Starting phenix.real_space_refine on Tue Aug 26 05:51:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufb_42190/08_2025/8ufb_42190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufb_42190/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ufb_42190/08_2025/8ufb_42190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufb_42190/08_2025/8ufb_42190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ufb_42190/08_2025/8ufb_42190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufb_42190/08_2025/8ufb_42190.map" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.80, per 1000 atoms: 0.20 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: 2.34 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.41 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: 5.83 Time building geometry restraints manager: 3.09 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: 0.01 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 26.890 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.580 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.021 0.003 ARG D 110 TYR 0.019 0.003 TYR A 309 PHE 0.023 0.001 PHE G 421 TRP 0.018 0.002 TRP Y 89 HIS 0.007 0.001 HIS I 80 Details of bonding type rmsd covalent geometry : bond 0.00263 (35548) covalent geometry : angle 0.57186 (48392) SS BOND : bond 0.00315 ( 96) SS BOND : angle 0.97248 ( 192) hydrogen bonds : bond 0.19483 ( 1150) hydrogen bonds : angle 8.23080 ( 2880) link_NAG-ASN : bond 0.00315 ( 8) link_NAG-ASN : angle 2.19116 ( 24) *********************** 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 : 1.315 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: 0.6840 (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: 0.7647 (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: 0.7985 (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: 0.8325 (p) REVERT: E 64 TYR cc_start: 0.7857 (m-80) cc_final: 0.7391 (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: 0.8788 (p) REVERT: E 334 ARG cc_start: 0.8312 (mtt180) cc_final: 0.8038 (mtt90) REVERT: F 65 LEU cc_start: 0.5560 (mt) cc_final: 0.5304 (mt) REVERT: G 174 PHE cc_start: 0.6821 (m-80) cc_final: 0.6383 (m-80) REVERT: G 277 ILE cc_start: 0.8266 (mt) cc_final: 0.8016 (mt) REVERT: G 299 ASP cc_start: 0.6747 (t0) cc_final: 0.6500 (t0) REVERT: J 11 VAL cc_start: 0.8664 (t) cc_final: 0.8058 (t) REVERT: J 134 ASN cc_start: 0.7093 (t0) cc_final: 0.6790 (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: 0.7180 (m100) outliers start: 0 outliers final: 0 residues processed: 1000 average time/residue: 0.1857 time to fit residues: 305.6438 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 : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 40.0000 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 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 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 223 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS E 126 HIS E 275 HIS F 80 HIS F 88 ASN ** G 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 ASN ** G 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 HIS H 80 ASN H 114 HIS H 160 GLN H 162 HIS H 302 ASN I 11 GLN J 28 HIS 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 213 HIS K 222 GLN K 253 HIS K 402 ASN ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.199974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.146541 restraints weight = 46281.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.147881 restraints weight = 30108.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.150263 restraints weight = 20004.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152063 restraints weight = 15406.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152095 restraints weight = 13387.724| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.119 35652 Z= 0.390 Angle : 0.887 11.857 48608 Z= 0.473 Chirality : 0.055 0.268 5360 Planarity : 0.007 0.066 6272 Dihedral : 5.810 59.706 4976 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.13 % Allowed : 8.41 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.12), residues: 4436 helix: 1.38 (0.23), residues: 476 sheet: 0.21 (0.14), residues: 1272 loop : 0.15 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 157 TYR 0.033 0.003 TYR G 122 PHE 0.030 0.003 PHE K 113 TRP 0.030 0.003 TRP B 327 HIS 0.014 0.003 HIS E 126 Details of bonding type rmsd covalent geometry : bond 0.00912 (35548) covalent geometry : angle 0.87307 (48392) SS BOND : bond 0.00958 ( 96) SS BOND : angle 1.93275 ( 192) hydrogen bonds : bond 0.05642 ( 1150) hydrogen bonds : angle 6.64473 ( 2880) link_NAG-ASN : bond 0.00872 ( 8) link_NAG-ASN : angle 5.13731 ( 24) *********************** 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 803 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 645 time to evaluate : 1.178 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 51 TYR cc_start: 0.7845 (p90) cc_final: 0.7631 (p90) REVERT: A 81 PHE cc_start: 0.8643 (m-80) cc_final: 0.8392 (m-80) REVERT: A 171 TRP cc_start: 0.8254 (t60) cc_final: 0.7361 (t-100) REVERT: A 214 LEU cc_start: 0.8730 (tp) cc_final: 0.8462 (tp) REVERT: A 217 ASN cc_start: 0.8593 (t0) cc_final: 0.8291 (t0) REVERT: A 378 LYS cc_start: 0.7512 (mttt) cc_final: 0.7106 (mtmt) REVERT: B 8 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7733 (mp10) REVERT: B 168 GLN cc_start: 0.8747 (tp40) cc_final: 0.8331 (tp-100) REVERT: B 232 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8023 (mmmm) REVERT: B 270 GLU cc_start: 0.8370 (tp30) cc_final: 0.8116 (mm-30) REVERT: B 300 ASP cc_start: 0.7407 (t0) cc_final: 0.7108 (t0) REVERT: B 323 LEU cc_start: 0.8729 (tp) cc_final: 0.8526 (tt) REVERT: B 342 GLU cc_start: 0.7874 (tp30) cc_final: 0.7633 (tp30) REVERT: B 394 ILE cc_start: 0.7828 (pt) cc_final: 0.7479 (tp) REVERT: C 25 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6821 (pttm) REVERT: C 60 MET cc_start: 0.3895 (mmm) cc_final: 0.3284 (mmm) REVERT: D 30 GLN cc_start: 0.8743 (tt0) cc_final: 0.8338 (tt0) REVERT: D 51 TYR cc_start: 0.8875 (p90) cc_final: 0.8471 (p90) REVERT: D 113 GLU cc_start: 0.8481 (mp0) cc_final: 0.7853 (mp0) REVERT: D 143 ARG cc_start: 0.6806 (mmm-85) cc_final: 0.6543 (mmt-90) REVERT: D 205 GLN cc_start: 0.8417 (mt0) cc_final: 0.7840 (mm-40) REVERT: D 252 LEU cc_start: 0.8443 (tp) cc_final: 0.8211 (tp) REVERT: D 391 TYR cc_start: 0.7721 (p90) cc_final: 0.7489 (p90) REVERT: E 64 TYR cc_start: 0.7978 (m-80) cc_final: 0.7096 (m-80) REVERT: E 136 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8162 (mt-10) REVERT: E 276 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7978 (mtpt) REVERT: E 291 LEU cc_start: 0.9400 (tp) cc_final: 0.8843 (tp) REVERT: E 302 ASN cc_start: 0.9203 (t0) cc_final: 0.8679 (t0) REVERT: E 310 ARG cc_start: 0.8425 (ptt90) cc_final: 0.7873 (ptp90) REVERT: E 327 TRP cc_start: 0.8986 (t-100) cc_final: 0.7151 (t-100) REVERT: E 334 ARG cc_start: 0.8550 (mtt180) cc_final: 0.7954 (mtt90) REVERT: E 336 TRP cc_start: 0.8918 (m-90) cc_final: 0.8444 (m-10) REVERT: F 15 TYR cc_start: 0.3986 (m-80) cc_final: 0.3604 (m-80) REVERT: F 101 ASP cc_start: 0.5111 (m-30) cc_final: 0.4395 (m-30) REVERT: G 24 TYR cc_start: 0.6034 (m-80) cc_final: 0.5567 (m-80) REVERT: G 205 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8473 (mm-40) REVERT: G 361 ASN cc_start: 0.8377 (m-40) cc_final: 0.8066 (m-40) REVERT: G 390 ASP cc_start: 0.8378 (t70) cc_final: 0.8145 (t0) REVERT: G 397 GLU cc_start: 0.8019 (tt0) cc_final: 0.7784 (tt0) REVERT: H 52 MET cc_start: 0.7588 (tpp) cc_final: 0.7065 (tpp) REVERT: H 107 ASP cc_start: 0.8485 (m-30) cc_final: 0.8275 (m-30) REVERT: H 126 HIS cc_start: 0.8585 (t70) cc_final: 0.8353 (t-90) REVERT: J 32 GLN cc_start: 0.8412 (tt0) cc_final: 0.8039 (tt0) REVERT: J 247 ASP cc_start: 0.7184 (m-30) cc_final: 0.6857 (t0) REVERT: J 279 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7732 (tt) REVERT: J 285 ASP cc_start: 0.8209 (m-30) cc_final: 0.7869 (t70) REVERT: J 382 LYS cc_start: 0.8241 (ptpp) cc_final: 0.7956 (mtpp) REVERT: K 35 GLU cc_start: 0.8164 (tt0) cc_final: 0.7766 (tt0) REVERT: K 62 LEU cc_start: 0.8643 (mt) cc_final: 0.8438 (mt) REVERT: K 160 GLN cc_start: 0.8012 (mt0) cc_final: 0.7377 (mt0) REVERT: K 166 MET cc_start: 0.8806 (ptt) cc_final: 0.8560 (ptp) REVERT: K 344 ASN cc_start: 0.8203 (t0) cc_final: 0.7810 (t0) REVERT: K 348 TRP cc_start: 0.6595 (m100) cc_final: 0.6351 (m100) REVERT: L 67 TYR cc_start: 0.6970 (p90) cc_final: 0.6596 (p90) outliers start: 158 outliers final: 99 residues processed: 738 average time/residue: 0.1777 time to fit residues: 219.1785 Evaluate side-chains 624 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 521 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 