Starting phenix.real_space_refine on Mon Jul 6 04:57:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ufc_42192/07_2026/8ufc_42192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufc_42192/07_2026/8ufc_42192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ufc_42192/07_2026/8ufc_42192.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ufc_42192/07_2026/8ufc_42192.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ufc_42192/07_2026/8ufc_42192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufc_42192/07_2026/8ufc_42192.map" model { file = "/net/cci-nas-00/data/ceres_data/8ufc_42192/07_2026/8ufc_42192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufc_42192/07_2026/8ufc_42192.cif" } resolution = 3.09 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= 0.001 sd= 0.059 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 8 9.91 5 S 240 5.16 5 C 21216 2.51 5 N 5828 2.21 5 O 6332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33624 Number of models: 1 Model: "" Number of chains: 28 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: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "W" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "X" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "Y" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} 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} Time building chain proxies: 7.38, per 1000 atoms: 0.22 Number of scatterers: 33624 At special positions: 0 Unit cell: (161.069, 171.879, 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 8 19.99 S 240 16.00 O 6332 8.00 N 5828 7.00 C 21216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=84, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.04 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=2.03 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=2.02 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=2.04 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=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.02 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=2.04 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=2.04 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 134 " " NAG B 501 " - " ASN B 315 " " NAG D 501 " - " ASN D 134 " " NAG E 501 " - " ASN E 315 " " NAG G 501 " - " ASN G 134 " " NAG H 501 " - " ASN H 315 " " NAG J 501 " - " ASN J 134 " " NAG K 501 " - " ASN K 315 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.5 seconds 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8008 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 86 sheets defined 16.1% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 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: 3.685A pdb=" N ALA E 410 " --> pdb=" O PRO E 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 40 removed outlier: 3.525A pdb=" N ALA F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 removed outlier: 4.392A 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 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: 3.692A pdb=" N ALA I 40 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 3.856A 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 removed outlier: 3.516A pdb=" N LYS J 246 " --> pdb=" O GLU J 242 " (cutoff:3.500A) 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: 3.603A 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 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: 4.536A 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: 4.429A 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: 3.568A pdb=" N LYS X 65 " --> pdb=" O GLY X 61 " (cutoff:3.500A) removed outlier: 4.547A 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: 4.685A 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 sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.539A 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: 4.760A pdb=" N THR A 36 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLN A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE A 38 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 128 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR A 46 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.338A 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: 5.439A pdb=" N ASP A 299 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS A 322 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 6.878A 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: 3.606A 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: 6.653A pdb=" N GLN B 48 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 36 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 27.786A pdb=" N ARG B 46 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 22.803A pdb=" N ASN B 69 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 16.976A pdb=" N GLN B 48 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 13.745A pdb=" N PHE B 67 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N SER B 50 " --> pdb=" O MET B 65 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N MET B 65 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N MET B 52 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N ALA B 63 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 54 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.608A 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: 4.377A 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 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: 6.378A pdb=" N PHE C 4 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR C 15 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 6 " --> pdb=" O ASN C 13 " (cutoff:3.500A) removed outlier: 8.057A 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: 9.607A 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: 8.225A 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: 6.034A pdb=" N VAL C 117 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.586A 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: 6.450A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE D 38 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR D 128 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR D 126 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR D 42 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL D 124 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 44 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR D 122 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR D 46 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS D 120 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TYR D 137 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 5.279A 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 186 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 184 through 186 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: 4.938A pdb=" N ASP D 299 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS D 322 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE D 316 " --> pdb=" O THR D 305 " (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: 4.625A pdb=" N ASN E 21 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 6.053A 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: 3.536A pdb=" N SER E 93 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN E 102 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 5.868A 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: 11.550A pdb=" N MET E 52 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ALA E 63 " --> pdb=" O MET E 52 " (cutoff:3.500A) removed outlier: 4.221A 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: 3.516A pdb=" N THR E 108 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N HIS E 126 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR E 110 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL E 124 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLY E 112 " --> pdb=" O CYS E 122 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS E 122 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N HIS E 114 " --> pdb=" O HIS E 120 " (cutoff:3.500A) removed outlier: 6.866A 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: 6.123A pdb=" N PHE F 4 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR F 15 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE F 6 " --> pdb=" O ASN F 13 " (cutoff:3.500A) removed outlier: 7.812A 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: 9.334A 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: 8.042A pdb=" N ALA F 115 " --> pdb=" O TRP F 134 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N TRP F 134 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL F 117 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 