Starting phenix.real_space_refine on Sun Aug 9 08:57:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ufb_42190/08_2026/8ufb_42190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufb_42190/08_2026/8ufb_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_2026/8ufb_42190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufb_42190/08_2026/8ufb_42190.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ufb_42190/08_2026/8ufb_42190.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ufb_42190/08_2026/8ufb_42190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ufb_42190/08_2026/8ufb_42190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufb_42190/08_2026/8ufb_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 8.50, per 1000 atoms: 0.25 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: 3.61 Conformation dependent library (CDL) restraints added in 1.8 seconds 8872 Ramachandran restraints generated. 4436 Oldfield, 0 Emsley, 4436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8256 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 90 sheets defined 16.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 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: 9.39 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11372 1.35 - 1.47: 8362 1.47 - 1.59: 15506 1.59 - 1.71: 0 1.71 - 1.83: 308 Bond restraints: 35548 Sorted by residual: bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" N ALA V 31 " pdb=" CA ALA V 31 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 bond pdb=" C1 NAG K 501 " pdb=" O5 NAG K 501 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" N ALA Y 31 " pdb=" CA ALA Y 31 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 bond pdb=" N ALA W 31 " pdb=" CA ALA W 31 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 ... (remaining 35543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 46139 1.20 - 2.40: 1773 2.40 - 3.60: 422 3.60 - 4.81: 54 4.81 - 6.01: 4 Bond angle restraints: 48392 Sorted by residual: angle pdb=" N GLU B 244 " pdb=" CA GLU B 244 " pdb=" C GLU B 244 " ideal model delta sigma weight residual 110.23 114.32 -4.09 1.45e+00 4.76e-01 7.94e+00 angle pdb=" C GLY B 243 " pdb=" N GLU B 244 " pdb=" CA GLU B 244 " ideal model delta sigma weight residual 120.71 124.54 -3.83 1.42e+00 4.96e-01 7.29e+00 angle pdb=" CA TYR J 309 " pdb=" CB TYR J 309 " pdb=" CG TYR J 309 " ideal model delta sigma weight residual 113.90 118.59 -4.69 1.80e+00 3.09e-01 6.78e+00 angle pdb=" CB ARG B 239 " pdb=" CG ARG B 239 " pdb=" CD ARG B 239 " ideal model delta sigma weight residual 111.30 117.04 -5.74 2.30e+00 1.89e-01 6.22e+00 angle pdb=" N TYR B 98 " pdb=" CA TYR B 98 " pdb=" C TYR B 98 " ideal model delta sigma weight residual 109.24 113.24 -4.00 1.63e+00 3.76e-01 6.03e+00 ... (remaining 48387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 20625 17.67 - 35.34: 701 35.34 - 53.02: 172 53.02 - 70.69: 40 70.69 - 88.36: 14 Dihedral angle restraints: 21552 sinusoidal: 8660 harmonic: 12892 Sorted by residual: dihedral pdb=" CB CYS J 329 " pdb=" SG CYS J 329 " pdb=" SG CYS J 371 " pdb=" CB CYS J 371 " ideal model delta sinusoidal sigma weight residual 93.00 146.87 -53.87 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CB CYS X 52 " pdb=" SG CYS X 52 " pdb=" SG CYS X 67 " pdb=" CB CYS X 67 " ideal model delta sinusoidal sigma weight residual 93.00 141.92 -48.92 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS V 52 " pdb=" SG CYS V 52 " pdb=" SG CYS V 67 " pdb=" CB CYS V 67 " ideal model delta sinusoidal sigma weight residual 93.00 137.29 -44.29 1 1.00e+01 1.00e-02 2.73e+01 ... (remaining 21549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3563 0.037 - 0.074: 1172 0.074 - 0.110: 452 0.110 - 0.147: 169 0.147 - 0.184: 4 Chirality restraints: 5360 Sorted by residual: chirality pdb=" C1 NAG K 501 " pdb=" ND2 ASN K 315 " pdb=" C2 NAG K 501 " pdb=" O5 NAG K 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CB ILE B 31 " pdb=" CA ILE B 31 " pdb=" CG1 ILE B 31 " pdb=" CG2 ILE B 31 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA ILE H 99 " pdb=" N ILE H 99 " pdb=" C ILE H 99 " pdb=" CB ILE H 99 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 5357 not shown) Planarity restraints: 6280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 239 " -0.317 9.50e-02 1.11e+02 1.42e-01 1.28e+01 pdb=" NE ARG B 239 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 239 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 239 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 239 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 84 " 0.231 9.50e-02 1.11e+02 1.04e-01 7.50e+00 pdb=" NE ARG B 84 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 84 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 84 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 84 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 110 " 0.211 9.50e-02 1.11e+02 9.54e-02 6.93e+00 pdb=" NE ARG D 110 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG D 110 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D 110 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 110 " 0.001 2.00e-02 2.50e+03 ... (remaining 6277 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3193 2.75 - 3.28: 33573 3.28 - 3.82: 56654 3.82 - 4.36: 68302 4.36 - 4.90: 120066 Nonbonded interactions: 281788 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 63 " pdb="CA CA Y 801 " model vdw 2.207 2.510 nonbonded pdb=" OD1 ASP Y 53 " pdb="CA CA Y 801 " model vdw 2.238 2.510 nonbonded pdb=" O TRP V 89 " pdb="CA CA V 802 " model vdw 2.247 2.510 nonbonded pdb=" O LYS H 398 " pdb=" NH1 ARG L 22 " model vdw 2.255 3.120 nonbonded pdb=" OG SER U 248 " pdb=" OE1 GLU U 250 " model vdw 2.269 3.040 ... (remaining 281783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 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: 1.710 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: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 36.120 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 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 are 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/Z covalent geometry : bond 0.00263 / 0.12 (35548) covalent geometry : angle 0.57186 / 0.31 (48392) SS BOND : bond 0.00315 / 0.21 ( 96) SS BOND : angle 0.97248 / 0.66 ( 192) hydrogen bonds : bond 0.19483 / 12.98 ( 1150) hydrogen bonds : angle 8.23080 / 5.67 ( 2880) link_NAG-ASN : bond 0.00315 / 0.15 ( 8) link_NAG-ASN : angle 2.19116 / 1.20 ( 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 : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 PHE cc_start: 0.7043 (m-80) cc_final: 0.6839 (m-80) REVERT: A 132 MET cc_start: 0.8063 (tpp) cc_final: 0.7804 (tpp) REVERT: A 171 TRP cc_start: 0.6890 (t60) cc_final: 0.6189 (t-100) REVERT: A 304 ILE cc_start: 0.8661 (mm) cc_final: 0.8249 (mt) REVERT: A 380 ASP cc_start: 0.6017 (m-30) cc_final: 0.5736 (m-30) REVERT: B 230 ASN cc_start: 0.7878 (m-40) cc_final: 0.7649 (m-40) REVERT: D 111 SER cc_start: 0.8854 (p) cc_final: 0.8650 (t) REVERT: D 136 THR cc_start: 0.8308 (t) cc_final: 0.7984 (m) REVERT: D 252 LEU cc_start: 0.8129 (tp) cc_final: 0.7798 (tp) REVERT: D 333 SER cc_start: 0.8838 (t) cc_final: 0.8326 (p) REVERT: E 64 TYR cc_start: 0.7857 (m-80) cc_final: 0.7390 (m-80) REVERT: E 136 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7801 (mt-10) REVERT: E 266 THR cc_start: 0.7532 (p) cc_final: 0.7287 (p) REVERT: E 291 LEU cc_start: 0.8949 (tp) cc_final: 0.8743 (tp) REVERT: E 302 ASN cc_start: 0.8083 (t0) cc_final: 0.7879 (t0) REVERT: E 326 THR cc_start: 0.9120 (m) cc_final: 0.8787 (p) REVERT: E 334 ARG cc_start: 0.8312 (mtt180) cc_final: 0.8039 (mtt90) REVERT: F 65 LEU cc_start: 0.5560 (mt) cc_final: 0.5305 (mt) REVERT: G 174 PHE cc_start: 0.6821 (m-80) cc_final: 0.6382 (m-80) REVERT: G 277 ILE cc_start: 0.8266 (mt) cc_final: 0.8017 (mt) REVERT: G 299 ASP cc_start: 0.6747 (t0) cc_final: 0.6499 (t0) REVERT: J 11 VAL cc_start: 0.8664 (t) cc_final: 0.8059 (t) REVERT: J 134 ASN cc_start: 0.7092 (t0) cc_final: 0.6791 (t0) REVERT: K 219 ASP cc_start: 0.7101 (t0) cc_final: 0.6756 (t0) REVERT: K 307 TRP cc_start: 0.7722 (m100) cc_final: 0.7179 (m100) outliers start: 0 outliers final: 0 residues processed: 1000 average time/residue: 0.2037 time to fit residues: 337.2150 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 : 1.512 ------------------------------------------------------------------------------- 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: 0.9980 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: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 275 HIS F 37 GLN F 80 HIS F 88 ASN ** G 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 ASN G 219 ASN G 231 HIS H 80 ASN H 114 HIS H 160 GLN H 162 HIS H 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 222 GLN K 253 HIS K 402 ASN V 42 ASN X 42 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.206582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153210 restraints weight = 45829.