Starting phenix.real_space_refine on Sun Jun 29 04:14:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufb_42190/06_2025/8ufb_42190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufb_42190/06_2025/8ufb_42190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ufb_42190/06_2025/8ufb_42190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufb_42190/06_2025/8ufb_42190.map" model { file = "/net/cci-nas-00/data/ceres_data/8ufb_42190/06_2025/8ufb_42190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufb_42190/06_2025/8ufb_42190.cif" } resolution = 3.89 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= 0.037 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: 5 Type Number sf(0) Gaussians Ca 12 9.91 5 S 264 5.16 5 C 21816 2.51 5 N 6012 2.21 5 O 6552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34656 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "B" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "C" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "D" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "E" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "F" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "G" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "H" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "I" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "J" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "K" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "L" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "V" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 588 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "W" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 588 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "X" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 588 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "Y" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 588 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "R" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "S" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "T" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "U" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 258 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.91, per 1000 atoms: 0.57 Number of scatterers: 34656 At special positions: 0 Unit cell: (162.15, 182.689, 202.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 12 19.99 S 264 16.00 O 6552 8.00 N 6012 7.00 C 21816 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=96, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.04 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 223 " distance=2.02 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 413 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 272 " distance=2.03 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 377 " distance=2.03 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 329 " - pdb=" SG CYS D 371 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 103 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 199 " - pdb=" SG CYS E 223 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 393 " - pdb=" SG CYS E 413 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 260 " - pdb=" SG CYS G 272 " distance=2.03 Simple disulfide: pdb=" SG CYS G 302 " - pdb=" SG CYS G 377 " distance=2.03 Simple disulfide: pdb=" SG CYS G 307 " - pdb=" SG CYS G 381 " distance=2.03 Simple disulfide: pdb=" SG CYS G 329 " - pdb=" SG CYS G 371 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 27 " distance=2.03 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 103 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 263 " distance=2.03 Simple disulfide: pdb=" SG CYS H 199 " - pdb=" SG CYS H 223 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 217 " distance=2.04 Simple disulfide: pdb=" SG CYS H 393 " - pdb=" SG CYS H 413 " distance=2.04 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 260 " - pdb=" SG CYS J 272 " distance=2.03 Simple disulfide: pdb=" SG CYS J 302 " - pdb=" SG CYS J 377 " distance=2.03 Simple disulfide: pdb=" SG CYS J 307 " - pdb=" SG CYS J 381 " distance=2.03 Simple disulfide: pdb=" SG CYS J 329 " - pdb=" SG CYS J 371 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 122 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 27 " distance=2.03 Simple disulfide: pdb=" SG CYS K 89 " - pdb=" SG CYS K 103 " distance=2.03 Simple disulfide: pdb=" SG CYS K 150 " - pdb=" SG CYS K 263 " distance=2.03 Simple disulfide: pdb=" SG CYS K 199 " - pdb=" SG CYS K 223 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 217 " distance=2.03 Simple disulfide: pdb=" SG CYS K 393 " - pdb=" SG CYS K 413 " distance=2.03 Simple disulfide: pdb=" SG CYS V 33 " - pdb=" SG CYS V 45 " distance=2.03 Simple disulfide: pdb=" SG CYS V 40 " - pdb=" SG CYS V 58 " distance=2.04 Simple disulfide: pdb=" SG CYS V 52 " - pdb=" SG CYS V 67 " distance=2.03 Simple disulfide: pdb=" SG CYS V 72 " - pdb=" SG CYS V 84 " distance=2.03 Simple disulfide: pdb=" SG CYS V 79 " - pdb=" SG CYS V 97 " distance=2.03 Simple disulfide: pdb=" SG CYS V 91 " - pdb=" SG CYS V 108 " distance=2.03 Simple disulfide: pdb=" SG CYS W 33 " - pdb=" SG CYS W 45 " distance=2.03 Simple disulfide: pdb=" SG CYS W 40 " - pdb=" SG CYS W 58 " distance=2.03 Simple disulfide: pdb=" SG CYS W 52 " - pdb=" SG CYS W 67 " distance=2.03 Simple disulfide: pdb=" SG CYS W 72 " - pdb=" SG CYS W 84 " distance=2.03 Simple disulfide: pdb=" SG CYS W 79 " - pdb=" SG CYS W 97 " distance=2.04 Simple disulfide: pdb=" SG CYS W 91 " - pdb=" SG CYS W 108 " distance=2.03 Simple disulfide: pdb=" SG CYS X 33 " - pdb=" SG CYS X 45 " distance=2.03 Simple disulfide: pdb=" SG CYS X 40 " - pdb=" SG CYS X 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 52 " - pdb=" SG CYS X 67 " distance=2.03 Simple disulfide: pdb=" SG CYS X 72 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 79 " - pdb=" SG CYS X 97 " distance=2.03 Simple disulfide: pdb=" SG CYS X 91 " - pdb=" SG CYS X 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 33 " - pdb=" SG CYS Y 45 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 40 " - pdb=" SG CYS Y 58 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 52 " - pdb=" SG CYS Y 67 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 72 " - pdb=" SG CYS Y 84 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 79 " - pdb=" SG CYS Y 97 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 91 " - pdb=" SG CYS Y 108 " distance=2.03 Simple disulfide: pdb=" SG CYS R 239 " - pdb=" SG CYS R 251 " distance=2.03 Simple disulfide: pdb=" SG CYS R 246 " - pdb=" SG CYS R 264 " distance=2.04 Simple disulfide: pdb=" SG CYS R 258 " - pdb=" SG CYS R 273 " distance=2.03 Simple disulfide: pdb=" SG CYS S 239 " - pdb=" SG CYS S 251 " distance=2.03 Simple disulfide: pdb=" SG CYS S 246 " - pdb=" SG CYS S 264 " distance=2.03 Simple disulfide: pdb=" SG CYS S 258 " - pdb=" SG CYS S 273 " distance=2.03 Simple disulfide: pdb=" SG CYS T 239 " - pdb=" SG CYS T 251 " distance=2.03 Simple disulfide: pdb=" SG CYS T 246 " - pdb=" SG CYS T 264 " distance=2.04 Simple disulfide: pdb=" SG CYS T 258 " - pdb=" SG CYS T 273 " distance=2.03 Simple disulfide: pdb=" SG CYS U 239 " - pdb=" SG CYS U 251 " distance=2.03 Simple disulfide: pdb=" SG CYS U 246 " - pdb=" SG CYS U 264 " distance=2.03 Simple disulfide: pdb=" SG CYS U 258 " - pdb=" SG CYS U 273 " distance=2.03 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 NAG-ASN " NAG A 501 " - " ASN A 134 " " NAG B 501 " - " ASN B 315 " " NAG D 501 " - " ASN D 134 " " NAG E 501 " - " ASN E 315 " " NAG G 501 " - " ASN G 134 " " NAG H 501 " - " ASN H 315 " " NAG J 501 " - " ASN J 134 " " NAG K 501 " - " ASN K 315 " Time building additional restraints: 8.17 Conformation dependent library (CDL) restraints added in 4.5 seconds 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8256 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 90 sheets defined 16.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.41 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 239 through 248 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 404 through 441 Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 348 through 360 Processing helix chain 'B' and resid 360 through 399 Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 239 through 248 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 404 through 441 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 8 through 12 Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 348 through 360 Processing helix chain 'E' and resid 360 through 399 Proline residue: E 396 - end of helix Processing helix chain 'E' and resid 406 through 413 removed outlier: 3.664A pdb=" N ALA E 410 " --> pdb=" O PRO E 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 40 Processing helix chain 'F' and resid 57 through 62 removed outlier: 4.382A pdb=" N SER F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 200 through 202 No H-bonds generated for 'chain 'G' and resid 200 through 202' Processing helix chain 'G' and resid 239 through 248 Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 257 through 260 Processing helix chain 'G' and resid 284 through 288 Processing helix chain 'G' and resid 290 through 294 Processing helix chain 'G' and resid 404 through 441 Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 8 through 12 Processing helix chain 'H' and resid 219 through 221 No H-bonds generated for 'chain 'H' and resid 219 through 221' Processing helix chain 'H' and resid 348 through 360 Processing helix chain 'H' and resid 360 through 399 Proline residue: H 396 - end of helix Processing helix chain 'H' and resid 406 through 413 Processing helix chain 'I' and resid 37 through 41 removed outlier: 3.702A pdb=" N ALA I 40 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE I 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 37 through 41' Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'J' and resid 112 through 116 Processing helix chain 'J' and resid 200 through 202 No H-bonds generated for 'chain 'J' and resid 200 through 202' Processing helix chain 'J' and resid 239 through 248 Processing helix chain 'J' and resid 251 through 256 Processing helix chain 'J' and resid 257 through 260 Processing helix chain 'J' and resid 284 through 288 Processing helix chain 'J' and resid 290 through 294 Processing helix chain 'J' and resid 404 through 441 removed outlier: 3.572A pdb=" N ARG J 440 " --> pdb=" O LEU J 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 8 through 12 Processing helix chain 'K' and resid 219 through 221 No H-bonds generated for 'chain 'K' and resid 219 through 221' Processing helix chain 'K' and resid 348 through 360 Processing helix chain 'K' and resid 360 through 399 Proline residue: K 396 - end of helix Processing helix chain 'K' and resid 406 through 413 Processing helix chain 'L' and resid 35 through 40 Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 57 through 61 Processing helix chain 'V' and resid 49 through 51 No H-bonds generated for 'chain 'V' and resid 49 through 51' Processing helix chain 'V' and resid 61 through 66 removed outlier: 4.163A pdb=" N ASN V 66 " --> pdb=" O SER V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 90 No H-bonds generated for 'chain 'V' and resid 