Starting phenix.real_space_refine on Sat May 24 13:08:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y75_33652/05_2025/7y75_33652.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y75_33652/05_2025/7y75_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_33652/05_2025/7y75_33652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y75_33652/05_2025/7y75_33652.map" model { file = "/net/cci-nas-00/data/ceres_data/7y75_33652/05_2025/7y75_33652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y75_33652/05_2025/7y75_33652.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.69, per 1000 atoms: 0.58 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: 6.89 Conformation dependent library (CDL) restraints added in 3.1 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: 2.50 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: 7.24 Time building geometry restraints manager: 7.87 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: 0.02 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: 0.990 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: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 57.310 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.500 ------------------------------------------------------------------------------- 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 : 10.11 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (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 TRP 0.015 0.002 TRP B 111 HIS 0.008 0.001 HIS A 241 PHE 0.016 0.002 PHE D 295 TYR 0.018 0.002 TYR A 385 ARG 0.007 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.01000 ( 22) link_NAG-ASN : angle 5.32260 ( 66) link_BETA1-4 : bond 0.00609 ( 16) link_BETA1-4 : angle 2.63897 ( 48) hydrogen bonds : bond 0.15337 ( 1219) hydrogen bonds : angle 6.04040 ( 3555) metal coordination : bond 0.44064 ( 4) SS BOND : bond 0.01221 ( 14) SS BOND : angle 7.56156 ( 28) covalent geometry : bond 0.00842 (25846) covalent geometry : angle 0.80457 (35078) *********************** 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 : 2.698 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: 0.8398 (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: 0.4948 (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: 0.3685 time to fit residues: 233.1679 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 : 2.566 ------------------------------------------------------------------------------- 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 255 optimal weight: 9.9990 chunk 228 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 154 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 236 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 274 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN B 237 ASN B 273 GLN ** 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 159 ASN A 210 ASN A 239 HIS 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 237 ASN ** D 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 98 GLN C 137 ASN C 159 ASN C 210 ASN C 239 HIS C 401 HIS C 437 ASN C 472 GLN C 493 HIS C 505 HIS F 422 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.173588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.096478 restraints weight = 36617.172| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.45 r_work: 0.2901 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25902 Z= 0.129 Angle : 0.642 16.677 35220 Z= 0.310 Chirality : 0.043 0.332 3902 Planarity : 0.004 0.073 4368 Dihedral : 11.038 77.250 4509 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.54 % Favored : 94.32 % Rotamer: Outliers : 3.60 % Allowed : 16.17 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.15), residues: 3030 helix: 0.15 (0.13), residues: 1668 sheet: -1.22 (0.44), residues: 142 loop : -2.42 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 391 HIS 0.003 0.001 HIS A 378 PHE 0.011 0.001 PHE A 684 TYR 0.046 0.001 TYR B 21 ARG 0.005 0.000 ARG F 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 22) link_NAG-ASN : angle 4.05792 ( 66) link_BETA1-4 : bond 0.00578 ( 16) link_BETA1-4 : angle 2.00811 ( 48) hydrogen bonds : bond 0.04650 ( 1219) hydrogen bonds : angle 4.35209 ( 3555) metal coordination : bond 0.00367 ( 4) SS BOND : bond 0.00847 ( 14) SS BOND : angle 1.37938 ( 28) covalent geometry : bond 0.00261 (25846) covalent geometry : angle 0.61301 (35078) *********************** 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 361 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 266 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 344 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6515 (p90) REVERT: B 361 GLU cc_start: 0.8372 (pt0) cc_final: 0.7540 (tm-30) REVERT: B 391 TRP cc_start: 0.7422 (m100) cc_final: 0.7040 (m100) REVERT: B 534 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4304 (tp) REVERT: B 537 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.5908 (mt0) REVERT: B 545 GLN cc_start: 0.7192 (mt0) cc_final: 0.6575 (mt0) REVERT: A 67 ASP cc_start: 0.8350 (m-30) cc_final: 0.7945 (m-30) REVERT: A 114 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8484 (mtpp) REVERT: A 142 LEU cc_start: 0.8740 (mt) cc_final: 0.8527 (mt) REVERT: A 564 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8877 (mp0) REVERT: A 719 ASP cc_start: 0.8190 (t0) cc_final: 0.7763 (t0) REVERT: E 369 TYR cc_start: 0.6108 (t80) cc_final: 0.5830 (t80) REVERT: E 392 PHE cc_start: 0.7504 (p90) cc_final: 0.7188 (p90) REVERT: E 406 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7946 (mt-10) REVERT: E 454 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.7992 (ttm170) REVERT: E 464 PHE cc_start: 0.8220 (m-80) cc_final: 0.7836 (m-80) REVERT: D 69 MET cc_start: 0.6217 (tpt) cc_final: 0.5824 (tpt) REVERT: D 344 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.6531 (p90) REVERT: D 361 GLU cc_start: 0.8377 (pt0) cc_final: 0.7545 (tm-30) REVERT: D 380 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7626 (tm-30) REVERT: D 385 MET cc_start: 0.7521 (mtm) cc_final: 0.7282 (mtm) REVERT: D 390 LEU cc_start: 0.6641 (tt) cc_final: 0.6408 (tt) REVERT: D 534 LEU cc_start: 0.5026 (OUTLIER) cc_final: 0.4087 (tp) REVERT: D 537 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.5930 (mt0) REVERT: C 60 GLN cc_start: 0.8532 (pm20) cc_final: 0.8316 (pm20) REVERT: C 67 ASP cc_start: 0.8452 (m-30) cc_final: 0.8049 (m-30) REVERT: C 114 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8459 (mtpp) REVERT: C 119 ILE cc_start: 0.8626 (pt) cc_final: 0.8380 (mt) REVERT: C 142 LEU cc_start: 0.8742 (mt) cc_final: 0.8502 (mt) REVERT: C 564 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8917 (mp0) REVERT: C 719 ASP cc_start: 0.8218 (t0) cc_final: 0.7797 (t0) REVERT: F 369 