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 308 THR Chi-restraints excluded: chain A residue 331 ILE 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 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 313 THR 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 25 LYS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 43 ASN 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 124 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 237 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 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 205 GLN Chi-restraints excluded: chain G residue 279 ILE 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 86 SER Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 302 ASN 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 19 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 126 THR 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 159 ASP 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 60 VAL Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain K residue 168 GLN 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 131 VAL 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 206 optimal weight: 10.0000 chunk 384 optimal weight: 7.9990 chunk 390 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 331 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 224 optimal weight: 0.2980 chunk 156 optimal weight: 1.9990 chunk 329 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 410 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 B 114 HIS ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS F 79 HIS F 136 GLN G 73 HIS ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN H 120 HIS J 100 ASN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 151 ASN K 194 GLN ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.205399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151681 restraints weight = 45772.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.153693 restraints weight = 29362.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.156164 restraints weight = 18355.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.158703 restraints weight = 14087.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.158648 restraints weight = 12023.155| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 35652 Z= 0.149 Angle : 0.604 10.796 48608 Z= 0.319 Chirality : 0.046 0.184 5360 Planarity : 0.005 0.058 6272 Dihedral : 5.148 54.787 4976 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.82 % Allowed : 12.04 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.13), residues: 4436 helix: 1.83 (0.24), residues: 476 sheet: 0.34 (0.14), residues: 1320 loop : 0.26 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 157 TYR 0.023 0.002 TYR H 360 PHE 0.018 0.002 PHE G 95 TRP 0.018 0.001 TRP J 142 HIS 0.009 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00344 (35548) covalent geometry : angle 0.58919 (48392) SS BOND : bond 0.00458 ( 96) SS BOND : angle 1.57982 ( 192) hydrogen bonds : bond 0.04098 ( 1150) hydrogen bonds : angle 6.11780 ( 2880) link_NAG-ASN : bond 0.00404 ( 8) link_NAG-ASN : angle 4.23724 ( 24) *********************** 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 703 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 595 time to evaluate : 1.002 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 7 MET cc_start: 0.7792 (ptm) cc_final: 0.7424 (ptp) REVERT: A 51 TYR cc_start: 0.7548 (p90) cc_final: 0.7204 (p90) REVERT: A 75 ASP cc_start: 0.8779 (t70) cc_final: 0.8397 (t70) REVERT: A 81 PHE cc_start: 0.8606 (m-80) cc_final: 0.8332 (m-80) REVERT: A 171 TRP cc_start: 0.8139 (t60) cc_final: 0.6863 (t-100) REVERT: A 217 ASN cc_start: 0.8580 (t0) cc_final: 0.8293 (t0) REVERT: A 262 ILE cc_start: 0.8595 (mm) cc_final: 0.8357 (mm) REVERT: A 271 ASN cc_start: 0.8305 (m-40) cc_final: 0.7909 (m110) REVERT: A 378 LYS cc_start: 0.7462 (mttt) cc_final: 0.7034 (mtmt) REVERT: A 400 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8053 (t) REVERT: B 8 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7618 (mp10) REVERT: B 163 TYR cc_start: 0.8361 (m-80) cc_final: 0.8086 (m-10) REVERT: B 168 GLN cc_start: 0.8702 (tp40) cc_final: 0.7994 (tp-100) REVERT: B 229 ASP cc_start: 0.5184 (t0) cc_final: 0.4935 (t0) REVERT: B 300 ASP cc_start: 0.7355 (t0) cc_final: 0.7099 (t0) REVERT: B 342 GLU cc_start: 0.7706 (tp30) cc_final: 0.7464 (tp30) REVERT: C 7 MET cc_start: 0.6295 (mpp) cc_final: 0.4862 (mmp) REVERT: C 60 MET cc_start: 0.3791 (mmm) cc_final: 0.3072 (mmm) REVERT: D 30 GLN cc_start: 0.8646 (tt0) cc_final: 0.8185 (tt0) REVERT: D 51 TYR cc_start: 0.8830 (p90) cc_final: 0.8351 (p90) REVERT: D 132 MET cc_start: 0.8114 (tpp) cc_final: 0.7769 (ttt) REVERT: D 143 ARG cc_start: 0.6747 (mmm-85) cc_final: 0.6311 (mmt-90) REVERT: D 152 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7235 (mp0) REVERT: D 176 ASN cc_start: 0.8114 (m110) cc_final: 0.7875 (m110) REVERT: D 252 LEU cc_start: 0.8481 (tp) cc_final: 0.8255 (tp) REVERT: E 64 TYR cc_start: 0.7904 (m-80) cc_final: 0.7592 (m-80) REVERT: E 136 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7983 (mt-10) REVERT: E 255 PRO cc_start: 0.9391 (Cg_endo) cc_final: 0.9182 (Cg_exo) REVERT: E 276 LYS cc_start: 0.8199 (mmtt) cc_final: 0.7966 (mtpt) REVERT: E 302 ASN cc_start: 0.9166 (t0) cc_final: 0.8638 (t0) REVERT: E 310 ARG cc_start: 0.8474 (ptt90) cc_final: 0.7911 (ptp90) REVERT: E 327 TRP cc_start: 0.8937 (t-100) cc_final: 0.7069 (t-100) REVERT: E 334 ARG cc_start: 0.8442 (mtt180) cc_final: 0.7875 (mtt90) REVERT: E 336 TRP cc_start: 0.8774 (m-90) cc_final: 0.8320 (m-10) REVERT: E 340 SER cc_start: 0.8879 (t) cc_final: 0.8630 (t) REVERT: F 15 TYR cc_start: 0.4029 (m-80) cc_final: 0.3499 (m-80) REVERT: F 101 ASP cc_start: 0.4646 (m-30) cc_final: 0.4352 (m-30) REVERT: G 24 TYR cc_start: 0.6048 (m-80) cc_final: 0.5504 (m-80) REVERT: G 75 ASP cc_start: 0.8892 (t0) cc_final: 0.8492 (t0) REVERT: G 152 GLU cc_start: 0.7296 (tp30) cc_final: 0.7018 (tp30) REVERT: G 223 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8469 (mm-40) REVERT: G 391 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7556 (p90) REVERT: H 52 MET cc_start: 0.7445 (tpp) cc_final: 0.6980 (tpp) REVERT: H 69 ASN cc_start: 0.6882 (t0) cc_final: 0.6062 (p0) REVERT: H 290 THR cc_start: 0.9096 (m) cc_final: 0.8504 (p) REVERT: J 32 GLN cc_start: 0.8404 (tt0) cc_final: 0.8041 (tt0) REVERT: J 156 LYS cc_start: 0.6662 (OUTLIER) cc_final: 0.6272 (mmtt) REVERT: J 175 ASP cc_start: 0.8010 (m-30) cc_final: 0.7555 (m-30) REVERT: J 205 GLN cc_start: 0.8245 (mt0) cc_final: 0.7948 (mm-40) REVERT: J 247 ASP cc_start: 0.7083 (m-30) cc_final: 0.6726 (t0) REVERT: J 279 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7655 (tt) REVERT: J 285 ASP cc_start: 0.8450 (m-30) cc_final: 0.7927 (t70) REVERT: J 299 ASP cc_start: 0.7856 (t0) cc_final: 0.7648 (t0) REVERT: J 382 LYS cc_start: 0.8219 (ptpp) cc_final: 0.7903 (mtpp) REVERT: K 35 GLU cc_start: 0.7937 (tt0) cc_final: 0.7580 (tt0) REVERT: K 79 ASP cc_start: 0.7361 (t0) cc_final: 0.7138 (t0) REVERT: K 80 ASN cc_start: 0.8404 (t0) cc_final: 0.8186 (t0) REVERT: K 197 TYR cc_start: 0.7807 (p90) cc_final: 0.7563 (p90) REVERT: K 256 PHE cc_start: 0.9069 (m-80) cc_final: 0.8623 (m-10) REVERT: K 344 ASN cc_start: 0.8288 (t0) cc_final: 0.7817 (t0) REVERT: L 60 MET cc_start: 0.5995 (mpp) cc_final: 0.5660 (mpp) outliers start: 108 outliers final: 66 residues processed: 657 average time/residue: 0.1701 time to fit residues: 190.2311 Evaluate side-chains 599 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 528 time to evaluate : 1.195 ------------------------------------------------------------------------------- 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 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 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 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 C residue 48 ILE 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 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 D residue 411 ILE Chi-restraints excluded: chain E residue 60 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 F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU 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 391 TYR Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 228 ILE 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 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 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 90 SER Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 168 GLN 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 L residue 3 THR 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 400 optimal weight: 5.9990 chunk 385 optimal weight: 0.0060 chunk 374 optimal weight: 0.8980 chunk 403 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 376 optimal weight: 0.9980 chunk 377 optimal weight: 0.3980 chunk 260 optimal weight: 0.0980 chunk 83 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 263 optimal weight: 4.