88 through 90' Processing helix chain 'V' and resid 99 through 104 removed outlier: 4.540A pdb=" N ASP V 102 " --> pdb=" O ASP V 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 51 No H-bonds generated for 'chain 'W' and resid 49 through 51' Processing helix chain 'W' and resid 88 through 90 No H-bonds generated for 'chain 'W' and resid 88 through 90' Processing helix chain 'W' and resid 100 through 108 Proline residue: W 105 - end of helix Processing helix chain 'X' and resid 49 through 52 removed outlier: 4.440A pdb=" N CYS X 52 " --> pdb=" O LEU X 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 49 through 52' Processing helix chain 'X' and resid 61 through 66 removed outlier: 3.610A pdb=" N LYS X 65 " --> pdb=" O GLY X 61 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN X 66 " --> pdb=" O SER X 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 61 through 66' Processing helix chain 'X' and resid 88 through 90 No H-bonds generated for 'chain 'X' and resid 88 through 90' Processing helix chain 'X' and resid 100 through 104 Processing helix chain 'Y' and resid 49 through 51 No H-bonds generated for 'chain 'Y' and resid 49 through 51' Processing helix chain 'Y' and resid 61 through 66 removed outlier: 4.686A pdb=" N ASN Y 66 " --> pdb=" O SER Y 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 90 No H-bonds generated for 'chain 'Y' and resid 88 through 90' Processing helix chain 'R' and resid 255 through 257 No H-bonds generated for 'chain 'R' and resid 255 through 257' Processing helix chain 'R' and resid 269 through 273 removed outlier: 3.577A pdb=" N CYS R 273 " --> pdb=" O GLU R 270 " (cutoff:3.500A) Processing helix chain 'S' and resid 255 through 257 No H-bonds generated for 'chain 'S' and resid 255 through 257' Processing helix chain 'S' and resid 269 through 273 Processing helix chain 'T' and resid 255 through 257 No H-bonds generated for 'chain 'T' and resid 255 through 257' Processing helix chain 'T' and resid 269 through 273 removed outlier: 3.558A pdb=" N CYS T 273 " --> pdb=" O GLU T 270 " (cutoff:3.500A) Processing helix chain 'U' and resid 255 through 257 No H-bonds generated for 'chain 'U' and resid 255 through 257' Processing helix chain 'U' and resid 269 through 273 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.548A pdb=" N LYS A 161 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.494A pdb=" N MET A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR A 36 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE A 38 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A 128 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 46 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LYS A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N SER A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 148 current: chain 'A' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 186 current: chain 'A' and resid 268 through 270 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 101 through 110 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA7, first strand: chain 'A' and resid 297 through 306 removed outlier: 5.392A pdb=" N ASP A 299 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LYS A 322 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 316 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA9, first strand: chain 'A' and resid 365 through 368 Processing sheet with id=AB1, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.642A pdb=" N CYS B 27 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.753A pdb=" N GLN B 48 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL B 36 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N SER B 50 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET B 68 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N LYS B 56 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N LEU B 62 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 72 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.472A pdb=" N ASP B 107 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 146 through 153 Processing sheet with id=AB6, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.523A pdb=" N VAL B 172 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 205 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AB9, first strand: chain 'B' and resid 272 through 276 Processing sheet with id=AC1, first strand: chain 'C' and resid 32 through 33 removed outlier: 6.382A pdb=" N PHE C 4 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR C 15 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 6 " --> pdb=" O ASN C 13 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR C 15 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 74 through 78 removed outlier: 9.579A pdb=" N ALA C 82 " --> pdb=" O PRO C 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 89 through 93 current: chain 'C' and resid 113 through 123 removed outlier: 8.217A pdb=" N ALA C 115 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N TRP C 134 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL C 117 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 132 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AC4, first strand: chain 'D' and resid 15 through 19 removed outlier: 6.470A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE D 38 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR D 128 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N THR D 126 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR D 42 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL D 124 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU D 44 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR D 122 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TYR D 46 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS D 120 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR D 137 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER D 141 " --> pdb=" O TYR D 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 140 through 148 current: chain 'D' and resid 184 through 187 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 184 through 187 current: chain 'D' and resid 268 through 270 Processing sheet with id=AC5, first strand: chain 'D' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 51 through 54 current: chain 'D' and resid 101 through 110 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AC7, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AC8, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AC9, first strand: chain 'D' and resid 297 through 306 removed outlier: 4.277A pdb=" N LEU D 300 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA D 320 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS D 302 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR D 318 " --> pdb=" O CYS D 302 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ILE D 304 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE D 316 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 344 through 347 Processing sheet with id=AD2, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AD3, first strand: chain 'E' and resid 17 through 22 removed outlier: 4.630A pdb=" N ASN E 21 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER E 25 " --> pdb=" O ASN E 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 33 through 37 removed outlier: 6.568A pdb=" N GLN E 48 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL E 36 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG E 46 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER E 93 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN E 102 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU E 91 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 52 through 56 removed outlier: 11.496A pdb=" N MET E 52 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N ALA E 63 " --> pdb=" O MET E 52 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY E 54 " --> pdb=" O ASP E 61 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.593A pdb=" N THR E 108 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS E 126 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR E 110 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL E 124 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N GLY E 112 " --> pdb=" O CYS E 122 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N CYS E 122 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N HIS E 114 " --> pdb=" O HIS E 120 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS E 120 " --> pdb=" O HIS E 114 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 146 through 153 Processing sheet with id=AD8, first strand: chain 'E' and resid 234 through 235 Processing sheet with id=AD9, first strand: chain 'E' and resid 172 through 173 Processing sheet with id=AE1, first strand: chain 'E' and resid 178 through 179 Processing sheet with id=AE2, first strand: chain 'E' and resid 272 through 276 Processing sheet with id=AE3, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.166A pdb=" N PHE F 4 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR F 15 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE F 6 " --> pdb=" O ASN F 13 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N TYR F 15 " --> pdb=" O PRO F 26 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 66 through 67 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 66 through 67 current: chain 'F' and resid 81 through 86 removed outlier: 9.311A pdb=" N ALA F 82 " --> pdb=" O PRO F 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 89 through 93 current: chain 'F' and resid 112 through 122 removed outlier: 8.058A pdb=" N ALA F 115 " --> pdb=" O TRP F 134 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N TRP F 134 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL F 117 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL F 132 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 2 through 8 removed outlier: 3.531A pdb=" N LYS G 161 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 15 through 19 removed outlier: 6.494A pdb=" N MET G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR G 36 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN G 130 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N TYR G 137 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER G 141 " --> pdb=" O TYR G 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 140 through 148 current: chain 'G' and resid 268 through 270 Processing sheet with id=AE7, first strand: chain 'G' and resid 41 through 48 removed outlier: 6.962A pdb=" N ALA G 121 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE G 47 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA G 119 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 54 current: chain 'G' and resid 101 through 110 No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AF1, first strand: chain 'G' and resid 204 through 206 Processing sheet with id=AF2, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AF3, first strand: chain 'G' and resid 297 through 306 removed outlier: 4.789A pdb=" N ASP G 299 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS G 322 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE G 316 " --> pdb=" O THR G 305 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 