TYR cc_start: 0.6700 (t80) cc_final: 0.6274 (t80) REVERT: F 392 PHE cc_start: 0.7513 (p90) cc_final: 0.7221 (p90) REVERT: F 406 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8077 (mt-10) REVERT: F 454 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.7968 (ttm170) REVERT: F 464 PHE cc_start: 0.8269 (m-80) cc_final: 0.7874 (m-80) outliers start: 95 outliers final: 47 residues processed: 348 average time/residue: 0.3161 time to fit residues: 179.5726 Evaluate side-chains 297 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 TYR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 195 VAL 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 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 295 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 343 VAL 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 626 SER Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 518 LEU Chi-restraints excluded: chain D residue 33 TYR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 195 VAL 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 558 VAL Chi-restraints excluded: chain D residue 579 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 150 GLU 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 358 ILE Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 401 HIS 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 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 147 optimal weight: 0.6980 chunk 272 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 270 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 218 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 268 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 34 HIS A 277 ASN A 378 HIS A 735 ASN D 273 GLN D 275 HIS ** D 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.173980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100513 restraints weight = 36506.187| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.71 r_work: 0.2893 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.730 25902 Z= 0.241 Angle : 0.595 14.980 35220 Z= 0.287 Chirality : 0.042 0.267 3902 Planarity : 0.004 0.046 4368 Dihedral : 9.824 77.130 4432 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.46 % Rotamer: Outliers : 3.48 % Allowed : 17.05 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3030 helix: 0.66 (0.13), residues: 1662 sheet: -1.02 (0.44), residues: 142 loop : -2.17 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 478 HIS 0.012 0.001 HIS C 34 PHE 0.012 0.001 PHE C 315 TYR 0.025 0.001 TYR B 21 ARG 0.004 0.000 ARG F 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00833 ( 22) link_NAG-ASN : angle 3.74486 ( 66) link_BETA1-4 : bond 0.00442 ( 16) link_BETA1-4 : angle 1.98957 ( 48) hydrogen bonds : bond 0.04211 ( 1219) hydrogen bonds : angle 4.13025 ( 3555) metal coordination : bond 0.51598 ( 4) SS BOND : bond 0.00826 ( 14) SS BOND : angle 1.42566 ( 28) covalent geometry : bond 0.00237 (25846) covalent geometry : angle 0.56735 (35078) *********************** 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 372 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 280 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 MET cc_start: 0.6389 (tpt) cc_final: 0.6034 (tpt) REVERT: B 344 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.6263 (p90) REVERT: B 361 GLU cc_start: 0.8446 (pt0) cc_final: 0.7492 (tm-30) REVERT: B 534 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.4299 (tp) REVERT: B 537 GLN cc_start: 0.6449 (OUTLIER) cc_final: 0.6008 (mt0) REVERT: B 545 GLN cc_start: 0.7211 (mt0) cc_final: 0.6680 (mt0) REVERT: A 60 GLN cc_start: 0.8577 (pm20) cc_final: 0.8322 (pm20) REVERT: A 67 ASP cc_start: 0.8431 (m-30) cc_final: 0.8011 (m-30) REVERT: A 114 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8501 (mtpp) REVERT: A 142 LEU cc_start: 0.8589 (mt) cc_final: 0.8347 (mt) REVERT: A 183 TYR cc_start: 0.9449 (OUTLIER) cc_final: 0.9071 (t80) REVERT: A 256 ILE cc_start: 0.9688 (OUTLIER) cc_final: 0.9350 (mm) REVERT: A 368 ASP cc_start: 0.8726 (m-30) cc_final: 0.8437 (m-30) REVERT: A 408 MET cc_start: 0.9454 (mmt) cc_final: 0.9238 (mmt) REVERT: A 564 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8853 (mp0) REVERT: A 719 ASP cc_start: 0.8250 (t0) cc_final: 0.7836 (t0) REVERT: E 369 TYR cc_start: 0.6412 (t80) cc_final: 0.6139 (t80) REVERT: E 392 PHE cc_start: 0.7595 (p90) cc_final: 0.7281 (p90) REVERT: E 406 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7923 (mt-10) REVERT: E 414 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8458 (mm-40) REVERT: E 454 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.7977 (ttm170) REVERT: E 464 PHE cc_start: 0.8160 (m-80) cc_final: 0.7800 (m-80) REVERT: D 115 HIS cc_start: 0.6666 (m-70) cc_final: 0.6375 (m-70) REVERT: D 141 LYS cc_start: 0.7956 (mmtp) cc_final: 0.7178 (mtmt) REVERT: D 344 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.6332 (p90) REVERT: D 361 GLU cc_start: 0.8430 (pt0) cc_final: 0.7612 (tm-30) REVERT: D 380 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7632 (tm-30) REVERT: D 385 MET cc_start: 0.7564 (mtm) cc_final: 0.7335 (mtm) REVERT: D 456 TRP cc_start: 0.7540 (m100) cc_final: 0.7007 (m100) REVERT: D 534 LEU cc_start: 0.5042 (OUTLIER) cc_final: 0.4079 (tp) REVERT: D 537 GLN cc_start: 0.6392 (OUTLIER) cc_final: 0.6012 (mt0) REVERT: D 545 GLN cc_start: 0.7018 (mt0) cc_final: 0.6445 (mt0) REVERT: C 34 HIS cc_start: 0.8154 (t70) cc_final: 0.7649 (m-70) REVERT: C 35 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8361 (mt-10) REVERT: C 60 GLN cc_start: 0.8607 (pm20) cc_final: 0.8354 (pm20) REVERT: C 67 ASP cc_start: 0.8401 (m-30) cc_final: 0.7993 (m-30) REVERT: C 114 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8489 (mtpp) REVERT: C 142 LEU cc_start: 0.8598 (mt) cc_final: 0.8389 (mt) REVERT: C 183 TYR cc_start: 0.9368 (OUTLIER) cc_final: 0.8964 (t80) REVERT: C 256 ILE cc_start: 0.9691 (OUTLIER) cc_final: 0.9349 (mm) REVERT: C 368 ASP cc_start: 0.8716 (m-30) cc_final: 0.8481 (m-30) REVERT: C 564 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8884 (mp0) REVERT: C 719 ASP cc_start: 0.8301 (t0) cc_final: 0.7867 (t0) REVERT: F 369 TYR cc_start: 0.6639 (t80) cc_final: 0.6236 (t80) REVERT: F 392 PHE cc_start: 0.7548 (p90) cc_final: 0.7342 (p90) REVERT: F 406 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8018 (mt-10) REVERT: F 454 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.7947 (ttm170) REVERT: F 464 PHE cc_start: 0.8233 (m-80) cc_final: 0.7904 (m-80) outliers start: 92 outliers final: 52 residues processed: 360 average time/residue: 0.3259 time to fit residues: 192.7075 Evaluate side-chains 316 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 2.494 ------------------------------------------------------------------------------- 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 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 183 TYR 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 343 VAL 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 611 SER Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 692 SER 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 488 CYS 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 121 LEU 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 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 C residue 62 MET Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 183 TYR 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 611 SER 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 399 SER Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 155 optimal weight: 2.9990 chunk 292 optimal weight: 9.9990 chunk 280 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 270 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 258 optimal weight: 0.9980 chunk 176 optimal weight: 30.0000 chunk 101 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** 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 = 0.4176 r_free = 0.4176 target = 0.174003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100900 restraints weight = 36827.634| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.74 r_work: 0.2880 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25902 Z= 0.116 Angle : 0.591 14.042 35220 Z= 0.284 Chirality : 0.041 0.276 3902 Planarity : 0.003 0.044 4368 Dihedral : 9.432 76.969 4425 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.25 % Favored : 94.62 % Rotamer: Outliers : 3.33 % Allowed : 17.95 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.15), residues: 3030 helix: 0.89 (0.13), residues: 1658 sheet: -0.93 (0.44), residues: 142 loop : -1.97 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 77 HIS 0.010 0.001 HIS C 34 PHE 0.012 0.001 PHE A 684 TYR 0.058 0.001 TYR D 21 ARG 0.003 0.000 ARG F 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 22) link_NAG-ASN : angle 3.63751 ( 66) link_BETA1-4 : bond 0.00464 ( 16) link_BETA1-4 : angle 1.94728 ( 48) hydrogen bonds : bond 0.04053 ( 1219) hydrogen bonds : angle 4.07016 ( 3555) metal coordination : bond 0.00495 ( 4) SS BOND : bond 0.00738 ( 14) SS BOND : angle 1.46619 ( 28) covalent geometry : bond 0.00258 (25846) covalent geometry : angle 0.56453 (35078) *********************** 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: 88 poor density : 267 time to evaluate : 2.513 Fit side-chains revert: symmetry clash REVERT: B 69 MET cc_start: 0.6359 (tpt) cc_final: 0.6044 (tpt) REVERT: B 344 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.5995 (p90) REVERT: B 380 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7318 (tm-30) REVERT: B 385 MET cc_start: 0.7355 (mtm) cc_final: 0.7140 (mtm) REVERT: B 387 VAL cc_start: 0.7611 (OUTLIER) cc_final: 0.7181 (p) REVERT: B 391 TRP cc_start: 0.7244 (m100) cc_final: 0.7003 (m100) REVERT: B 534 LEU cc_start: 0.5305 (OUTLIER) cc_final: 0.4278 (tp) REVERT: B 545 GLN cc_start: 0.7208 (mt0) cc_final: 0.6607 (mt0) REVERT: A 60 GLN cc_start: 0.8584 (pm20) cc_final: 0.8330 (pm20) REVERT: A 67 ASP cc_start: 0.8448 (m-30) cc_final: 0.8006 (m-30) REVERT: A 114 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8477 (mtpp) REVERT: A 142 LEU cc_start: 0.8526 (mt) cc_final: 0.8316 (mt) REVERT: A 183 TYR cc_start: 0.9508 (OUTLIER) cc_final: 0.9227 (t80) REVERT: A 256 ILE cc_start: 0.9689 (OUTLIER) cc_final: 0.9358 (mm) REVERT: A 325 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8005 (tp-100) REVERT: A 368 ASP cc_start: 0.8732 (m-30) cc_final: 0.8514 (m-30) REVERT: A 408 MET cc_start: 0.9454 (mmt) cc_final: 0.9243 (mmt) REVERT: A 564 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8867 (mp0) REVERT: A 719 ASP cc_start: 0.8267 (t0) cc_final: 0.7864 (t0) REVERT: E 392 PHE cc_start: 0.7541 (p90) cc_final: 0.7275 (p90) REVERT: E 406 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8015 (mt-10) REVERT: E 442 ASP cc_start: 0.8035 (m-30) cc_final: 0.7699 (m-30) REVERT: E 454 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.7967 (ttm170) REVERT: E 464 PHE cc_start: 0.8141 (m-80) cc_final: 0.7822 (m-80) REVERT: E 509 ARG cc_start: 0.6139 (mtt-85) cc_final: 0.5502 (mtt90) REVERT: D 69 MET cc_start: 0.6144 (tpt) cc_final: 0.5748 (tpt) REVERT: D 322 ASP cc_start: 0.7786 (m-30) cc_final: 0.7449 (m-30) REVERT: D 344 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.6001 (p90) REVERT: D 380 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7651 (tm-30) REVERT: D 456 TRP cc_start: 0.7564 (m100) cc_final: 0.6991 (m100) REVERT: D 476 GLU cc_start: 0.5254 (mm-30) cc_final: 0.4619 (tp30) REVERT: D 534 LEU cc_start: 0.5162 (OUTLIER) cc_final: 0.4154 (tp) REVERT: D 545 GLN cc_start: 0.6992 (mt0) cc_final: 0.6436 (mt0) REVERT: C 34 HIS cc_start: 0.8127 (t70) cc_final: 0.7619 (m-70) REVERT: C 35 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8366 (mt-10) REVERT: C 60 GLN cc_start: 0.8618 (pm20) cc_final: 0.8322 (pm20) REVERT: C 67 ASP cc_start: 0.8426 (m-30) cc_final: 0.7999 (m-30) REVERT: C 114 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8475 (mtpp) REVERT: C 256 ILE cc_start: 0.9683 (OUTLIER) cc_final: 0.9351 (mm) REVERT: C 368 ASP cc_start: 0.8728 (m-30) cc_final: 0.8509 (m-30) REVERT: C 564 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8832 (mp0) REVERT: C 719 ASP cc_start: 0.8308 (t0) cc_final: 0.7878 (t0) REVERT: F 369 TYR cc_start: 0.6615 (t80) cc_final: 0.6246 (t80) REVERT: F 392 PHE cc_start: 0.7535 (p90) cc_final: 0.7321 (p90) REVERT: F 406 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8083 (mt-10) REVERT: F 454 ARG cc_start: 0.8421 (ttm-80) cc_final: 0.7927 (ttm170) REVERT: F 464 PHE cc_start: 0.8192 (m-80) cc_final: 0.7904 (m-80) outliers start: 88 outliers final: 54 residues processed: 338 average time/residue: 0.3157 time to fit residues: 174.8181 Evaluate side-chains 320 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 258 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 387 VAL Chi-restraints excluded: chain B residue 390 LEU 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 78 THR 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 256 ILE Chi-restraints excluded: chain A residue 295 ASP 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 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 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 121 LEU Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 212 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 C residue 62 MET Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 