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154762 restraints weight = 29935.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.157633 restraints weight = 19908.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.158575 restraints weight = 15019.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.159296 restraints weight = 12965.202| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 35652 Z= 0.320 Angle : 0.815 11.701 48608 Z= 0.433 Chirality : 0.053 0.250 5360 Planarity : 0.006 0.059 6272 Dihedral : 5.544 59.949 4976 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.76 % Allowed : 8.23 % Favored : 88.01 % 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 are not related in a simple way. whole: 0.58 (0.12), residues: 4436 helix: 1.62 (0.23), residues: 476 sheet: 0.24 (0.14), residues: 1336 loop : 0.35 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 157 TYR 0.027 0.003 TYR G 122 PHE 0.027 0.003 PHE K 113 TRP 0.028 0.003 TRP B 327 HIS 0.026 0.003 HIS B 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.32 (35548) covalent geometry : angle 0.79957 / 0.43 (48392) SS BOND : bond 0.00723 / 0.51 ( 96) SS BOND : angle 1.91769 / 1.41 ( 192) hydrogen bonds : bond 0.05244 / 3.53 ( 1150) hydrogen bonds : angle 6.51369 / 4.46 ( 2880) link_NAG-ASN : bond 0.00844 / 0.42 ( 8) link_NAG-ASN : angle 5.16819 / 2.94 ( 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: 144 poor density : 659 time to evaluate : 1.252 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 51 TYR cc_start: 0.7778 (p90) cc_final: 0.7543 (p90) REVERT: A 81 PHE cc_start: 0.8606 (m-80) cc_final: 0.8320 (m-80) REVERT: A 171 TRP cc_start: 0.8154 (t60) cc_final: 0.6885 (t-100) REVERT: A 214 LEU cc_start: 0.8668 (tp) cc_final: 0.8446 (tp) REVERT: A 217 ASN cc_start: 0.8463 (t0) cc_final: 0.8158 (t0) REVERT: A 378 LYS cc_start: 0.7526 (mttt) cc_final: 0.7127 (mtmt) REVERT: B 8 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: B 168 GLN cc_start: 0.8723 (tp40) cc_final: 0.8324 (tp-100) REVERT: B 270 GLU cc_start: 0.8333 (tp30) cc_final: 0.8096 (mm-30) REVERT: B 300 ASP cc_start: 0.7285 (t0) cc_final: 0.6971 (t0) REVERT: B 342 GLU cc_start: 0.7728 (tp30) cc_final: 0.7527 (tp30) REVERT: C 60 MET cc_start: 0.3884 (mmm) cc_final: 0.3209 (mmm) REVERT: D 30 GLN cc_start: 0.8745 (tt0) cc_final: 0.8336 (tt0) REVERT: D 51 TYR cc_start: 0.8842 (p90) cc_final: 0.8550 (p90) REVERT: D 113 GLU cc_start: 0.8328 (mp0) cc_final: 0.7792 (mp0) REVERT: D 143 ARG cc_start: 0.6869 (mmm-85) cc_final: 0.6519 (mtt-85) REVERT: D 205 GLN cc_start: 0.8380 (mt0) cc_final: 0.7873 (mm-40) REVERT: D 252 LEU cc_start: 0.8496 (tp) cc_final: 0.8256 (tp) REVERT: E 64 TYR cc_start: 0.7940 (m-80) cc_final: 0.7060 (m-80) REVERT: E 136 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8113 (mt-10) REVERT: E 175 HIS cc_start: 0.6628 (p90) cc_final: 0.6406 (p90) REVERT: E 276 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7952 (mtpt) REVERT: E 291 LEU cc_start: 0.9396 (tp) cc_final: 0.8830 (tp) REVERT: E 302 ASN cc_start: 0.9150 (t0) cc_final: 0.8631 (t0) REVERT: E 310 ARG cc_start: 0.8426 (ptt90) cc_final: 0.7911 (ptp90) REVERT: E 326 THR cc_start: 0.9301 (m) cc_final: 0.8895 (p) REVERT: E 327 TRP cc_start: 0.8946 (t-100) cc_final: 0.7071 (t-100) REVERT: E 334 ARG cc_start: 0.8511 (mtt180) cc_final: 0.8076 (mtt90) REVERT: F 15 TYR cc_start: 0.4038 (m-80) cc_final: 0.3561 (m-80) REVERT: F 88 ASN cc_start: 0.6057 (OUTLIER) cc_final: 0.5824 (m-40) REVERT: F 101 ASP cc_start: 0.5236 (m-30) cc_final: 0.4459 (m-30) REVERT: G 24 TYR cc_start: 0.5985 (m-80) cc_final: 0.5505 (m-80) REVERT: G 75 ASP cc_start: 0.8926 (t0) cc_final: 0.8586 (t0) REVERT: G 205 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8455 (mm-40) REVERT: G 206 SER cc_start: 0.9166 (t) cc_final: 0.8935 (m) REVERT: G 342 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6711 (mm-30) REVERT: G 361 ASN cc_start: 0.8331 (m-40) cc_final: 0.8068 (m-40) REVERT: G 397 GLU cc_start: 0.7972 (tt0) cc_final: 0.7735 (tt0) REVERT: H 52 MET cc_start: 0.7544 (tpp) cc_final: 0.7028 (tpp) REVERT: H 251 LYS cc_start: 0.7647 (mtpt) cc_final: 0.7418 (mtpt) REVERT: J 32 GLN cc_start: 0.8436 (tt0) cc_final: 0.8141 (tt0) REVERT: J 175 ASP cc_start: 0.8217 (m-30) cc_final: 0.7576 (m-30) REVERT: J 187 ASN cc_start: 0.9064 (m-40) cc_final: 0.8598 (m-40) REVERT: J 279 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7562 (tt) REVERT: J 285 ASP cc_start: 0.8166 (m-30) cc_final: 0.7793 (t70) REVERT: J 382 LYS cc_start: 0.8156 (ptpp) cc_final: 0.7809 (mtpt) REVERT: K 35 GLU cc_start: 0.8108 (tt0) cc_final: 0.7735 (tt0) REVERT: K 84 ARG cc_start: 0.8283 (ptt90) cc_final: 0.7895 (ptt-90) REVERT: K 126 HIS cc_start: 0.8504 (t-170) cc_final: 0.8271 (t-170) REVERT: K 344 ASN cc_start: 0.8197 (t0) cc_final: 0.7775 (t0) REVERT: K 348 TRP cc_start: 0.6576 (m100) cc_final: 0.6372 (m100) REVERT: L 87 ASN cc_start: 0.5220 (p0) cc_final: 0.4989 (p0) REVERT: L 118 LEU cc_start: 0.4703 (tt) cc_final: 0.4478 (tp) outliers start: 144 outliers final: 86 residues processed: 744 average time/residue: 0.1941 time to fit residues: 243.8755 Evaluate side-chains 622 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 532 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 20 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 88 ASN Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 205 GLN 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 114 VAL Chi-restraints excluded: chain I residue 144 THR Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 126 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain K residue 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 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 234 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 206 optimal weight: 10.0000 chunk 384 optimal weight: 7.9990 chunk 390 optimal weight: 20.0000 chunk 261 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 224 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 329 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 410 optimal weight: 30.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS D 253 ASN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN F 79 HIS F 88 ASN F 136 GLN G 73 HIS G 219 ASN 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** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.204375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150371 restraints weight = 45850.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.152233 restraints weight = 29819.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.155174 restraints weight = 19326.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.157438 restraints weight = 14127.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.157411 restraints weight = 12377.816| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 35652 Z= 0.190 Angle : 0.622 10.383 48608 Z= 0.329 Chirality : 0.047 0.188 5360 Planarity : 0.005 0.052 6272 Dihedral : 5.126 55.548 4976 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.45 % Allowed : 11.52 % Favored : 85.03 % 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 are not related in a simple way. whole: 0.59 (0.13), residues: 4436 helix: 1.83 (0.24), residues: 476 sheet: 0.33 (0.14), residues: 1308 loop : 0.27 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 26 TYR 0.023 0.002 TYR J 309 PHE 0.019 0.002 PHE G 95 TRP 0.017 0.001 TRP H 327 HIS 0.013 0.001 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (35548) covalent geometry : angle 0.60951 / 0.33 (48392) SS BOND : bond 0.00549 / 0.37 ( 96) SS BOND : angle 1.62677 / 1.16 ( 192) hydrogen bonds : bond 0.04228 / 2.88 ( 1150) hydrogen bonds : angle 6.11902 / 4.19 ( 2880) link_NAG-ASN : bond 0.00461 / 0.23 ( 8) link_NAG-ASN : angle 3.78622 / 2.22 ( 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 709 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 577 time to evaluate : 1.170 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 7 MET cc_start: 0.7806 (ptm) cc_final: 0.7431 (ptp) REVERT: A 51 TYR cc_start: 0.7564 (p90) cc_final: 0.7170 (p90) REVERT: A 81 PHE cc_start: 0.8645 (m-80) cc_final: 0.8336 (m-80) REVERT: A 171 TRP cc_start: 0.8136 (t60) cc_final: 0.6861 (t-100) REVERT: A 217 ASN cc_start: 0.8520 (t0) cc_final: 0.8244 (t0) REVERT: A 378 LYS cc_start: 0.7465 (mttt) cc_final: 0.7040 (mtmt) REVERT: B 8 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7610 (mp10) REVERT: B 168 GLN cc_start: 0.8714 (tp40) cc_final: 0.7974 (tp-100) REVERT: B 229 ASP cc_start: 0.5171 (t0) cc_final: 0.4921 (t0) REVERT: B 270 GLU cc_start: 0.8314 (tp30) cc_final: 0.8107 (mm-30) REVERT: B 300 ASP cc_start: 0.7328 (t0) cc_final: 0.7121 (t0) REVERT: B 342 GLU cc_start: 0.7724 (tp30) cc_final: 0.7496 (tp30) REVERT: C 7 MET cc_start: 0.6159 (mpp) cc_final: 0.4813 (mmp) REVERT: C 60 MET cc_start: 0.3806 (mmm) cc_final: 0.3105 (mmm) REVERT: D 30 GLN cc_start: 0.8664 (tt0) cc_final: 0.8169 (tt0) REVERT: D 51 TYR cc_start: 0.8835 (p90) cc_final: 0.8422 (p90) REVERT: D 143 ARG cc_start: 0.6775 (mmm-85) cc_final: 0.6278 (mmt-90) REVERT: D 252 LEU cc_start: 0.8503 (tp) cc_final: 0.8241 (tp) REVERT: E 136 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8095 (mt-10) REVERT: E 175 HIS cc_start: 0.6726 (p90) cc_final: 0.6479 (p90) REVERT: E 276 LYS cc_start: 0.8201 (mmtt) cc_final: 0.7990 (mtpt) REVERT: E 291 LEU cc_start: 0.9330 (tp) cc_final: 0.8904 (tp) REVERT: E 302 ASN cc_start: 0.9162 (t0) cc_final: 0.8661 (t0) REVERT: E 310 ARG cc_start: 0.8496 (ptt90) cc_final: 0.7919 (ptp90) REVERT: E 327 TRP cc_start: 0.8933 (t-100) cc_final: 0.7064 (t-100) REVERT: E 334 ARG cc_start: 0.8377 (mtt180) cc_final: 0.7806 (mtt90) REVERT: E 336 TRP cc_start: 0.8812 (m-90) cc_final: 0.8306 (m-10) REVERT: E 340 SER cc_start: 0.8852 (t) cc_final: 0.8581 (t) REVERT: F 15 TYR cc_start: 0.3941 (m-80) cc_final: 0.3439 (m-80) REVERT: F 88 ASN cc_start: 0.5885 (OUTLIER) cc_final: 0.5319 (m-40) REVERT: F 101 ASP cc_start: 0.4452 (m-30) cc_final: 0.4134 (m-30) REVERT: G 24 TYR cc_start: 0.6080 (m-80) cc_final: 0.5536 (m-80) REVERT: G 75 ASP cc_start: 0.8894 (t0) cc_final: 0.8460 (t0) REVERT: G 152 GLU cc_start: 0.7292 (tp30) cc_final: 0.7040 (tp30) REVERT: G 223 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8513 (mm-40) REVERT: G 342 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6775 (mm-30) REVERT: G 361 ASN cc_start: 0.8551 (m-40) cc_final: 0.8136 (m-40) REVERT: G 391 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7332 (p90) REVERT: H 69 ASN cc_start: 0.6880 (t0) cc_final: 0.6180 (p0) REVERT: H 290 THR cc_start: 0.9149 (m) cc_final: 0.8527 (p) REVERT: J 32 GLN cc_start: 0.8421 (tt0) cc_final: 0.8064 (tt0) REVERT: J 156 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6246 (mmtt) REVERT: J 247 ASP cc_start: 0.6879 (t0) cc_final: 0.6563 (t0) REVERT: J 279 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7746 (tt) REVERT: J 285 ASP cc_start: 0.8438 (m-30) cc_final: 0.7885 (t70) REVERT: J 299 ASP cc_start: 0.7871 (t0) cc_final: 0.7663 (t0) REVERT: J 382 LYS cc_start: 0.8161 (ptpp) cc_final: 0.7902 (mtpp) REVERT: K 35 GLU cc_start: 0.7929 (tt0) cc_final: 0.7580 (tt0) REVERT: K 79 ASP cc_start: 0.7390 (t0) cc_final: 0.7160 (t0) REVERT: K 256 PHE cc_start: 0.9173 (m-80) cc_final: 0.8739 (m-10) REVERT: K 344 ASN cc_start: 0.8312 (t0) cc_final: 0.7864 (t0) REVERT: L 60 MET cc_start: 0.6054 (mpp) cc_final: 0.5697 (mpp) REVERT: L 67 TYR cc_start: 0.6890 (p90) cc_final: 0.6550 (p90) outliers start: 132 outliers final: 89 residues processed: 653 average time/residue: 0.1874 time to fit residues: 209.7858 Evaluate side-chains 613 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 519 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 335 SER 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 B residue 318 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 88 ASN 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 300 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 401 SER 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 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 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 149 VAL Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 372 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 400 optimal weight: 4.9990 chunk 385 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 69.4343 > 50:) chunk 374 optimal weight: 3.9990 chunk 403 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 376 optimal weight: 1.9990 chunk 377 optimal weight: 1.9990 chunk 260 optimal weight: 0.0970 chunk 83 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 69 ASN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 213 HIS ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS F 37 GLN G 183 HIS K 102 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.203162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149327 restraints weight = 45977.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.152175 restraints weight = 29971.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154770 restraints weight = 18792.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155675 restraints weight = 13756.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.155830 restraints weight = 12992.549| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 35652 Z= 0.184 Angle : 0.634 27.326 48608 Z= 0.327 Chirality : 0.046 0.274 5360 Planarity : 0.005 0.047 6272 Dihedral : 5.224 57.147 4976 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.87 % Allowed : 12.33 % Favored : 83.80 % 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 are not related in a simple way. whole: 0.40 (0.13), residues: 4436 helix: 1.92 (0.24), residues: 476 sheet: 0.13 (0.14), residues: 1324 loop : 0.12 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 119 TYR 0.024 0.002 TYR D 321 PHE 0.016 0.002 PHE F 24 TRP 0.031 0.001 TRP T 256 HIS 0.010 0.001 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (35548) covalent geometry : angle 0.60582 / 0.32 (48392) SS BOND : bond 0.00399 / 0.28 ( 96) SS BOND : angle 1.54539 / 1.08 ( 192) hydrogen bonds : bond 0.03947 / 2.68 ( 1150) hydrogen bonds : angle 5.93241 / 4.06 ( 2880) link_NAG-ASN : bond 0.00554 / 0.28 ( 8) link_NAG-ASN : angle 7.47264 / 4.20 ( 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 713 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 565 time to evaluate : 1.235 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: A 7 MET cc_start: 0.7821 (ptm) cc_final: 0.7448 (ptp) REVERT: A 171 TRP cc_start: 0.8253 (t60) cc_final: 0.7452 (t-100) REVERT: A 217 ASN cc_start: 0.8507 (t0) cc_final: 0.8189 (t0) REVERT: A 367 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7688 (mtpp) REVERT: A 378 LYS cc_start: 0.7518 (mttt) cc_final: 0.7084 (mtmt) REVERT: B 8 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: B 61 ASP cc_start: 0.6815 (t0) cc_final: 0.5552 (p0) REVERT: B 168 GLN cc_start: 0.8789 (tt0) cc_final: 0.8245 (tp-100) REVERT: B 232 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8105 (mmmm) REVERT: B 270 GLU cc_start: 0.8387 (tp30) cc_final: 0.8183 (mm-30) REVERT: B 300 ASP cc_start: 0.7351 (t0) cc_final: 0.7101 (t0) REVERT: C 60 MET cc_start: 0.3989 (mmm) cc_final: 0.3258 (mmm) REVERT: D 30 GLN cc_start: 0.8757 (tt0) cc_final: 0.8362 (tt0) REVERT: D 51 TYR cc_start: 0.8880 (p90) cc_final: 0.8242 (p90) REVERT: D 143 ARG cc_start: 0.6741 (mmm-85) cc_final: 0.6339 (mmt-90) REVERT: D 252 LEU cc_start: 0.8469 (tp) cc_final: 0.8265 (tp) REVERT: E 35 GLU cc_start: 0.7949 (tt0) cc_final: 0.7743 (tt0) REVERT: E 136 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8099 (mt-10) REVERT: E 166 MET cc_start: 0.7726 (ptm) cc_final: 0.7436 (ptp) REVERT: E 175 HIS cc_start: 0.6734 (p90) cc_final: 0.6455 (p90) REVERT: E 302 ASN cc_start: 0.9170 (t0) cc_final: 0.8639 (t0) REVERT: E 310 ARG cc_start: 0.8508 (ptt90) cc_final: 0.8063 (ptp90) REVERT: E 327 TRP cc_start: 0.8932 (t-100) cc_final: 0.7069 (t-100) REVERT: E 334 ARG cc_start: 0.8364 (mtt180) cc_final: 0.8135 (mtt90) REVERT: E 336 TRP cc_start: 0.8765 (m-90) cc_final: 0.8249 (m-10) REVERT: E 340 SER cc_start: 0.8899 (t) cc_final: 0.8657 (t) REVERT: F 15 TYR cc_start: 0.4128 (m-80) cc_final: 0.3627 (m-80) REVERT: F 101 ASP cc_start: 0.4841 (m-30) cc_final: 0.4536 (m-30) REVERT: G 24 TYR cc_start: 0.6152 (m-80) cc_final: 0.5587 (m-80) REVERT: G 254 ASP cc_start: 0.8479 (t70) cc_final: 0.8072 (t0) REVERT: G 342 GLU cc_start: 0.7557 (mt-10) cc_final: 0.6895 (mm-30) REVERT: G 361 ASN cc_start: 0.8520 (m-40) cc_final: 0.8148 (m-40) REVERT: G 391 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7276 (p90) REVERT: H 69 ASN cc_start: 0.6986 (t0) cc_final: 0.6304 (p0) REVERT: H 290 THR cc_start: 0.9156 (m) cc_final: 0.8552 (p) REVERT: J 32 GLN cc_start: 0.8351 (tt0) cc_final: 0.7982 (tt0) REVERT: J 156 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6311 (mmtt) REVERT: J 175 ASP cc_start: 0.7990 (m-30) cc_final: 0.7642 (m-30) REVERT: J 247 ASP cc_start: 0.6954 (t0) cc_final: 0.6663 (t0) REVERT: J 279 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7677 (tt) REVERT: J 299 ASP cc_start: 0.7920 (t0) cc_final: 0.7694 (t0) REVERT: J 382 LYS cc_start: 0.8190 (ptpp) cc_final: 0.7892 (mtpp) REVERT: K 35 GLU cc_start: 0.7952 (tt0) cc_final: 0.7614 (tt0) REVERT: K 50 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8886 (p) REVERT: K 79 ASP cc_start: 0.7398 (t0) cc_final: 0.7120 (t0) REVERT: K 256 PHE cc_start: 0.9147 (m-80) cc_final: 0.8822 (m-10) REVERT: K 344 ASN cc_start: 0.8375 (t0) cc_final: 0.7856 (t0) REVERT: L 60 MET cc_start: 0.6145 (mpp) cc_final: 0.5837 (mpp) REVERT: L 67 TYR cc_start: 0.6931 (p90) cc_final: 0.6573 (p90) outliers start: 148 outliers final: 113 residues processed: 647 average time/residue: 0.1831 time to fit residues: 204.9030 Evaluate side-chains 641 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 522 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 66 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 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 335 SER Chi-restraints excluded: chain A residue 367 LYS 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 85 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR 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 289 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain E residue 296 SER Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 62 CYS 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 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 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 309 GLU Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 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 279 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 372 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 227 LEU Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 324 GLU 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 83 VAL Chi-restraints excluded: chain L residue 116 ILE Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain L residue 139 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 221 optimal weight: 2.9990 chunk 294 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 242 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 428 optimal weight: 20.0000 chunk 256 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 ASN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 ASN H 285 HIS I 28 HIS J 28 HIS ** J 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN K 402 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.200022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146726 restraints weight = 46596.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.148809 restraints weight = 31688.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.151545 restraints weight = 19769.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154094 restraints weight = 14067.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.154067 restraints weight = 12545.048| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 35652 Z= 0.221 Angle : 0.651 22.323 48608 Z= 0.339 Chirality : 0.048 0.268 5360 Planarity : 0.005 0.061 6272 Dihedral : 5.271 58.353 4976 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.44 % Allowed : 13.01 % Favored : 82.55 % 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 are not related in a simple way. whole: 0.05 (0.13), residues: 4436 helix: 1.62 (0.24), residues: 500 sheet: -0.09 (0.14), residues: 1344 loop : -0.13 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 119 TYR 0.024 0.002 TYR B 235 PHE 0.017 0.002 PHE D 288 TRP 0.017 0.002 TRP H 327 HIS 0.035 0.002 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (35548) covalent geometry : angle 0.62937 / 0.33 (48392) SS BOND : bond 0.00428 / 0.30 ( 96) SS BOND : angle 1.49379 / 1.05 ( 192) hydrogen bonds : bond 0.04123 / 2.78 ( 1150) hydrogen bonds : angle 5.91378 / 4.05 ( 2880) link_NAG-ASN : bond 0.00799 / 0.38 ( 8) link_NAG-ASN : angle 6.41837 / 3.63 ( 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 703 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 533 time to evaluate : 1.214 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 7 MET cc_start: 0.7853 (ptm) cc_final: 0.7489 (ptp) REVERT: A 20 GLU cc_start: 0.8417 (pm20) cc_final: 0.7885 (pm20) REVERT: A 120 LYS cc_start: 0.8290 (mttt) cc_final: 0.7894 (mttp) REVERT: A 136 THR cc_start: 0.7264 (OUTLIER) cc_final: 0.6670 (m) REVERT: A 171 TRP cc_start: 0.8334 (t60) cc_final: 0.7296 (t-100) REVERT: A 217 ASN cc_start: 0.8570 (t0) cc_final: 0.8223 (t0) REVERT: A 367 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7677 (mtpp) REVERT: A 378 LYS cc_start: 0.7633 (mttt) cc_final: 0.7236 (mtmt) REVERT: A 403 ILE cc_start: 0.8654 (mt) cc_final: 0.8121 (tt) REVERT: A 421 PHE cc_start: 0.4878 (OUTLIER) cc_final: 0.4382 (t80) REVERT: B 8 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7666 (mp10) REVERT: B 168 GLN cc_start: 0.8746 (tt0) cc_final: 0.8431 (tp-100) REVERT: B 232 LYS cc_start: 0.8409 (mmtt) cc_final: 0.8040 (mmmm) REVERT: B 270 GLU cc_start: 0.8396 (tp30) cc_final: 0.8166 (mm-30) REVERT: B 300 ASP cc_start: 0.7446 (t0) cc_final: 0.7226 (t0) REVERT: B 339 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6804 (mm-30) REVERT: B 394 ILE cc_start: 0.8093 (pt) cc_final: 0.7687 (tp) REVERT: C 7 MET cc_start: 0.6266 (mpp) cc_final: 0.4833 (mmp) REVERT: C 60 MET cc_start: 0.4127 (mmm) cc_final: 0.3604 (mmm) REVERT: D 30 GLN cc_start: 0.8666 (tt0) cc_final: 0.8426 (tt0) REVERT: D 143 ARG cc_start: 0.6806 (mmm-85) cc_final: 0.6386 (mmt-90) REVERT: E 136 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8144 (mt-10) REVERT: E 175 HIS cc_start: 0.6963 (p90) cc_final: 0.6705 (p90) REVERT: E 302 ASN cc_start: 0.9155 (t0) cc_final: 0.8611 (t0) REVERT: E 310 ARG cc_start: 0.8476 (ptt90) cc_final: 0.8078 (ptp90) REVERT: E 327 TRP cc_start: 0.8907 (t-100) cc_final: 0.7072 (t-100) REVERT: E 334 ARG cc_start: 0.8644 (mtt180) cc_final: 0.8138 (mtt90) REVERT: E 336 TRP cc_start: 0.8767 (m-90) cc_final: 0.8305 (m-10) REVERT: F 15 TYR cc_start: 0.4289 (m-80) cc_final: 0.3778 (m-80) REVERT: F 88 ASN cc_start: 0.6288 (OUTLIER) cc_final: 0.6017 (m-40) REVERT: F 101 ASP cc_start: 0.5078 (m-30) cc_final: 0.4753 (m-30) REVERT: G 152 GLU cc_start: 0.7271 (tp30) cc_final: 0.6732 (tp30) REVERT: G 254 ASP cc_start: 0.8256 (t70) cc_final: 0.7957 (t0) REVERT: G 299 ASP cc_start: 0.7423 (t0) cc_final: 0.6778 (t0) REVERT: G 361 ASN cc_start: 0.8580 (m-40) cc_final: 0.8202 (m-40) REVERT: G 391 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7303 (p90) REVERT: H 69 ASN cc_start: 0.7013 (t0) cc_final: 0.6303 (p0) REVERT: H 290 THR cc_start: 0.9208 (m) cc_final: 0.8644 (p) REVERT: J 32 GLN cc_start: 0.8254 (tt0) cc_final: 0.7897 (tt0) REVERT: J 156 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6346 (mmtt) REVERT: J 247 ASP cc_start: 0.6935 (t0) cc_final: 0.6673 (t0) REVERT: J 382 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7388 (mptt) REVERT: K 35 GLU cc_start: 0.7960 (tt0) cc_final: 0.7603 (tt0) REVERT: K 52 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7048 (ttm) REVERT: K 327 TRP cc_start: 0.9288 (t-100) cc_final: 0.8513 (t-100) REVERT: K 344 ASN cc_start: 0.8479 (t0) cc_final: 0.8058 (t0) REVERT: L 60 MET cc_start: 0.6238 (mpp) cc_final: 0.5806 (mpp) REVERT: L 67 TYR cc_start: 0.7022 (p90) cc_final: 0.6620 (p90) outliers start: 170 outliers final: 132 residues processed: 635 average time/residue: 0.1790 time to fit residues: 195.9812 Evaluate side-chains 632 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 492 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 66 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 73 GLN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 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 75 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain E residue 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 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 88 ASN 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 62 CYS Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 313 THR Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 337 VAL Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 375 VAL Chi-restraints excluded: chain J residue 388 ILE Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 107 ASP Chi-restraints excluded: chain K residue 143 GLU Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 172 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 257 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 326 THR Chi-restraints excluded: chain K residue 376 MET Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 27 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 164 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 390 optimal weight: 20.0000 chunk 299 optimal weight: 9.9990 chunk 419 optimal weight: 40.0000 chunk 231 optimal weight: 10.0000 chunk 369 optimal weight: 3.9990 chunk 407 optimal weight: 9.9990 chunk 99 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 HIS ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN D 28 HIS D 219 ASN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN J 205 GLN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN K 402 ASN W 83 GLN W 107 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.198476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.145470 restraints weight = 46343.