344 through 346 Processing sheet with id=AF5, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AF6, first strand: chain 'H' and resid 17 through 22 removed outlier: 5.345A pdb=" N ASP H 18 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N SER H 29 " --> pdb=" O ASP H 18 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N CYS H 27 " --> pdb=" O PRO H 20 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 25 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 33 through 37 removed outlier: 8.611A pdb=" N ILE H 33 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER H 50 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU H 35 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 10.254A pdb=" N SER H 50 " --> pdb=" O MET H 68 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N MET H 68 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR H 64 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N LYS H 56 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N LEU H 62 " --> pdb=" O LYS H 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 72 through 77 current: chain 'H' and resid 88 through 102 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 88 through 102 current: chain 'H' and resid 118 through 128 Processing sheet with id=AF8, first strand: chain 'H' and resid 146 through 153 Processing sheet with id=AF9, first strand: chain 'H' and resid 234 through 235 Processing sheet with id=AG1, first strand: chain 'H' and resid 172 through 173 Processing sheet with id=AG2, first strand: chain 'H' and resid 178 through 179 Processing sheet with id=AG3, first strand: chain 'H' and resid 272 through 276 Processing sheet with id=AG4, first strand: chain 'I' and resid 32 through 33 removed outlier: 3.725A pdb=" N GLY I 14 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR I 15 " --> pdb=" O PRO I 26 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 74 through 78 removed outlier: 9.764A pdb=" N ALA I 82 " --> pdb=" O PRO I 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 89 through 93 current: chain 'I' and resid 113 through 122 removed outlier: 8.829A pdb=" N VAL I 114 " --> pdb=" O TRP I 134 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP I 134 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER I 130 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY I 120 " --> pdb=" O ALA I 128 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA I 128 " --> pdb=" O GLY I 120 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASN I 122 " --> pdb=" O ARG I 126 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG I 126 " --> pdb=" O ASN I 122 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.571A pdb=" N LYS J 161 " --> pdb=" O ASP J 282 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 15 through 19 removed outlier: 6.597A pdb=" N MET J 132 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR J 36 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN J 130 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE J 38 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR J 128 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR J 126 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR J 42 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL J 124 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU J 44 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR J 122 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR J 46 " --> pdb=" O LYS J 120 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYS J 120 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR J 137 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N SER J 141 " --> pdb=" O TYR J 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 140 through 148 current: chain 'J' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 184 through 186 current: chain 'J' and resid 268 through 270 Processing sheet with id=AG8, first strand: chain 'J' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 51 through 54 current: chain 'J' and resid 101 through 110 No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AH1, first strand: chain 'J' and resid 204 through 206 Processing sheet with id=AH2, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AH3, first strand: chain 'J' and resid 296 through 306 removed outlier: 6.048A pdb=" N VAL J 297 " --> pdb=" O SER J 324 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER J 324 " --> pdb=" O VAL J 297 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP J 299 " --> pdb=" O LYS J 322 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS J 322 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE J 316 " --> pdb=" O THR J 305 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 344 through 346 Processing sheet with id=AH5, first strand: chain 'J' and resid 388 through 389 Processing sheet with id=AH6, first strand: chain 'K' and resid 17 through 19 removed outlier: 3.695A pdb=" N CYS K 27 " --> pdb=" O CYS K 19 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 33 through 37 removed outlier: 8.477A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU K 35 " --> pdb=" O GLN K 48 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N SER K 50 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N MET K 68 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR K 64 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LYS K 56 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N LEU K 62 " --> pdb=" O LYS K 56 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 82 through 84 removed outlier: 3.595A pdb=" N THR K 108 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS K 126 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR K 110 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL K 124 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLY K 112 " --> pdb=" O CYS K 122 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N CYS K 122 " --> pdb=" O GLY K 112 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HIS K 114 " --> pdb=" O HIS K 120 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N HIS K 120 " --> pdb=" O HIS K 114 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 146 through 153 Processing sheet with id=AI1, first strand: chain 'K' and resid 234 through 235 Processing sheet with id=AI2, first strand: chain 'K' and resid 172 through 173 Processing sheet with id=AI3, first strand: chain 'K' and resid 178 through 179 Processing sheet with id=AI4, first strand: chain 'K' and resid 272 through 276 Processing sheet with id=AI5, first strand: chain 'L' and resid 32 through 33 removed outlier: 3.764A pdb=" N GLY L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TYR L 15 " --> pdb=" O PRO L 26 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY L 54 " --> pdb=" O VAL L 23 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 74 through 78 removed outlier: 8.960A pdb=" N ALA L 82 " --> pdb=" O PRO L 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 89 through 93 current: chain 'L' and resid 113 through 122 removed outlier: 9.027A pdb=" N VAL L 114 " --> pdb=" O TRP L 134 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TRP L 134 " --> pdb=" O VAL L 114 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER L 130 " --> pdb=" O LEU L 118 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY L 120 " --> pdb=" O ALA L 128 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA L 128 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN L 122 " --> pdb=" O ARG L 126 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ARG L 126 " --> pdb=" O ASN L 122 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 37 through 39 Processing sheet with id=AI8, first strand: chain 'V' and resid 76 through 78 Processing sheet with id=AI9, first strand: chain 'W' and resid 37 through 39 Processing sheet with id=AJ1, first strand: chain 'W' and resid 76 through 78 Processing sheet with id=AJ2, first strand: chain 'X' and resid 37 through 39 Processing sheet with id=AJ3, first strand: chain 'X' and resid 76 through 78 Processing sheet with id=AJ4, first strand: chain 'Y' and resid 37 through 39 Processing sheet with id=AJ5, first strand: chain 'Y' and resid 76 through 78 Processing sheet with id=AJ6, first strand: chain 'R' and resid 243 through 245 Processing sheet with id=AJ7, first strand: chain 'S' and resid 243 through 245 Processing sheet with id=AJ8, first strand: chain 'T' and resid 243 through 245 Processing sheet with id=AJ9, first strand: chain 'U' and resid 243 through 245 1150 hydrogen bonds defined for protein. 2880 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: 13.85 Time building geometry restraints manager: 9.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11372 1.35 - 1.47: 8362 1.47 - 1.59: 15506 1.59 - 1.71: 0 1.71 - 1.83: 308 Bond restraints: 35548 Sorted by residual: bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" N ALA V 31 " pdb=" CA ALA V 31 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 bond pdb=" C1 NAG K 501 " pdb=" O5 NAG K 501 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" N ALA Y 31 " pdb=" CA ALA Y 31 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N ALA W 31 " pdb=" CA ALA W 31 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 ... (remaining 35543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 46139 1.20 - 2.40: 1773 2.40 - 3.60: 422 3.60 - 4.81: 54 4.81 - 6.01: 4 Bond angle restraints: 48392 Sorted by residual: angle pdb=" N GLU B 244 " pdb=" CA GLU B 244 " pdb=" C GLU B 244 " ideal model delta sigma weight residual 110.23 114.32 -4.09 1.45e+00 4.76e-01 7.94e+00 angle pdb=" C GLY B 243 " pdb=" N GLU B 244 " pdb=" CA GLU B 244 " ideal model delta sigma weight residual 120.71 124.54 -3.83 1.42e+00 4.96e-01 7.29e+00 angle pdb=" CA TYR J 309 " pdb=" CB TYR J 309 " pdb=" CG TYR J 309 " ideal model delta sigma weight residual 113.90 118.59 -4.69 1.80e+00 3.09e-01 6.78e+00 angle pdb=" CB ARG B 239 " pdb=" CG ARG B 239 " pdb=" CD ARG B 239 " ideal model delta sigma weight residual 111.30 117.04 -5.74 2.30e+00 1.89e-01 6.22e+00 angle pdb=" N TYR B 98 " pdb=" CA TYR B 98 " pdb=" C TYR B 98 " ideal model delta sigma weight residual 109.24 113.24 -4.00 1.63e+00 3.76e-01 6.03e+00 ... (remaining 48387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 20625 17.67 - 35.34: 701 35.34 - 53.02: 172 53.02 - 70.69: 40 70.69 - 88.36: 14 Dihedral angle restraints: 21552 sinusoidal: 8660 harmonic: 12892 Sorted by residual: dihedral pdb=" CB CYS J 329 " pdb=" SG CYS J 329 " pdb=" SG CYS J 371 " pdb=" CB CYS J 371 " ideal model delta sinusoidal sigma weight residual 93.00 146.87 -53.87 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CB CYS X 52 " pdb=" SG CYS X 52 " pdb=" SG CYS X 67 " pdb=" CB CYS X 67 " ideal model delta sinusoidal sigma weight residual 93.00 141.92 -48.92 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS V 52 " pdb=" SG CYS V 52 " pdb=" SG CYS V 67 " pdb=" CB CYS V 67 " ideal model delta sinusoidal sigma weight residual 93.00 137.29 -44.29 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 21549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3563 0.037 - 0.074: 1172 0.074 - 0.110: 452 0.110 - 0.147: 169 0.147 - 0.184: 4 Chirality restraints: 5360 Sorted by residual: chirality pdb=" C1 