LEU 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 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 427 ASP 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 379 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 157 optimal weight: 6.9990 chunk 279 optimal weight: 8.9990 chunk 255 optimal weight: 0.9990 chunk 280 optimal weight: 6.9990 chunk 25 optimal weight: 0.0770 chunk 299 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 276 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 537 GLN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 96 GLN D 275 HIS D 537 GLN ** D 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.173611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098701 restraints weight = 36821.567| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.68 r_work: 0.2864 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25902 Z= 0.125 Angle : 0.589 13.298 35220 Z= 0.282 Chirality : 0.042 0.265 3902 Planarity : 0.003 0.041 4368 Dihedral : 8.911 76.476 4414 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Rotamer: Outliers : 3.07 % Allowed : 18.41 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3030 helix: 1.01 (0.13), residues: 1662 sheet: -0.09 (0.46), residues: 122 loop : -1.94 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 77 HIS 0.009 0.001 HIS C 34 PHE 0.018 0.001 PHE E 347 TYR 0.031 0.001 TYR B 21 ARG 0.005 0.000 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 22) link_NAG-ASN : angle 3.63222 ( 66) link_BETA1-4 : bond 0.00415 ( 16) link_BETA1-4 : angle 1.94008 ( 48) hydrogen bonds : bond 0.04088 ( 1219) hydrogen bonds : angle 4.01943 ( 3555) metal coordination : bond 0.00303 ( 4) SS BOND : bond 0.00730 ( 14) SS BOND : angle 1.46234 ( 28) covalent geometry : bond 0.00287 (25846) covalent geometry : angle 0.56262 (35078) *********************** 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 347 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 266 time to evaluate : 2.682 Fit side-chains revert: symmetry clash REVERT: B 69 MET cc_start: 0.6283 (tpt) cc_final: 0.5985 (tpt) REVERT: B 322 ASP cc_start: 0.7819 (m-30) cc_final: 0.7464 (m-30) REVERT: B 344 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.5866 (p90) REVERT: B 380 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7421 (tm-30) REVERT: B 387 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7089 (p) REVERT: B 476 GLU cc_start: 0.5007 (mm-30) cc_final: 0.4453 (tp30) REVERT: B 534 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.4390 (tp) REVERT: B 545 GLN cc_start: 0.7180 (mt0) cc_final: 0.6571 (mt0) REVERT: A 67 ASP cc_start: 0.8469 (m-30) cc_final: 0.8018 (m-30) REVERT: A 114 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8457 (mtpp) REVERT: A 183 TYR cc_start: 0.9530 (OUTLIER) cc_final: 0.9319 (t80) REVERT: A 256 ILE cc_start: 0.9675 (OUTLIER) cc_final: 0.9357 (mm) REVERT: A 325 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8009 (tp-100) REVERT: A 368 ASP cc_start: 0.8751 (m-30) cc_final: 0.8459 (m-30) REVERT: A 564 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8839 (mp0) REVERT: A 719 ASP cc_start: 0.8376 (t0) cc_final: 0.7968 (t0) REVERT: E 392 PHE cc_start: 0.7525 (p90) cc_final: 0.7271 (p90) REVERT: E 406 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8047 (mt-10) REVERT: E 442 ASP cc_start: 0.8002 (m-30) cc_final: 0.7727 (m-30) REVERT: E 454 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.7961 (ttm170) REVERT: E 464 PHE cc_start: 0.8080 (m-80) cc_final: 0.7750 (m-80) REVERT: E 509 ARG cc_start: 0.6106 (mtt-85) cc_final: 0.5625 (mtt90) REVERT: D 69 MET cc_start: 0.6257 (tpt) cc_final: 0.5916 (tpt) REVERT: D 322 ASP cc_start: 0.7809 (m-30) cc_final: 0.7467 (m-30) REVERT: D 344 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.5901 (p90) REVERT: D 380 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7666 (tm-30) REVERT: D 456 TRP cc_start: 0.7573 (m100) cc_final: 0.7000 (m100) REVERT: D 476 GLU cc_start: 0.5141 (mm-30) cc_final: 0.4574 (tp30) REVERT: D 503 TRP cc_start: 0.4215 (m100) cc_final: 0.3498 (m-90) REVERT: D 534 LEU cc_start: 0.5228 (OUTLIER) cc_final: 0.4238 (tp) REVERT: D 545 GLN cc_start: 0.7030 (mt0) cc_final: 0.6448 (mt0) REVERT: C 34 HIS cc_start: 0.8162 (t70) cc_final: 0.7651 (m-70) REVERT: C 60 GLN cc_start: 0.8627 (pm20) cc_final: 0.8356 (pm20) REVERT: C 67 ASP cc_start: 0.8434 (m-30) cc_final: 0.7998 (m-30) REVERT: C 114 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8459 (mtpp) REVERT: C 183 TYR cc_start: 0.9478 (OUTLIER) cc_final: 0.9172 (t80) REVERT: C 256 ILE cc_start: 0.9676 (OUTLIER) cc_final: 0.9361 (mm) REVERT: C 368 ASP cc_start: 0.8743 (m-30) cc_final: 0.8503 (m-30) REVERT: C 564 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8840 (mp0) REVERT: C 719 ASP cc_start: 0.8410 (t0) cc_final: 0.8029 (t0) REVERT: F 369 TYR cc_start: 0.6756 (t80) cc_final: 0.6316 (t80) REVERT: F 406 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7953 (mt-10) REVERT: F 454 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.7908 (ttm170) REVERT: F 464 PHE cc_start: 0.8175 (m-80) cc_final: 0.7897 (m-80) outliers start: 81 outliers final: 55 residues processed: 333 average time/residue: 0.3252 time to fit residues: 175.9432 Evaluate side-chains 320 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 256 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 534 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 78 THR 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 256 ILE Chi-restraints excluded: chain A residue 295 ASP 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 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 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 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 424 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 78 THR 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 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 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: 0.9980 chunk 160 optimal weight: 2.9990 chunk 265 optimal weight: 0.5980 chunk 261 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 281 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 148 optimal weight: 0.0980 chunk 266 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS D 243 ASN ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.174525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102295 restraints weight = 36684.053| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.76 r_work: 0.2895 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 25902 Z= 0.108 Angle : 0.579 12.558 35220 Z= 0.277 Chirality : 0.041 0.266 3902 Planarity : 0.003 0.037 4368 Dihedral : 8.551 75.524 4410 