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS E 114 HIS E 120 HIS E 194 GLN G 183 HIS ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN ** 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 = 0.4298 r_free = 0.4298 target = 0.210125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.155598 restraints weight = 45633.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.158571 restraints weight = 29425.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.161283 restraints weight = 18506.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.163111 restraints weight = 13654.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.163150 restraints weight = 11822.413| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35652 Z= 0.102 Angle : 0.573 25.831 48608 Z= 0.292 Chirality : 0.045 0.231 5360 Planarity : 0.004 0.048 6272 Dihedral : 4.963 59.781 4976 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.27 % Allowed : 13.79 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.13), residues: 4436 helix: 2.08 (0.24), residues: 480 sheet: 0.30 (0.14), residues: 1296 loop : 0.38 (0.12), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 157 TYR 0.024 0.001 TYR H 235 PHE 0.025 0.001 PHE A 399 TRP 0.031 0.001 TRP T 256 HIS 0.010 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00222 (35548) covalent geometry : angle 0.54789 (48392) SS BOND : bond 0.00291 ( 96) SS BOND : angle 1.30176 ( 192) hydrogen bonds : bond 0.03443 ( 1150) hydrogen bonds : angle 5.71226 ( 2880) link_NAG-ASN : bond 0.00398 ( 8) link_NAG-ASN : angle 6.70998 ( 24) *********************** 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 665 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 578 time to evaluate : 1.332 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: 0.7646 (ptm) cc_final: 0.7324 (ptp) REVERT: A 81 PHE cc_start: 0.8605 (m-80) cc_final: 0.8253 (m-80) REVERT: A 171 TRP cc_start: 0.8104 (t60) cc_final: 0.6884 (t-100) REVERT: A 217 ASN cc_start: 0.8335 (t0) cc_final: 0.8068 (t0) REVERT: A 262 ILE cc_start: 0.8562 (mm) cc_final: 0.8328 (mm) REVERT: A 271 ASN cc_start: 0.8219 (m-40) cc_final: 0.7829 (m110) REVERT: A 378 LYS cc_start: 0.7565 (mttt) cc_final: 0.7108 (mtmt) REVERT: B 8 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7630 (mp10) REVERT: B 52 MET cc_start: 0.7013 (mmm) cc_final: 0.6715 (tpp) REVERT: B 68 MET cc_start: 0.6681 (mtp) cc_final: 0.6468 (mtp) REVERT: B 82 HIS cc_start: 0.8329 (p-80) cc_final: 0.8109 (p90) REVERT: B 163 TYR cc_start: 0.8436 (m-80) cc_final: 0.8143 (m-10) REVERT: B 168 GLN cc_start: 0.8714 (tt0) cc_final: 0.8174 (tp-100) REVERT: B 232 LYS cc_start: 0.8390 (mmtt) cc_final: 0.8089 (mmmm) REVERT: B 235 TYR cc_start: 0.6553 (t80) cc_final: 0.6285 (t80) REVERT: B 289 PRO cc_start: 0.9110 (Cg_exo) cc_final: 0.8886 (Cg_endo) REVERT: B 300 ASP cc_start: 0.7301 (t0) cc_final: 0.7049 (t0) REVERT: B 317 THR cc_start: 0.8782 (m) cc_final: 0.8514 (p) REVERT: C 60 MET cc_start: 0.3738 (mmm) cc_final: 0.3147 (mmm) REVERT: D 51 TYR cc_start: 0.8808 (p90) cc_final: 0.8180 (p90) REVERT: D 132 MET cc_start: 0.7979 (tpp) cc_final: 0.7749 (ttt) REVERT: D 143 ARG cc_start: 0.6564 (mmm-85) cc_final: 0.6196 (mmt-90) REVERT: D 152 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7257 (mp0) REVERT: D 252 LEU cc_start: 0.8476 (tp) cc_final: 0.8209 (tp) REVERT: E 166 MET cc_start: 0.7616 (ptm) cc_final: 0.7413 (ptp) REVERT: E 302 ASN cc_start: 0.9145 (t0) cc_final: 0.8600 (t0) REVERT: E 310 ARG cc_start: 0.8446 (ptt90) cc_final: 0.8066 (ptp90) REVERT: E 327 TRP cc_start: 0.8919 (t-100) cc_final: 0.7116 (t-100) REVERT: E 334 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7990 (mtt90) REVERT: E 336 TRP cc_start: 0.8765 (m-90) cc_final: 0.8234 (m-10) REVERT: E 340 SER cc_start: 0.8844 (t) cc_final: 0.8610 (t) REVERT: F 15 TYR cc_start: 0.3853 (m-80) cc_final: 0.3407 (m-80) REVERT: F 101 ASP cc_start: 0.4614 (m-30) cc_final: 0.4211 (m-30) REVERT: G 21 ARG cc_start: 0.7204 (ttt-90) cc_final: 0.6958 (ttt90) REVERT: G 24 TYR cc_start: 0.6049 (m-80) cc_final: 0.5375 (m-80) REVERT: G 51 TYR cc_start: 0.8292 (p90) cc_final: 0.8078 (p90) REVERT: G 75 ASP cc_start: 0.8723 (t0) cc_final: 0.8352 (t0) REVERT: G 100 ASN cc_start: 0.8439 (t0) cc_final: 0.8136 (t0) REVERT: G 283 ILE cc_start: 0.8415 (mm) cc_final: 0.8109 (mt) REVERT: H 69 ASN cc_start: 0.6836 (t0) cc_final: 0.6245 (p0) REVERT: H 290 THR cc_start: 0.9143 (m) cc_final: 0.8691 (p) REVERT: J 32 GLN cc_start: 0.8295 (tt0) cc_final: 0.7885 (tt0) REVERT: J 81 PHE cc_start: 0.8869 (m-80) cc_final: 0.8337 (m-10) REVERT: J 205 GLN cc_start: 0.8002 (mt0) cc_final: 0.7761 (mm-40) REVERT: J 247 ASP cc_start: 0.6923 (m-30) cc_final: 0.6677 (t0) REVERT: J 285 ASP cc_start: 0.8578 (m-30) cc_final: 0.7953 (t70) REVERT: J 299 ASP cc_start: 0.7926 (t0) cc_final: 0.7671 (t0) REVERT: J 333 SER cc_start: 0.7863 (t) cc_final: 0.7621 (m) REVERT: J 382 LYS cc_start: 0.8158 (ptpp) cc_final: 0.7884 (mtpp) REVERT: J 404 SER cc_start: 0.8360 (p) cc_final: 0.7882 (t) REVERT: K 35 GLU cc_start: 0.7949 (tt0) cc_final: 0.7560 (tt0) REVERT: K 50 SER cc_start: 0.9087 (OUTLIER) cc_final: 0.8587 (p) REVERT: K 52 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6844 (ttm) REVERT: K 79 ASP cc_start: 0.7392 (t0) cc_final: 0.7161 (t0) REVERT: K 80 ASN cc_start: 0.8120 (t0) cc_final: 0.7811 (t0) REVERT: K 90 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7756 (p) REVERT: K 256 PHE cc_start: 0.9079 (m-80) cc_final: 0.8668 (m-10) REVERT: K 323 LEU cc_start: 0.7776 (tt) cc_final: 0.7515 (tp) REVERT: K 344 ASN cc_start: 0.8237 (t0) cc_final: 0.7722 (t0) REVERT: L 60 MET cc_start: 0.5975 (mpp) cc_final: 0.5661 (mpp) REVERT: L 67 TYR cc_start: 0.6810 (p90) cc_final: 0.6453 (p90) outliers start: 87 outliers final: 54 residues processed: 628 average time/residue: 0.1689 time to fit residues: 181.4209 Evaluate side-chains 576 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 518 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 230 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 73 GLN 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 350 HIS Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 381 CYS 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 66 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 155 HIS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 339 GLU Chi-restraints excluded: chain H residue 363 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 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 375 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 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 376 MET Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 130 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 221 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 219 optimal weight: 7.9990 chunk 217 optimal weight: 0.0980 chunk 242 optimal weight: 7.9990 chunk 282 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 428 optimal weight: 20.0000 chunk 256 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- 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 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN C 80 HIS D 219 ASN F 136 GLN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 ASN H 160 GLN I 28 HIS ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 102 GLN K 120 HIS ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN K 288 HIS ** V 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 83 GLN W 107 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.198774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.146004 restraints weight = 47234.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.150333 restraints weight = 29891.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151510 restraints weight = 17441.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.151888 restraints weight = 14172.