NAG K 501 " pdb=" ND2 ASN K 315 " pdb=" C2 NAG K 501 " pdb=" O5 NAG K 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB ILE B 31 " pdb=" CA ILE B 31 " pdb=" CG1 ILE B 31 " pdb=" CG2 ILE B 31 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA ILE H 99 " pdb=" N ILE H 99 " pdb=" C ILE H 99 " pdb=" CB ILE H 99 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 5357 not shown) Planarity restraints: 6280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 239 " -0.317 9.50e-02 1.11e+02 1.42e-01 1.28e+01 pdb=" NE ARG B 239 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 239 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 239 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 239 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 84 " 0.231 9.50e-02 1.11e+02 1.04e-01 7.50e+00 pdb=" NE ARG B 84 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 84 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 84 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 84 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 110 " 0.211 9.50e-02 1.11e+02 9.54e-02 6.93e+00 pdb=" NE ARG D 110 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG D 110 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D 110 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 110 " 0.001 2.00e-02 2.50e+03 ... (remaining 6277 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3193 2.75 - 3.28: 33573 3.28 - 3.82: 56654 3.82 - 4.36: 68302 4.36 - 4.90: 120066 Nonbonded interactions: 281788 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 63 " pdb="CA CA Y 801 " model vdw 2.207 2.510 nonbonded pdb=" OD1 ASP Y 53 " pdb="CA CA Y 801 " model vdw 2.238 2.510 nonbonded pdb=" O TRP V 89 " pdb="CA CA V 802 " model vdw 2.247 2.510 nonbonded pdb=" O LYS H 398 " pdb=" NH1 ARG L 22 " model vdw 2.255 3.120 nonbonded pdb=" OG SER U 248 " pdb=" OE1 GLU U 250 " model vdw 2.269 3.040 ... (remaining 281783 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.350 Check model and map are aligned: 0.240 Set scattering table: 0.330 Process input model: 77.800 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.230 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: 85.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 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 : 0.003 0.036 35652 Z= 0.122 Angle : 0.576 6.008 48608 Z= 0.312 Chirality : 0.045 0.184 5360 Planarity : 0.007 0.142 6272 Dihedral : 10.017 88.359 13008 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 0.76 (0.12), residues: 4436 helix: 0.99 (0.23), residues: 508 sheet: 0.61 (0.14), residues: 1332 loop : 0.49 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 89 HIS 0.007 0.001 HIS I 80 PHE 0.023 0.001 PHE G 421 TYR 0.019 0.003 TYR A 309 ARG 0.021 0.003 ARG D 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 8) link_NAG-ASN : angle 2.19116 ( 24) hydrogen bonds : bond 0.19483 ( 1150) hydrogen bonds : angle 8.23080 ( 2880) SS BOND : bond 0.00315 ( 96) SS BOND : angle 0.97248 ( 192) covalent geometry : bond 0.00263 (35548) covalent geometry : angle 0.57186 (48392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1000 time to evaluate : 3.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.7043 (m-80) cc_final: 0.6839 (m-80) REVERT: A 132 MET cc_start: 0.8063 (tpp) cc_final: 0.7804 (tpp) REVERT: A 171 TRP cc_start: 0.6890 (t60) cc_final: 0.6188 (t-100) REVERT: A 304 ILE cc_start: 0.8661 (mm) cc_final: 0.8249 (mt) REVERT: A 380 ASP cc_start: 0.6017 (m-30) cc_final: 0.5736 (m-30) REVERT: B 230 ASN cc_start: 0.7878 (m-40) cc_final: 0.7649 (m-40) REVERT: D 111 SER cc_start: 0.8854 (p) cc_final: 0.8650 (t) REVERT: D 136 THR cc_start: 0.8308 (t) cc_final: 0.7984 (m) REVERT: D 252 LEU cc_start: 0.8129 (tp) cc_final: 0.7798 (tp) REVERT: D 333 SER cc_start: 0.8838 (t) cc_final: 0.8326 (p) REVERT: E 64 TYR cc_start: 0.7857 (m-80) cc_final: 0.7390 (m-80) REVERT: E 136 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7801 (mt-10) REVERT: E 266 THR cc_start: 0.7532 (p) cc_final: 0.7286 (p) REVERT: E 291 LEU cc_start: 0.8949 (tp) cc_final: 0.8743 (tp) REVERT: E 302 ASN cc_start: 0.8083 (t0) cc_final: 0.7879 (t0) REVERT: E 326 THR cc_start: 0.9120 (m) cc_final: 0.8787 (p) REVERT: E 334 ARG cc_start: 0.8312 (mtt180) cc_final: 0.8039 (mtt90) REVERT: F 65 LEU cc_start: 0.5560 (mt) cc_final: 0.5305 (mt) REVERT: G 174 PHE cc_start: 0.6821 (m-80) cc_final: 0.6382 (m-80) REVERT: G 277 ILE cc_start: 0.8266 (mt) cc_final: 0.8017 (mt) REVERT: G 299 ASP cc_start: 0.6747 (t0) cc_final: 0.6499 (t0) REVERT: J 11 VAL cc_start: 0.8664 (t) cc_final: 0.8059 (t) REVERT: J 134 ASN cc_start: 0.7093 (t0) cc_final: 0.6791 (t0) REVERT: K 219 ASP cc_start: 0.7101 (t0) cc_final: 0.6756 (t0) REVERT: K 307 TRP cc_start: 0.7721 (m100) cc_final: 0.7179 (m100) outliers start: 0 outliers final: 0 residues processed: 1000 average time/residue: 0.4539 time to fit residues: 746.7535 Evaluate side-chains 577 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 3.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 9.9990 chunk 333 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 344 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 256 optimal weight: 0.6980 chunk 399 optimal weight: 4.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS C 79 HIS D 73 HIS ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS F 37 GLN F 80 HIS ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 ASN G 219 ASN G 231 HIS H 80 ASN H 114 HIS H 160 GLN H 162 HIS H 168 GLN I 11 GLN J 236 GLN J 271 ASN K 114 HIS ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN K 194 GLN K 222 GLN K 253 HIS K 402 ASN ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.208229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153940 restraints weight = 45465.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.156053 restraints weight = 29756.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.159096 restraints weight = 19071.901| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 35652 Z= 0.291 Angle : 0.780 10.883 48608 Z= 0.415 Chirality : 0.051 0.241 5360 Planarity : 0.006 0.064 6272 Dihedral : 5.385 59.545 4976 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.53 % Allowed : 8.20 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.69 (0.13), residues: 4436 helix: 1.73 (0.24), residues: 476 sheet: 0.32 (0.14), residues: 1328 loop : 0.42 (0.12), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 327 HIS 0.018 0.002 HIS B 275 PHE 0.026 0.003 PHE K 113 TYR 0.025 0.003 TYR G 122 ARG 0.009 0.001 ARG E 157 Details of bonding type rmsd link_NAG-ASN : bond 0.00782 ( 8) link_NAG-ASN : angle 4.67639 ( 24) hydrogen bonds : bond 0.05059 ( 1150) hydrogen bonds : angle 6.45474 ( 2880) SS BOND : bond 0.00633 ( 96) SS BOND : angle 1.86093 ( 192) covalent geometry : bond 0.00681 (35548) covalent geometry : angle 0.76628 (48392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 657 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.8564 (m-80) cc_final: 0.8285 (m-80) REVERT: A 171 TRP cc_start: 0.8078 (t60) cc_final: 0.6878 (t-100) REVERT: A 217 ASN cc_start: 0.8451 (t0) cc_final: 0.8131 (t0) REVERT: A 271 ASN cc_start: 0.8305 (m-40) cc_final: 0.7937 (m110) REVERT: B 8 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: B 52 MET cc_start: 0.7560 (mmm) cc_final: 0.6836 (tpp) REVERT: B 68 MET cc_start: 0.6650 (mtp) cc_final: 0.6419 (tpp) REVERT: B 168 GLN cc_start: 0.8712 (tp40) cc_final: 0.8299 (tp-100) REVERT: B 232 LYS cc_start: 0.8486 (mmtt) cc_final: 0.7447 (mmmt) REVERT: B 270 GLU cc_start: 0.8346 (tp30) cc_final: 0.8120 (mm-30) REVERT: B 300 ASP cc_start: 0.7208 (t0) cc_final: 0.6908 (t0) REVERT: C 60 MET cc_start: 0.3758 (mmm) cc_final: 0.3084 (mmm) REVERT: D 30 GLN cc_start: 0.8732 (tt0) cc_final: 0.8352 (tt0) REVERT: D 51 TYR cc_start: 0.8831 (p90) cc_final: 0.8562 (p90) REVERT: D 113 GLU cc_start: 0.8331 (mp0) cc_final: 0.7787 (mp0) REVERT: D 143 ARG cc_start: 0.6808 (mmm-85) cc_final: 0.6452 (mtt-85) REVERT: D 205 GLN cc_start: 0.8350 (mt0) cc_final: 0.7888 (mm-40) REVERT: D 252 LEU cc_start: 0.8478 (tp) cc_final: 0.8232 (tp) REVERT: E 64 TYR cc_start: 0.7957 (m-80) cc_final: 0.7049 (m-80) REVERT: E 136 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8285 (mt-10) REVERT: E 276 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7942 (mtpt) REVERT: E 291 LEU cc_start: 0.9401 (tp) cc_final: 0.8858 (tp) REVERT: E 302 ASN cc_start: 0.9150 (t0) cc_final: 0.8614 (t0) REVERT: E 310 ARG cc_start: 0.8441 (ptt90) cc_final: 0.7903 (ptp90) REVERT: E 326 THR cc_start: 0.9309 (m) cc_final: 0.8893 (p) REVERT: E 327 TRP cc_start: 0.8940 (t-100) cc_final: 0.7041 (t-100) REVERT: E 334 ARG cc_start: 0.8488 (mtt180) cc_final: 0.8058 (mtt90) REVERT: F 15 TYR cc_start: 0.3886 (m-80) cc_final: 0.3452 (m-80) REVERT: F 101 ASP cc_start: 0.5177 (m-30) cc_final: 0.4384 (m-30) REVERT: G 24 TYR cc_start: 0.5992 (m-80) cc_final: 0.5445 (m-80) REVERT: G 75 ASP cc_start: 0.8846 (t0) cc_final: 0.8464 (t0) REVERT: G 205 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8498 (mm-40) REVERT: G 206 SER cc_start: 0.9195 (t) cc_final: 0.8935 (m) REVERT: G 223 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8522 (mm-40) REVERT: G 300 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8530 (mm) REVERT: G 390 ASP cc_start: 0.8229 (t70) cc_final: 0.8017 (t0) REVERT: G 397 GLU cc_start: 0.7960 (tt0) cc_final: 0.7757 (tt0) REVERT: H 52 MET cc_start: 0.7582 (tpp) cc_final: 0.7057 (tpp) REVERT: H 251 LYS cc_start: 0.7592 (mtpt) cc_final: 0.7364 (mtpt) REVERT: J 32 GLN cc_start: 0.8419 (tt0) cc_final: 0.8103 (tt0) REVERT: J 175 ASP cc_start: 0.8220 (m-30) cc_final: 0.7578 (m-30) REVERT: J 187 ASN cc_start: 0.9043 (m-40) cc_final: 0.8572 (m-40) REVERT: J 279 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7643 (tt) REVERT: J 285 ASP cc_start: 0.8229 (m-30) cc_final: 0.7860 (t70) REVERT: J 382 LYS cc_start: 0.8102 (ptpp) cc_final: 0.7772 (mtpt) REVERT: K 35 GLU cc_start: 0.8054 (tt0) cc_final: 0.7725 (tt0) REVERT: K 344 ASN cc_start: 0.8124 (t0) cc_final: 0.7710 (t0) REVERT: L 60 MET cc_start: 0.6100 (mpp) cc_final: 0.5882 (mpp) REVERT: L 67 TYR cc_start: 0.6803 (p90) cc_final: 0.6434 (p90) REVERT: L 87 ASN cc_start: 0.5238 (p0) cc_final: 0.5009 (p0) REVERT: L 118 LEU cc_start: 0.4613 (tt) cc_final: 0.4407 (tp) outliers start: 135 outliers final: 81 residues processed: 738 average time/residue: 0.4533 time to fit residues: 567.2706 Evaluate side-chains 623 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 538 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 205 GLN Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 234 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 237 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 340 optimal weight: 7.9990 chunk 199 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 342 optimal weight: 7.9990 chunk 139 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 95 HIS B 114 HIS ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN D 271 ASN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS E 118 ASN E 194 GLN F 37 GLN F 79 HIS F 136 GLN G 73 HIS G 219 ASN H 80 ASN H 120 HIS J 30 GLN J 100 ASN K 120 HIS ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 ASN ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.206498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.152148 restraints weight = 45550.