start: 0.6176 (tpt) cc_final: 0.5920 (tpt) REVERT: D 100 MET cc_start: 0.7114 (ptt) cc_final: 0.6762 (ptp) REVERT: D 380 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7500 (tm-30) REVERT: D 401 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7425 (ppp) REVERT: D 451 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6499 (mm-30) REVERT: D 476 GLU cc_start: 0.4984 (mm-30) cc_final: 0.4562 (tp30) REVERT: D 503 TRP cc_start: 0.3880 (m100) cc_final: 0.3319 (m-90) REVERT: D 534 LEU cc_start: 0.4984 (OUTLIER) cc_final: 0.4062 (tp) REVERT: D 545 GLN cc_start: 0.7155 (mt0) cc_final: 0.6565 (mt0) REVERT: C 34 HIS cc_start: 0.8153 (t-90) cc_final: 0.7781 (m-70) REVERT: C 35 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8285 (mt-10) REVERT: C 67 ASP cc_start: 0.8344 (m-30) cc_final: 0.7910 (m-30) REVERT: C 114 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8450 (mtpp) REVERT: C 325 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8054 (tp-100) REVERT: C 368 ASP cc_start: 0.8678 (m-30) cc_final: 0.8472 (m-30) REVERT: C 527 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8812 (tt0) REVERT: C 564 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8895 (mp0) REVERT: C 596 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.8961 (mtpt) REVERT: F 369 TYR cc_start: 0.6927 (t80) cc_final: 0.6572 (t80) REVERT: F 406 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8039 (mt-10) REVERT: F 454 ARG cc_start: 0.8436 (ttm-80) cc_final: 0.7874 (ttm170) outliers start: 79 outliers final: 62 residues processed: 332 average time/residue: 0.1524 time to fit residues: 82.8724 Evaluate side-chains 329 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 256 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 596 LYS Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 623 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 451 GLU Chi-restraints excluded: chain D residue 469 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 611 SER Chi-restraints excluded: chain C residue 623 SER Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 95 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 139 GLN ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 718 ASN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.174161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.096292 restraints weight = 35999.308| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.38 r_work: 0.2888 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25902 Z= 0.136 Angle : 0.616 14.656 35220 Z= 0.296 Chirality : 0.043 0.418 3902 Planarity : 0.004 0.047 4368 Dihedral : 8.153 59.930 4409 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 2.92 % Allowed : 21.21 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.01 (0.16), residues: 3030 helix: 1.20 (0.13), residues: 1674 sheet: 0.14 (0.49), residues: 120 loop : -1.75 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 493 TYR 0.029 0.001 TYR D 21 PHE 0.013 0.001 PHE C 684 TRP 0.030 0.001 TRP D 505 HIS 0.004 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00320 (25846) covalent geometry : angle 0.59497 (35078) SS BOND : bond 0.00850 ( 14) SS BOND : angle 1.69250 ( 28) hydrogen bonds : bond 0.04136 ( 1219) hydrogen bonds : angle 3.97881 ( 3555) metal coordination : bond 0.00302 ( 4) link_BETA1-4 : bond 0.00406 ( 16) link_BETA1-4 : angle 1.93702 ( 48) link_NAG-ASN : bond 0.00417 ( 22) link_NAG-ASN : angle 3.21586 ( 66) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10045.48 seconds wall clock time: 171 minutes 2.95 seconds (10262.95 seconds total)