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.149090 restraints weight = 30431.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.150627 restraints weight = 17738.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.150977 restraints weight = 14849.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.151616 restraints weight = 13841.586| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.006 0.076 35652 Z= 0.239 Angle : 0.665 21.926 48608 Z= 0.346 Chirality : 0.048 0.359 5360 Planarity : 0.005 0.051 6272 Dihedral : 5.342 59.800 4976 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.81 % Allowed : 13.95 % 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 are not related in a simple way. whole: -0.15 (0.13), residues: 4436 helix: 1.54 (0.23), residues: 500 sheet: -0.21 (0.14), residues: 1364 loop : -0.30 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 89 TYR 0.021 0.002 TYR G 309 PHE 0.021 0.002 PHE H 256 TRP 0.016 0.002 TRP H 327 HIS 0.009 0.001 HIS J 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (35548) covalent geometry : angle 0.64358 / 0.34 (48392) SS BOND : bond 0.00465 / 0.32 ( 96) SS BOND : angle 1.47392 / 1.02 ( 192) hydrogen bonds : bond 0.04198 / 2.84 ( 1150) hydrogen bonds : angle 5.96052 / 4.09 ( 2880) link_NAG-ASN : bond 0.00730 / 0.35 ( 8) link_NAG-ASN : angle 6.53235 / 3.74 ( 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 695 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 511 time to evaluate : 1.288 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: 0.7769 (ptm) cc_final: 0.7406 (ptp) REVERT: A 13 ILE cc_start: 0.9292 (mm) cc_final: 0.9080 (mm) REVERT: A 120 LYS cc_start: 0.8214 (mttt) cc_final: 0.7841 (mttp) REVERT: A 136 THR cc_start: 0.7206 (OUTLIER) cc_final: 0.6572 (m) REVERT: A 171 TRP cc_start: 0.8325 (t60) cc_final: 0.7182 (t-100) REVERT: A 217 ASN cc_start: 0.8653 (t0) cc_final: 0.8272 (t0) REVERT: A 367 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7573 (mtpp) REVERT: A 378 LYS cc_start: 0.7702 (mttt) cc_final: 0.7275 (mtmt) REVERT: A 391 TYR cc_start: 0.8984 (OUTLIER) cc_final: 0.7082 (p90) REVERT: A 403 ILE cc_start: 0.8719 (mt) cc_final: 0.8071 (tt) REVERT: A 421 PHE cc_start: 0.4982 (OUTLIER) cc_final: 0.4377 (t80) REVERT: B 8 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7705 (mp10) REVERT: B 61 ASP cc_start: 0.7013 (t0) cc_final: 0.5495 (p0) REVERT: B 168 GLN cc_start: 0.8796 (tt0) cc_final: 0.8503 (tp-100) REVERT: B 232 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8056 (mmmm) REVERT: B 270 GLU cc_start: 0.8359 (tp30) cc_final: 0.8091 (mm-30) REVERT: B 339 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7008 (mm-30) REVERT: C 7 MET cc_start: 0.6206 (mpp) cc_final: 0.5642 (mpp) REVERT: C 60 MET cc_start: 0.4215 (mmm) cc_final: 0.3724 (mmm) REVERT: C 83 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8502 (m) REVERT: C 104 ARG cc_start: 0.5151 (mtt-85) cc_final: 0.4552 (mtt-85) REVERT: D 30 GLN cc_start: 0.8674 (tt0) cc_final: 0.8436 (tt0) REVERT: D 143 ARG cc_start: 0.6801 (mmm-85) cc_final: 0.6300 (mmt-90) REVERT: D 385 LYS cc_start: 0.7798 (tppt) cc_final: 0.7462 (tppt) REVERT: E 136 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8091 (mt-10) REVERT: E 175 HIS cc_start: 0.7041 (p90) cc_final: 0.6756 (p90) REVERT: E 302 ASN cc_start: 0.9158 (t0) cc_final: 0.8617 (t0) REVERT: E 310 ARG cc_start: 0.8507 (ptt90) cc_final: 0.8101 (ptp90) REVERT: E 327 TRP cc_start: 0.8910 (t-100) cc_final: 0.7078 (t-100) REVERT: E 334 ARG cc_start: 0.8589 (mtt180) cc_final: 0.8190 (mtt90) REVERT: F 15 TYR cc_start: 0.4413 (m-80) cc_final: 0.3884 (m-80) REVERT: F 101 ASP cc_start: 0.5255 (m-30) cc_final: 0.4866 (m-30) REVERT: G 67 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6524 (mm-40) REVERT: G 152 GLU cc_start: 0.7258 (tp30) cc_final: 0.6820 (tp30) REVERT: G 299 ASP cc_start: 0.7518 (t0) cc_final: 0.6800 (t0) REVERT: G 361 ASN cc_start: 0.8594 (m-40) cc_final: 0.8266 (m-40) REVERT: G 391 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7293 (p90) REVERT: H 290 THR cc_start: 0.9212 (m) cc_final: 0.8672 (p) REVERT: J 156 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6516 (mmtt) REVERT: J 247 ASP cc_start: 0.7095 (t0) cc_final: 0.6806 (t0) REVERT: K 35 GLU cc_start: 0.8040 (tt0) cc_final: 0.7671 (tt0) REVERT: K 327 TRP cc_start: 0.9313 (t-100) cc_final: 0.8501 (t-100) REVERT: K 344 ASN cc_start: 0.8595 (t0) cc_final: 0.8149 (t0) REVERT: L 52 GLU cc_start: 0.5541 (tt0) cc_final: 0.5276 (tt0) REVERT: L 60 MET cc_start: 0.6177 (mpp) cc_final: 0.5637 (mpp) outliers start: 184 outliers final: 144 residues processed: 631 average time/residue: 0.1897 time to fit residues: 204.1371 Evaluate side-chains 641 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 488 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 107 TYR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 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 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 72 THR 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 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 229 ILE 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 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 75 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 LYS Chi-restraints excluded: chain E residue 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 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 11 VAL 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 300 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 378 LYS Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 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 151 ASN Chi-restraints excluded: chain H residue 197 TYR 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 324 GLU 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 19 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 291 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 408 TRP Chi-restraints excluded: chain J residue 413 VAL Chi-restraints excluded: chain J residue 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 107 ASP 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 180 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 373 optimal weight: 4.9990 chunk 402 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 426 optimal weight: 20.0000 chunk 382 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 HIS ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 HIS ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 ASN G 394 GLN ** G 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 32 GLN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN K 402 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.196081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144198 restraints weight = 47116.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146645 restraints weight = 29521.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.148192 restraints weight = 19856.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.149623 restraints weight = 15641.