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154278 restraints weight = 29663.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.156874 restraints weight = 18620.123| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 35652 Z= 0.168 Angle : 0.604 10.094 48608 Z= 0.319 Chirality : 0.046 0.199 5360 Planarity : 0.005 0.053 6272 Dihedral : 4.990 55.595 4976 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.19 % Allowed : 11.34 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.13), residues: 4436 helix: 2.00 (0.24), residues: 476 sheet: 0.33 (0.14), residues: 1324 loop : 0.43 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 327 HIS 0.009 0.001 HIS K 126 PHE 0.030 0.002 PHE K 113 TYR 0.023 0.002 TYR J 309 ARG 0.007 0.001 ARG E 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 8) link_NAG-ASN : angle 3.83738 ( 24) hydrogen bonds : bond 0.04094 ( 1150) hydrogen bonds : angle 6.02302 ( 2880) SS BOND : bond 0.00403 ( 96) SS BOND : angle 1.64855 ( 192) covalent geometry : bond 0.00391 (35548) covalent geometry : angle 0.59045 (48392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 600 time to evaluate : 4.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7666 (p90) cc_final: 0.7439 (p90) REVERT: A 81 PHE cc_start: 0.8619 (m-80) cc_final: 0.8317 (m-80) REVERT: A 171 TRP cc_start: 0.8134 (t60) cc_final: 0.6900 (t-100) REVERT: A 217 ASN cc_start: 0.8520 (t0) cc_final: 0.8225 (t0) REVERT: A 271 ASN cc_start: 0.8226 (m-40) cc_final: 0.7884 (m110) REVERT: B 8 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: B 163 TYR cc_start: 0.8387 (m-80) cc_final: 0.8113 (m-10) REVERT: B 168 GLN cc_start: 0.8694 (tp40) cc_final: 0.8062 (tp-100) REVERT: B 229 ASP cc_start: 0.5145 (t0) cc_final: 0.4899 (t0) REVERT: B 270 GLU cc_start: 0.8386 (tp30) cc_final: 0.8155 (mm-30) REVERT: B 300 ASP cc_start: 0.7358 (t0) cc_final: 0.7087 (t0) REVERT: B 321 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6698 (mt-10) REVERT: C 7 MET cc_start: 0.6110 (mpp) cc_final: 0.4788 (mmp) REVERT: C 60 MET cc_start: 0.3674 (mmm) cc_final: 0.2994 (mmm) REVERT: D 30 GLN cc_start: 0.8667 (tt0) cc_final: 0.8282 (tt0) REVERT: D 51 TYR cc_start: 0.8816 (p90) cc_final: 0.8420 (p90) REVERT: D 252 LEU cc_start: 0.8454 (tp) cc_final: 0.8173 (tp) REVERT: E 136 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8265 (mt-10) REVERT: E 276 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7967 (mtpt) REVERT: E 291 LEU cc_start: 0.9364 (tp) cc_final: 0.8938 (tp) REVERT: E 302 ASN cc_start: 0.9168 (t0) cc_final: 0.8658 (t0) REVERT: E 310 ARG cc_start: 0.8489 (ptt90) cc_final: 0.7908 (ptp90) REVERT: E 327 TRP cc_start: 0.8943 (t-100) cc_final: 0.7108 (t-100) REVERT: E 336 TRP cc_start: 0.8827 (m-90) cc_final: 0.8387 (m-10) REVERT: E 340 SER cc_start: 0.8884 (t) cc_final: 0.8599 (t) REVERT: F 15 TYR cc_start: 0.3953 (m-80) cc_final: 0.3460 (m-80) REVERT: F 101 ASP cc_start: 0.4381 (m-30) cc_final: 0.4101 (m-30) REVERT: F 105 PRO cc_start: 0.8057 (Cg_endo) cc_final: 0.7801 (Cg_exo) REVERT: G 24 TYR cc_start: 0.6029 (m-80) cc_final: 0.5490 (m-80) REVERT: G 75 ASP cc_start: 0.8846 (t0) cc_final: 0.8467 (t0) REVERT: G 223 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8519 (mm-40) REVERT: G 342 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6749 (mm-30) REVERT: G 394 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8581 (mm-40) REVERT: H 69 ASN cc_start: 0.6859 (t0) cc_final: 0.6165 (p0) REVERT: H 290 THR cc_start: 0.9138 (m) cc_final: 0.8524 (p) REVERT: J 32 GLN cc_start: 0.8430 (tt0) cc_final: 0.8048 (tt0) REVERT: J 81 PHE cc_start: 0.8848 (m-80) cc_final: 0.8391 (m-10) REVERT: J 156 LYS cc_start: 0.6632 (OUTLIER) cc_final: 0.6288 (mmtt) REVERT: J 175 ASP cc_start: 0.8275 (m-30) cc_final: 0.7559 (m-30) REVERT: J 187 ASN cc_start: 0.8969 (m-40) cc_final: 0.8471 (m-40) REVERT: J 205 GLN cc_start: 0.8268 (mt0) cc_final: 0.7995 (mm-40) REVERT: J 247 ASP cc_start: 0.6880 (t0) cc_final: 0.6543 (t0) REVERT: J 279 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7732 (tt) REVERT: J 285 ASP cc_start: 0.8464 (m-30) cc_final: 0.7925 (t70) REVERT: J 299 ASP cc_start: 0.7936 (t0) cc_final: 0.7710 (t0) REVERT: J 382 LYS cc_start: 0.8195 (ptpp) cc_final: 0.7815 (mtpt) REVERT: K 35 GLU cc_start: 0.7944 (tt0) cc_final: 0.7618 (tt0) REVERT: K 79 ASP cc_start: 0.7359 (t0) cc_final: 0.7083 (t0) REVERT: K 126 HIS cc_start: 0.8404 (t-170) cc_final: 0.8183 (t-170) REVERT: K 256 PHE cc_start: 0.9125 (m-80) cc_final: 0.8554 (m-10) REVERT: K 344 ASN cc_start: 0.8198 (t0) cc_final: 0.7702 (t0) REVERT: L 67 TYR cc_start: 0.6863 (p90) cc_final: 0.6524 (p90) outliers start: 122 outliers final: 81 residues processed: 669 average time/residue: 0.4773 time to fit residues: 547.0208 Evaluate side-chains 606 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 522 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 372 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 130 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 242 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 157 optimal weight: 0.4980 chunk 46 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 353 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 417 optimal weight: 50.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 213 HIS ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS E 285 HIS F 136 GLN ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 HIS ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.201164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148690 restraints weight = 46297.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.149891 restraints weight = 30493.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.152263 restraints weight = 19688.587| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 35652 Z= 0.234 Angle : 0.680 26.788 48608 Z= 0.354 Chirality : 0.048 0.225 5360 Planarity : 0.005 0.068 6272 Dihedral : 5.382 57.797 4976 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.36 % Allowed : 12.15 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 0.35 (0.13), residues: 4436 helix: 1.86 (0.24), residues: 476 sheet: 0.04 (0.13), residues: 1372 loop : 0.13 (0.13), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP T 256 HIS 0.010 0.002 HIS B 277 PHE 0.023 0.002 PHE K 113 TYR 0.025 0.002 TYR J 89 ARG 0.006 0.001 ARG G 21 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 8) link_NAG-ASN : angle 7.19237 ( 24) hydrogen bonds : bond 0.04271 ( 1150) hydrogen bonds : angle 5.99380 ( 2880) SS BOND : bond 0.00485 ( 96) SS BOND : angle 1.60761 ( 192) covalent geometry : bond 0.00547 (35548) covalent geometry : angle 0.65469 (48392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 540 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7572 (p90) cc_final: 0.7184 (p90) REVERT: A 171 TRP cc_start: 0.8328 (t60) cc_final: 0.7386 (t-100) REVERT: A 217 ASN cc_start: 0.8536 (t0) cc_final: 0.8181 (t0) REVERT: A 367 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7694 (mtpp) REVERT: A 378 LYS cc_start: 0.7546 (mttt) cc_final: 0.7086 (mtmt) REVERT: A 403 ILE cc_start: 0.8724 (mt) cc_final: 0.8275 (tt) REVERT: B 8 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7929 (mp10) REVERT: B 68 MET cc_start: 0.7053 (mtp) cc_final: 0.6557 (tpp) REVERT: B 168 GLN cc_start: 0.8769 (tt0) cc_final: 0.8444 (tp-100) REVERT: B 232 LYS cc_start: 0.8297 (mmmm) cc_final: 0.8081 (mmmm) REVERT: B 235 TYR cc_start: 0.6895 (t80) cc_final: 0.6638 (t80) REVERT: B 270 GLU cc_start: 0.8424 (tp30) cc_final: 0.8114 (mm-30) REVERT: B 300 ASP cc_start: 0.7456 (t0) cc_final: 0.7217 (t0) REVERT: B 321 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6601 (mt-10) REVERT: C 60 MET cc_start: 0.4072 (mmm) cc_final: 0.3424 (mmm) REVERT: D 30 GLN cc_start: 0.8714 (tt0) cc_final: 0.8356 (tt0) REVERT: D 51 TYR cc_start: 0.8910 (p90) cc_final: 0.8317 (p90) REVERT: D 143 ARG cc_start: 0.6765 (mmm-85) cc_final: 0.6379 (mmt-90) REVERT: D 386 ASP cc_start: 0.8140 (m-30) cc_final: 0.7699 (m-30) REVERT: E 302 ASN cc_start: 0.9173 (t0) cc_final: 0.8623 (t0) REVERT: E 310 ARG cc_start: 0.8465 (ptt90) cc_final: 0.8049 (ptp90) REVERT: E 327 TRP cc_start: 0.8906 (t-100) cc_final: 0.6998 (t-100) REVERT: E 336 TRP cc_start: 0.8842 (m-90) cc_final: 0.8365 (m-10) REVERT: F 15 TYR cc_start: 0.4302 (m-80) cc_final: 0.3915 (m-80) REVERT: G 24 TYR cc_start: 0.6214 (m-80) cc_final: 0.5803 (m-80) REVERT: G 342 GLU cc_start: 0.7576 (mt-10) cc_final: 0.6840 (mm-30) REVERT: G 361 ASN cc_start: 0.8573 (m-40) cc_final: 0.8215 (m-40) REVERT: G 394 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8684 (mm-40) REVERT: H 52 MET cc_start: 0.7491 (tpp) cc_final: 0.7269 (tpp) REVERT: H 69 ASN cc_start: 0.7040 (t0) cc_final: 0.6360 (p0) REVERT: H 290 THR cc_start: 0.9169 (m) cc_final: 0.8637 (p) REVERT: J 32 GLN cc_start: 0.8383 (tt0) cc_final: 0.7997 (tt0) REVERT: J 156 LYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6358 (mmtt) REVERT: J 247 ASP cc_start: 0.7057 (t0) cc_final: 0.6747 (t0) REVERT: J 299 ASP cc_start: 0.8011 (t0) cc_final: 0.7787 (t0) REVERT: J 382 LYS cc_start: 0.8225 (ptpp) cc_final: 0.7922 (mtpp) REVERT: K 35 GLU cc_start: 0.7965 (tt0) cc_final: 0.7591 (tt0) REVERT: K 52 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6870 (ttm) REVERT: K 79 ASP cc_start: 0.7351 (t0) cc_final: 0.7094 (t0) REVERT: K 276 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7779 (mtpt) REVERT: K 327 TRP cc_start: 0.9272 (t-100) cc_final: 0.8483 (t-100) REVERT: K 344 ASN cc_start: 0.8405 (t0) cc_final: 0.7896 (t0) REVERT: L 60 MET cc_start: 0.6022 (mpp) cc_final: 0.5819 (mpp) REVERT: L 67 TYR cc_start: 0.7043 (p90) cc_final: 0.6698 (p90) outliers start: 167 outliers final: 126 residues processed: 633 average time/residue: 0.4048 time to fit residues: 438.8209 Evaluate side-chains 627 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 496 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 372 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 251 LYS Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 372 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 234 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 240 optimal weight: 20.0000 chunk 420 optimal weight: 5.9990 chunk 330 optimal weight: 8.9990 chunk 327 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 355 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 421 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 175 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS B 69 ASN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 GLN H 285 HIS ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 83 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.199282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145992 restraints weight = 46669.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149692 restraints weight = 30066.