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 2.92 % Allowed : 19.36 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3030 helix: 1.20 (0.13), residues: 1644 sheet: 0.07 (0.48), residues: 120 loop : -1.84 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 391 HIS 0.008 0.001 HIS C 34 PHE 0.013 0.001 PHE E 347 TYR 0.024 0.001 TYR B 21 ARG 0.003 0.000 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 22) link_NAG-ASN : angle 3.44597 ( 66) link_BETA1-4 : bond 0.00440 ( 16) link_BETA1-4 : angle 1.89094 ( 48) hydrogen bonds : bond 0.03795 ( 1219) hydrogen bonds : angle 3.96839 ( 3555) metal coordination : bond 0.00147 ( 4) SS BOND : bond 0.00645 ( 14) SS BOND : angle 1.28810 ( 28) covalent geometry : bond 0.00238 (25846) covalent geometry : angle 0.55537 (35078) *********************** 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 346 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 269 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 MET cc_start: 0.6265 (tpt) cc_final: 0.6017 (tpt) REVERT: B 380 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 401 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7374 (ppp) REVERT: B 476 GLU cc_start: 0.5066 (mm-30) cc_final: 0.4453 (tp30) REVERT: B 534 LEU cc_start: 0.5464 (OUTLIER) cc_final: 0.4421 (tp) REVERT: B 545 GLN cc_start: 0.7207 (mt0) cc_final: 0.6607 (mt0) REVERT: A 67 ASP cc_start: 0.8399 (m-30) cc_final: 0.7974 (m-30) REVERT: A 114 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8492 (mtpp) REVERT: A 256 ILE cc_start: 0.9665 (OUTLIER) cc_final: 0.9354 (mm) REVERT: A 325 GLN cc_start: 0.8660 (tm-30) cc_final: 0.7984 (tp-100) REVERT: A 368 ASP cc_start: 0.8713 (m-30) cc_final: 0.8486 (m-30) REVERT: A 408 MET cc_start: 0.9443 (mmt) cc_final: 0.9242 (mmt) REVERT: A 527 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8803 (tt0) REVERT: A 564 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8802 (mp0) REVERT: A 719 ASP cc_start: 0.8357 (t0) cc_final: 0.7981 (t0) REVERT: E 392 PHE cc_start: 0.7664 (p90) cc_final: 0.7442 (p90) REVERT: E 406 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8059 (mt-10) REVERT: E 442 ASP cc_start: 0.8025 (m-30) cc_final: 0.7749 (m-30) REVERT: E 454 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.7903 (ttm170) REVERT: E 464 PHE cc_start: 0.8058 (m-80) cc_final: 0.7779 (m-80) REVERT: E 509 ARG cc_start: 0.6061 (mtt-85) cc_final: 0.5622 (mtt90) REVERT: D 69 MET cc_start: 0.6111 (tpt) cc_final: 0.5770 (tpt) REVERT: D 380 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7684 (tm-30) REVERT: D 456 TRP cc_start: 0.7508 (m100) cc_final: 0.6955 (m100) REVERT: D 476 GLU cc_start: 0.5073 (mm-30) cc_final: 0.4492 (tp30) REVERT: D 503 TRP cc_start: 0.4156 (m100) cc_final: 0.3460 (m-90) REVERT: D 534 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4227 (tp) REVERT: C 34 HIS cc_start: 0.8147 (t70) cc_final: 0.7678 (m-70) REVERT: C 35 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8265 (mt-10) REVERT: C 60 GLN cc_start: 0.8630 (pm20) cc_final: 0.8352 (pm20) REVERT: C 67 ASP cc_start: 0.8389 (m-30) cc_final: 0.7941 (m-30) REVERT: C 114 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8466 (mtpp) REVERT: C 256 ILE cc_start: 0.9665 (OUTLIER) cc_final: 0.9360 (mm) REVERT: C 325 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8033 (tp-100) REVERT: C 368 ASP cc_start: 0.8707 (m-30) cc_final: 0.8472 (m-30) REVERT: C 527 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8796 (tt0) REVERT: C 564 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8798 (mp0) REVERT: C 719 ASP cc_start: 0.8373 (t0) cc_final: 0.7965 (t0) REVERT: F 369 TYR cc_start: 0.6767 (t80) cc_final: 0.6345 (t80) REVERT: F 406 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7974 (mt-10) REVERT: F 464 PHE cc_start: 0.8130 (m-80) cc_final: 0.7881 (m-80) outliers start: 77 outliers final: 48 residues processed: 333 average time/residue: 0.3277 time to fit residues: 179.4719 Evaluate side-chains 316 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 2.599 ------------------------------------------------------------------------------- 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 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 344 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 295 ASP 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 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 434 ILE Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL 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 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 424 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 91 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 362 THR Chi-restraints excluded: chain C residue 401 HIS Chi-restraints excluded: chain C residue 427 ASP 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 399 SER Chi-restraints excluded: chain F residue 434 ILE Chi-restraints excluded: chain F residue 518 LEU 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 224 optimal weight: 0.5980 chunk 198 optimal weight: 10.0000 chunk 175 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 275 HIS ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.175640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.097666 restraints weight = 36321.597| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.52 r_work: 0.2893 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25902 Z= 0.113 Angle : 0.584 12.003 35220 Z= 0.280 Chirality : 0.041 0.264 3902 Planarity : 0.003 0.034 4368 Dihedral : 8.398 74.186 4400 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.72 % Rotamer: Outliers : 2.80 % Allowed : 19.73 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.16), residues: 3030 helix: 1.19 (0.13), residues: 1674 sheet: 0.03 (0.47), residues: 120 loop : -1.83 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 391 HIS 0.008 0.001 HIS C 34 PHE 0.011 0.001 PHE A 684 TYR 0.021 0.001 TYR B 21 ARG 0.003 0.000 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00781 ( 22) link_NAG-ASN : angle 3.25901 ( 66) link_BETA1-4 : bond 0.00435 ( 16) link_BETA1-4 : angle 1.87661 ( 48) hydrogen bonds : bond 0.03806 ( 1219) hydrogen bonds : angle 3.94904 ( 3555) metal coordination : bond 0.00197 ( 4) SS BOND : bond 0.01034 ( 14) SS BOND : angle 1.51891 ( 28) covalent geometry : bond 0.00253 (25846) covalent geometry : angle 0.56194 (35078) *********************** 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 343 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 269 time to evaluate : 2.