6.955A 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 Processing sheet with id=AE6, first strand: chain 'G' and resid 15 through 19 removed outlier: 6.486A pdb=" N MET G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR G 36 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN G 130 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE G 38 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR G 128 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR G 126 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR G 42 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL G 124 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU G 44 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR G 122 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR G 46 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LYS G 120 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR G 137 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 5.414A 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 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 184 through 186 current: chain 'G' and resid 268 through 270 Processing sheet with id=AE7, 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=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'G' and resid 204 through 206 Processing sheet with id=AF1, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AF2, first strand: chain 'G' and resid 297 through 306 removed outlier: 4.772A pdb=" N ASP G 299 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS G 322 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE G 316 " --> pdb=" O THR G 305 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 344 through 346 Processing sheet with id=AF4, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AF5, first strand: chain 'H' and resid 17 through 22 removed outlier: 5.294A pdb=" N ASP H 18 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER H 29 " --> pdb=" O ASP H 18 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N CYS H 27 " --> pdb=" O PRO H 20 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER H 25 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 33 through 37 removed outlier: 8.596A pdb=" N ILE H 33 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER H 50 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 10.244A pdb=" N SER H 50 " --> pdb=" O MET H 68 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N MET H 68 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR H 64 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N LYS H 56 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N LEU H 62 " --> pdb=" O LYS H 56 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 82 through 84 removed outlier: 3.695A pdb=" N THR H 108 " --> pdb=" O HIS H 126 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N HIS H 126 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR H 110 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL H 124 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLY H 112 " --> pdb=" O CYS H 122 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS H 122 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS H 114 " --> pdb=" O HIS H 120 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N HIS H 120 " --> pdb=" O HIS H 114 " (cutoff:3.500A) 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: 3.703A pdb=" N GLY I 14 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 7.992A 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: 9.812A 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: 8.853A pdb=" N VAL I 114 " --> pdb=" O TRP I 134 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP I 134 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER I 130 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY I 120 " --> pdb=" O ALA I 128 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA I 128 " --> pdb=" O GLY I 120 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASN I 122 " --> pdb=" O ARG I 126 " (cutoff:3.500A) removed outlier: 6.854A 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: 3.560A 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: 6.564A pdb=" N MET J 132 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR J 36 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLN J 130 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE J 38 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR J 128 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR J 126 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR J 42 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL J 124 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU J 44 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR J 122 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR J 46 " --> pdb=" O LYS J 120 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS J 120 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR J 137 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 5.310A 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: 6.047A pdb=" N VAL J 297 " --> pdb=" O SER J 324 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER J 324 " --> pdb=" O VAL J 297 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP J 299 " --> pdb=" O LYS J 322 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS J 322 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.794A 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: 3.639A 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: 8.478A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N SER K 50 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N MET K 68 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N TYR K 64 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N LYS K 56 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 9.552A 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: 3.549A pdb=" N THR K 108 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS K 126 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N THR K 110 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL K 124 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLY K 112 " --> pdb=" O CYS K 122 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N CYS K 122 " --> pdb=" O GLY K 112 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N HIS K 114 " --> pdb=" O HIS K 120 " (cutoff:3.500A) removed outlier: 6.846A 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: 3.743A pdb=" N GLY L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TYR L 15 " --> pdb=" O PRO L 26 " (cutoff:3.500A) removed outlier: 3.530A 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: 8.984A 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: 9.040A pdb=" N VAL L 114 " --> pdb=" O TRP L 134 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP L 134 " --> pdb=" O VAL L 114 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER L 130 " --> pdb=" O LEU L 118 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY L 120 " --> pdb=" O ALA L 128 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA L 128 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASN L 122 " --> pdb=" O ARG L 126 " (cutoff:3.500A) removed outlier: 6.996A 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 1135 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.48 Time building geometry restraints manager: 3.67 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: 11000 1.35 - 1.47: 8258 1.47 - 1.59: 14962 1.59 - 1.71: 0 1.71 - 1.83: 284 Bond restraints: 34504 Sorted by residual: bond pdb=" C1 NAG K 501 " pdb=" O5 NAG K 501 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 NAG H 501 " pdb=" O5 NAG H 501 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" N ALA X 31 " pdb=" CA ALA X 31 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+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 2.89e+00 ... (remaining 34499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 44207 1.28 - 2.56: 2234 2.56 - 3.84: 503 3.84 - 5.11: 49 5.11 - 6.39: 3 Bond angle restraints: 46996 Sorted by residual: angle pdb=" N ASN Y 66 " pdb=" CA ASN Y 66 " pdb=" C ASN Y 66 " ideal model delta sigma weight residual 112.90 117.67 -4.77 1.31e+00 5.83e-01 1.33e+01 angle pdb=" N LYS Y 65 " pdb=" CA LYS Y 65 " pdb=" C LYS Y 65 " ideal model delta sigma weight residual 111.07 114.69 -3.62 1.07e+00 8.73e-01 1.15e+01 angle pdb=" N VAL A 55 " pdb=" CA VAL A 55 " pdb=" C VAL A 55 " ideal model delta sigma weight residual 108.15 111.01 -2.86 9.90e-01 1.02e+00 8.35e+00 angle pdb=" N ALA H 42 " pdb=" CA ALA H 42 " pdb=" C ALA H 42 " ideal model delta sigma weight residual 109.11 113.07 -3.96 1.42e+00 4.96e-01 7.76e+00 