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.151358 restraints weight = 17464.528| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 35652 Z= 0.240 Angle : 0.666 22.525 48608 Z= 0.347 Chirality : 0.048 0.276 5360 Planarity : 0.005 0.061 6272 Dihedral : 5.364 57.505 4976 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.44 % Allowed : 13.56 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.02 (0.12), residues: 4436 helix: 1.59 (0.23), residues: 500 sheet: -0.14 (0.14), residues: 1372 loop : -0.18 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 142 HIS 0.036 0.002 HIS B 213 PHE 0.024 0.002 PHE K 113 TYR 0.023 0.002 TYR J 89 ARG 0.010 0.001 ARG B 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00854 ( 8) link_NAG-ASN : angle 6.58162 ( 24) hydrogen bonds : bond 0.04220 ( 1150) hydrogen bonds : angle 5.98437 ( 2880) SS BOND : bond 0.00443 ( 96) SS BOND : angle 1.54461 ( 192) covalent geometry : bond 0.00564 (35548) covalent geometry : angle 0.64349 (48392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 521 time to evaluate : 3.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8383 (pm20) cc_final: 0.7823 (pm20) REVERT: A 120 LYS cc_start: 0.8285 (mttt) cc_final: 0.7895 (mttp) REVERT: A 136 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.6739 (m) REVERT: A 168 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8761 (p) REVERT: A 171 TRP cc_start: 0.8353 (t60) cc_final: 0.7364 (t-100) REVERT: A 217 ASN cc_start: 0.8645 (t0) cc_final: 0.8311 (t0) REVERT: A 367 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7545 (mtpp) REVERT: A 378 LYS cc_start: 0.7644 (mttt) cc_final: 0.7236 (mtmt) REVERT: A 403 ILE cc_start: 0.8784 (mt) cc_final: 0.8179 (tt) REVERT: A 421 PHE cc_start: 0.5000 (OUTLIER) cc_final: 0.4442 (t80) REVERT: B 8 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: B 68 MET cc_start: 0.6834 (mtp) cc_final: 0.6411 (tpp) REVERT: B 168 GLN cc_start: 0.8779 (tt0) cc_final: 0.8501 (tp-100) REVERT: B 235 TYR cc_start: 0.6901 (t80) cc_final: 0.6620 (t80) REVERT: B 300 ASP cc_start: 0.7463 (t0) cc_final: 0.7257 (t0) REVERT: B 321 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6458 (mt-10) REVERT: B 339 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6780 (mm-30) REVERT: C 7 MET cc_start: 0.6267 (mpp) cc_final: 0.4967 (mmp) REVERT: C 60 MET cc_start: 0.4114 (mmm) cc_final: 0.3600 (mmm) REVERT: D 30 GLN cc_start: 0.8709 (tt0) cc_final: 0.8412 (tt0) REVERT: D 132 MET cc_start: 0.8111 (tpp) cc_final: 0.7569 (ttt) REVERT: D 143 ARG cc_start: 0.6822 (mmm-85) cc_final: 0.6428 (mmt-90) REVERT: D 312 ASP cc_start: 0.8672 (t0) cc_final: 0.8424 (t0) REVERT: E 302 ASN cc_start: 0.9164 (t0) cc_final: 0.8627 (t0) REVERT: E 310 ARG cc_start: 0.8477 (ptt90) cc_final: 0.8084 (ptp90) REVERT: E 327 TRP cc_start: 0.8936 (t-100) cc_final: 0.6965 (t-100) REVERT: E 336 TRP cc_start: 0.8815 (m-90) cc_final: 0.8405 (m-10) REVERT: F 15 TYR cc_start: 0.4628 (m-80) cc_final: 0.4138 (m-80) REVERT: F 101 ASP cc_start: 0.5131 (m-30) cc_final: 0.4649 (m-30) REVERT: G 24 TYR cc_start: 0.6298 (m-80) cc_final: 0.5979 (m-80) REVERT: G 214 LEU cc_start: 0.7999 (tp) cc_final: 0.7791 (tp) REVERT: G 361 ASN cc_start: 0.8618 (m-40) cc_final: 0.8221 (m-40) REVERT: G 391 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7420 (p90) REVERT: G 394 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8629 (mm-40) REVERT: H 69 ASN cc_start: 0.7002 (t0) cc_final: 0.6274 (p0) REVERT: H 266 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7841 (p) REVERT: H 290 THR cc_start: 0.9179 (m) cc_final: 0.8660 (p) REVERT: J 32 GLN cc_start: 0.8326 (tt0) cc_final: 0.7991 (tt0) REVERT: J 156 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6392 (mmtt) REVERT: J 175 ASP cc_start: 0.8099 (m-30) cc_final: 0.7544 (m-30) REVERT: J 247 ASP cc_start: 0.7011 (t0) cc_final: 0.6720 (t0) REVERT: J 382 LYS cc_start: 0.8228 (ptpp) cc_final: 0.7369 (mptt) REVERT: K 35 GLU cc_start: 0.7923 (tt0) cc_final: 0.7604 (tt0) REVERT: K 327 TRP cc_start: 0.9309 (t-100) cc_final: 0.8457 (t-100) REVERT: K 344 ASN cc_start: 0.8508 (t0) cc_final: 0.8080 (t0) REVERT: L 52 GLU cc_start: 0.5487 (tt0) cc_final: 0.5248 (tt0) REVERT: L 60 MET cc_start: 0.6135 (mpp) cc_final: 0.5767 (mpp) outliers start: 170 outliers final: 130 residues processed: 626 average time/residue: 0.4361 time to fit residues: 466.0771 Evaluate side-chains 625 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 487 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 175 HIS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 372 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 408 TRP Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 234 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain K residue 376 MET Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain V residue 78 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 397 optimal weight: 4.9990 chunk 289 optimal weight: 0.7980 chunk 252 optimal weight: 1.9990 chunk 308 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 418 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 424 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS D 28 HIS D 439 HIS F 136 GLN G 183 HIS ** G 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.203247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150236 restraints weight = 46055.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.152041 restraints weight = 32230.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155404 restraints weight = 19635.024| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.139 35652 Z= 0.132 Angle : 0.584 21.646 48608 Z= 0.301 Chirality : 0.045 0.297 5360 Planarity : 0.005 0.053 6272 Dihedral : 5.058 56.427 4976 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.61 % Allowed : 14.99 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: 0.11 (0.13), residues: 4436 helix: 1.82 (0.24), residues: 492 sheet: -0.06 (0.14), residues: 1372 loop : -0.11 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP T 256 HIS 0.007 0.001 HIS B 277 PHE 0.021 0.002 PHE K 113 TYR 0.021 0.002 TYR H 235 ARG 0.008 0.000 ARG B 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00975 ( 8) link_NAG-ASN : angle 6.32378 ( 24) hydrogen bonds : bond 0.03520 ( 1150) hydrogen bonds : angle 5.72624 ( 2880) SS BOND : bond 0.00322 ( 96) SS BOND : angle 1.29021 ( 192) covalent geometry : bond 0.00311 (35548) covalent geometry : angle 0.56194 (48392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 536 time to evaluate : 3.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.7753 (ptm) cc_final: 0.7358 (ptp) REVERT: A 120 LYS cc_start: 0.8152 (mttt) cc_final: 0.7763 (mttp) REVERT: A 136 THR cc_start: 0.6964 (OUTLIER) cc_final: 0.6344 (m) REVERT: A 171 TRP cc_start: 0.8248 (t60) cc_final: 0.7182 (t-100) REVERT: A 217 ASN cc_start: 0.8547 (t0) cc_final: 0.8200 (t0) REVERT: A 378 LYS cc_start: 0.7617 (mttt) cc_final: 0.7216 (mtmt) REVERT: A 403 ILE cc_start: 0.8664 (mt) cc_final: 0.7999 (tt) REVERT: A 421 PHE cc_start: 0.4823 (OUTLIER) cc_final: 0.4329 (t80) REVERT: B 8 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: B 68 MET cc_start: 0.6729 (mtp) cc_final: 0.6077 (tpp) REVERT: B 168 GLN cc_start: 0.8683 (tt0) cc_final: 0.8418 (tp-100) REVERT: B 300 ASP cc_start: 0.7449 (t0) cc_final: 0.7241 (t0) REVERT: B 321 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6463 (mt-10) REVERT: B 339 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6725 (mm-30) REVERT: C 7 MET cc_start: 0.6214 (mpp) cc_final: 0.4803 (mmp) REVERT: C 60 MET cc_start: 0.4097 (mmm) cc_final: 0.3587 (mmm) REVERT: C 83 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8518 (m) REVERT: D 51 TYR cc_start: 0.8898 (p90) cc_final: 0.8348 (p90) REVERT: D 132 MET cc_start: 0.8144 (tpp) cc_final: 0.7649 (ttt) REVERT: D 143 ARG cc_start: 0.6685 (mmm-85) cc_final: 0.6168 (mmt-90) REVERT: D 152 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7377 (mp0) REVERT: D 312 ASP cc_start: 0.8644 (t0) cc_final: 0.8349 (t0) REVERT: D 386 ASP cc_start: 0.8112 (m-30) cc_final: 0.7765 (m-30) REVERT: E 302 ASN cc_start: 0.9167 (t0) cc_final: 0.8595 (t0) REVERT: E 310 ARG cc_start: 0.8491 (ptt90) cc_final: 0.8105 (ptp90) REVERT: E 327 TRP cc_start: 0.8949 (t-100) cc_final: 0.7036 (t-100) REVERT: E 336 TRP cc_start: 0.8744 (m-90) cc_final: 0.8318 (m-10) REVERT: F 15 TYR cc_start: 0.4553 (m-80) cc_final: 0.4093 (m-80) REVERT: F 101 ASP cc_start: 0.4833 (m-30) cc_final: 0.4252 (m-30) REVERT: G 24 TYR cc_start: 0.6187 (m-80) cc_final: 0.5883 (m-80) REVERT: G 342 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6493 (mm-30) REVERT: G 390 ASP cc_start: 0.8061 (t70) cc_final: 0.7784 (t0) REVERT: G 391 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7531 (p90) REVERT: G 394 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8558 (mm-40) REVERT: H 266 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7786 (p) REVERT: H 290 THR cc_start: 0.9179 (m) cc_final: 0.8805 (p) REVERT: J 32 GLN cc_start: 0.8310 (tt0) cc_final: 0.7922 (tt0) REVERT: J 175 ASP cc_start: 0.7956 (m-30) cc_final: 0.7693 (m-30) REVERT: J 247 ASP cc_start: 0.6931 (t0) cc_final: 0.6657 (t0) REVERT: K 35 GLU cc_start: 0.7925 (tt0) cc_final: 0.7557 (tt0) REVERT: K 52 MET cc_start: 0.7552 (ttt) cc_final: 0.7210 (ttm) REVERT: K 327 TRP cc_start: 0.9283 (t-100) cc_final: 0.8554 (t-100) REVERT: K 344 ASN cc_start: 0.8428 (t0) cc_final: 0.8020 (t0) REVERT: L 60 MET cc_start: 0.6195 (mpp) cc_final: 0.5775 (mpp) REVERT: L 67 TYR cc_start: 0.7026 (p90) cc_final: 0.6549 (p90) outliers start: 138 outliers final: 98 residues processed: 623 average time/residue: 0.4147 time to fit residues: 441.2266 Evaluate side-chains 606 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 502 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 175 HIS Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 372 THR Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 408 TRP Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 376 MET Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain V residue 78 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 149 optimal weight: 3.9990 chunk 328 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 270 optimal weight: 8.9990 chunk 359 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 411 optimal weight: 50.0000 chunk 419 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 213 HIS ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 HIS C 66 GLN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 HIS F 136 GLN G 187 ASN ** G 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 HIS ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN W 107 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.194881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144957 restraints weight = 47574.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.146259 restraints weight = 29482.