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.152270 restraints weight = 14012.769| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 35652 Z= 0.306 Angle : 0.748 21.903 48608 Z= 0.393 Chirality : 0.051 0.313 5360 Planarity : 0.006 0.067 6272 Dihedral : 5.461 59.847 4976 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.49 % Allowed : 13.04 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.12), residues: 4436 helix: 1.40 (0.23), residues: 496 sheet: -0.09 (0.14), residues: 1332 loop : -0.21 (0.12), residues: 2608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 112 TYR 0.034 0.003 TYR A 46 PHE 0.042 0.003 PHE K 113 TRP 0.022 0.002 TRP H 336 HIS 0.037 0.002 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00721 (35548) covalent geometry : angle 0.72654 (48392) SS BOND : bond 0.00512 ( 96) SS BOND : angle 1.69466 ( 192) hydrogen bonds : bond 0.04772 ( 1150) hydrogen bonds : angle 6.08231 ( 2880) link_NAG-ASN : bond 0.01007 ( 8) link_NAG-ASN : angle 6.76495 ( 24) *********************** 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 715 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 543 time to evaluate : 1.012 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 20 GLU cc_start: 0.8336 (pm20) cc_final: 0.7747 (pm20) REVERT: A 120 LYS cc_start: 0.8289 (mttt) cc_final: 0.7898 (mttp) REVERT: A 136 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7407 (m) REVERT: A 171 TRP cc_start: 0.8411 (t60) cc_final: 0.7320 (t-100) REVERT: A 217 ASN cc_start: 0.8631 (t0) cc_final: 0.8239 (t0) REVERT: A 367 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7583 (mtpp) REVERT: A 378 LYS cc_start: 0.7615 (mttt) cc_final: 0.7126 (mtmt) REVERT: A 395 HIS cc_start: 0.8046 (p90) cc_final: 0.7822 (p-80) REVERT: A 421 PHE cc_start: 0.4964 (OUTLIER) cc_final: 0.4420 (t80) REVERT: B 8 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7659 (mp10) REVERT: B 113 PHE cc_start: 0.7604 (p90) cc_final: 0.7330 (p90) REVERT: B 168 GLN cc_start: 0.8769 (tt0) cc_final: 0.8315 (mm-40) REVERT: B 300 ASP cc_start: 0.7492 (t0) cc_final: 0.7282 (t0) REVERT: B 313 THR cc_start: 0.8438 (p) cc_final: 0.8173 (p) REVERT: B 339 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6766 (mm-30) REVERT: B 394 ILE cc_start: 0.8070 (pt) cc_final: 0.7631 (tp) REVERT: C 60 MET cc_start: 0.4146 (mmm) cc_final: 0.3717 (mmm) REVERT: D 88 MET cc_start: 0.8087 (mmm) cc_final: 0.7865 (mmm) REVERT: D 132 MET cc_start: 0.7974 (tpp) cc_final: 0.7768 (ttt) REVERT: D 143 ARG cc_start: 0.6779 (mmm-85) cc_final: 0.6569 (mmt-90) REVERT: D 175 ASP cc_start: 0.7878 (m-30) cc_final: 0.7628 (m-30) REVERT: E 166 MET cc_start: 0.7955 (ptm) cc_final: 0.7702 (ptp) REVERT: E 302 ASN cc_start: 0.9176 (t0) cc_final: 0.8612 (t0) REVERT: E 310 ARG cc_start: 0.8424 (ptt90) cc_final: 0.8047 (ptp90) REVERT: E 327 TRP cc_start: 0.8950 (t-100) cc_final: 0.6950 (t-100) REVERT: E 334 ARG cc_start: 0.8671 (mtt180) cc_final: 0.8164 (mtt90) REVERT: E 336 TRP cc_start: 0.8770 (m-90) cc_final: 0.8355 (m-10) REVERT: F 15 TYR cc_start: 0.4117 (m-80) cc_final: 0.3731 (m-80) REVERT: F 101 ASP cc_start: 0.4939 (m-30) cc_final: 0.4670 (m-30) REVERT: G 24 TYR cc_start: 0.6314 (m-80) cc_final: 0.5981 (m-80) REVERT: G 51 TYR cc_start: 0.8380 (p90) cc_final: 0.8105 (p90) REVERT: G 299 ASP cc_start: 0.7438 (t0) cc_final: 0.6868 (t0) REVERT: G 361 ASN cc_start: 0.8631 (m-40) cc_final: 0.8290 (m-40) REVERT: G 387 HIS cc_start: 0.8122 (m170) cc_final: 0.7811 (m170) REVERT: H 52 MET cc_start: 0.7575 (tpp) cc_final: 0.7373 (tpp) REVERT: H 64 TYR cc_start: 0.8003 (m-80) cc_final: 0.7794 (m-80) REVERT: H 69 ASN cc_start: 0.7001 (t0) cc_final: 0.6232 (p0) REVERT: H 266 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8029 (p) REVERT: H 290 THR cc_start: 0.9234 (m) cc_final: 0.8646 (p) REVERT: J 32 GLN cc_start: 0.8349 (tt0) cc_final: 0.7961 (tt0) REVERT: J 156 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6456 (mmtt) REVERT: J 247 ASP cc_start: 0.7351 (m-30) cc_final: 0.6969 (t0) REVERT: J 299 ASP cc_start: 0.8035 (t0) cc_final: 0.7819 (t0) REVERT: J 382 LYS cc_start: 0.8269 (ptpp) cc_final: 0.7392 (mptt) REVERT: K 35 GLU cc_start: 0.8072 (tt0) cc_final: 0.7645 (tt0) REVERT: K 171 LEU cc_start: 0.7965 (mt) cc_final: 0.7459 (mt) REVERT: K 327 TRP cc_start: 0.9313 (t-100) cc_final: 0.8508 (t-100) REVERT: K 344 ASN cc_start: 0.8452 (t0) cc_final: 0.8006 (t0) REVERT: L 60 MET cc_start: 0.6093 (mpp) cc_final: 0.5713 (mpp) outliers start: 172 outliers final: 131 residues processed: 643 average time/residue: 0.1654 time to fit residues: 182.1579 Evaluate side-chains 647 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 510 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 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 298 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 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 266 THR Chi-restraints excluded: chain B residue 291 LEU 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 B residue 366 ILE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 48 ILE 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 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 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 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 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 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 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 62 CYS Chi-restraints excluded: chain G residue 157 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 406 THR Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 197 TYR Chi-restraints excluded: chain H residue 266 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 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 274 VAL 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 16 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 85 THR 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 234 VAL Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 291 LEU 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 27 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 116 ILE 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 164 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 390 optimal weight: 6.9990 chunk 299 optimal weight: 6.9990 chunk 419 optimal weight: 9.9990 chunk 231 optimal weight: 8.9990 chunk 369 optimal weight: 0.0970 chunk 407 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 overall best weight: 3.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS ** 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** C 80 HIS D 28 HIS ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 ASN ** J 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN L 37 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.198713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.145823 restraints weight = 46453.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.149324 restraints weight = 29722.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.151452 restraints weight = 18377.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.151841 restraints weight = 13592.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.152484 restraints weight = 13224.855| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35652 Z= 0.227 Angle : 0.652 21.219 48608 Z= 0.340 Chirality : 0.048 0.365 5360 Planarity : 0.005 0.055 6272 Dihedral : 5.291 59.290 4976 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.94 % Allowed : 14.81 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.12), residues: 4436 helix: 1.51 (0.23), residues: 500 sheet: -0.12 (0.14), residues: 1312 loop : -0.33 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 119 TYR 0.022 0.002 TYR A 46 PHE 0.027 0.002 PHE G 95 TRP 0.021 0.002 TRP A 142 HIS 0.009 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00530 (35548) covalent geometry : angle 0.63113 (48392) SS BOND : bond 0.00417 ( 96) SS BOND : angle 1.43469 ( 192) hydrogen bonds : bond 0.04100 ( 1150) hydrogen bonds : angle 5.93055 ( 2880) link_NAG-ASN : bond 0.00796 ( 8) link_NAG-ASN : angle 6.34797 ( 24) *********************** 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 672 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 521 time to evaluate : 0.920 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 13 ILE cc_start: 0.9298 (mm) cc_final: 0.9063 (mm) REVERT: A 120 LYS cc_start: 0.8246 (mttt) cc_final: 0.7859 (mttp) REVERT: A 142 TRP cc_start: 0.7520 (m-10) cc_final: 0.7264 (m-10) REVERT: A 171 TRP cc_start: 0.8311 (t60) cc_final: 0.7202 (t-100) REVERT: A 187 ASN cc_start: 0.9218 (t0) cc_final: 0.8828 (t0) REVERT: A 217 ASN cc_start: 0.8619 (t0) cc_final: 0.8271 (t0) REVERT: A 306 GLU cc_start: 0.7584 (tt0) cc_final: 0.7367 (mt-10) REVERT: A 342 GLU cc_start: 0.8267 (mp0) cc_final: 0.7472 (tt0) REVERT: A 367 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7604 (mtpp) REVERT: A 378 LYS cc_start: 0.7665 (mttt) cc_final: 0.7210 (mtmt) REVERT: A 391 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.6939 (p90) REVERT: A 395 HIS cc_start: 0.8006 (p90) cc_final: 0.7796 (p-80) REVERT: A 403 ILE cc_start: 0.8682 (mt) cc_final: 0.8137 (tt) REVERT: A 421 