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.149821 restraints weight = 13904.570| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 35652 Z= 0.309 Angle : 0.746 21.856 48608 Z= 0.390 Chirality : 0.051 0.591 5360 Planarity : 0.006 0.053 6272 Dihedral : 5.687 59.235 4976 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.22 % Allowed : 14.24 % 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 are not related in a simple way. whole: -0.62 (0.12), residues: 4436 helix: 1.05 (0.23), residues: 524 sheet: -0.34 (0.14), residues: 1272 loop : -0.72 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 310 TYR 0.026 0.003 TYR G 309 PHE 0.034 0.003 PHE H 256 TRP 0.020 0.002 TRP H 327 HIS 0.012 0.002 HIS J 332 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.31 (35548) covalent geometry : angle 0.72425 / 0.38 (48392) SS BOND : bond 0.00523 / 0.36 ( 96) SS BOND : angle 1.54387 / 1.09 ( 192) hydrogen bonds : bond 0.04710 / 3.18 ( 1150) hydrogen bonds : angle 6.17685 / 4.25 ( 2880) link_NAG-ASN : bond 0.00855 / 0.42 ( 8) link_NAG-ASN : angle 7.05748 / 4.17 ( 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: 200 poor density : 509 time to evaluate : 1.269 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 120 LYS cc_start: 0.8265 (mttt) cc_final: 0.7920 (mttp) REVERT: A 136 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.6618 (m) REVERT: A 171 TRP cc_start: 0.8364 (t60) cc_final: 0.7163 (t-100) REVERT: A 217 ASN cc_start: 0.8818 (t0) cc_final: 0.8424 (t0) REVERT: A 342 GLU cc_start: 0.8206 (mp0) cc_final: 0.7441 (tt0) REVERT: A 367 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7620 (mtpp) REVERT: A 378 LYS cc_start: 0.7762 (mttt) cc_final: 0.7313 (mtmt) REVERT: A 391 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.7159 (p90) REVERT: A 421 PHE cc_start: 0.4810 (OUTLIER) cc_final: 0.4005 (t80) REVERT: B 8 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: B 168 GLN cc_start: 0.8743 (tt0) cc_final: 0.8300 (mm-40) REVERT: B 232 LYS cc_start: 0.8429 (mmtt) cc_final: 0.7917 (mmmm) REVERT: C 60 MET cc_start: 0.4158 (mmm) cc_final: 0.3682 (mmm) REVERT: C 104 ARG cc_start: 0.5070 (mtt-85) cc_final: 0.4746 (mtt-85) REVERT: D 143 ARG cc_start: 0.6908 (mmm-85) cc_final: 0.6534 (mmt-90) REVERT: D 175 ASP cc_start: 0.7911 (m-30) cc_final: 0.7679 (m-30) REVERT: D 247 ASP cc_start: 0.7897 (t70) cc_final: 0.7289 (t0) REVERT: D 380 ASP cc_start: 0.8104 (p0) cc_final: 0.7865 (p0) REVERT: E 136 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8229 (mt-10) REVERT: E 175 HIS cc_start: 0.7044 (p90) cc_final: 0.6721 (p90) REVERT: E 302 ASN cc_start: 0.9049 (t0) cc_final: 0.8598 (t0) REVERT: E 310 ARG cc_start: 0.8573 (ptt90) cc_final: 0.8110 (ptp90) REVERT: E 327 TRP cc_start: 0.8911 (t-100) cc_final: 0.7026 (t-100) REVERT: E 334 ARG cc_start: 0.8660 (mtt180) cc_final: 0.8408 (mtt90) REVERT: F 15 TYR cc_start: 0.4335 (m-80) cc_final: 0.3809 (m-80) REVERT: F 88 ASN cc_start: 0.7311 (t0) cc_final: 0.7080 (m-40) REVERT: F 101 ASP cc_start: 0.5459 (m-30) cc_final: 0.5077 (m-30) REVERT: G 67 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6739 (mm-40) REVERT: G 152 GLU cc_start: 0.7377 (tp30) cc_final: 0.6971 (tp30) REVERT: G 299 ASP cc_start: 0.7583 (t0) cc_final: 0.6877 (t0) REVERT: G 301 GLU cc_start: 0.8091 (mp0) cc_final: 0.7384 (mp0) REVERT: G 361 ASN cc_start: 0.8618 (m-40) cc_final: 0.8289 (m-40) REVERT: G 391 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7239 (p90) REVERT: H 266 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7903 (p) REVERT: H 290 THR cc_start: 0.9173 (m) cc_final: 0.8645 (p) REVERT: J 156 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6526 (mmtt) REVERT: J 247 ASP cc_start: 0.7179 (t0) cc_final: 0.6848 (t0) REVERT: J 291 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7958 (mt) REVERT: K 35 GLU cc_start: 0.8065 (tt0) cc_final: 0.7598 (tt0) REVERT: K 327 TRP cc_start: 0.9357 (t-100) cc_final: 0.8464 (t-100) REVERT: K 344 ASN cc_start: 0.8627 (t0) cc_final: 0.8179 (t0) REVERT: L 27 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6832 (mt) REVERT: L 60 MET cc_start: 0.6022 (mpp) cc_final: 0.5398 (mpp) REVERT: L 67 TYR cc_start: 0.7222 (p90) cc_final: 0.6680 (p90) outliers start: 200 outliers final: 160 residues processed: 636 average time/residue: 0.1853 time to fit residues: 202.4006 Evaluate side-chains 654 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 483 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 187 ASN Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 302 CYS Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 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 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 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 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 31 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 184 LYS 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 19 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 67 GLN Chi-restraints excluded: chain G residue 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 92 VAL Chi-restraints excluded: chain H residue 151 ASN 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 92 VAL Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 47 ILE Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 156 LYS Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 265 GLU Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 305 THR Chi-restraints excluded: chain J residue 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 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 50 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 79 ASP Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 107 ASP 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 276 LYS 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 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 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: 0.9980 chunk 371 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 319 optimal weight: 0.9990 chunk 193 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS B 194 GLN B 275 HIS D 35 ASN D 439 HIS E 114 HIS F 136 GLN ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 ASN G 439 HIS H 151 ASN J 32 GLN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN K 402 ASN ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.202878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.149762 restraints weight = 46084.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.152874 restraints weight = 30709.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.155347 restraints weight = 19141.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.158385 restraints weight = 13720.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.157884 restraints weight = 12308.745| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 35652 Z= 0.118 Angle : 0.594 20.647 48608 Z= 0.305 Chirality : 0.046 0.843 5360 Planarity : 0.005 0.049 6272 Dihedral : 5.161 55.816 4976 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.48 % Allowed : 17.58 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4436 helix: 1.78 (0.24), residues: 492 sheet: -0.31 (0.14), residues: 1372 loop : -0.32 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 310 TYR 0.030 0.002 TYR C 49 PHE 0.018 0.002 PHE G 421 TRP 0.025 0.001 TRP J 142 HIS 0.010 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (35548) covalent geometry : angle 0.57297 / 0.30 (48392) SS BOND : bond 0.00358 / 0.26 ( 96) SS BOND : angle 1.17416 / 0.79 ( 192) hydrogen bonds : bond 0.03448 / 2.37 ( 1150) hydrogen bonds : angle 5.71994 / 3.92 ( 2880) link_NAG-ASN : bond 0.00863 / 0.41 ( 8) link_NAG-ASN : angle 6.53599 / 3.84 ( 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 626 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 531 time to evaluate : 1.210 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 7 MET cc_start: 0.7817 (ptm) cc_final: 0.7432 (ptp) REVERT: A 13 ILE cc_start: 0.9255 (mm) cc_final: 0.9032 (mm) REVERT: A 67 GLN cc_start: 0.8773 (mp10) cc_final: 0.8544 (mp10) REVERT: A 120 LYS cc_start: 0.8132 (mttt) cc_final: 0.7818 (mttp) REVERT: A 136 THR cc_start: 0.7082 (OUTLIER) cc_final: 0.6407 (m) REVERT: A 171 TRP cc_start: 0.8129 (t60) cc_final: 0.6905 (t-100) REVERT: A 217 ASN cc_start: 0.8667 (t0) cc_final: 0.8359 (t0) REVERT: A 342 GLU cc_start: 0.8132 (mp0) cc_final: 0.7455 (tt0) REVERT: A 378 LYS cc_start: 0.7574 (mttt) cc_final: 0.7191 (mtmt) REVERT: A 403 ILE cc_start: 0.8612 (mt) cc_final: 0.7926 (tt) REVERT: A 421 PHE cc_start: 0.4877 (OUTLIER) cc_final: 0.4207 (t80) REVERT: B 8 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7692 (mp10) REVERT: B 26 ARG cc_start: 0.6680 (ttm-80) cc_final: 0.6438 (ttm-80) REVERT: B 163 TYR cc_start: 0.8500 (m-80) cc_final: 0.8106 (m-10) REVERT: B 168 GLN cc_start: 0.8689 (tt0) cc_final: 0.8288 (tp-100) REVERT: B 232 LYS cc_start: 0.8353 (mmtt) cc_final: 0.7887 (mmmm) REVERT: C 7 MET cc_start: 0.6014 (mpp) cc_final: 0.4658 (mmp) REVERT: C 60 MET cc_start: 0.4135 (mmm) cc_final: 0.3734 (mmm) REVERT: C 86 GLU cc_start: 0.6574 (tp30) cc_final: 0.5893 (tt0) REVERT: D 51 TYR cc_start: 0.8898 (p90) cc_final: 0.8379 (p90) REVERT: D 142 TRP cc_start: 0.8034 (m-10) cc_final: 0.7771 (m100) REVERT: D 143 ARG cc_start: 0.6713 (mmm-85) cc_final: 0.6208 (mmt90) REVERT: D 247 ASP cc_start: 0.7627 (t70) cc_final: 0.6989 (t0) REVERT: D 380 ASP cc_start: 0.8033 (p0) cc_final: 0.7775 (p0) REVERT: E 302 ASN cc_start: 0.9125 (t0) cc_final: 0.8575 (t0) REVERT: E 310 ARG cc_start: 0.8561 (ptt90) cc_final: 0.8131 (ptp90) REVERT: E 327 TRP cc_start: 0.8930 (t-100) cc_final: 0.7104 (t-100) REVERT: E 334 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8124 (mtt90) REVERT: F 15 TYR cc_start: 0.4195 (m-80) cc_final: 0.3664 (m-80) REVERT: F 101 ASP cc_start: 0.5242 (m-30) cc_final: 0.4717 (m-30) REVERT: G 100 ASN cc_start: 0.8551 (t0) cc_final: 0.8218 (t0) REVERT: G 299 ASP cc_start: 0.7576 (t0) cc_final: 0.6661 (t0) REVERT: G 301 GLU cc_start: 0.8145 (mp0) cc_final: 0.7349 (mp0) REVERT: G 342 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6327 (mm-30) REVERT: G 391 TYR cc_start: 0.7712 (OUTLIER) cc_final: 0.7045 (p90) REVERT: H 266 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7771 (p) REVERT: H 290 THR cc_start: 0.9171 (m) cc_final: 0.8645 (p) REVERT: I 43 LEU cc_start: 0.6289 (mm) cc_final: 0.5881 (mm) REVERT: J 175 ASP cc_start: 0.7913 (m-30) cc_final: 0.7616 (m-30) REVERT: J 247 ASP cc_start: 0.6955 (t0) cc_final: 0.6677 (t0) REVERT: K 35 GLU cc_start: 0.7953 (tt0) cc_final: 0.7514 (tt0) REVERT: K 80 ASN cc_start: 0.8669 (t0) cc_final: 0.8434 (p0) REVERT: K 90 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8180 (p) REVERT: K 135 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7607 (mtp-110) REVERT: K 167 HIS cc_start: 0.7339 (m-70) cc_final: 0.6550 (m170) REVERT: K 256 PHE cc_start: 0.9132 (m-10) cc_final: 0.8535 (m-10) REVERT: K 262 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8395 (mttm) REVERT: K 327 TRP cc_start: 0.9304 (t-100) cc_final: 0.8617 (t-100) REVERT: K 333 LYS cc_start: 0.8314 (mmmm) cc_final: 0.7670 (mtmt) REVERT: K 344 ASN cc_start: 0.8580 (t0) cc_final: 0.8155 (t0) REVERT: L 52 GLU cc_start: 0.5892 (tt0) cc_final: 0.5431 (tt0) REVERT: L 60 MET cc_start: 0.6063 (mpp) cc_final: 0.5681 (mpp) outliers start: 95 outliers final: 68 residues processed: 590 average time/residue: 0.1775 time to fit residues: 178.1489 Evaluate side-chains 570 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 494 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 294 THR 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 66 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain 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 208 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 391 TYR 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 179 SER Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 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 376 THR Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 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 206 SER Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 354 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 50 SER Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 135 ARG 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 262 LYS Chi-restraints excluded: chain K residue 276 LYS 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 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: 8.9990 chunk 202 optimal weight: 4.9990 chunk 401 optimal weight: 30.0000 chunk 163 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 325 optimal weight: 0.6980 chunk 240 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 380 optimal weight: 6.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 HIS ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 ASN K 80 ASN K 120 HIS ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN K 402 ASN ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148602 restraints weight = 46145.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151638 restraints weight = 30712.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154440 restraints weight = 19241.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.155321 restraints weight = 13547.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.155612 restraints weight = 13025.074| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35652 Z= 0.148 Angle : 0.608 20.565 48608 Z= 0.311 Chirality : 0.048 1.141 5360 Planarity : 0.005 0.046 6272 Dihedral : 5.086 57.349 4976 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 2.53 % Allowed : 18.08 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4436 helix: 1.80 (0.24), residues: 492 sheet: -0.13 (0.14), residues: 1288 loop : -0.38 (0.12), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 21 TYR 0.027 0.002 TYR J 137 PHE 0.051 0.002 PHE K 113 TRP 0.033 0.001 TRP A 142 HIS 0.010 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (35548) covalent geometry : angle 0.58659 / 0.31 (48392) SS BOND : bond 0.00324 / 0.23 ( 96) SS BOND : angle 1.25318 / 0.84 ( 192) hydrogen bonds : bond 0.03571 / 2.43 ( 1150) hydrogen bonds : angle 5.67674 / 3.90 ( 2880) link_NAG-ASN : bond 0.00903 / 0.43 ( 8) link_NAG-ASN : angle 6.58600 / 3.89 ( 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 600 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 503 time to evaluate : 1.040 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 13 ILE cc_start: 0.9251 (mm) cc_final: 0.9049 (mm) REVERT: A 120 LYS cc_start: 0.8161 (mttt) cc_final: 0.7854 (mttp) REVERT: A 142 TRP cc_start: 0.7691 (m-10) cc_final: 0.7337 (m-10) REVERT: A 171 TRP cc_start: 0.8169 (t60) cc_final: 0.6983 (t-100) REVERT: A 217 ASN cc_start: 0.8668 (t0) cc_final: 0.8318 (t0) REVERT: A 342 GLU cc_start: 0.8145 (mp0) cc_final: 0.7439 (tt0) REVERT: A 378 LYS cc_start: 0.7573 (mttt) cc_final: 0.7198 (mtmt) REVERT: A 403 ILE cc_start: 0.8636 (mt) cc_final: 0.7951 (tt) REVERT: A 421 PHE cc_start: 0.4875 (OUTLIER) cc_final: 0.4262 (t80) REVERT: B 8 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7795 (mp10) REVERT: B 163 TYR cc_start: 0.8476 (m-80) cc_final: 0.8153 (m-10) REVERT: B 168 GLN cc_start: 0.8685 (tt0) cc_final: 0.8329 (tp-100) REVERT: B 174 ASP cc_start: 0.8031 (t0) cc_final: 0.7523 (t70) REVERT: C 7 MET cc_start: 0.6116 (mpp) cc_final: 0.4749 (mmp) REVERT: C 60 MET cc_start: 0.4250 (mmm) cc_final: 0.3841 (mmm) REVERT: C 86 GLU cc_start: 0.6673 (tp30) cc_final: 0.5816 (tt0) REVERT: D 30 GLN cc_start: 0.8381 (tt0) cc_final: 0.8110 (tt0) REVERT: D 247 ASP cc_start: 0.7820 (t70) cc_final: 0.7093 (t0) REVERT: E 68 MET cc_start: 0.7829 (mmm) cc_final: 0.7621 (mmm) REVERT: E 302 ASN cc_start: 0.9126 (t0) cc_final: 0.8578 (t0) REVERT: E 327 TRP cc_start: 0.8932 (t-100) cc_final: 0.6993 (t-100) REVERT: E 334 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8109 (mtt90) REVERT: F 15 TYR cc_start: 0.4405 (m-80) cc_final: 0.3837 (m-80) REVERT: F 101 ASP cc_start: 0.5330 (m-30) cc_final: 0.4813 (m-30) REVERT: G 152 GLU cc_start: 0.7186 (tp30) cc_final: 0.6821 (tp30) REVERT: G 176 ASN cc_start: 0.8535 (p0) cc_final: 0.8247 (t0) REVERT: G 299 ASP cc_start: 0.7580 (t0) cc_final: 0.6865 (t0) REVERT: G 306 GLU cc_start: 0.8418 (tp30) cc_final: 0.8152 (tp30) REVERT: G 342 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6336 (mm-30) REVERT: G 391 TYR cc_start: 0.7814 (OUTLIER) cc_final: 0.7185 (p90) REVERT: H 266 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7774 (p) REVERT: H 290 THR cc_start: 0.9203 (m) cc_final: 0.8645 (p) REVERT: I 43 LEU cc_start: 0.6408 (mm) cc_final: 0.5998 (mm) REVERT: J 175 ASP cc_start: 0.7974 (m-30) cc_final: 0.7688 (m-30) REVERT: J 247 ASP cc_start: 0.7198 (t0) cc_final: 0.6954 (t0) REVERT: K 35 GLU cc_start: 0.8082 (tt0) cc_final: 0.7682 (tt0) REVERT: K 90 SER cc_start: 0.8672 (OUTLIER) cc_final: 0.8361 (p) REVERT: K 135 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7626 (mtp-110) REVERT: K 262 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8404 (mttm) REVERT: K 327 TRP cc_start: 0.9306 (t-100) cc_final: 0.8465 (t-100) REVERT: K 344 ASN cc_start: 0.8586 (t0) cc_final: 0.8184 (t0) REVERT: L 52 GLU cc_start: 0.5791 (tt0) cc_final: 0.5412 (tt0) REVERT: L 60 MET cc_start: 0.6055 (mpp) cc_final: 0.5560 (mpp) outliers start: 97 outliers final: 79 residues processed: 571 average time/residue: 0.1808 time to fit residues: 176.1385 Evaluate side-chains 568 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 482 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 153 THR 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 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 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 391 TYR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 439 HIS Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 288 HIS Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 354 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 50 SER Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 135 ARG 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 262 LYS Chi-restraints excluded: chain K residue 276 LYS Chi-restraints excluded: chain K residue 326 THR 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 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: 2.9990 chunk 266 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 247 optimal weight: 0.7980 chunk 414 optimal weight: 6.9990 chunk 437 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 334 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS ** H 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.202668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149643 restraints weight = 46238.