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147157 restraints weight = 20404.093| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.096 35652 Z= 0.365 Angle : 0.817 22.102 48608 Z= 0.428 Chirality : 0.053 0.502 5360 Planarity : 0.006 0.064 6272 Dihedral : 5.906 59.784 4976 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.41 % Allowed : 14.16 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % 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: -0.68 (0.12), residues: 4436 helix: 0.84 (0.22), residues: 528 sheet: -0.37 (0.14), residues: 1304 loop : -0.74 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 336 HIS 0.032 0.002 HIS D 439 PHE 0.041 0.003 PHE H 256 TYR 0.034 0.003 TYR J 89 ARG 0.010 0.001 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00903 ( 8) link_NAG-ASN : angle 7.02555 ( 24) hydrogen bonds : bond 0.05161 ( 1150) hydrogen bonds : angle 6.30732 ( 2880) SS BOND : bond 0.00611 ( 96) SS BOND : angle 1.70373 ( 192) covalent geometry : bond 0.00857 (35548) covalent geometry : angle 0.79620 (48392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 497 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 LYS cc_start: 0.8317 (mttt) cc_final: 0.8013 (mttp) REVERT: A 136 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.6943 (m) REVERT: A 171 TRP cc_start: 0.8457 (t60) cc_final: 0.7225 (t-100) REVERT: A 217 ASN cc_start: 0.8769 (t0) cc_final: 0.8366 (t0) REVERT: A 367 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7623 (mtpp) REVERT: A 378 LYS cc_start: 0.7793 (mttt) cc_final: 0.7325 (mtmt) REVERT: A 391 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.7264 (p90) REVERT: A 421 PHE cc_start: 0.4801 (OUTLIER) cc_final: 0.4065 (t80) REVERT: B 8 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: B 68 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.6454 (mmm) REVERT: B 168 GLN cc_start: 0.8748 (tt0) cc_final: 0.8364 (mm-40) REVERT: B 321 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6557 (mt-10) REVERT: B 339 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7045 (mm-30) REVERT: C 60 MET cc_start: 0.4202 (mmm) cc_final: 0.3665 (mmm) REVERT: D 51 TYR cc_start: 0.8993 (p90) cc_final: 0.8488 (p90) REVERT: D 143 ARG cc_start: 0.6999 (mmm-85) cc_final: 0.6702 (mmt-90) REVERT: D 357 PHE cc_start: 0.8937 (p90) cc_final: 0.8690 (p90) REVERT: D 380 ASP cc_start: 0.8103 (p0) cc_final: 0.7854 (p0) REVERT: E 302 ASN cc_start: 0.9140 (t0) cc_final: 0.8625 (t0) REVERT: E 310 ARG cc_start: 0.8549 (ptt90) cc_final: 0.8114 (ptp90) REVERT: E 327 TRP cc_start: 0.8970 (t-100) cc_final: 0.7088 (t-100) REVERT: F 15 TYR cc_start: 0.4814 (m-80) cc_final: 0.4369 (m-80) REVERT: F 101 ASP cc_start: 0.5289 (m-30) cc_final: 0.5037 (m-30) REVERT: G 10 LYS cc_start: 0.7764 (mttt) cc_final: 0.7467 (mtpp) REVERT: G 67 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6778 (mm-40) REVERT: G 162 LEU cc_start: 0.8655 (tp) cc_final: 0.8409 (tp) REVERT: G 219 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.7773 (m110) REVERT: G 229 ILE cc_start: 0.9118 (mt) cc_final: 0.8884 (mm) REVERT: G 239 SER cc_start: 0.8811 (t) cc_final: 0.8429 (p) REVERT: G 299 ASP cc_start: 0.7553 (t0) cc_final: 0.6844 (t0) REVERT: G 361 ASN cc_start: 0.8723 (m-40) cc_final: 0.8346 (m-40) REVERT: G 390 ASP cc_start: 0.8194 (t70) cc_final: 0.7866 (t0) REVERT: G 391 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7039 (p90) REVERT: H 266 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8005 (p) REVERT: H 290 THR cc_start: 0.9160 (m) cc_final: 0.8674 (p) REVERT: J 247 ASP cc_start: 0.7297 (t0) cc_final: 0.7017 (t0) REVERT: K 35 GLU cc_start: 0.8073 (tt0) cc_final: 0.7666 (tt0) REVERT: K 52 MET cc_start: 0.7932 (ttt) cc_final: 0.7608 (ttm) REVERT: K 135 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7566 (mtp-110) REVERT: K 327 TRP cc_start: 0.9333 (t-100) cc_final: 0.8434 (t-100) REVERT: K 344 ASN cc_start: 0.8705 (t0) cc_final: 0.8300 (t0) REVERT: L 67 TYR cc_start: 0.7275 (p90) cc_final: 0.6821 (p90) outliers start: 207 outliers final: 160 residues processed: 629 average time/residue: 0.4219 time to fit residues: 451.0670 Evaluate side-chains 634 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 463 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 175 HIS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 326 THR Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 67 GLN Chi-restraints excluded: chain G residue 219 ASN Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 309 TYR Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 372 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 408 TRP Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 288 HIS Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain H residue 399 LEU Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 362 ILE Chi-restraints excluded: chain J residue 372 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 403 ILE Chi-restraints excluded: chain J residue 408 TRP Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 415 VAL Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 135 ARG Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 234 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain K residue 376 MET Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain V residue 78 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 257 optimal weight: 0.7980 chunk 225 optimal weight: 0.3980 chunk 42 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 331 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 433 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 269 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS F 136 GLN G 439 HIS H 151 ASN H 288 HIS J 32 GLN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.201550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.147965 restraints weight = 46363.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.152093 restraints weight = 29020.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.153720 restraints weight = 17121.020| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 35652 Z= 0.130 Angle : 0.613 20.890 48608 Z= 0.315 Chirality : 0.047 0.798 5360 Planarity : 0.005 0.049 6272 Dihedral : 5.331 56.069 4976 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 3.03 % Allowed : 17.19 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.22 (0.13), residues: 4436 helix: 1.42 (0.23), residues: 516 sheet: -0.16 (0.14), residues: 1348 loop : -0.40 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 256 HIS 0.038 0.001 HIS B 213 PHE 0.022 0.002 PHE G 81 TYR 0.027 0.002 TYR B 235 ARG 0.006 0.000 ARG H 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00828 ( 8) link_NAG-ASN : angle 6.61765 ( 24) hydrogen bonds : bond 0.03570 ( 1150) hydrogen bonds : angle 5.81009 ( 2880) SS BOND : bond 0.00297 ( 96) SS BOND : angle 1.24109 ( 192) covalent geometry : bond 0.00297 (35548) covalent geometry : angle 0.59120 (48392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 532 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8870 (mp10) cc_final: 0.8601 (mp10) REVERT: A 120 LYS cc_start: 0.8120 (mttt) cc_final: 0.7770 (mttp) REVERT: A 171 TRP cc_start: 0.8246 (t60) cc_final: 0.7045 (t-100) REVERT: A 217 ASN cc_start: 0.8768 (t0) cc_final: 0.8396 (t0) REVERT: A 378 LYS cc_start: 0.7596 (mttt) cc_final: 0.7184 (mtmt) REVERT: A 403 ILE cc_start: 0.8581 (mt) cc_final: 0.8069 (tt) REVERT: A 421 PHE cc_start: 0.5074 (OUTLIER) cc_final: 0.4324 (t80) REVERT: B 8 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: B 68 MET cc_start: 0.6605 (mtp) cc_final: 0.6069 (tpp) REVERT: B 163 TYR cc_start: 0.8538 (m-80) cc_final: 0.8180 (m-10) REVERT: B 168 GLN cc_start: 0.8676 (tt0) cc_final: 0.8241 (tp-100) REVERT: B 174 ASP cc_start: 0.8124 (t0) cc_final: 0.7543 (t70) REVERT: B 339 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6836 (mm-30) REVERT: C 7 MET cc_start: 0.5949 (mpp) cc_final: 0.4646 (mmp) REVERT: C 60 MET cc_start: 0.4101 (mmm) cc_final: 0.3678 (mmm) REVERT: C 86 GLU cc_start: 0.6609 (tp30) cc_final: 0.5881 (tt0) REVERT: C 104 ARG cc_start: 0.5297 (mtt-85) cc_final: 0.4723 (tpp80) REVERT: D 51 TYR cc_start: 0.8927 (p90) cc_final: 0.8514 (p90) REVERT: D 143 ARG cc_start: 0.6608 (mmm-85) cc_final: 0.6173 (mmt90) REVERT: D 152 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7314 (mp0) REVERT: D 200 SER cc_start: 0.9250 (t) cc_final: 0.9006 (m) REVERT: D 357 PHE cc_start: 0.8818 (p90) cc_final: 0.8602 (p90) REVERT: D 380 ASP cc_start: 0.8067 (p0) cc_final: 0.7832 (p0) REVERT: E 302 ASN cc_start: 0.9138 (t0) cc_final: 0.8547 (t0) REVERT: E 310 ARG cc_start: 0.8565 (ptt90) cc_final: 0.8116 (ptp90) REVERT: E 327 TRP cc_start: 0.8961 (t-100) cc_final: 0.7037 (t-100) REVERT: F 15 TYR cc_start: 0.4555 (m-80) cc_final: 0.4092 (m-80) REVERT: F 101 ASP cc_start: 0.5128 (m-30) cc_final: 0.4578 (m-30) REVERT: G 10 LYS cc_start: 0.7589 (mttt) cc_final: 0.7312 (mtpp) REVERT: G 24 TYR cc_start: 0.6576 (m-10) cc_final: 0.6244 (m-80) REVERT: G 67 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6812 (mm-40) REVERT: G 100 ASN cc_start: 0.8569 (t0) cc_final: 0.8221 (t0) REVERT: G 299 ASP cc_start: 0.7450 (t0) cc_final: 0.6688 (t0) REVERT: G 342 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6347 (mm-30) REVERT: G 390 ASP cc_start: 0.8029 (t70) cc_final: 0.7744 (t0) REVERT: G 391 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.7126 (p90) REVERT: H 251 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7045 (ttpp) REVERT: H 266 THR cc_start: 0.8193 (OUTLIER) cc_final: 0.7797 (p) REVERT: H 290 THR cc_start: 0.9115 (m) cc_final: 0.8756 (p) REVERT: J 247 ASP cc_start: 0.7083 (t0) cc_final: 0.6762 (t0) REVERT: K 35 GLU cc_start: 0.7956 (tt0) cc_final: 0.7499 (tt0) REVERT: K 327 TRP cc_start: 0.9340 (t-100) cc_final: 0.8393 (t-100) REVERT: K 344 ASN cc_start: 0.8558 (t0) cc_final: 0.8103 (t0) REVERT: L 60 MET cc_start: 0.6000 (mpp) cc_final: 0.5719 (mpp) outliers start: 116 outliers final: 96 residues processed: 607 average time/residue: 0.4069 time to fit residues: 422.7876 Evaluate side-chains 593 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 492 time to evaluate : 3.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 439 HIS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 175 HIS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 136 GLN Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 67 GLN Chi-restraints excluded: chain G residue 372 THR Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 408 TRP Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 288 HIS Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 376 MET Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain V residue 78 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 182 optimal weight: 20.0000 chunk 383 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 393 optimal weight: 5.9990 chunk 265 optimal weight: 40.0000 chunk 271 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 HIS ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN G 439 HIS H 155 HIS H 288 HIS H 302 ASN J 32 GLN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.195276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.142931 restraints weight = 47200.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144651 restraints weight = 29997.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146151 restraints weight = 21449.631| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 35652 Z= 0.328 Angle : 0.778 21.426 48608 Z= 0.406 Chirality : 0.055 1.329 5360 Planarity : 0.006 0.058 6272 Dihedral : 5.760 59.812 4976 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 3.84 % Allowed : 16.77 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.71 (0.12), residues: 4436 helix: 1.21 (0.23), residues: 504 sheet: -0.50 (0.14), residues: 1292 loop : -0.75 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 327 HIS 0.032 0.002 HIS D 439 PHE 0.035 0.003 PHE H 256 TYR 0.040 0.003 TYR A 46 ARG 0.008 0.001 ARG H 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 8) link_NAG-ASN : angle 7.02950 ( 24) hydrogen bonds : bond 0.04871 ( 1150) hydrogen bonds : angle 6.16131 ( 2880) SS BOND : bond 0.00560 ( 96) SS BOND : angle 1.62617 ( 192) covalent geometry : bond 0.00770 (35548) covalent geometry : angle 0.75697 (48392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 474 time to evaluate : 3.