PHE cc_start: 0.4946 (OUTLIER) cc_final: 0.4356 (t80) REVERT: B 8 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: B 168 GLN cc_start: 0.8640 (tt0) cc_final: 0.8319 (tp-100) REVERT: B 232 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8042 (mmmm) REVERT: B 266 THR cc_start: 0.6781 (OUTLIER) cc_final: 0.6517 (p) REVERT: B 313 THR cc_start: 0.8383 (p) cc_final: 0.8143 (p) REVERT: B 339 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6876 (mm-30) REVERT: B 394 ILE cc_start: 0.8200 (pt) cc_final: 0.7796 (tp) REVERT: C 7 MET cc_start: 0.6060 (mpp) cc_final: 0.4773 (mmp) REVERT: C 60 MET cc_start: 0.4230 (mmm) cc_final: 0.3726 (mmm) REVERT: D 30 GLN cc_start: 0.8494 (tt0) cc_final: 0.8172 (tt0) REVERT: D 51 TYR cc_start: 0.8934 (p90) cc_final: 0.8374 (p90) REVERT: D 132 MET cc_start: 0.8052 (tpp) cc_final: 0.7788 (ttt) REVERT: D 143 ARG cc_start: 0.6742 (mmm-85) cc_final: 0.6499 (mmt-90) REVERT: D 152 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7376 (mp0) REVERT: D 385 LYS cc_start: 0.7745 (tppt) cc_final: 0.7462 (tppt) REVERT: E 302 ASN cc_start: 0.9137 (t0) cc_final: 0.8573 (t0) REVERT: E 310 ARG cc_start: 0.8461 (ptt90) cc_final: 0.8099 (ptp90) REVERT: E 327 TRP cc_start: 0.8967 (t-100) cc_final: 0.6965 (t-100) REVERT: E 334 ARG cc_start: 0.8620 (mtt180) cc_final: 0.8115 (mtt90) REVERT: E 336 TRP cc_start: 0.8745 (m-90) cc_final: 0.8314 (m-10) REVERT: F 15 TYR cc_start: 0.4095 (m-80) cc_final: 0.3679 (m-80) REVERT: F 101 ASP cc_start: 0.5225 (m-30) cc_final: 0.4950 (m-30) REVERT: G 10 LYS cc_start: 0.7485 (mttt) cc_final: 0.7258 (mtpp) REVERT: G 67 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6433 (mm-40) REVERT: G 299 ASP cc_start: 0.7538 (t0) cc_final: 0.6721 (t0) REVERT: G 301 GLU cc_start: 0.8156 (mp0) cc_final: 0.7491 (mp0) REVERT: G 361 ASN cc_start: 0.8659 (m-40) cc_final: 0.8316 (m-40) REVERT: G 388 ILE cc_start: 0.9016 (mm) cc_final: 0.8806 (mm) REVERT: G 390 ASP cc_start: 0.8091 (t70) cc_final: 0.7811 (t0) REVERT: G 391 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7339 (p90) REVERT: H 52 MET cc_start: 0.7598 (tpp) cc_final: 0.7396 (tpp) REVERT: H 290 THR cc_start: 0.9164 (m) cc_final: 0.8607 (p) REVERT: J 175 ASP cc_start: 0.8002 (m-30) cc_final: 0.7705 (m-30) REVERT: J 247 ASP cc_start: 0.7091 (m-30) cc_final: 0.6785 (t0) REVERT: J 382 LYS cc_start: 0.8165 (ptpp) cc_final: 0.7388 (mptt) REVERT: K 35 GLU cc_start: 0.8008 (tt0) cc_final: 0.7552 (tt0) REVERT: K 52 MET cc_start: 0.7511 (ttm) cc_final: 0.7308 (ttp) REVERT: K 327 TRP cc_start: 0.9286 (t-100) cc_final: 0.8445 (t-100) REVERT: K 344 ASN cc_start: 0.8573 (t0) cc_final: 0.8102 (t0) REVERT: L 52 GLU cc_start: 0.5540 (tt0) cc_final: 0.5279 (tt0) REVERT: L 60 MET cc_start: 0.6256 (mpp) cc_final: 0.5755 (mpp) outliers start: 151 outliers final: 124 residues processed: 615 average time/residue: 0.1702 time to fit residues: 178.3478 Evaluate side-chains 634 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 503 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 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 178 VAL 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 367 LYS 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 73 GLN Chi-restraints excluded: chain B residue 85 THR 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 266 THR Chi-restraints excluded: chain B residue 291 LEU 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 121 VAL Chi-restraints excluded: chain D residue 11 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 294 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 391 TYR 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 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 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 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 62 CYS Chi-restraints excluded: chain G residue 67 GLN 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 318 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 G residue 432 VAL 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 294 THR 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 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 124 VAL 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 291 ILE 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 408 TRP 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 60 VAL Chi-restraints excluded: chain K residue 90 SER 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 291 LEU Chi-restraints excluded: chain K residue 323 LEU 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 7 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 180 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 328 optimal weight: 1.9990 chunk 373 optimal weight: 4.9990 chunk 402 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 181 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 426 optimal weight: 50.0000 chunk 382 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 ASN B 162 HIS ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 HIS C 80 HIS ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 HIS J 32 GLN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN Y 83 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.193987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145169 restraints weight = 47469.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145727 restraints weight = 29980.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.146739 restraints weight = 20335.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.147575 restraints weight = 16759.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.147785 restraints weight = 14642.463| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.140 35652 Z= 0.383 Angle : 0.811 21.257 48608 Z= 0.427 Chirality : 0.054 0.741 5360 Planarity : 0.006 0.060 6272 Dihedral : 5.909 59.395 4976 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.36 % Allowed : 14.11 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.12), residues: 4436 helix: 0.83 (0.22), residues: 528 sheet: -0.49 (0.14), residues: 1284 loop : -0.82 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 205 TYR 0.034 0.003 TYR A 76 PHE 0.033 0.003 PHE D 288 TRP 0.026 0.002 TRP A 142 HIS 0.013 0.002 HIS J 332 Details of bonding type rmsd covalent geometry : bond 0.00900 (35548) covalent geometry : angle 0.79073 (48392) SS BOND : bond 0.00598 ( 96) SS BOND : angle 1.64877 ( 192) hydrogen bonds : bond 0.05151 ( 1150) hydrogen bonds : angle 6.31562 ( 2880) link_NAG-ASN : bond 0.01059 ( 8) link_NAG-ASN : angle 7.04372 ( 24) *********************** 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 709 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 504 time to evaluate : 1.076 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 120 LYS cc_start: 0.8285 (mttt) cc_final: 0.7925 (mttp) REVERT: A 171 TRP cc_start: 0.8512 (t60) cc_final: 0.7269 (t-100) REVERT: A 217 ASN cc_start: 0.8826 (t0) cc_final: 0.8404 (t0) REVERT: A 342 GLU cc_start: 0.8294 (mp0) cc_final: 0.7568 (tt0) REVERT: A 367 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7596 (mtpp) REVERT: A 378 LYS cc_start: 0.7772 (mttt) cc_final: 0.7314 (mtmt) REVERT: A 391 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.7327 (p90) REVERT: A 400 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7784 (t) REVERT: A 421 PHE cc_start: 0.4925 (OUTLIER) cc_final: 0.4023 (t80) REVERT: B 8 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7654 (mp10) REVERT: B 168 GLN cc_start: 0.8733 (tt0) cc_final: 0.8324 (mm-40) REVERT: B 174 ASP cc_start: 0.8163 (t0) cc_final: 0.7846 (t70) REVERT: B 232 LYS cc_start: 0.8473 (mmtt) cc_final: 0.7968 (mmmm) REVERT: B 313 THR cc_start: 0.8558 (p) cc_final: 0.8342 (p) REVERT: B 402 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7705 (m-40) REVERT: C 7 MET cc_start: 0.5845 (mpp) cc_final: 0.5275 (mpp) REVERT: C 60 MET cc_start: 0.4471 (mmm) cc_final: 0.3977 (mmm) REVERT: C 80 HIS cc_start: 0.6437 (OUTLIER) cc_final: 0.6225 (m90) REVERT: C 104 ARG cc_start: 0.5438 (mtt-85) cc_final: 0.4967 (mtt-85) REVERT: D 30 GLN cc_start: 0.8617 (tt0) cc_final: 0.8355 (tt0) REVERT: D 143 ARG cc_start: 0.6962 (mmm-85) cc_final: 0.6567 (mmt-90) REVERT: D 175 ASP cc_start: 0.7924 (m-30) cc_final: 0.7720 (m-30) REVERT: E 302 ASN cc_start: 0.9035 (t0) cc_final: 0.8588 (t0) REVERT: E 310 ARG cc_start: 0.8619 (ptt90) cc_final: 0.8185 (ptp90) REVERT: E 319 THR cc_start: 0.8615 (p) cc_final: 0.8286 (t) REVERT: E 327 TRP cc_start: 0.8960 (t-100) cc_final: 0.6973 (t-100) REVERT: E 334 ARG cc_start: 0.8667 (mtt180) cc_final: 0.8378 (mtt90) REVERT: F 15 TYR cc_start: 0.4350 (m-80) cc_final: 0.3802 (m-80) REVERT: F 101 ASP cc_start: 0.5589 (m-30) cc_final: 