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 MET cc_start: 0.6243 (tpt) cc_final: 0.5988 (tpt) REVERT: B 328 LEU cc_start: 0.7571 (tp) cc_final: 0.7326 (tt) REVERT: B 380 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7608 (tm-30) REVERT: B 401 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7370 (ppp) REVERT: B 456 TRP cc_start: 0.7652 (m100) cc_final: 0.7067 (m100) REVERT: B 476 GLU cc_start: 0.5108 (mm-30) cc_final: 0.4659 (tp30) REVERT: B 508 MET cc_start: 0.6816 (mmm) cc_final: 0.6063 (mtt) REVERT: B 534 LEU cc_start: 0.5462 (OUTLIER) cc_final: 0.4407 (tp) REVERT: B 545 GLN cc_start: 0.7185 (mt0) cc_final: 0.6586 (mt0) REVERT: A 67 ASP cc_start: 0.8425 (m-30) cc_final: 0.7975 (m-30) REVERT: A 114 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8475 (mtpp) REVERT: A 256 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9356 (mm) REVERT: A 325 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8024 (tp-100) REVERT: A 527 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8777 (tt0) REVERT: A 564 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8804 (mp0) REVERT: E 406 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7969 (mt-10) REVERT: E 454 ARG cc_start: 0.8387 (ttm-80) cc_final: 0.7959 (ttm170) REVERT: E 464 PHE cc_start: 0.8116 (m-80) cc_final: 0.7862 (m-80) REVERT: D 69 MET cc_start: 0.6129 (tpt) cc_final: 0.5802 (tpt) REVERT: D 380 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7745 (tm-30) REVERT: D 456 TRP cc_start: 0.7495 (m100) cc_final: 0.6942 (m100) REVERT: D 476 GLU cc_start: 0.4947 (mm-30) cc_final: 0.4407 (tp30) REVERT: D 503 TRP cc_start: 0.4148 (m100) cc_final: 0.3466 (m-90) REVERT: D 534 LEU cc_start: 0.5172 (OUTLIER) cc_final: 0.4183 (tp) REVERT: C 34 HIS cc_start: 0.8135 (t70) cc_final: 0.7656 (m-70) REVERT: C 35 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8254 (mt-10) REVERT: C 67 ASP cc_start: 0.8385 (m-30) cc_final: 0.7945 (m-30) REVERT: C 114 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8463 (mtpp) REVERT: C 256 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9361 (mm) REVERT: C 325 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8030 (tp-100) REVERT: C 332 MET cc_start: 0.8961 (ttp) cc_final: 0.8735 (ttm) REVERT: C 368 ASP cc_start: 0.8693 (m-30) cc_final: 0.8456 (m-30) REVERT: C 527 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8775 (tt0) REVERT: C 564 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8805 (mp0) REVERT: C 719 ASP cc_start: 0.8397 (t0) cc_final: 0.8000 (t0) REVERT: F 369 TYR cc_start: 0.6820 (t80) cc_final: 0.6494 (t80) REVERT: F 406 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7981 (mt-10) REVERT: F 464 PHE cc_start: 0.8099 (m-80) cc_final: 0.7866 (m-80) outliers start: 74 outliers final: 55 residues processed: 331 average time/residue: 0.3186 time to fit residues: 173.0523 Evaluate side-chains 320 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 258 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 175 LEU 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 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 78 THR 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 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 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 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 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 283 ASN 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 424 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 244 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 89 optimal weight: 0.0470 chunk 27 optimal weight: 5.9990 chunk 192 optimal weight: 0.0040 chunk 133 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 174 optimal weight: 0.8980 chunk 235 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.5090 ------------------------------------------------------------------------------- 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 275 HIS ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.176855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099301 restraints weight = 36194.798| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.36 r_work: 0.2939 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25902 Z= 0.101 Angle : 0.572 11.418 35220 Z= 0.274 Chirality : 0.041 0.278 3902 Planarity : 0.003 0.033 4368 Dihedral : 8.176 71.970 4398 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.75 % Rotamer: Outliers : 2.58 % Allowed : 20.34 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 3030 helix: 1.28 (0.13), residues: 1668 sheet: -0.04 (0.47), residues: 122 loop : -1.76 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 478 HIS 0.007 0.001 HIS C 34 PHE 0.027 0.001 PHE E 347 TYR 0.061 0.001 TYR D 21 ARG 0.003 0.000 ARG E 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 22) link_NAG-ASN : angle 3.12053 ( 66) link_BETA1-4 : bond 0.00443 ( 16) link_BETA1-4 : angle 1.85630 ( 48) hydrogen bonds : bond 0.03572 ( 1219) hydrogen bonds : angle 3.90280 ( 3555) metal coordination : bond 0.00089 ( 4) SS BOND : bond 0.00686 ( 14) SS BOND : angle 1.32283 ( 28) covalent geometry : bond 0.00216 (25846) covalent geometry : angle 0.55109 (35078) *********************** 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 342 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 2.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 MET cc_start: 0.6193 (tpt) cc_final: 0.5955 (tpt) REVERT: B 241 TRP cc_start: 0.7496 (m100) cc_final: 0.6502 (m100) REVERT: B 328 LEU cc_start: 0.7374 (tp) cc_final: 0.7128 (tt) REVERT: B 380 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7588 (tm-30) REVERT: B 401 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7396 (ppp) REVERT: B 476 GLU cc_start: 0.5148 (mm-30) cc_final: 0.4607 (tp30) REVERT: B 534 LEU cc_start: 0.5392 (OUTLIER) cc_final: 0.4330 (tp) REVERT: B 545 GLN cc_start: 0.7196 (mt0) cc_final: 0.6594 (mt0) REVERT: A 67 ASP cc_start: 0.8397 (m-30) cc_final: 0.7941 (m-30) REVERT: A 114 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8378 (mtpp) REVERT: A 256 ILE cc_start: 0.9653 (OUTLIER) cc_final: 0.9344 (mm) REVERT: A 325 GLN cc_start: 0.8665 (tm-30) cc_final: 0.7997 (tp-100) REVERT: A 527 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8700 (tt0) REVERT: A 564 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8754 (mp0) REVERT: E 406 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8008 (mt-10) REVERT: E 454 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.7932 (ttm170) REVERT: E 464 PHE cc_start: 0.7909 (m-80) cc_final: 0.7633 (m-80) REVERT: D 69 MET cc_start: 0.6173 (tpt) cc_final: 0.5861 (tpt) REVERT: D 100 MET cc_start: 0.7049 (ptt) cc_final: 0.6479 (ptp) REVERT: D 241 TRP cc_start: 0.7349 (m100) cc_final: 0.6253 (m100) REVERT: D 328 LEU cc_start: 0.7413 (tp) cc_final: 0.7176 (tt) REVERT: D 380 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7670 (tm-30) REVERT: D 456 TRP cc_start: 0.7499 (m100) cc_final: 0.6958 (m100) REVERT: D 476 GLU cc_start: 0.4955 (mm-30) cc_final: 0.4441 (tp30) REVERT: D 503 TRP cc_start: 0.4076 (m100) cc_final: 0.3472 (m-90) REVERT: D 534 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4213 (tp) REVERT: C 34 HIS cc_start: 0.8056 (t70) cc_final: 0.7663 (m90) REVERT: C 35 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8178 (mm-30) REVERT: C 67 ASP cc_start: 0.8406 (m-30) cc_final: 0.7943 (m-30) REVERT: C 114 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8412 (mtpp) REVERT: C 256 ILE cc_start: 0.9656 (OUTLIER) cc_final: 0.9351 (mm) REVERT: C 325 GLN cc_start: 0.8648 (tm-30) cc_final: 0.7998 (tp-100) REVERT: C 368 ASP cc_start: 0.8634 (m-30) cc_final: 0.8398 (m-30) REVERT: C 527 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: C 564 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8744 (mp0) REVERT: C 719 ASP cc_start: 0.8308 (t0) cc_final: 0.7936 (t0) REVERT: F 369 TYR cc_start: 0.6896 (t80) cc_final: 0.6596 (t80) REVERT: F 406 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8012 (mt-10) REVERT: F 464 PHE cc_start: 0.8059 (m-80) cc_final: 0.7845 (m-80) outliers start: 68 outliers final: 50 residues processed: 333 average time/residue: 0.3307 time to fit residues: 180.6386 Evaluate side-chains 324 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 401 MET Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 150 GLU 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 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 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 309 CYS Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 TYR Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 183 TYR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 227 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 292 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS D 275 HIS ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN C 277 ASN F 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.174043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100848 restraints weight = 36645.698| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.54 r_work: 0.2884 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25902 Z= 0.131 Angle : 0.597 11.087 35220 Z= 0.287 Chirality : 0.043 0.423 3902 Planarity : 0.003 0.054 4368 Dihedral : 8.094 68.940 4398 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.62 % Rotamer: Outliers : 2.61 % Allowed : 20.23 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 3030 helix: 1.27 (0.13), residues: 1668 sheet: -0.03 (0.47), residues: 120 loop : -1.74 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.008 0.001 HIS C 34 PHE 0.028 0.001 PHE E 347 TYR 0.052 0.001 TYR D 21 ARG 0.007 0.000 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 22) link_NAG-ASN : angle 3.09326 ( 66) link_BETA1-4 : bond 0.00396 ( 16) link_BETA1-4 : angle 1.88956 ( 48) hydrogen bonds : bond 0.03980 ( 1219) hydrogen bonds : angle 3.94535 ( 3555) metal coordination : bond 0.00277 ( 4) SS BOND : bond 0.00685 ( 14) SS BOND : angle 1.39268 ( 28) covalent geometry : bond 0.00304 (25846) covalent geometry : angle 0.57766 (35078) *********************** 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 340 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 271 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 MET cc_start: 0.6218 (tpt) cc_final: 0.5995 (tpt) REVERT: B 380 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7624 (tm-30) REVERT: B 401 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7413 (ppp) REVERT: B 476 GLU cc_start: 0.5232 (mm-30) cc_final: 0.4813 (tp30) REVERT: B 534 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.4304 (tp) REVERT: B 545 GLN cc_start: 0.7254 (mt0) cc_final: 0.6643 (mt0) REVERT: A 67 ASP cc_start: 0.8460 (m-30) cc_final: 0.7999 (m-30) REVERT: A 114 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8441 (mtpp) REVERT: A 256 ILE cc_start: 0.9672 (OUTLIER) cc_final: 0.9365 (mm) REVERT: A 325 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8010 (tp-100) REVERT: A 527 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8796 (tt0) REVERT: A 564 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8788 (mp0) REVERT: E 406 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8028 (mt-10) REVERT: E 454 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.7958 (ttm170) REVERT: E 464 PHE cc_start: 0.7817 (m-80) cc_final: 0.7535 (m-80) REVERT: D 69 MET cc_start: 0.6203 (tpt) cc_final: 0.5887 (tpt) REVERT: D 100 MET cc_start: 0.7141 (ptt) cc_final: 0.6694 (ptp) REVERT: D 380 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7723 (tm-30) REVERT: D 456 TRP cc_start: 0.7549 (m100) cc_final: 0.6975 (m100) REVERT: D 476 GLU cc_start: 0.5063 (mm-30) cc_final: 0.4598 (tp30) REVERT: D 503 TRP cc_start: 0.4061 (m100) cc_final: 0.3422 (m-90) REVERT: D 534 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4182 (tp) REVERT: C 34 HIS cc_start: 0.8127 (t70) cc_final: 0.7663 (m-70) REVERT: C 67 ASP cc_start: 0.8469 (m-30) cc_final: 0.8009 (m-30) REVERT: C 114 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8453 (mtpp) REVERT: C 256 ILE cc_start: 0.9664 (OUTLIER) cc_final: 0.9361 (mm) REVERT: C 325 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8038 (tp-100) REVERT: C 527 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8806 (tt0) REVERT: C 564 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8773 (mp0) REVERT: F 369 TYR cc_start: 0.6927 (t80) cc_final: 0.6632 (t80) REVERT: F 406 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8048 (mt-10) REVERT: F 464 PHE cc_start: 0.8052 (m-80) cc_final: 0.7852 (m-80) outliers start: 69 outliers final: 54 residues processed: 331 average time/residue: 0.3205 time to fit residues: 173.6822 Evaluate side-chains 321 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 260 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 175 LEU 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 337 LYS Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain A residue 78 THR 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 427 ASP 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 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 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 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 424 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 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 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 394 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 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 33 optimal weight: 0.7980 chunk 292 