angle pdb=" N TRP H 327 " pdb=" CA TRP H 327 " pdb=" C TRP H 327 " ideal model delta sigma weight residual 109.96 105.35 4.61 1.68e+00 3.54e-01 7.53e+00 ... (remaining 46991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 20070 17.95 - 35.91: 592 35.91 - 53.86: 159 53.86 - 71.82: 39 71.82 - 89.77: 16 Dihedral angle restraints: 20876 sinusoidal: 8368 harmonic: 12508 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 93.00 148.40 -55.40 1 1.00e+01 1.00e-02 4.15e+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 93.00 142.94 -49.94 1 1.00e+01 1.00e-02 3.42e+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 93.00 137.69 -44.69 1 1.00e+01 1.00e-02 2.78e+01 ... (remaining 20873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3269 0.035 - 0.071: 1279 0.071 - 0.106: 460 0.106 - 0.141: 197 0.141 - 0.177: 19 Chirality restraints: 5224 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 7.79e-01 chirality pdb=" CA PRO B 286 " pdb=" N PRO B 286 " pdb=" C PRO B 286 " pdb=" CB PRO B 286 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA CYS D 371 " pdb=" N CYS D 371 " pdb=" C CYS D 371 " pdb=" CB CYS D 371 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 5221 not shown) Planarity restraints: 6088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 84 " 0.274 9.50e-02 1.11e+02 1.23e-01 1.06e+01 pdb=" NE ARG B 84 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 84 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 84 " -0.009 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 K 239 " -0.277 9.50e-02 1.11e+02 1.24e-01 9.72e+00 pdb=" NE ARG K 239 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG K 239 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG K 239 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG K 239 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 110 " 0.240 9.50e-02 1.11e+02 1.08e-01 9.56e+00 pdb=" NE ARG D 110 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 110 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG D 110 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG D 110 " -0.000 2.00e-02 2.50e+03 ... (remaining 6085 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1990 2.73 - 3.27: 32508 3.27 - 3.81: 54575 3.81 - 4.36: 67618 4.36 - 4.90: 118904 Nonbonded interactions: 275595 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 63 " pdb="CA CA Y 201 " model vdw 2.186 2.510 nonbonded pdb=" OD1 ASP Y 53 " pdb="CA CA Y 201 " model vdw 2.206 2.510 nonbonded pdb=" O TRP V 89 " pdb="CA CA V 202 " model vdw 2.254 2.510 nonbonded pdb=" O TRP Y 50 " pdb="CA CA Y 201 " model vdw 2.264 2.510 nonbonded pdb=" O LYS H 398 " pdb=" NH1 ARG L 22 " model vdw 2.280 3.120 ... (remaining 275590 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 '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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.340 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 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 0.040 34596 Z= 0.114 Angle : 0.658 6.393 47188 Z= 0.370 Chirality : 0.046 0.177 5224 Planarity : 0.008 0.124 6080 Dihedral : 9.954 89.771 12616 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.74 (0.12), residues: 4304 helix: 0.73 (0.22), residues: 488 sheet: 0.62 (0.14), residues: 1320 loop : 0.51 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG D 110 TYR 0.028 0.005 TYR D 309 PHE 0.022 0.002 PHE G 421 TRP 0.032 0.004 TRP Y 89 HIS 0.011 0.002 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (34504) covalent geometry : angle 0.65281 / 0.37 (46996) SS BOND : bond 0.00407 / 0.28 ( 84) SS BOND : angle 1.24629 / 0.83 ( 168) hydrogen bonds : bond 0.20200 / 13.71 ( 1135) hydrogen bonds : angle 8.42540 / 5.92 ( 2853) link_NAG-ASN : bond 0.00257 / 0.12 ( 8) link_NAG-ASN : angle 2.48148 / 1.35 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 687 time to evaluate : 1.117 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: B 168 GLN cc_start: 0.7746 (tt0) cc_final: 0.7514 (tt0) REVERT: E 4 THR cc_start: 0.8797 (t) cc_final: 0.8227 (p) REVERT: G 148 TYR cc_start: 0.7404 (m-80) cc_final: 0.6978 (m-80) REVERT: H 236 ASN cc_start: 0.8814 (p0) cc_final: 0.8581 (p0) REVERT: I 67 TYR cc_start: 0.6804 (p90) cc_final: 0.6570 (p90) REVERT: J 98 THR cc_start: 0.7919 (p) cc_final: 0.7634 (m) REVERT: K 52 MET cc_start: 0.7667 (mmm) cc_final: 0.7401 (mmm) outliers start: 0 outliers final: 0 residues processed: 687 average time/residue: 0.2100 time to fit residues: 231.5420 Evaluate side-chains 442 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 223 GLN B 8 GLN B 102 GLN B 213 HIS B 230 ASN B 236 ASN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN D 223 GLN D 356 HIS E 80 ASN E 120 HIS E 151 ASN E 175 HIS E 213 HIS E 275 HIS F 37 GLN F 79 HIS G 28 HIS H 114 HIS H 346 HIS I 11 GLN K 21 ASN K 213 HIS K 346 HIS V 42 ASN W 37 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.181746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130499 restraints weight = 37398.859| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.48 r_work: 0.3265 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.121 34596 Z= 0.330 Angle : 0.723 10.760 47188 Z= 0.384 Chirality : 0.053 0.227 5224 Planarity : 0.005 0.059 6080 Dihedral : 5.725 87.909 4840 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.91 % Allowed : 5.58 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.43 (0.12), residues: 4304 helix: 1.26 (0.24), residues: 492 sheet: 0.35 (0.14), residues: 1312 loop : 0.15 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 135 TYR 0.031 0.003 TYR J 309 PHE 0.031 0.003 PHE C 24 TRP 0.021 0.002 TRP B 327 HIS 0.012 0.002 HIS K 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00816 / 0.33 (34504) covalent geometry : angle 0.71442 / 0.38 (46996) SS BOND : bond 0.00622 / 0.38 ( 84) SS BOND : angle 1.83490 / 1.13 ( 168) hydrogen bonds : bond 0.04683 / 3.16 ( 1135) hydrogen bonds : angle 6.34022 / 4.44 ( 2853) link_NAG-ASN : bond 0.00391 / 0.19 ( 8) link_NAG-ASN : angle 2.33345 / 1.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 451 time to evaluate : 1.300 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: A 99 GLU cc_start: 0.7758 (mp0) cc_final: 0.7298 (mp0) REVERT: A 141 SER cc_start: 0.8176 (t) cc_final: 0.7801 (p) REVERT: A 161 LYS cc_start: 0.8633 (ttpt) cc_final: 0.7986 (ttmt) REVERT: A 290 ARG cc_start: 0.8168 (mtp85) cc_final: 0.7930 (mtp85) REVERT: A 344 ASP cc_start: 0.8480 (p0) cc_final: 0.8273 (p0) REVERT: B 60 VAL cc_start: 0.7679 (p) cc_final: 0.7332 (t) REVERT: B 339 GLU cc_start: 0.7611 (mp0) cc_final: 0.7399 (mp0) REVERT: D 45 GLU cc_start: 0.8598 (tp30) cc_final: 0.8353 (mm-30) REVERT: D 109 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7922 (mt-10) REVERT: D 134 ASN cc_start: 0.8714 (t0) cc_final: 0.8446 (t0) REVERT: D 146 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8508 (t0) REVERT: D 282 ASP cc_start: 0.8137 (t0) cc_final: 0.7807 (t0) REVERT: D 301 GLU cc_start: 0.7612 (tp30) cc_final: 0.7200 (pm20) REVERT: D 344 ASP cc_start: 0.8567 (p0) cc_final: 0.8236 (p0) REVERT: E 171 LEU cc_start: 0.8785 (mm) cc_final: 0.8496 (mt) REVERT: F 7 MET cc_start: 0.5655 (mmt) cc_final: 0.5240 (mmp) REVERT: F 78 TRP cc_start: 0.6164 (OUTLIER) cc_final: 0.5164 (p-90) REVERT: F 117 VAL cc_start: 0.6740 (t) cc_final: 0.6412 (m) REVERT: G 82 SER cc_start: 0.9090 (p) cc_final: 0.8714 (m) REVERT: G 148 TYR cc_start: 0.8814 (m-80) cc_final: 0.8489 (m-80) REVERT: G 163 ILE cc_start: 0.7680 (mt) cc_final: 0.7474 (mp) REVERT: G 212 ASN cc_start: 0.8661 (m-40) cc_final: 0.8303 (p0) REVERT: G 343 ASN cc_start: 0.8226 (m-40) cc_final: 0.7971 (m-40) REVERT: G 373 SER cc_start: 0.7742 (t) cc_final: 0.7261 (m) REVERT: H 129 GLU cc_start: 0.8694 (pt0) cc_final: 0.8469 (pt0) REVERT: H 166 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8827 (ptp) REVERT: H 302 ASN cc_start: 0.8196 (t0) cc_final: 0.7964 (m-40) REVERT: H 358 ASN cc_start: 0.8631 (m-40) cc_final: 0.8326 (m110) REVERT: H 376 MET cc_start: 0.6214 (mmp) cc_final: 0.4915 (mtp) REVERT: I 7 MET cc_start: 0.6125 (OUTLIER) cc_final: 0.5594 (mmt) REVERT: J 98 THR cc_start: 0.9050 (p) cc_final: 0.8648 (m) REVERT: J 125 HIS cc_start: 0.7335 (m90) cc_final: 0.7072 (m90) REVERT: J 322 LYS cc_start: 0.7755 (mttp) cc_final: 0.7305 (mtmt) REVERT: J 343 ASN cc_start: 0.8512 (m-40) cc_final: 0.7977 (m-40) REVERT: J 412 LYS cc_start: 0.7192 (mttt) cc_final: 0.6883 (mtpt) REVERT: K 21 ASN cc_start: 0.9253 (OUTLIER) cc_final: 0.9011 (t0) REVERT: K 102 GLN cc_start: 0.8704 (mt0) cc_final: 0.8394 (tt0) REVERT: K 339 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7450 (mp0) REVERT: Y 63 ASP cc_start: 0.4698 (t0) cc_final: 0.4434 (t0) outliers start: 71 outliers