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8803 (mp10) cc_final: 0.8580 (mp10) REVERT: A 120 LYS cc_start: 0.8311 (mttt) cc_final: 0.7997 (mttp) REVERT: A 136 THR cc_start: 0.7306 (OUTLIER) cc_final: 0.6574 (m) REVERT: A 171 TRP cc_start: 0.8444 (t60) cc_final: 0.7087 (t-100) REVERT: A 217 ASN cc_start: 0.8821 (t0) cc_final: 0.8380 (t0) REVERT: A 342 GLU cc_start: 0.8334 (mp0) cc_final: 0.7566 (tt0) REVERT: A 378 LYS cc_start: 0.7794 (mttt) cc_final: 0.7376 (mtmt) REVERT: A 391 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.7274 (p90) REVERT: A 421 PHE cc_start: 0.5006 (OUTLIER) cc_final: 0.4118 (t80) REVERT: B 8 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7886 (mp10) REVERT: B 68 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6346 (mmm) REVERT: B 168 GLN cc_start: 0.8675 (tt0) cc_final: 0.8350 (tp-100) REVERT: B 174 ASP cc_start: 0.8264 (t0) cc_final: 0.7912 (t70) REVERT: C 7 MET cc_start: 0.5930 (mpp) cc_final: 0.5459 (mpp) REVERT: C 60 MET cc_start: 0.4176 (mmm) cc_final: 0.3734 (mmm) REVERT: D 51 TYR cc_start: 0.9014 (p90) cc_final: 0.8620 (p90) REVERT: D 143 ARG cc_start: 0.6833 (mmm-85) cc_final: 0.6203 (mmt90) REVERT: D 357 PHE cc_start: 0.8993 (p90) cc_final: 0.8701 (p90) REVERT: D 380 ASP cc_start: 0.8205 (p0) cc_final: 0.7968 (p0) REVERT: E 205 ARG cc_start: 0.5865 (mmt-90) cc_final: 0.5602 (mmm160) REVERT: E 302 ASN cc_start: 0.9054 (t0) cc_final: 0.8585 (t0) REVERT: E 310 ARG cc_start: 0.8619 (ptt90) cc_final: 0.8178 (ptp90) REVERT: E 327 TRP cc_start: 0.8967 (t-100) cc_final: 0.7170 (t-100) REVERT: F 15 TYR cc_start: 0.4624 (m-80) cc_final: 0.4084 (m-80) REVERT: F 101 ASP cc_start: 0.5395 (m-30) cc_final: 0.5071 (m-30) REVERT: G 67 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6819 (mm-40) REVERT: G 162 LEU cc_start: 0.8674 (tp) cc_final: 0.8447 (tp) REVERT: G 247 ASP cc_start: 0.7870 (m-30) cc_final: 0.7621 (t70) REVERT: G 299 ASP cc_start: 0.7609 (t0) cc_final: 0.6725 (t0) REVERT: G 301 GLU cc_start: 0.8130 (mp0) cc_final: 0.7371 (mp0) REVERT: G 361 ASN cc_start: 0.8631 (m-40) cc_final: 0.8326 (m-40) REVERT: G 390 ASP cc_start: 0.8148 (t70) cc_final: 0.7822 (t0) REVERT: G 391 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7047 (p90) REVERT: H 266 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8017 (p) REVERT: H 290 THR cc_start: 0.9142 (m) cc_final: 0.8667 (p) REVERT: I 123 GLU cc_start: 0.5924 (tt0) cc_final: 0.5697 (tt0) REVERT: J 247 ASP cc_start: 0.7291 (t0) cc_final: 0.7001 (t0) REVERT: K 35 GLU cc_start: 0.8022 (tt0) cc_final: 0.7618 (tt0) REVERT: K 52 MET cc_start: 0.7798 (ttt) cc_final: 0.7559 (ttm) REVERT: K 327 TRP cc_start: 0.9360 (t-100) cc_final: 0.8389 (t-100) REVERT: K 344 ASN cc_start: 0.8671 (t0) cc_final: 0.8252 (t0) REVERT: L 27 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6893 (mt) REVERT: L 60 MET cc_start: 0.5891 (mpp) cc_final: 0.5550 (mpp) REVERT: L 67 TYR cc_start: 0.7306 (p90) cc_final: 0.6807 (p90) outliers start: 147 outliers final: 123 residues processed: 568 average time/residue: 0.4414 time to fit residues: 428.9003 Evaluate side-chains 596 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 464 time to evaluate : 3.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 175 HIS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 136 GLN Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 67 GLN Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 408 TRP Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 288 HIS Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 316 ILE Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 372 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 408 TRP Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 19 CYS Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 151 ASN Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain K residue 376 MET Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain V residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 397 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 chunk 417 optimal weight: 0.0570 chunk 413 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 chunk 235 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 325 optimal weight: 0.8980 chunk 335 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN G 439 HIS H 102 GLN H 288 HIS J 32 GLN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.203476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.150231 restraints weight = 46241.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.154639 restraints weight = 29057.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156289 restraints weight = 17490.291| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 35652 Z= 0.121 Angle : 0.619 20.416 48608 Z= 0.316 Chirality : 0.048 1.134 5360 Planarity : 0.005 0.050 6272 Dihedral : 5.296 59.726 4976 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer: Outliers : 2.38 % Allowed : 18.47 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.36 (0.13), residues: 4436 helix: 1.49 (0.23), residues: 516 sheet: -0.28 (0.14), residues: 1296 loop : -0.52 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP T 256 HIS 0.016 0.001 HIS K 213 PHE 0.021 0.002 PHE G 421 TYR 0.027 0.002 TYR B 235 ARG 0.008 0.000 ARG H 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00937 ( 8) link_NAG-ASN : angle 6.59223 ( 24) hydrogen bonds : bond 0.03530 ( 1150) hydrogen bonds : angle 5.76073 ( 2880) SS BOND : bond 0.00302 ( 96) SS BOND : angle 1.23388 ( 192) covalent geometry : bond 0.00278 (35548) covalent geometry : angle 0.59753 (48392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 509 time to evaluate : 3.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8781 (mp10) cc_final: 0.8580 (mp10) REVERT: A 120 LYS cc_start: 0.8077 (mttt) cc_final: 0.7779 (mttp) REVERT: A 171 TRP cc_start: 0.8294 (t60) cc_final: 0.7036 (t-100) REVERT: A 217 ASN cc_start: 0.8628 (t0) cc_final: 0.8185 (t0) REVERT: A 342 GLU cc_start: 0.8161 (mp0) cc_final: 0.7488 (tt0) REVERT: A 378 LYS cc_start: 0.7614 (mttt) cc_final: 0.7190 (mtmt) REVERT: A 421 PHE cc_start: 0.4813 (OUTLIER) cc_final: 0.4030 (t80) REVERT: B 8 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: B 68 MET cc_start: 0.6525 (mtp) cc_final: 0.6192 (tpp) REVERT: B 163 TYR cc_start: 0.8536 (m-80) cc_final: 0.8183 (m-10) REVERT: B 167 HIS cc_start: 0.7843 (m170) cc_final: 0.7531 (m-70) REVERT: B 168 GLN cc_start: 0.8549 (tt0) cc_final: 0.8200 (tp-100) REVERT: B 174 ASP cc_start: 0.8240 (t0) cc_final: 0.7816 (t70) REVERT: C 7 MET cc_start: 0.5945 (mpp) cc_final: 0.4672 (mmp) REVERT: C 60 MET cc_start: 0.4207 (mmm) cc_final: 0.3774 (mmm) REVERT: C 86 GLU cc_start: 0.6589 (tp30) cc_final: 0.5794 (tt0) REVERT: D 51 TYR cc_start: 0.8935 (p90) cc_final: 0.8716 (p90) REVERT: D 152 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7539 (mp0) REVERT: D 200 SER cc_start: 0.9238 (t) cc_final: 0.9017 (m) REVERT: D 357 PHE cc_start: 0.8879 (p90) cc_final: 0.8574 (p90) REVERT: D 380 ASP cc_start: 0.8077 (p0) cc_final: 0.7845 (p0) REVERT: E 205 ARG cc_start: 0.5874 (mmt-90) cc_final: 0.5597 (mmm160) REVERT: E 302 ASN cc_start: 0.9098 (t0) cc_final: 0.8506 (t0) REVERT: E 310 ARG cc_start: 0.8552 (ptt90) cc_final: 0.8094 (ptp90) REVERT: E 327 TRP cc_start: 0.8941 (t-100) cc_final: 0.7120 (t-100) REVERT: F 15 TYR cc_start: 0.4561 (m-80) cc_final: 0.4053 (m-80) REVERT: F 101 ASP cc_start: 0.5328 (m-30) cc_final: 0.4786 (m-30) REVERT: G 100 ASN cc_start: 0.8535 (t0) cc_final: 0.8177 (t0) REVERT: G 247 ASP cc_start: 0.7735 (m-30) cc_final: 0.7436 (t70) REVERT: G 299 ASP cc_start: 0.7551 (t0) cc_final: 0.6661 (t0) REVERT: G 390 ASP cc_start: 0.8060 (t70) cc_final: 0.7783 (t0) REVERT: G 391 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7139 (p90) REVERT: H 266 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7844 (p) REVERT: H 290 THR cc_start: 0.9070 (m) cc_final: 0.8750 (p) REVERT: I 7 MET cc_start: 0.5239 (tmm) cc_final: 0.5013 (tpp) REVERT: I 17 CYS cc_start: 0.7559 (t) cc_final: 0.6878 (m) REVERT: J 247 ASP cc_start: 0.7070 (t0) cc_final: 0.6789 (t0) REVERT: K 35 GLU cc_start: 0.7978 (tt0) cc_final: 0.7508 (tt0) REVERT: K 52 MET cc_start: 0.7430 (ttt) cc_final: 0.7165 (ttm) REVERT: K 90 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8379 (p) REVERT: K 327 TRP cc_start: 0.9313 (t-100) cc_final: 0.8427 (t-100) REVERT: K 344 ASN cc_start: 0.8592 (t0) cc_final: 0.8167 (t0) REVERT: L 60 MET cc_start: 0.5941 (mpp) cc_final: 0.5617 (mpp) outliers start: 91 outliers final: 81 residues processed: 566 average time/residue: 0.4153 time to fit residues: 402.9307 Evaluate side-chains 570 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 484 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 175 HIS Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 439 HIS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 90 SER Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 288 HIS Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 125 HIS Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 376 MET Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain V residue 78 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 44 optimal weight: 7.9990 chunk 284 optimal weight: 9.9990 chunk 270 optimal weight: 1.9990 chunk 289 optimal weight: 0.4980 chunk 135 optimal weight: 4.9990 chunk 233 optimal weight: 8.9990 chunk 307 optimal weight: 0.0570 chunk 300 optimal weight: 10.0000 chunk 424 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 213 HIS ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN G 439 HIS H 288 HIS K 21 ASN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.201491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150833 restraints weight = 46781.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.150895 restraints weight = 31771.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.153327 restraints weight = 21458.374| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 35652 Z= 0.167 Angle : 0.632 20.472 48608 Z= 0.324 Chirality : 0.049 1.068 5360 Planarity : 0.005 0.049 6272 Dihedral : 5.225 56.905 4976 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 2.85 % Allowed : 18.21 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.36 (0.13), residues: 4436 helix: 1.50 (0.23), residues: 516 sheet: -0.28 (0.14), residues: 1296 loop : -0.52 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP J 142 HIS 0.019 0.001 HIS G 439 PHE 0.022 0.002 PHE E 113 TYR 0.023 0.002 TYR A 46 ARG 0.008 0.000 ARG H 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00935 ( 8) link_NAG-ASN : angle 6.69152 ( 24) hydrogen bonds : bond 0.03716 ( 1150) hydrogen bonds : angle 5.71839 ( 2880) SS BOND : bond 0.00331 ( 96) SS BOND : angle 1.28668 ( 192) covalent geometry : bond 0.00394 (35548) covalent geometry : angle 0.61020 (48392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12589.23 seconds wall clock time: 222 minutes 9.44 seconds (13329.44 seconds total)