0.5166 (m-30) REVERT: G 10 LYS cc_start: 0.7830 (mttt) cc_final: 0.7503 (mtpp) REVERT: G 67 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.6844 (mm-40) REVERT: G 229 ILE cc_start: 0.9145 (mt) cc_final: 0.8901 (mm) REVERT: G 299 ASP cc_start: 0.7616 (t0) cc_final: 0.7074 (t0) REVERT: G 361 ASN cc_start: 0.8722 (m-40) cc_final: 0.8383 (m-40) REVERT: G 388 ILE cc_start: 0.9192 (mm) cc_final: 0.8951 (mm) REVERT: G 390 ASP cc_start: 0.8131 (t70) cc_final: 0.7841 (t0) REVERT: G 391 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.6929 (p90) REVERT: H 219 ASP cc_start: 0.7581 (t0) cc_final: 0.7214 (t70) REVERT: H 266 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8033 (p) REVERT: H 290 THR cc_start: 0.9180 (m) cc_final: 0.8638 (p) REVERT: J 156 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6706 (mmtt) REVERT: J 247 ASP cc_start: 0.7304 (m-30) cc_final: 0.6840 (t0) REVERT: J 265 GLU cc_start: 0.7917 (mp0) cc_final: 0.7603 (mp0) REVERT: J 291 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7883 (mt) REVERT: K 35 GLU cc_start: 0.8089 (tt0) cc_final: 0.7616 (tt0) REVERT: K 52 MET cc_start: 0.7704 (ttm) cc_final: 0.7503 (ttp) REVERT: K 327 TRP cc_start: 0.9331 (t-100) cc_final: 0.8469 (t-100) REVERT: K 333 LYS cc_start: 0.8372 (mmmm) cc_final: 0.7698 (mtmt) REVERT: K 344 ASN cc_start: 0.8693 (t0) cc_final: 0.8235 (t0) REVERT: L 27 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6866 (mt) REVERT: L 60 MET cc_start: 0.6119 (mpp) cc_final: 0.5473 (mpp) REVERT: L 67 TYR cc_start: 0.7285 (p90) cc_final: 0.6735 (p90) outliers start: 205 outliers final: 162 residues processed: 635 average time/residue: 0.1709 time to fit residues: 184.5432 Evaluate side-chains 649 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 474 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 80 VAL 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 178 VAL 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 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 66 SER 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 85 THR 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 172 VAL Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 291 LEU 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 B residue 366 ILE Chi-restraints excluded: chain B residue 402 ASN Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 80 HIS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 11 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 87 PHE 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 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 294 THR Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 391 TYR 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 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 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 220 VAL 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 354 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain F residue 3 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 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 62 CYS Chi-restraints excluded: chain G residue 67 GLN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 222 LEU 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 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 G residue 432 VAL 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 197 TYR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 266 THR 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 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 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 337 VAL 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 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 22 CYS 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 92 VAL Chi-restraints excluded: chain K residue 124 VAL 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 281 ILE Chi-restraints excluded: chain K residue 291 LEU 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 7 MET Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 69 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 83 VAL Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 92 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 52 optimal weight: 2.9990 chunk 371 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 319 optimal weight: 0.6980 chunk 193 optimal weight: 20.0000 chunk 218 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 204 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 B 194 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS F 136 GLN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 ASN G 439 HIS H 140 HIS ** H 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN J 130 GLN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.202146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.149826 restraints weight = 46176.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153024 restraints weight = 29079.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155250 restraints weight = 18107.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156203 restraints weight = 13287.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.156533 restraints weight = 12424.265| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35652 Z= 0.118 Angle : 0.600 20.070 48608 Z= 0.311 Chirality : 0.046 0.381 5360 Planarity : 0.005 0.051 6272 Dihedral : 5.226 53.678 4976 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.80 % Favored : 97.18 % Rotamer: Outliers : 2.35 % Allowed : 17.82 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.13), residues: 4436 helix: 1.49 (0.23), residues: 516 sheet: -0.29 (0.14), residues: 1368 loop : -0.39 (0.12), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 157 TYR 0.027 0.002 TYR E 235 PHE 0.020 0.002 PHE A 399 TRP 0.035 0.001 TRP A 142 HIS 0.032 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00264 (35548) covalent geometry : angle 0.58186 (48392) SS BOND : bond 0.00319 ( 96) SS BOND : angle 1.21921 ( 192) hydrogen bonds : bond 0.03517 ( 1150) hydrogen bonds : angle 5.80130 ( 2880) link_NAG-ASN : bond 0.00949 ( 8) link_NAG-ASN : angle 5.95081 ( 24) *********************** 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 633 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 543 time to evaluate : 1.104 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: A 13 ILE cc_start: 0.9268 (mm) cc_final: 0.9058 (mm) REVERT: A 120 LYS cc_start: 0.8204 (mttt) cc_final: 0.7912 (mttp) REVERT: A 171 TRP cc_start: 0.8215 (t60) cc_final: 0.7028 (t-100) REVERT: A 217 ASN cc_start: 0.8614 (t0) cc_final: 0.8309 (t0) REVERT: A 342 GLU cc_start: 0.8123 (mp0) cc_final: 0.7401 (tt0) REVERT: A 378 LYS cc_start: 0.7565 (mttt) cc_final: 0.7191 (mtmt) REVERT: A 403 ILE cc_start: 0.8652 (mt) cc_final: 0.7968 (tt) REVERT: A 421 PHE cc_start: 0.4669 (OUTLIER) cc_final: 0.3927 (t80) REVERT: B 8 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7742 (mp10) REVERT: B 26 ARG cc_start: 0.6701 (ttm-80) cc_final: 0.6454 (ttm-80) REVERT: B 52 MET cc_start: 0.7166 (mmm) cc_final: 0.6610 (tpp) REVERT: B 163 TYR cc_start: 0.8508 (m-80) cc_final: 0.8127 (m-10) REVERT: B 168 GLN cc_start: 0.8503 (tt0) cc_final: 0.8092 (mm-40) REVERT: B 232 LYS cc_start: 0.8381 (mmtt) cc_final: 0.7922 (mmmm) REVERT: B 313 THR cc_start: 0.8459 (p) cc_final: 0.8222 (p) REVERT: B 339 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6862 (mm-30) REVERT: C 7 MET cc_start: 0.5853 (mpp) cc_final: 0.4480 (mmp) REVERT: C 60 MET cc_start: 0.4126 (mmm) cc_final: 0.3707 (mmm) REVERT: C 86 GLU cc_start: 0.6552 (tp30) cc_final: 0.5867 (tt0) REVERT: D 51 TYR cc_start: 0.8897 (p90) cc_final: 0.8418 (p90) REVERT: D 113 GLU cc_start: 0.8004 (mp0) cc_final: 0.7639 (mp0) REVERT: D 143 ARG cc_start: 0.6600 (mmm-85) cc_final: 0.6181 (mmt90) REVERT: D 152 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7611 (mp0) REVERT: D 247 ASP cc_start: 0.7598 (t70) cc_final: 0.6935 (t0) REVERT: E 302 ASN cc_start: 0.9110 (t0) cc_final: 0.8553 (t0) REVERT: E 310 ARG cc_start: 0.8492 (ptt90) cc_final: 0.8102 (ptp90) REVERT: E 319 THR cc_start: 0.8458 (p) cc_final: 0.8154 (t) REVERT: E 327 TRP cc_start: 0.8952 (t-100) cc_final: 0.6960 (t-100) REVERT: E 334 ARG cc_start: 0.8556 (mtt180) cc_final: 0.8162 (mtt90) REVERT: F 15 TYR cc_start: 0.4079 (m-80) cc_final: 0.3585 (m-80) REVERT: F 101 ASP cc_start: 0.5385 (m-30) cc_final: 0.4723 (m-30) REVERT: G 10 LYS cc_start: 0.7579 (mttt) cc_final: 0.7323 (mtpp) REVERT: G 51 TYR cc_start: 0.8205 (p90) cc_final: 0.7999 (p90) REVERT: G 100 ASN cc_start: 0.8514 (t0) cc_final: 0.8226 (t0) REVERT: G 299 ASP cc_start: 0.7627 (t0) cc_final: 0.6948 (t0) REVERT: G 342 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6278 (mm-30) REVERT: G 390 ASP cc_start: 0.8022 (t70) cc_final: 0.7777 (t0) REVERT: G 391 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7025 (p90) REVERT: H 266 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7853 (p) REVERT: H 290 THR cc_start: 0.9185 (m) cc_final: 0.8656 (p) REVERT: I 7 MET cc_start: 0.3989 (tpt) cc_final: 0.3144 (mmm) REVERT: I 126 ARG cc_start: 0.6064 (mtm180) cc_final: 0.5796 (mtm180) REVERT: J 175 ASP cc_start: 0.7879 (m-30) cc_final: 0.7612 (m-30) REVERT: J 247 ASP cc_start: 0.6879 (m-30) cc_final: 0.6603 (t0) REVERT: J 265 GLU cc_start: 0.7789 (mp0) cc_final: 0.7564 (mp0) REVERT: K 35 GLU cc_start: 0.7843 (tt0) cc_final: 0.7407 (tt0) REVERT: K 50 SER cc_start: 0.8987 (t) cc_final: 0.8739 (p) REVERT: K 167 HIS cc_start: 0.7452 (m-70) cc_final: 0.7174 (m-70) REVERT: K 323 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7657 (tp) REVERT: K 327 TRP cc_start: 0.9270 (t-100) cc_final: 0.8572 (t-100) REVERT: K 333 LYS cc_start: 0.8227 (mmmm) cc_final: 0.7537 (mtmt) REVERT: K 344 ASN cc_start: 0.8616 (t0) cc_final: 0.8185 (t0) REVERT: L 52 GLU cc_start: 0.5892 (tt0) cc_final: 0.5425 (tt0) REVERT: L 60 MET cc_start: 0.6010 (mpp) cc_final: 0.5553 (mpp) outliers start: 90 outliers final: 69 residues processed: 598 average time/residue: 0.1727 time to fit residues: 175.0061 Evaluate side-chains 577 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 503 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 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 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 73 GLN Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 135 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 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 107 ASP Chi-restraints excluded: chain E residue 175 HIS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 354 VAL 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 G residue 6 VAL Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 90 SER 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 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 92 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 274 VAL 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 K residue 16 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 323 LEU Chi-restraints excluded: chain K residue 376 MET Chi-restraints excluded: chain L residue 56 VAL 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 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 61 optimal weight: 20.0000 chunk 202 optimal weight: 0.9990 chunk 401 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 chunk 325 optimal weight: 3.9990 chunk 240 optimal weight: 20.0000 chunk 216 optimal weight: 9.9990 chunk 221 optimal weight: 0.6980 chunk 380 optimal weight: 5.9990 chunk 91 optimal weight: 0.0060 overall best weight: 1.3402 ------------------------------------------------------------------------------- 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 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 HIS D 441 HIS ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 HIS ** H 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.202112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149602 restraints weight = 46232.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.153429 restraints weight = 29485.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.155642 restraints weight = 18119.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.155789 restraints weight = 13073.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.156555 restraints weight = 12984.478| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 35652 Z= 0.128 Angle : 0.596 20.016 48608 Z= 0.306 Chirality : 0.046 0.703 5360 Planarity : 0.005 0.047 6272 Dihedral : 5.059 53.965 4976 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.63 % Favored : 96.35 % Rotamer: Outliers : 2.17 % Allowed : 18.50 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.13), residues: 4436 helix: 1.84 (0.24), residues: 492 sheet: -0.16 (0.14), residues: 1328 loop : -0.35 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 440 TYR 0.022 0.002 TYR E 235 PHE 0.021 0.002 PHE K 113 TRP 0.030 0.001 TRP A 142 HIS 0.012 0.001 HIS D 439 Details of bonding type rmsd covalent geometry : bond 0.00297 (35548) covalent geometry : angle 0.57526 (48392) SS BOND : bond 0.00341 ( 96) SS BOND : angle 1.19431 ( 192) hydrogen bonds : bond 0.03465 ( 1150) hydrogen bonds : angle 5.63936 ( 2880) link_NAG-ASN : bond 0.01475 ( 8) link_NAG-ASN : angle 6.44179 ( 24) *********************** 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 604 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 521 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.9262 (mm) cc_final: 0.9030 (mm) REVERT: A 120 LYS cc_start: 0.8181 (mttt) cc_final: 0.7890 (mttp) REVERT: A 171 TRP cc_start: 0.8234 (t60) cc_final: 0.7010 (t-100) REVERT: A 217 ASN cc_start: 0.8596 (t0) cc_final: 0.8247 (t0) REVERT: A 342 GLU cc_start: 0.8131 (mp0) cc_final: 0.7448 (tt0) REVERT: A 378 LYS cc_start: 0.7538 (mttt) cc_final: 0.7161 (mtmt) REVERT: A 421 PHE cc_start: 0.4879 (OUTLIER) cc_final: 0.4213 (t80) REVERT: B 8 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7767 (mp10) REVERT: B 168 GLN cc_start: 0.8508 (tt0) cc_final: 0.8049 (tp-100) REVERT: B 174 ASP cc_start: 0.8120 (t0) cc_final: 0.7648 (t70) REVERT: B 232 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8070 (mmmm) REVERT: B 313 THR cc_start: 0.8355 (p) cc_final: 0.8125 (p) REVERT: B 317 THR cc_start: 0.8913 (m) cc_final: 0.8573 (p) REVERT: B 339 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6879 (mm-30) REVERT: C 7 MET cc_start: 0.5940 (mpp) cc_final: 0.4660 (mmp) REVERT: C 60 MET cc_start: 0.4201 (mmm) cc_final: 0.3784 (mmm) REVERT: C 86 GLU cc_start: 0.6615 (tp30) cc_final: 0.5790 (tt0) REVERT: D 113 GLU cc_start: 0.8057 (mp0) cc_final: 0.7638 (mp0) REVERT: D 143 ARG cc_start: 0.6600 (mmm-85) cc_final: 0.6209 (mmt90) REVERT: D 152 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7517 (mp0) REVERT: D 247 ASP cc_start: 0.7781 (t70) cc_final: 0.7119 (t0) REVERT: E 302 ASN cc_start: 0.9106 (t0) cc_final: 0.8545 (t0) REVERT: E 319 THR cc_start: 0.8426 (p) cc_final: 0.8135 (t) REVERT: E 327 TRP cc_start: 0.8940 (t-100) cc_final: 0.7076 (t-100) REVERT: E 334 ARG cc_start: 0.8619 (mtt180) cc_final: 0.8148 (mtt90) REVERT: F 15 TYR cc_start: 0.4099 (m-80) cc_final: 0.3633 (m-80) REVERT: F 101 ASP cc_start: 0.5255 (m-30) cc_final: 0.4603 (m-30) REVERT: G 10 LYS cc_start: 0.7579 (mttt) cc_final: 0.7329 (mtpp) REVERT: G 100 ASN cc_start: 0.8549 (t0) cc_final: 0.8205 (t0) REVERT: G 299 ASP cc_start: 0.7588 (t0) cc_final: 0.6921 (t0) REVERT: G 342 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6310 (mm-30) REVERT: G 390 ASP cc_start: 0.7963 (t70) cc_final: 0.7706 (t0) REVERT: G 391 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6986 (p90) REVERT: H 138 TYR cc_start: 0.9279 (p90) cc_final: 0.8975 (p90) REVERT: H 166 MET cc_start: 0.8284 (mtm) cc_final: 0.7926 (mtp) REVERT: H 266 THR cc_start: 0.8238 (OUTLIER) cc_final: 0.7826 (p) REVERT: H 290 THR cc_start: 0.9141 (m) cc_final: 0.8538 (p) REVERT: J 20 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7161 (pm20) REVERT: J 247 ASP cc_start: 0.7058 (m-30) cc_final: 0.6810 (t0) REVERT: J 265 GLU cc_start: 0.7830 (mp0) cc_final: 0.7568 (mp0) REVERT: K 35 GLU cc_start: 0.7879 (tt0) cc_final: 0.7452 (tt0) REVERT: K 50 SER cc_start: 0.9039 (t) cc_final: 0.8672 (p) REVERT: K 90 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8354 (p) REVERT: K 167 HIS cc_start: 0.7345 (m-70) cc_final: 0.7090 (m-70) REVERT: K 323 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7657 (tp) REVERT: K 344 ASN cc_start: 0.8561 (t0) cc_final: 0.8149 (t0) REVERT: L 52 GLU cc_start: 0.5790 (tt0) cc_final: 0.5405 (tt0) REVERT: L 60 MET cc_start: 0.6004 (mpp) cc_final: 0.5546 (mpp) outliers start: 83 outliers final: 66 residues processed: 572 average time/residue: 0.1765 time to fit residues: 171.6481 Evaluate side-chains 575 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 502 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 255 VAL 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 73 GLN Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 208 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 60 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 291 LEU 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 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 228 ILE 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 11 VAL Chi-restraints excluded: chain J residue 20 GLU 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 274 VAL 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 22 CYS Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain K residue 323 LEU Chi-restraints excluded: chain K residue 376 MET Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain L residue 56 VAL 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 118 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 218 optimal weight: 0.9980 chunk 266 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 247 optimal weight: 0.8980 chunk 414 optimal weight: 6.9990 chunk 437 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 HIS ** H 346 HIS ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.203027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151284 restraints weight = 46331.