final: 47 residues processed: 497 average time/residue: 0.1981 time to fit residues: 162.7826 Evaluate side-chains 445 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 393 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 160 GLN Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 84 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 270 optimal weight: 1.9990 chunk 411 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 360 optimal weight: 5.9990 chunk 304 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 HIS B 102 GLN B 168 GLN B 213 HIS B 230 ASN B 236 ASN B 253 HIS C 79 HIS D 77 GLN D 176 ASN D 223 GLN H 344 ASN ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.181990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.129310 restraints weight = 37314.832| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.62 r_work: 0.3284 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34596 Z= 0.152 Angle : 0.553 7.389 47188 Z= 0.292 Chirality : 0.046 0.196 5224 Planarity : 0.004 0.060 6080 Dihedral : 5.354 87.029 4840 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.73 % Allowed : 7.58 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.47 (0.13), residues: 4304 helix: 1.84 (0.24), residues: 472 sheet: 0.22 (0.14), residues: 1280 loop : 0.16 (0.12), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 84 TYR 0.026 0.001 TYR K 197 PHE 0.019 0.001 PHE C 24 TRP 0.014 0.001 TRP B 327 HIS 0.010 0.001 HIS K 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (34504) covalent geometry : angle 0.54285 / 0.29 (46996) SS BOND : bond 0.00394 / 0.26 ( 84) SS BOND : angle 1.60417 / 1.05 ( 168) hydrogen bonds : bond 0.03957 / 2.68 ( 1135) hydrogen bonds : angle 5.90741 / 4.12 ( 2853) link_NAG-ASN : bond 0.00581 / 0.29 ( 8) link_NAG-ASN : angle 2.30844 / 1.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 439 time to evaluate : 1.475 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: A 45 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8218 (mm-30) REVERT: A 99 GLU cc_start: 0.7561 (mp0) cc_final: 0.6857 (mp0) REVERT: A 161 LYS cc_start: 0.8584 (ttpt) cc_final: 0.7890 (ttmt) REVERT: A 207 ARG cc_start: 0.8996 (mmt180) cc_final: 0.8594 (mmt180) REVERT: A 290 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7955 (mtp85) REVERT: B 60 VAL cc_start: 0.7573 (p) cc_final: 0.7246 (t) REVERT: B 339 GLU cc_start: 0.7652 (mp0) cc_final: 0.7372 (mp0) REVERT: D 45 GLU cc_start: 0.8648 (tp30) cc_final: 0.8412 (mm-30) REVERT: D 109 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7943 (mt-10) REVERT: D 142 TRP cc_start: 0.8396 (m100) cc_final: 0.7990 (m100) REVERT: D 146 ASP cc_start: 0.8881 (m-30) cc_final: 0.8586 (t0) REVERT: D 176 ASN cc_start: 0.8563 (t0) cc_final: 0.8253 (t0) REVERT: D 282 ASP cc_start: 0.8176 (t0) cc_final: 0.7833 (t0) REVERT: D 299 ASP cc_start: 0.8192 (t0) cc_final: 0.7932 (m-30) REVERT: D 301 GLU cc_start: 0.7543 (tp30) cc_final: 0.7062 (pm20) REVERT: D 328 ASN cc_start: 0.7705 (t0) cc_final: 0.7435 (t0) REVERT: D 344 ASP cc_start: 0.8504 (p0) cc_final: 0.8226 (p0) REVERT: E 171 LEU cc_start: 0.8704 (mm) cc_final: 0.8385 (mt) REVERT: E 399 LEU cc_start: 0.7231 (mp) cc_final: 0.6995 (mp) REVERT: F 78 TRP cc_start: 0.6474 (OUTLIER) cc_final: 0.5497 (p-90) REVERT: G 82 SER cc_start: 0.8998 (p) cc_final: 0.8646 (m) REVERT: G 105 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8151 (mt-10) REVERT: G 148 TYR cc_start: 0.8847 (m-80) cc_final: 0.8480 (m-80) REVERT: G 163 ILE cc_start: 0.7612 (mt) cc_final: 0.7385 (mp) REVERT: G 212 ASN cc_start: 0.8619 (m-40) cc_final: 0.8257 (p0) REVERT: G 299 ASP cc_start: 0.7919 (t0) cc_final: 0.7194 (t0) REVERT: G 343 ASN cc_start: 0.8165 (m-40) cc_final: 0.7886 (m-40) REVERT: G 373 SER cc_start: 0.7652 (t) cc_final: 0.7256 (m) REVERT: G 394 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8335 (mm-40) REVERT: G 421 PHE cc_start: 0.6376 (OUTLIER) cc_final: 0.4978 (t80) REVERT: H 65 MET cc_start: 0.8588 (ttp) cc_final: 0.8257 (ttp) REVERT: H 77 LYS cc_start: 0.9021 (mttt) cc_final: 0.8589 (tttm) REVERT: H 129 GLU cc_start: 0.8726 (pt0) cc_final: 0.8368 (pt0) REVERT: H 186 LYS cc_start: 0.6209 (tttt) cc_final: 0.5786 (ttpt) REVERT: H 196 LYS cc_start: 0.7555 (tttt) cc_final: 0.7100 (tttm) REVERT: H 299 SER cc_start: 0.9268 (p) cc_final: 0.9063 (t) REVERT: H 310 ARG cc_start: 0.8534 (ptp-110) cc_final: 0.8113 (ptp90) REVERT: H 376 MET cc_start: 0.6307 (mmp) cc_final: 0.5032 (mtp) REVERT: I 60 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.6214 (ttt) REVERT: J 98 THR cc_start: 0.8990 (p) cc_final: 0.8592 (m) REVERT: J 322 LYS cc_start: 0.7584 (mttp) cc_final: 0.7166 (mtmt) REVERT: J 343 ASN cc_start: 0.8615 (m-40) cc_final: 0.8073 (m-40) REVERT: J 412 LYS cc_start: 0.7177 (mttt) cc_final: 0.6895 (mtpt) REVERT: K 147 GLU cc_start: 0.8525 (tt0) cc_final: 0.8170 (tt0) REVERT: K 339 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7333 (mp0) REVERT: K 376 MET cc_start: 0.7164 (mmt) cc_final: 0.6929 (mmt) REVERT: Y 63 ASP cc_start: 0.4622 (t0) cc_final: 0.4368 (t0) outliers start: 64 outliers final: 43 residues processed: 481 average time/residue: 0.2110 time to fit residues: 167.5047 Evaluate side-chains 445 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 399 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 234 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 413 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 394 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 298 optimal weight: 0.1980 chunk 395 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 204 optimal weight: 3.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 HIS B 168 GLN B 213 HIS B 230 ASN B 236 ASN D 223 GLN E 140 HIS E 144 HIS E 213 HIS H 277 HIS J 32 GLN J 328 ASN J 395 HIS K 21 ASN ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 181 HIS K 213 HIS L 80 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.179395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.127517 restraints weight = 37246.585| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.51 r_work: 0.3252 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 34596 Z= 0.350 Angle : 0.700 11.514 47188 Z= 0.366 Chirality : 0.052 0.214 5224 Planarity : 0.006 0.057 6080 Dihedral : 5.783 84.482 4840 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.54 % Allowed : 8.50 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.02 (0.12), residues: 4304 helix: 1.29 (0.24), residues: 504 sheet: -0.07 (0.14), residues: 1336 loop : -0.16 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 207 TYR 0.034 0.003 TYR J 309 PHE 0.029 0.003 PHE C 24 TRP 0.019 0.002 TRP B 327 HIS 0.007 0.002 HIS H 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00866 / 0.35 (34504) covalent geometry : angle 0.68743 / 0.36 (46996) SS BOND : bond 0.00517 / 0.34 ( 84) SS BOND : angle 2.01841 / 1.39 ( 168) hydrogen bonds : bond 0.04316 / 2.93 ( 1135) hydrogen bonds : angle 6.02826 / 4.22 ( 2853) link_NAG-ASN : bond 0.00646 / 0.34 ( 8) link_NAG-ASN : angle 2.96940 / 1.68 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 424 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7621 (tptt) cc_final: 0.6869 (ttmt) REVERT: A 99 GLU cc_start: 0.7702 (mp0) cc_final: 0.7273 (mp0) REVERT: A 152 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8567 (mt-10) REVERT: A 161 LYS cc_start: 0.8613 (ttpt) cc_final: 0.7945 (ttmt) REVERT: A 290 ARG cc_start: 0.8306 (mtp85) cc_final: 0.8088 (mmt180) REVERT: A 344 ASP cc_start: 0.8506 (p0) cc_final: 0.8227 (p0) REVERT: A 437 PHE cc_start: 0.7054 (t80) cc_final: 0.6698 (t80) REVERT: B 60 VAL cc_start: 0.7657 (p) cc_final: 0.7276 (t) REVERT: B 80 ASN cc_start: 0.7904 (m-40) cc_final: 0.7492 (t0) REVERT: B 296 SER cc_start: 0.9076 (OUTLIER) cc_final: 0.8836 (t) REVERT: B 339 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: C 134 TRP cc_start: 0.6579 (m-90) cc_final: 0.6143 (m-90) REVERT: D 45 GLU cc_start: 0.8614 (tp30) cc_final: 0.8255 (mm-30) REVERT: D 134 ASN cc_start: 0.8772 (t0) cc_final: 0.8566 (t0) REVERT: D 146 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8391 (t0) REVERT: D 282 ASP cc_start: 0.8113 (t0) cc_final: 0.7798 (t0) REVERT: D 299 ASP cc_start: 0.8228 (t0) cc_final: 0.7967 (m-30) REVERT: D 301 GLU cc_start: 0.7474 (tp30) cc_final: 0.7018 (pm20) REVERT: D 344 ASP cc_start: 0.8619 (p0) cc_final: 0.8211 (p0) REVERT: D 385 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7465 (mmtm) REVERT: E 171 LEU cc_start: 0.8698 (mm) cc_final: 0.8470 (mm) REVERT: E 399 LEU cc_start: 0.7341 (mp) cc_final: 0.7078 (mp) REVERT: F 7 MET cc_start: 0.5132 (mmt) cc_final: 0.4780 (mmp) REVERT: F 78 TRP cc_start: 0.6440 (OUTLIER) cc_final: 0.5581 (p-90) REVERT: G 82 SER cc_start: 0.9058 (p) cc_final: 0.8729 (m) REVERT: G 148 TYR cc_start: 0.8832 (m-80) cc_final: 0.8467 (m-80) REVERT: G 163 ILE cc_start: 0.7605 (mt) cc_final: 0.7378 (mp) REVERT: G 212 ASN cc_start: 0.8644 (m-40) cc_final: 0.8429 (p0) REVERT: G 299 ASP cc_start: 0.7833 (t0) cc_final: 0.7111 (t0) REVERT: G 343 ASN cc_start: 0.8119 (m-40) cc_final: 0.7830 (m-40) REVERT: G 373 SER cc_start: 0.7562 (t) cc_final: 0.7087 (m) REVERT: G 421 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.5131 (t80) REVERT: H 77 LYS cc_start: 0.9080 (mttt) cc_final: 0.8814 (mtpp) REVERT: H 86 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8470 (p) REVERT: H 186 LYS cc_start: 0.6247 (tttt) cc_final: 0.5839 (ttpt) REVERT: H 196 LYS cc_start: 0.7603 (tttt) cc_final: 0.7096 (tttm) REVERT: I 60 MET cc_start: 0.6618 (OUTLIER) cc_final: 0.6219 (ttt) REVERT: J 98 THR cc_start: 0.9064 (p) cc_final: 0.8683 (m) REVERT: J 322 LYS cc_start: 0.7742 (mttp) cc_final: 0.7357 (mtmt) REVERT: J 412 LYS cc_start: 0.7234 (mttt) cc_final: 0.6956 (mtpt) REVERT: K 21 ASN cc_start: 0.9287 (OUTLIER) cc_final: 0.8790 (t0) REVERT: K 69 ASN cc_start: 0.8249 (t0) cc_final: 0.8006 (t0) REVERT: K 102 GLN cc_start: 0.8711 (mt0) cc_final: 0.8481 (mt0) REVERT: K 339 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7328 (mp0) REVERT: K 376 MET cc_start: 0.7300 (mmt) cc_final: 0.7048 (mmt) REVERT: L 60 MET cc_start: 0.6400 (mtm) cc_final: 0.6084 (mtm) REVERT: L 78 TRP cc_start: 0.7441 (p-90) cc_final: 0.6812 (p-90) REVERT: V 38 PHE cc_start: 0.7805 (t80) cc_final: 0.7350 (t80) REVERT: V 60 ASP cc_start: 0.7985 (t0) cc_final: 0.7507 (p0) REVERT: Y 63 ASP cc_start: 0.5099 (t0) cc_final: 0.4817 (t0) outliers start: 94 outliers final: 66 residues processed: 486 average time/residue: 0.2035 time to fit residues: 163.2746 Evaluate side-chains 479 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 405 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 413 VAL 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 208 ILE Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 91 optimal weight: 20.0000 chunk 361 optimal weight: 8.9990 chunk 399 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 321 optimal weight: 0.8980 chunk 261 optimal weight: 8.9990 chunk 422 optimal weight: 0.0020 chunk 386 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 409 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 HIS B 168 GLN B 213 HIS B 230 ASN D 176 ASN D 223 GLN E 213 HIS K 21 ASN ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.182379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.133634 restraints weight = 37242.422| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.38 r_work: 0.3300 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34596 Z= 0.173 Angle : 0.560 8.439 47188 Z= 0.295 Chirality : 0.046 0.188 5224 Planarity : 0.004 0.046 6080 Dihedral : 5.459 83.188 4840 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.43 % Allowed : 8.98 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.08 (0.13), residues: 4304 helix: 1.62 (0.24), residues: 496 sheet: -0.09 (0.14), residues: 1296 loop : -0.10 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 242 TYR 0.026 0.002 TYR K 197 PHE 0.019 0.001 PHE C 24 TRP 0.015 0.001 TRP D 142 HIS 0.007 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (34504) covalent geometry : angle 0.55272 / 0.29 (46996) SS BOND : bond 0.00397 / 0.28 ( 84) SS BOND : angle 1.41668 / 0.96 ( 168) hydrogen bonds : bond 0.03642 / 2.47 ( 1135) hydrogen bonds : angle 5.76221 / 4.03 ( 2853) link_NAG-ASN : bond 0.00318 / 0.16 ( 8) link_NAG-ASN : angle 2.16687 / 1.25 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 411 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7752 (mp0) cc_final: 0.7346 (mp0) REVERT: A 161 LYS cc_start: 0.8577 (ttpt) cc_final: 0.7948 (ttmt) REVERT: A 207 ARG cc_start: 0.8983 (mmt180) cc_final: 0.8664 (mmt180) REVERT: A 290 ARG cc_start: 0.8354 (mtp85) cc_final: 0.8112 (mmt180) REVERT: A 344 ASP cc_start: 0.8478 (p0) cc_final: 0.8229 (p0) REVERT: B 60 VAL cc_start: 0.7720 (p) cc_final: 0.7398 (t) REVERT: B 80 ASN cc_start: 0.7900 (m-40) cc_final: 0.7536 (t0) REVERT: B 321 GLU cc_start: 0.8371 (pt0) cc_final: 0.8159 (pt0) REVERT: B 339 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: C 104 ARG cc_start: 0.7110 (mtt-85) cc_final: 0.6343 (mtt-85) REVERT: D 37 ARG cc_start: 0.8775 (mtm-85) cc_final: 0.8443 (mtm110) REVERT: D 45 GLU cc_start: 0.8535 (tp30) cc_final: 0.8219 (mm-30) REVERT: D 142 TRP cc_start: 0.8482 (m100) cc_final: 0.8045 (m100) REVERT: D 146 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8409 (t0) REVERT: D 282 ASP cc_start: 0.8013 (t0) cc_final: 0.7664 (t70) REVERT: D 301 GLU cc_start: 0.7525 (tp30) cc_final: 0.7183 (pm20) REVERT: D 344 ASP cc_start: 0.8432 (p0) cc_final: 0.8018 (p0) REVERT: D 385 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7475 (mmtm) REVERT: E 77 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8417 (tttm) REVERT: E 171 LEU cc_start: 0.8761 (mm) cc_final: 0.8529 (mm) REVERT: E 399 LEU cc_start: 0.7308 (mp) cc_final: 0.6992 (mp) REVERT: F 4 PHE cc_start: 0.6999 (m-80) cc_final: 0.6640 (m-80) REVERT: F 7 MET cc_start: 0.5135 (mmt) cc_final: 0.4784 (mmp) REVERT: F 78 TRP cc_start: 0.6570 (OUTLIER) cc_final: 0.5634 (p-90) REVERT: G 7 MET cc_start: 0.8578 (ptm) cc_final: 0.8314 (ptp) REVERT: G 82 SER cc_start: 0.8987 (p) cc_final: 0.8684 (m) REVERT: G 105 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8062 (mt-10) REVERT: G 136 THR cc_start: 0.8694 (p) cc_final: 0.8429 (m) REVERT: G 148 TYR cc_start: 0.8771 (m-80) cc_final: 0.8477 (m-80) REVERT: G 163 ILE cc_start: 0.7767 (mt) cc_final: 0.7557 (mp) REVERT: G 299 ASP cc_start: 0.7889 (t0) cc_final: 0.7235 (t0) REVERT: G 343 ASN cc_start: 0.8109 (m-40) cc_final: 0.7828 (m-40) REVERT: G 373 SER cc_start: 0.7654 (t) cc_final: 0.7233 (m) REVERT: G 394 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8252 (mm-40) REVERT: G 421 PHE cc_start: 0.6324 (OUTLIER) cc_final: 0.5175 (t80) REVERT: H 77 LYS cc_start: 0.8956 (mttt) cc_final: 0.8695 (mtpp) REVERT: H 86 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8398 (p) REVERT: H 186 LYS cc_start: 0.6350 (tttt) cc_final: 0.5774 (ttpt) REVERT: H 196 LYS cc_start: 0.7672 (tttt) cc_final: 0.7292 (tttm) REVERT: J 98 THR cc_start: 0.9038 (p) cc_final: 0.8668 (m) REVERT: J 343 ASN cc_start: 0.8598 (m-40) cc_final: 0.8147 (m-40) REVERT: J 412 LYS cc_start: 0.7296 (mttt) cc_final: 0.7040 (mtpt) REVERT: K 69 ASN cc_start: 0.8250 (t0) cc_final: 0.8030 (t0) REVERT: K 102 GLN cc_start: 0.8600 (mt0) cc_final: 0.8393 (mt0) REVERT: K 339 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7332 (mp0) REVERT: L 60 MET cc_start: 0.6407 (mtm) cc_final: 0.6047 (mtm) REVERT: L 78 TRP cc_start: 0.7566 (p-90) cc_final: 0.6725 (p-90) REVERT: V 38 PHE cc_start: 0.7911 (t80) cc_final: 0.7396 (t80) REVERT: V 60 ASP cc_start: 0.7946 (t0) cc_final: 0.7516 (p0) REVERT: Y 63 ASP cc_start: 0.5157 (t0) cc_final: 0.4906 (t0) outliers start: 90 outliers final: 64 residues processed: 475 average time/residue: 0.2047 time to fit residues: 160.0397 Evaluate side-chains 472 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 403 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 319 VAL 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 208 ILE Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain X residue 58 CYS Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 271 optimal weight: 5.9990 chunk 256 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 390 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 275 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 317 optimal weight: 0.0040 chunk 333 optimal weight: 4.9990 chunk 313 optimal weight: 3.