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.152310 restraints weight = 30263.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.154860 restraints weight = 19288.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.158642 restraints weight = 13816.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.157893 restraints weight = 11687.904| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35652 Z= 0.132 Angle : 0.600 20.353 48608 Z= 0.306 Chirality : 0.048 1.082 5360 Planarity : 0.005 0.066 6272 Dihedral : 4.997 57.813 4976 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 2.38 % Allowed : 18.50 % Favored : 79.13 % 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 are not related in a simple way. whole: -0.09 (0.13), residues: 4436 helix: 1.83 (0.24), residues: 492 sheet: -0.08 (0.14), residues: 1280 loop : -0.37 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 310 TYR 0.027 0.002 TYR J 137 PHE 0.036 0.002 PHE G 95 TRP 0.019 0.001 TRP A 142 HIS 0.011 0.001 HIS G 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (35548) covalent geometry : angle 0.57912 / 0.30 (48392) SS BOND : bond 0.00293 / 0.21 ( 96) SS BOND : angle 1.18385 / 0.80 ( 192) hydrogen bonds : bond 0.03429 / 2.34 ( 1150) hydrogen bonds : angle 5.60039 / 3.84 ( 2880) link_NAG-ASN : bond 0.00966 / 0.47 ( 8) link_NAG-ASN : angle 6.45917 / 3.81 ( 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 592 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 501 time to evaluate : 1.005 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 120 LYS cc_start: 0.8139 (mttt) cc_final: 0.7843 (mttp) REVERT: A 171 TRP cc_start: 0.8112 (t60) cc_final: 0.6948 (t-100) REVERT: A 217 ASN cc_start: 0.8657 (t0) cc_final: 0.8319 (t0) REVERT: A 342 GLU cc_start: 0.8127 (mp0) cc_final: 0.7466 (tt0) REVERT: A 378 LYS cc_start: 0.7549 (mttt) cc_final: 0.7175 (mtmt) REVERT: A 403 ILE cc_start: 0.8635 (mt) cc_final: 0.8073 (tt) REVERT: A 421 PHE cc_start: 0.4877 (OUTLIER) cc_final: 0.4279 (t80) REVERT: B 8 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7723 (mp10) REVERT: B 163 TYR cc_start: 0.8478 (m-80) cc_final: 0.8069 (m-10) REVERT: B 168 GLN cc_start: 0.8676 (tt0) cc_final: 0.8309 (tp-100) REVERT: B 174 ASP cc_start: 0.7915 (t0) cc_final: 0.7454 (t70) REVERT: C 7 MET cc_start: 0.6115 (mpp) cc_final: 0.4760 (mmp) REVERT: C 60 MET cc_start: 0.4222 (mmm) cc_final: 0.3819 (mmm) REVERT: C 86 GLU cc_start: 0.6622 (tp30) cc_final: 0.5802 (tt0) REVERT: E 302 ASN cc_start: 0.9093 (t0) cc_final: 0.8545 (t0) REVERT: E 327 TRP cc_start: 0.8945 (t-100) cc_final: 0.7033 (t-100) REVERT: E 334 ARG cc_start: 0.8551 (mtt180) cc_final: 0.8078 (mtt90) REVERT: F 15 TYR cc_start: 0.4055 (m-80) cc_final: 0.3594 (m-80) REVERT: F 101 ASP cc_start: 0.5451 (m-30) cc_final: 0.4867 (m-30) REVERT: F 105 PRO cc_start: 0.8307 (Cg_endo) cc_final: 0.8057 (Cg_exo) REVERT: G 67 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6560 (mm-40) REVERT: G 299 ASP cc_start: 0.7596 (t0) cc_final: 0.6891 (t0) REVERT: G 391 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7176 (p90) REVERT: H 266 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7830 (p) REVERT: H 290 THR cc_start: 0.9115 (m) cc_final: 0.8539 (p) REVERT: I 17 CYS cc_start: 0.7421 (t) cc_final: 0.6781 (m) REVERT: I 43 LEU cc_start: 0.6446 (mm) cc_final: 0.6027 (mm) REVERT: J 175 ASP cc_start: 0.7952 (m-30) cc_final: 0.7649 (m-30) REVERT: J 247 ASP cc_start: 0.7170 (t0) cc_final: 0.6944 (t0) REVERT: K 35 GLU cc_start: 0.8042 (tt0) cc_final: 0.7635 (tt0) REVERT: K 90 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8290 (p) REVERT: K 135 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7647 (mtp-110) REVERT: K 167 HIS cc_start: 0.7340 (m-70) cc_final: 0.7036 (m-70) REVERT: K 262 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8385 (mttm) REVERT: K 276 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7901 (mtmm) REVERT: K 327 TRP cc_start: 0.9280 (t-100) cc_final: 0.8587 (t-100) REVERT: K 344 ASN cc_start: 0.8559 (t0) cc_final: 0.8169 (t0) REVERT: L 52 GLU cc_start: 0.5819 (tt0) cc_final: 0.5435 (tt0) REVERT: L 60 MET cc_start: 0.5985 (mpp) cc_final: 0.5513 (mpp) outliers start: 91 outliers final: 74 residues processed: 560 average time/residue: 0.1772 time to fit residues: 169.4735 Evaluate side-chains 573 residues out of total 3828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 490 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 294 THR 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 66 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 126 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 237 VAL Chi-restraints excluded: chain D residue 381 CYS Chi-restraints excluded: chain D residue 391 TYR 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 354 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 4 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 13 ILE Chi-restraints excluded: chain G residue 67 GLN Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 391 TYR Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 364 THR Chi-restraints excluded: chain H residue 387 CYS Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 279 ILE Chi-restraints excluded: chain J residue 289 THR 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 434 LEU Chi-restraints excluded: chain K residue 16 ILE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 90 SER Chi-restraints excluded: chain K residue 135 ARG 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 262 LYS Chi-restraints excluded: chain K residue 276 LYS 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 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: 20.0000 chunk 100 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 340 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 283 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 212 optimal weight: 7.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 HIS ** D 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 439 HIS H 302 ASN ** H 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 HIS ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.202436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149583 restraints weight = 46142.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.153480 restraints weight = 29919.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.155354 restraints weight = 17899.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.155701 restraints weight = 13821.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156053 restraints weight = 12981.077| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35652 Z= 0.138 Angle : 0.605 20.283 48608 Z= 0.307 Chirality : 0.048 0.958 5360 Planarity : 0.005 0.047 6272 Dihedral : 4.973 55.855 4976 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.83 % Favored : 96.15 % Rotamer: Outliers : 2.56 % Allowed : 18.39 % Favored : 79.05 % 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 are not related in a simple way. whole: -0.03 (0.13), residues: 4436 helix: 1.88 (0.24), residues: 492 sheet: -0.07 (0.14), residues: 1360 loop : -0.31 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 310 TYR 0.023 0.002 TYR B 235 PHE 0.037 0.002 PHE G 95 TRP 0.035 0.001 TRP A 142 HIS 0.012 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (35548) covalent geometry : angle 0.58413 / 0.30 (48392) SS BOND : bond 0.00307 / 0.22 ( 96) SS BOND : angle 1.17227 / 0.79 ( 192) hydrogen bonds : bond 0.03433 / 2.33 ( 1150) hydrogen bonds : angle 5.54755 / 3.81 ( 2880) link_NAG-ASN : bond 0.00991 / 0.48 ( 8) link_NAG-ASN : angle 6.50597 / 3.79 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6156.11 seconds wall clock time: 107 minutes 23.92 seconds (6443.92 seconds total)