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.154273 restraints weight = 29547.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.155571 restraints weight = 17455.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.156782 restraints weight = 14226.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.156786 restraints weight = 13056.787| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 35652 Z= 0.124 Angle : 0.593 19.888 48608 Z= 0.303 Chirality : 0.047 0.983 5360 Planarity : 0.005 0.045 6272 Dihedral : 4.977 59.334 4976 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 2.12 % Allowed : 18.70 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.13), residues: 4436 helix: 1.90 (0.24), residues: 492 sheet: -0.08 (0.14), residues: 1320 loop : -0.32 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 440 TYR 0.026 0.002 TYR J 137 PHE 0.028 0.001 PHE J 95 TRP 0.025 0.001 TRP K 233 HIS 0.010 0.001 HIS K 213 Details of bonding type rmsd covalent geometry : bond 0.00288 (35548) covalent geometry : angle 0.57282 (48392) SS BOND : bond 0.00295 ( 96) SS BOND : angle 1.16222 ( 192) hydrogen bonds : bond 0.03382 ( 1150) hydrogen bonds : angle 5.57030 ( 2880) link_NAG-ASN : bond 0.00931 ( 8) link_NAG-ASN : angle 6.24394 ( 24) ********************** 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 590 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 509 time to evaluate : 1.226 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 13 ILE cc_start: 0.9250 (mm) cc_final: 0.9028 (mm) REVERT: A 120 LYS cc_start: 0.8141 (mttt) cc_final: 0.7826 (mttp) REVERT: A 171 TRP cc_start: 0.8229 (t60) cc_final: 0.7004 (t-100) REVERT: A 217 ASN cc_start: 0.8623 (t0) cc_final: 0.8266 (t0) REVERT: A 342 GLU cc_start: 0.8073 (mp0) cc_final: 0.7411 (tt0) REVERT: A 378 LYS cc_start: 0.7517 (mttt) cc_final: 0.7165 (mtmt) REVERT: A 403 ILE cc_start: 0.8646 (mt) cc_final: 0.7947 (tt) REVERT: A 421 PHE cc_start: 0.4803 (OUTLIER) cc_final: 0.4197 (t80) REVERT: B 8 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7805 (mp10) REVERT: B 168 GLN cc_start: 0.8497 (tt0) cc_final: 0.8062 (tp-100) REVERT: B 174 ASP cc_start: 0.8041 (t0) cc_final: 0.7609 (t70) REVERT: B 313 THR cc_start: 0.8338 (p) cc_final: 0.8112 (p) REVERT: B 317 THR cc_start: 0.8848 (m) cc_final: 0.8563 (p) REVERT: B 339 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6891 (mm-30) REVERT: C 7 MET cc_start: 0.6058 (mpp) cc_final: 0.4851 (mmp) REVERT: C 60 MET cc_start: 0.4163 (mmm) cc_final: 0.3757 (mmm) REVERT: C 86 GLU cc_start: 0.6607 (tp30) cc_final: 0.5783 (tt0) REVERT: D 113 GLU cc_start: 0.8040 (mp0) cc_final: 0.7611 (mp0) REVERT: D 152 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7450 (mp0) REVERT: D 200 SER cc_start: 0.9288 (t) cc_final: 0.9077 (m) REVERT: E 302 ASN cc_start: 0.9107 (t0) cc_final: 0.8560 (t0) REVERT: E 319 THR cc_start: 0.8414 (p) cc_final: 0.8135 (t) REVERT: E 327 TRP cc_start: 0.8930 (t-100) cc_final: 0.7046 (t-100) REVERT: E 334 ARG cc_start: 0.8600 (mtt180) cc_final: 0.8146 (mtt90) REVERT: F 15 TYR cc_start: 0.3918 (m-80) cc_final: 0.3516 (m-80) REVERT: F 101 ASP cc_start: 0.5235 (m-30) cc_final: 0.4580 (m-30) REVERT: G 10 LYS cc_start: 0.7560 (mttt) cc_final: 0.7306 (mtpp) REVERT: G 100 ASN cc_start: 0.8513 (t0) cc_final: 0.8152 (t0) REVERT: G 299 ASP cc_start: 0.7575 (t0) cc_final: 0.6858 (t0) REVERT: G 342 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6353 (mm-30) REVERT: G 390 ASP cc_start: 0.7977 (t70) cc_final: 0.7727 (t0) REVERT: G 391 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.6963 (p90) REVERT: H 266 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.8002 (p) REVERT: H 290 THR cc_start: 0.9126 (m) cc_final: 0.8520 (p) REVERT: I 123 GLU cc_start: 0.5378 (OUTLIER) cc_final: 0.5033 (tt0) REVERT: J 20 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: J 175 ASP cc_start: 0.7906 (m-30) cc_final: 0.7497 (m-30) REVERT: J 247 ASP cc_start: 0.7164 (m-30) cc_final: 0.6955 (t0) REVERT: J 265 GLU cc_start: 0.7797 (mp0) cc_final: 0.7546 (mp0) REVERT: K 35 GLU cc_start: 0.7876 (tt0) cc_final: 0.7424 (tt0) REVERT: K 90 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.8325 (p) REVERT: K 167 HIS cc_start: 0.7333 (m-70) cc_final: 0.7044 (m-70) REVERT: K 323 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7664 (tp) REVERT: K 324 GLU cc_start: 0.7659 (tt0) cc_final: 0.7173 (pt0) REVERT: K 327 TRP cc_start: 0.9263 (t-100) cc_final: 0.8625 (t-100) REVERT: K 344 ASN cc_start: 0.8593 (t0) cc_final: 0.8224 (t0) REVERT: L 52 GLU cc_start: 0.5804 (tt0) cc_final: 0.5414 (tt0) REVERT: L 60 MET cc_start: 0.5938 (mpp) cc_final: 0.5454 (mpp) outliers start: 81 outliers final: 68 residues processed: 559 average time/residue: 0.1685 time to fit residues: 161.2785 Evaluate side-chains 568 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 492 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 153 THR 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 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain D residue 47 ILE 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 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 188 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 291 LEU 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 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 6 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 90 SER 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 123 GLU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 20 GLU 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 274 VAL 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 375 VAL Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 90 SER 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 291 LEU Chi-restraints excluded: chain K residue 323 LEU Chi-restraints excluded: chain K residue 376 MET Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain L residue 56 VAL 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 118 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 390 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 31 optimal weight: 0.5980 chunk 340 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 212 optimal weight: 0.4980 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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** D 130 GLN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 HIS H 302 ASN ** H 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 ASN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148988 restraints weight = 46746.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.152203 restraints weight = 27068.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.154151 restraints weight = 19111.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.155292 restraints weight = 14929.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155725 restraints weight = 13198.819| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 35652 Z= 0.168 Angle : 0.619 19.961 48608 Z= 0.319 Chirality : 0.049 1.054 5360 Planarity : 0.005 0.045 6272 Dihedral : 5.064 57.871 4976 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.37 % Favored : 95.60 % Rotamer: Outliers : 2.32 % Allowed : 18.68 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.13), residues: 4436 helix: 1.90 (0.24), residues: 492 sheet: -0.07 (0.14), residues: 1328 loop : -0.39 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 310 TYR 0.027 0.002 TYR A 46 PHE 0.024 0.002 PHE J 95 TRP 0.036 0.001 TRP K 233 HIS 0.010 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00395 (35548) covalent geometry : angle 0.59985 (48392) SS BOND : bond 0.00329 ( 96) SS BOND : angle 1.22285 ( 192) hydrogen bonds : bond 0.03631 ( 1150) hydrogen bonds : angle 5.60887 ( 2880) link_NAG-ASN : bond 0.00916 ( 8) link_NAG-ASN : angle 6.24269 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5478.39 seconds wall clock time: 95 minutes 32.13 seconds (5732.13 seconds total)