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN B 213 HIS D 176 ASN D 223 GLN E 21 ASN E 230 ASN G 176 ASN ** K 168 GLN ** 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 = 0.4023 r_free = 0.4023 target = 0.181504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132903 restraints weight = 37077.793| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.43 r_work: 0.3289 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 34596 Z= 0.208 Angle : 0.577 9.217 47188 Z= 0.302 Chirality : 0.047 0.190 5224 Planarity : 0.005 0.044 6080 Dihedral : 5.407 81.262 4840 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.62 % Allowed : 9.52 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.07 (0.13), residues: 4304 helix: 1.62 (0.24), residues: 504 sheet: -0.10 (0.14), residues: 1324 loop : -0.11 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 242 TYR 0.027 0.002 TYR J 309 PHE 0.021 0.002 PHE C 24 TRP 0.015 0.001 TRP B 327 HIS 0.004 0.001 HIS J 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 (34504) covalent geometry : angle 0.56718 / 0.30 (46996) SS BOND : bond 0.00432 / 0.26 ( 84) SS BOND : angle 1.66442 / 1.13 ( 168) hydrogen bonds : bond 0.03644 / 2.47 ( 1135) hydrogen bonds : angle 5.70690 / 3.99 ( 2853) link_NAG-ASN : bond 0.00324 / 0.17 ( 8) link_NAG-ASN : angle 2.04970 / 1.19 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 417 time to evaluate : 1.289 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 61 LYS cc_start: 0.7665 (tptt) cc_final: 0.6987 (ttmt) REVERT: A 99 GLU cc_start: 0.7734 (mp0) cc_final: 0.7250 (mp0) REVERT: A 161 LYS cc_start: 0.8590 (ttpt) cc_final: 0.7949 (ttmt) REVERT: A 207 ARG cc_start: 0.9007 (mmt180) cc_final: 0.8681 (mmt180) REVERT: A 290 ARG cc_start: 0.8344 (mtp85) cc_final: 0.8101 (mmt180) REVERT: A 344 ASP cc_start: 0.8481 (p0) cc_final: 0.8209 (p0) REVERT: A 421 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.5990 (t80) REVERT: B 60 VAL cc_start: 0.7701 (p) cc_final: 0.7365 (t) REVERT: B 80 ASN cc_start: 0.7909 (m-40) cc_final: 0.7506 (t0) REVERT: C 45 LYS cc_start: 0.6860 (tttt) cc_final: 0.6399 (mmtt) REVERT: C 104 ARG cc_start: 0.7184 (mtt-85) cc_final: 0.6400 (mtt-85) REVERT: D 45 GLU cc_start: 0.8577 (tp30) cc_final: 0.8259 (mm-30) REVERT: D 146 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8496 (t0) REVERT: D 282 ASP cc_start: 0.8070 (t0) cc_final: 0.7733 (t70) REVERT: D 301 GLU cc_start: 0.7551 (tp30) cc_final: 0.7087 (pm20) REVERT: D 344 ASP cc_start: 0.8515 (p0) cc_final: 0.8096 (p0) REVERT: D 385 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7490 (mmtm) REVERT: E 77 LYS cc_start: 0.8761 (mtpt) cc_final: 0.8429 (tttm) REVERT: E 339 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7664 (mm-30) REVERT: E 399 LEU cc_start: 0.7277 (mp) cc_final: 0.6927 (mp) REVERT: F 4 PHE cc_start: 0.6931 (m-80) cc_final: 0.6423 (m-80) REVERT: F 7 MET cc_start: 0.5104 (mmt) cc_final: 0.4749 (mmp) REVERT: F 78 TRP cc_start: 0.6436 (OUTLIER) cc_final: 0.5598 (p-90) REVERT: G 82 SER cc_start: 0.9000 (p) cc_final: 0.8725 (m) REVERT: G 105 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8114 (mt-10) REVERT: G 148 TYR cc_start: 0.8788 (m-80) cc_final: 0.8455 (m-80) REVERT: G 163 ILE cc_start: 0.7735 (mt) cc_final: 0.7518 (mp) REVERT: G 299 ASP cc_start: 0.7942 (t0) cc_final: 0.7308 (t0) REVERT: G 343 ASN cc_start: 0.8074 (m-40) cc_final: 0.7818 (m-40) REVERT: G 373 SER cc_start: 0.7879 (t) cc_final: 0.7386 (m) REVERT: G 394 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8275 (mm-40) REVERT: G 421 PHE cc_start: 0.6176 (OUTLIER) cc_final: 0.5051 (t80) REVERT: H 77 LYS cc_start: 0.8959 (mttt) cc_final: 0.8692 (mtpp) REVERT: H 86 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8406 (p) REVERT: H 186 LYS cc_start: 0.6379 (tttt) cc_final: 0.5791 (ttpt) REVERT: H 196 LYS cc_start: 0.7617 (tttt) cc_final: 0.7312 (ttpp) REVERT: J 98 THR cc_start: 0.9033 (p) cc_final: 0.8674 (m) REVERT: J 343 ASN cc_start: 0.8623 (m-40) cc_final: 0.8160 (m-40) REVERT: J 412 LYS cc_start: 0.7226 (mttt) cc_final: 0.6962 (mtpt) REVERT: K 64 TYR cc_start: 0.8351 (m-80) cc_final: 0.8114 (m-10) REVERT: K 102 GLN cc_start: 0.8645 (mt0) cc_final: 0.8435 (mt0) REVERT: K 284 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8767 (mt) REVERT: K 339 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7332 (mp0) REVERT: L 60 MET cc_start: 0.6313 (mtm) cc_final: 0.5941 (mtm) REVERT: L 78 TRP cc_start: 0.7522 (p-90) cc_final: 0.6706 (p-90) REVERT: V 38 PHE cc_start: 0.7835 (t80) cc_final: 0.7315 (t80) REVERT: V 60 ASP cc_start: 0.7942 (t0) cc_final: 0.7477 (p0) REVERT: Y 63 ASP cc_start: 0.5281 (t0) cc_final: 0.5043 (t0) outliers start: 97 outliers final: 80 residues processed: 480 average time/residue: 0.2124 time to fit residues: 167.2812 Evaluate side-chains 493 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 407 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 413 VAL 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 136 GLU Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain K residue 323 LEU Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain X residue 58 CYS Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 266 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 372 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 249 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 234 optimal weight: 8.9990 chunk 415 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 HIS D 176 ASN ** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN E 21 ASN ** K 168 GLN ** 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 = 0.4033 r_free = 0.4033 target = 0.182805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132658 restraints weight = 37352.956| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.32 r_work: 0.3348 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 34596 Z= 0.098 Angle : 0.497 7.684 47188 Z= 0.260 Chirality : 0.044 0.172 5224 Planarity : 0.004 0.040 6080 Dihedral : 4.961 79.398 4840 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.59 % Allowed : 10.84 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.30 (0.13), residues: 4304 helix: 1.98 (0.24), residues: 496 sheet: 0.01 (0.14), residues: 1332 loop : 0.04 (0.13), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 440 TYR 0.025 0.001 TYR K 197 PHE 0.015 0.001 PHE G 421 TRP 0.020 0.001 TRP D 142 HIS 0.011 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (34504) covalent geometry : angle 0.49059 / 0.26 (46996) SS BOND : bond 0.00249 / 0.15 ( 84) SS BOND : angle 1.12863 / 0.76 ( 168) hydrogen bonds : bond 0.03148 / 2.14 ( 1135) hydrogen bonds : angle 5.40389 / 3.77 ( 2853) link_NAG-ASN : bond 0.00257 / 0.12 ( 8) link_NAG-ASN : angle 2.18914 / 1.22 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 435 time to evaluate : 1.124 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 61 LYS cc_start: 0.7757 (tptt) cc_final: 0.7038 (ttmt) REVERT: A 99 GLU cc_start: 0.7563 (mp0) cc_final: 0.7159 (mp0) REVERT: A 161 LYS cc_start: 0.8520 (ttpt) cc_final: 0.7879 (ttmt) REVERT: A 207 ARG cc_start: 0.9006 (mmt180) cc_final: 0.8641 (mmt180) REVERT: A 293 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6288 (tm-30) REVERT: A 306 GLU cc_start: 0.8079 (tt0) cc_final: 0.7765 (pt0) REVERT: A 344 ASP cc_start: 0.8454 (p0) cc_final: 0.8141 (p0) REVERT: A 421 PHE cc_start: 0.7126 (OUTLIER) cc_final: 0.6006 (t80) REVERT: B 60 VAL cc_start: 0.7638 (p) cc_final: 0.7334 (t) REVERT: B 80 ASN cc_start: 0.7772 (m-40) cc_final: 0.7397 (t0) REVERT: B 339 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6647 (mt-10) REVERT: C 104 ARG cc_start: 0.7105 (mtt-85) cc_final: 0.6394 (mtt-85) REVERT: D 37 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8524 (mtm-85) REVERT: D 45 GLU cc_start: 0.8582 (tp30) cc_final: 0.8325 (mm-30) REVERT: D 282 ASP cc_start: 0.8093 (t0) cc_final: 0.7735 (t70) REVERT: D 301 GLU cc_start: 0.7468 (tp30) cc_final: 0.7043 (pm20) REVERT: D 344 ASP cc_start: 0.8443 (p0) cc_final: 0.8046 (p0) REVERT: D 385 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7476 (mmtm) REVERT: E 171 LEU cc_start: 0.8680 (mm) cc_final: 0.8343 (mt) REVERT: E 339 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7636 (mm-30) REVERT: E 399 LEU cc_start: 0.7269 (mp) cc_final: 0.6958 (mp) REVERT: F 4 PHE cc_start: 0.6825 (m-80) cc_final: 0.6356 (m-80) REVERT: F 7 MET cc_start: 0.5143 (mmt) cc_final: 0.4873 (mmp) REVERT: F 78 TRP cc_start: 0.6421 (OUTLIER) cc_final: 0.5492 (p-90) REVERT: G 7 MET cc_start: 0.8552 (ptm) cc_final: 0.8237 (ptp) REVERT: G 82 SER cc_start: 0.8988 (p) cc_final: 0.8747 (m) REVERT: G 105 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8046 (mt-10) REVERT: G 148 TYR cc_start: 0.8758 (m-80) cc_final: 0.8530 (m-80) REVERT: G 163 ILE cc_start: 0.7679 (mt) cc_final: 0.7459 (mp) REVERT: G 299 ASP cc_start: 0.7912 (t0) cc_final: 0.7388 (t0) REVERT: G 313 PHE cc_start: 0.8892 (m-80) cc_final: 0.8585 (m-10) REVERT: G 343 ASN cc_start: 0.8144 (m-40) cc_final: 0.7923 (m-40) REVERT: G 373 SER cc_start: 0.7975 (t) cc_final: 0.7491 (m) REVERT: G 421 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.5063 (t80) REVERT: H 77 LYS cc_start: 0.8877 (mttt) cc_final: 0.8649 (mtpp) REVERT: H 186 LYS cc_start: 0.6483 (tttt) cc_final: 0.5872 (ttpt) REVERT: H 196 LYS cc_start: 0.7593 (tttt) cc_final: 0.7309 (ttpp) REVERT: J 98 THR cc_start: 0.9004 (p) cc_final: 0.8637 (m) REVERT: J 130 GLN cc_start: 0.8612 (mt0) cc_final: 0.8307 (mt0) REVERT: J 132 MET cc_start: 0.8658 (ttm) cc_final: 0.8425 (tpt) REVERT: J 343 ASN cc_start: 0.8602 (m-40) cc_final: 0.8145 (m-40) REVERT: J 412 LYS cc_start: 0.7244 (mttt) cc_final: 0.7000 (mtpt) REVERT: K 64 TYR cc_start: 0.8299 (m-80) cc_final: 0.8077 (m-10) REVERT: K 339 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7340 (mp0) REVERT: L 60 MET cc_start: 0.6447 (mtm) cc_final: 0.6035 (mtm) REVERT: L 78 TRP cc_start: 0.7495 (p-90) cc_final: 0.6798 (p-90) REVERT: V 38 PHE cc_start: 0.7802 (t80) cc_final: 0.7224 (t80) REVERT: V 60 ASP cc_start: 0.7888 (t0) cc_final: 0.7463 (p0) REVERT: Y 63 ASP cc_start: 0.5375 (t0) cc_final: 0.5153 (t0) outliers start: 59 outliers final: 42 residues processed: 468 average time/residue: 0.1978 time to fit residues: 152.0305 Evaluate side-chains 448 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 402 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 189 ASP Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain X residue 58 CYS Chi-restraints excluded: chain Y residue 46 ILE Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 406 optimal weight: 1.9990 chunk 298 optimal weight: 0.0670 chunk 139 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 314 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 405 optimal weight: 0.0870 chunk 21 optimal weight: 6.9990 overall best weight: 2.