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 300 optimal weight: 0.7980 chunk 270 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN ** B 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS ** D 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.175223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.097034 restraints weight = 36190.580| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.35 r_work: 0.2901 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2436 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= 0.134 Angle : 0.600 10.845 35220 Z= 0.289 Chirality : 0.043 0.385 3902 Planarity : 0.003 0.038 4368 Dihedral : 8.014 65.503 4398 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.31 % Favored : 94.59 % Rotamer: Outliers : 2.58 % Allowed : 20.49 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 3030 helix: 1.23 (0.13), residues: 1686 sheet: -0.14 (0.46), residues: 122 loop : -1.72 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 509 HIS 0.008 0.001 HIS C 34 PHE 0.033 0.001 PHE E 347 TYR 0.052 0.001 TYR D 21 ARG 0.012 0.000 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 22) link_NAG-ASN : angle 3.03401 ( 66) link_BETA1-4 : bond 0.00404 ( 16) link_BETA1-4 : angle 1.90258 ( 48) hydrogen bonds : bond 0.04009 ( 1219) hydrogen bonds : angle 3.96810 ( 3555) metal coordination : bond 0.00313 ( 4) SS BOND : bond 0.00672 ( 14) SS BOND : angle 1.36009 ( 28) covalent geometry : bond 0.00313 (25846) covalent geometry : angle 0.58084 (35078) ********************** 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 329 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 261 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 MET cc_start: 0.6202 (tpt) cc_final: 0.5965 (tpt) REVERT: B 241 TRP cc_start: 0.7433 (m100) cc_final: 0.6369 (m100) REVERT: B 380 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7577 (tm-30) REVERT: B 401 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7407 (ppp) REVERT: B 456 TRP cc_start: 0.7535 (m100) cc_final: 0.6962 (m100) REVERT: B 476 GLU cc_start: 0.5222 (mm-30) cc_final: 0.4774 (tp30) REVERT: B 534 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.4356 (tp) REVERT: B 545 GLN cc_start: 0.7231 (mt0) cc_final: 0.6629 (mt0) REVERT: A 67 ASP cc_start: 0.8409 (m-30) cc_final: 0.7936 (m-30) REVERT: A 114 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8399 (mtpp) REVERT: A 256 ILE cc_start: 0.9671 (OUTLIER) cc_final: 0.9359 (mm) REVERT: A 325 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8000 (tp-100) REVERT: A 527 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8778 (tt0) REVERT: A 564 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8776 (mp0) REVERT: E 406 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8003 (mt-10) REVERT: E 454 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.7936 (ttm170) REVERT: E 464 PHE cc_start: 0.7797 (m-80) cc_final: 0.7511 (m-80) REVERT: D 69 MET cc_start: 0.6165 (tpt) cc_final: 0.5867 (tpt) REVERT: D 100 MET cc_start: 0.7050 (ptt) cc_final: 0.6713 (ptp) REVERT: D 380 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7678 (tm-30) REVERT: D 456 TRP cc_start: 0.7538 (m100) cc_final: 0.6947 (m100) REVERT: D 476 GLU cc_start: 0.5083 (mm-30) cc_final: 0.4648 (tp30) REVERT: D 503 TRP cc_start: 0.4053 (m100) cc_final: 0.3482 (m-90) REVERT: D 534 LEU cc_start: 0.5141 (OUTLIER) cc_final: 0.4186 (tp) REVERT: C 34 HIS cc_start: 0.8115 (t70) cc_final: 0.7691 (m-70) REVERT: C 35 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8139 (mm-30) REVERT: C 67 ASP cc_start: 0.8452 (m-30) cc_final: 0.7985 (m-30) REVERT: C 114 LYS cc_start: 0.8661 (mtmt) cc_final: 0.8409 (mtpp) REVERT: C 183 TYR cc_start: 0.9594 (OUTLIER) cc_final: 0.9247 (t80) REVERT: C 256 ILE cc_start: 0.9666 (OUTLIER) cc_final: 0.9359 (mm) REVERT: C 325 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8019 (tp-100) REVERT: C 527 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8768 (tt0) REVERT: C 564 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8770 (mp0) REVERT: F 369 TYR cc_start: 0.6961 (t80) cc_final: 0.6667 (t80) REVERT: F 406 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8011 (mt-10) REVERT: F 464 PHE cc_start: 0.8024 (m-80) cc_final: 0.7785 (m-80) outliers start: 68 outliers final: 53 residues processed: 322 average time/residue: 0.3193 time to fit residues: 168.0984 Evaluate side-chains 319 residues out of total 2640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 258 time to evaluate : 2.586 ------------------------------------------------------------------------------- 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 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 401 MET Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain A residue 78 THR 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 427 ASP 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 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 121 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 283 ASN 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 424 ILE Chi-restraints excluded: chain D residue 534 LEU 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 427 ASP 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 394 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 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 213 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.175626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097581 restraints weight = 36183.572| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.37 r_work: 0.2920 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25902 Z= 0.111 Angle : 0.594 13.291 35220 Z= 0.284 Chirality : 0.042 0.432 3902 Planarity : 0.003 0.040 4368 Dihedral : 7.899 61.737 4398 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.69 % Rotamer: Outliers : 2.31 % Allowed : 20.53 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 3030 helix: 1.31 (0.13), residues: 1696 sheet: -0.10 (0.47), residues: 120 loop : -1.69 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 509 HIS 0.007 0.001 HIS C 34 PHE 0.034 0.001 PHE E 347 TYR 0.051 0.001 TYR D 21 ARG 0.003 0.000 ARG E 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00513 ( 22) link_NAG-ASN : angle 2.94779 ( 66) link_BETA1-4 : bond 0.00419 ( 16) link_BETA1-4 : angle 1.88412 ( 48) hydrogen bonds : bond 0.03769 ( 1219) hydrogen bonds : angle 3.95799 ( 3555) metal coordination : bond 0.00179 ( 4) SS BOND : bond 0.00752 ( 14) SS BOND : angle 1.52844 ( 28) covalent geometry : bond 0.00249 (25846) covalent geometry : angle 0.57501 (35078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19632.85 seconds wall clock time: 337 minutes 31.87 seconds (20251.87 seconds total)