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 HIS D 223 GLN E 213 HIS F 37 GLN I 11 GLN K 168 GLN V 83 GLN W 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.180906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129846 restraints weight = 37280.049| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.49 r_work: 0.3303 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34596 Z= 0.172 Angle : 0.539 7.344 47188 Z= 0.281 Chirality : 0.046 0.202 5224 Planarity : 0.005 0.110 6080 Dihedral : 5.029 77.305 4840 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.81 % Allowed : 11.30 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.25 (0.13), residues: 4304 helix: 2.01 (0.24), residues: 496 sheet: -0.02 (0.14), residues: 1332 loop : -0.02 (0.13), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 152 TYR 0.025 0.002 TYR J 309 PHE 0.018 0.001 PHE C 24 TRP 0.025 0.001 TRP D 142 HIS 0.023 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (34504) covalent geometry : angle 0.53244 / 0.28 (46996) SS BOND : bond 0.00318 / 0.20 ( 84) SS BOND : angle 1.25375 / 0.84 ( 168) hydrogen bonds : bond 0.03317 / 2.26 ( 1135) hydrogen bonds : angle 5.43358 / 3.79 ( 2853) link_NAG-ASN : bond 0.00257 / 0.13 ( 8) link_NAG-ASN : angle 2.42339 / 1.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 403 time to evaluate : 1.355 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: A 61 LYS cc_start: 0.7727 (tptt) cc_final: 0.6981 (ttmt) REVERT: A 96 CYS cc_start: 0.7478 (m) cc_final: 0.7018 (m) REVERT: A 99 GLU cc_start: 0.7573 (mp0) cc_final: 0.7133 (mp0) REVERT: A 161 LYS cc_start: 0.8536 (ttpt) cc_final: 0.7863 (ttmt) REVERT: A 207 ARG cc_start: 0.9041 (mmt180) cc_final: 0.8658 (mmt180) REVERT: A 290 ARG cc_start: 0.8246 (mtp85) cc_final: 0.8007 (mmt180) REVERT: A 293 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6251 (tm-30) REVERT: A 306 GLU cc_start: 0.8013 (tt0) cc_final: 0.7564 (pt0) REVERT: A 344 ASP cc_start: 0.8466 (p0) cc_final: 0.8179 (p0) REVERT: A 421 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.5958 (t80) REVERT: B 60 VAL cc_start: 0.7584 (p) cc_final: 0.7251 (t) REVERT: B 339 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6726 (mt-10) REVERT: C 45 LYS cc_start: 0.6817 (tttt) cc_final: 0.6288 (mmtt) REVERT: C 104 ARG cc_start: 0.7248 (mtt-85) cc_final: 0.6451 (mtt-85) REVERT: D 45 GLU cc_start: 0.8643 (tp30) cc_final: 0.8357 (mm-30) REVERT: D 282 ASP cc_start: 0.8160 (t0) cc_final: 0.7806 (t70) REVERT: D 301 GLU cc_start: 0.7522 (tp30) cc_final: 0.7002 (pm20) REVERT: D 344 ASP cc_start: 0.8497 (p0) cc_final: 0.8066 (p0) REVERT: D 385 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7448 (mmtm) REVERT: E 171 LEU cc_start: 0.8683 (mm) cc_final: 0.8306 (mt) REVERT: E 339 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7651 (mm-30) REVERT: E 399 LEU cc_start: 0.7276 (mp) cc_final: 0.6945 (mp) REVERT: F 4 PHE cc_start: 0.6726 (m-80) cc_final: 0.6148 (m-80) REVERT: F 7 MET cc_start: 0.5047 (mmt) cc_final: 0.4707 (mmp) REVERT: F 78 TRP cc_start: 0.6290 (OUTLIER) cc_final: 0.5407 (p-90) REVERT: G 7 MET cc_start: 0.8524 (ptm) cc_final: 0.8223 (ptp) REVERT: G 82 SER cc_start: 0.9009 (p) cc_final: 0.8749 (m) REVERT: G 105 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8173 (mt-10) REVERT: G 148 TYR cc_start: 0.8769 (m-80) cc_final: 0.8515 (m-80) REVERT: G 163 ILE cc_start: 0.7608 (mt) cc_final: 0.7374 (mp) REVERT: G 299 ASP cc_start: 0.7920 (t0) cc_final: 0.7299 (t0) REVERT: G 343 ASN cc_start: 0.8165 (m-40) cc_final: 0.7919 (m-40) REVERT: G 373 SER cc_start: 0.8063 (t) cc_final: 0.7494 (m) REVERT: G 421 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5109 (t80) REVERT: H 77 LYS cc_start: 0.8900 (mttt) cc_final: 0.8628 (mtpp) REVERT: H 186 LYS cc_start: 0.6384 (tttt) cc_final: 0.5777 (ttpt) REVERT: H 196 LYS cc_start: 0.7397 (tttt) cc_final: 0.7093 (tttp) REVERT: H 272 LEU cc_start: 0.8266 (mt) cc_final: 0.7995 (mm) REVERT: J 98 THR cc_start: 0.9003 (p) cc_final: 0.8621 (m) REVERT: J 343 ASN cc_start: 0.8626 (m-40) cc_final: 0.8147 (m-40) REVERT: J 412 LYS cc_start: 0.7152 (mttt) cc_final: 0.6909 (mtpt) REVERT: K 102 GLN cc_start: 0.8625 (mt0) cc_final: 0.8407 (mt0) REVERT: K 284 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8725 (mt) REVERT: K 339 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7287 (mp0) REVERT: L 60 MET cc_start: 0.6403 (mtm) cc_final: 0.5925 (mtm) REVERT: L 78 TRP cc_start: 0.7451 (p-90) cc_final: 0.6657 (p-90) REVERT: V 38 PHE cc_start: 0.7775 (t80) cc_final: 0.7237 (t80) REVERT: V 60 ASP cc_start: 0.7913 (t0) cc_final: 0.7411 (p0) REVERT: Y 63 ASP cc_start: 0.5291 (t0) cc_final: 0.5071 (t0) outliers start: 67 outliers final: 52 residues processed: 446 average time/residue: 0.1964 time to fit residues: 144.7102 Evaluate side-chains 455 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 398 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain X residue 58 CYS Chi-restraints excluded: chain Y residue 46 ILE Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 238 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 371 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 GLN B 213 HIS C 28 HIS D 223 GLN E 213 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.181583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.129328 restraints weight = 37066.435| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.51 r_work: 0.3277 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 34596 Z= 0.218 Angle : 0.576 8.814 47188 Z= 0.300 Chirality : 0.047 0.188 5224 Planarity : 0.005 0.042 6080 Dihedral : 5.179 74.411 4840 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.02 % Allowed : 11.27 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.11 (0.13), residues: 4304 helix: 1.92 (0.24), residues: 496 sheet: -0.10 (0.14), residues: 1324 loop : -0.13 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 152 TYR 0.027 0.002 TYR J 309 PHE 0.021 0.002 PHE C 24 TRP 0.030 0.001 TRP D 142 HIS 0.009 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.22 (34504) covalent geometry : angle 0.56791 / 0.30 (46996) SS BOND : bond 0.00369 / 0.23 ( 84) SS BOND : angle 1.39774 / 0.94 ( 168) hydrogen bonds : bond 0.03483 / 2.37 ( 1135) hydrogen bonds : angle 5.53944 / 3.87 ( 2853) link_NAG-ASN : bond 0.00312 / 0.16 ( 8) link_NAG-ASN : angle 2.61899 / 1.34 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 399 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7766 (tptt) cc_final: 0.6986 (ttmt) REVERT: A 99 GLU cc_start: 0.7556 (mp0) cc_final: 0.7060 (mp0) REVERT: A 161 LYS cc_start: 0.8560 (ttpt) cc_final: 0.7892 (ttmt) REVERT: A 207 ARG cc_start: 0.9030 (mmt180) cc_final: 0.8716 (mmt180) REVERT: A 293 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6167 (tm-30) REVERT: A 306 GLU cc_start: 0.8038 (tt0) cc_final: 0.7568 (pt0) REVERT: A 344 ASP cc_start: 0.8475 (p0) cc_final: 0.8207 (p0) REVERT: A 421 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.5950 (t80) REVERT: B 60 VAL cc_start: 0.7546 (p) cc_final: 0.7189 (t) REVERT: B 80 ASN cc_start: 0.7851 (m-40) cc_final: 0.7409 (t0) REVERT: B 152 ARG cc_start: 0.8845 (mtp180) cc_final: 0.8492 (mtt180) REVERT: B 296 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8724 (t) REVERT: B 339 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6696 (mt-10) REVERT: C 104 ARG cc_start: 0.7297 (mtt-85) cc_final: 0.6477 (mtt-85) REVERT: D 45 GLU cc_start: 0.8647 (tp30) cc_final: 0.8331 (mm-30) REVERT: D 282 ASP cc_start: 0.8145 (t0) cc_final: 0.7804 (t70) REVERT: D 301 GLU cc_start: 0.7537 (tp30) cc_final: 0.7004 (pm20) REVERT: D 344 ASP cc_start: 0.8508 (p0) cc_final: 0.8073 (p0) REVERT: D 385 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7456 (mmtm) REVERT: E 171 LEU cc_start: 0.8702 (mm) cc_final: 0.8307 (mt) REVERT: E 399 LEU cc_start: 0.7285 (mp) cc_final: 0.6900 (mp) REVERT: F 4 PHE cc_start: 0.6878 (m-80) cc_final: 0.6233 (m-80) REVERT: F 7 MET cc_start: 0.5040 (mmt) cc_final: 0.4703 (mmp) REVERT: F 78 TRP cc_start: 0.6383 (OUTLIER) cc_final: 0.5518 (p-90) REVERT: G 7 MET cc_start: 0.8518 (ptm) cc_final: 0.8241 (ptp) REVERT: G 82 SER cc_start: 0.9016 (p) cc_final: 0.8748 (m) REVERT: G 105 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8202 (mt-10) REVERT: G 148 TYR cc_start: 0.8739 (m-80) cc_final: 0.8456 (m-80) REVERT: G 163 ILE cc_start: 0.7678 (mt) cc_final: 0.7444 (mp) REVERT: G 299 ASP cc_start: 0.7843 (t0) cc_final: 0.7394 (t0) REVERT: G 343 ASN cc_start: 0.8189 (m-40) cc_final: 0.7958 (m-40) REVERT: G 373 SER cc_start: 0.8130 (t) cc_final: 0.7543 (m) REVERT: G 421 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5125 (t80) REVERT: H 77 LYS cc_start: 0.8939 (mttt) cc_final: 0.8644 (mtpp) REVERT: H 86 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8474 (p) REVERT: H 186 LYS cc_start: 0.6397 (tttt) cc_final: 0.5998 (ttpt) REVERT: H 196 LYS cc_start: 0.7386 (tttt) cc_final: 0.7085 (tttp) REVERT: H 376 MET cc_start: 0.6227 (mmp) cc_final: 0.5860 (mmt) REVERT: J 98 THR cc_start: 0.8996 (p) cc_final: 0.8620 (m) REVERT: J 343 ASN cc_start: 0.8613 (m-40) cc_final: 0.8123 (m-40) REVERT: J 412 LYS cc_start: 0.7154 (mttt) cc_final: 0.6893 (mtpt) REVERT: K 102 GLN cc_start: 0.8670 (mt0) cc_final: 0.8456 (mt0) REVERT: K 284 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8765 (mt) REVERT: K 339 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7265 (mp0) REVERT: L 60 MET cc_start: 0.6404 (mtm) cc_final: 0.5927 (mtm) REVERT: V 38 PHE cc_start: 0.7807 (t80) cc_final: 0.7321 (t80) REVERT: V 60 ASP cc_start: 0.7934 (t0) cc_final: 0.7478 (p0) REVERT: Y 63 ASP cc_start: 0.5214 (t0) cc_final: 0.4985 (t0) outliers start: 75 outliers final: 62 residues processed: 449 average time/residue: 0.2000 time to fit residues: 148.7832 Evaluate side-chains 470 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 401 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 331 ILE Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain X residue 58 CYS Chi-restraints excluded: chain Y residue 46 ILE Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 79 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 177 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 8 optimal weight: 0.0070 chunk 189 optimal weight: 0.9980 chunk 243 optimal weight: 9.9990 chunk 351 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 114 HIS D 176 ASN D 223 GLN E 213 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.189034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138728 restraints weight = 37541.040| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.55 r_work: 0.3384 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 34596 Z= 0.101 Angle : 0.503 7.561 47188 Z= 0.264 Chirality : 0.044 0.184 5224 Planarity : 0.004 0.041 6080 Dihedral : 4.889 72.078 4840 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.43 % Allowed : 11.87 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % 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: 0.30 (0.13), residues: 4304 helix: 2.12 (0.24), residues: 496 sheet: 0.01 (0.14), residues: 1324 loop : -0.00 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 440 TYR 0.023 0.001 TYR K 197 PHE 0.021 0.001 PHE G 95 TRP 0.027 0.001 TRP D 142 HIS 0.039 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (34504) covalent geometry : angle 0.49625 / 0.26 (46996) SS BOND : bond 0.00234 / 0.16 ( 84) SS BOND : angle 1.27008 / 0.88 ( 168) hydrogen bonds : bond 0.03062 / 2.09 ( 1135) hydrogen bonds : angle 5.32367 / 3.72 ( 2853) link_NAG-ASN : bond 0.00224 / 0.11 ( 8) link_NAG-ASN : angle 2.21380 / 1.20 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 403 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7658 (tptt) cc_final: 0.6856 (ttmt) REVERT: A 99 GLU cc_start: 0.7434 (mp0) cc_final: 0.6945 (mp0) REVERT: A 161 LYS cc_start: 0.8543 (ttpt) cc_final: 0.7890 (ttmt) REVERT: A 207 ARG cc_start: 0.9036 (mmt180) cc_final: 0.8653 (mmt180) REVERT: A 293 GLU cc_start: 0.7556 (mm-30) cc_final: 0.6263 (tm-30) REVERT: A 306 GLU cc_start: 0.8077 (tt0) cc_final: 0.7638 (pt0) REVERT: A 344 ASP cc_start: 0.8435 (p0) cc_final: 0.8157 (p0) REVERT: A 421 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.5925 (t80) REVERT: B 60 VAL cc_start: 0.7528 (p) cc_final: 0.7190 (t) REVERT: B 80 ASN cc_start: 0.7633 (m-40) cc_final: 0.7202 (t0) REVERT: B 339 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6678 (mt-10) REVERT: C 104 ARG cc_start: 0.7246 (mtt-85) cc_final: 0.6501 (mtt-85) REVERT: D 45 GLU cc_start: 0.8633 (tp30) cc_final: 0.8366 (mm-30) REVERT: D 282 ASP cc_start: 0.8101 (t0) cc_final: 0.7750 (t70) REVERT: D 301 GLU cc_start: 0.7481 (tp30) cc_final: 0.7001 (pm20) REVERT: D 344 ASP cc_start: 0.8449 (p0) cc_final: 0.8011 (p0) REVERT: E 171 LEU cc_start: 0.8658 (mm) cc_final: 0.8272 (mt) REVERT: E 399 LEU cc_start: 0.7128 (mp) cc_final: 0.6812 (mp) REVERT: F 4 PHE cc_start: 0.6671 (m-80) cc_final: 0.6068 (m-80) REVERT: F 7 MET cc_start: 0.5039 (mmt) cc_final: 0.4741 (mmp) REVERT: G 7 MET cc_start: 0.8500 (ptm) cc_final: 0.8154 (ptp) REVERT: G 82 SER cc_start: 0.8981 (p) cc_final: 0.8774 (m) REVERT: G 105 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8119 (mt-10) REVERT: G 148 TYR cc_start: 0.8672 (m-80) cc_final: 0.8452 (m-80) REVERT: G 163 ILE cc_start: 0.7640 (mt) cc_final: 0.7399 (mp) REVERT: G 299 ASP cc_start: 0.7756 (t0) cc_final: 0.7356 (t0) REVERT: G 313 PHE cc_start: 0.8941 (m-80) cc_final: 0.8564 (m-10) REVERT: G 343 ASN cc_start: 0.8111 (m-40) cc_final: 0.7872 (m-40) REVERT: G 373 SER cc_start: 0.8205 (t) cc_final: 0.7662 (m) REVERT: G 421 PHE cc_start: 0.6175 (OUTLIER) cc_final: 0.5111 (t80) REVERT: H 77 LYS cc_start: 0.8892 (mttt) cc_final: 0.8632 (mtpp) REVERT: H 186 LYS cc_start: 0.6447 (tttt) cc_final: 0.5846 (ttpt) REVERT: H 196 LYS cc_start: 0.7519 (tttt) cc_final: 0.7117 (tttm) REVERT: H 376 MET cc_start: 0.6194 (mmp) cc_final: 0.5839 (mmt) REVERT: J 98 THR cc_start: 0.9018 (p) cc_final: 0.8634 (m) REVERT: J 132 MET cc_start: 0.8673 (ttm) cc_final: 0.8427 (tpt) REVERT: J 343 ASN cc_start: 0.8625 (m-40) cc_final: 0.8130 (m-40) REVERT: J 412 LYS cc_start: 0.7173 (mttt) cc_final: 0.6930 (mtpt) REVERT: K 339 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7305 (mp0) REVERT: L 60 MET cc_start: 0.6289 (mtm) cc_final: 0.5815 (mtm) REVERT: V 38 PHE cc_start: 0.7761 (t80) cc_final: 0.7226 (t80) REVERT: V 60 ASP cc_start: 0.7872 (t0) cc_final: 0.7409 (p0) REVERT: Y 63 ASP cc_start: 0.5272 (t0) cc_final: 0.5046 (t0) outliers start: 53 outliers final: 45 residues processed: 435 average time/residue: 0.2082 time to fit residues: 150.0216 Evaluate side-chains 441 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 393 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 77 ASN Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain X residue 58 CYS Chi-restraints excluded: chain Y residue 46 ILE Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 252 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 chunk 242 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 11 optimal weight: 0.2980 chunk 240 optimal weight: 7.9990 chunk 372 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 HIS B 236 ASN D 223 GLN E 213 HIS J 130 GLN K 80 ASN W 39 GLN Y 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.182846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134157 restraints weight = 37355.139| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.21 r_work: 0.3348 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 34596 Z= 0.208 Angle : 0.564 7.539 47188 Z= 0.294 Chirality : 0.047 0.189 5224 Planarity : 0.005 0.042 6080 Dihedral : 5.071 69.036 4840 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.81 % Allowed : 11.70 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.13), residues: 4304 helix: 2.00 (0.24), residues: 496 sheet: -0.09 (0.14), residues: 1324 loop : -0.12 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 37 TYR 0.027 0.002 TYR J 309 PHE 0.020 0.002 PHE C 24 TRP 0.028 0.001 TRP D 142 HIS 0.005 0.001 HIS J 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 (34504) covalent geometry : angle 0.55651 / 0.29 (46996) SS BOND : bond 0.00433 / 0.26 ( 84) SS BOND : angle 1.41814 / 0.94 ( 168) hydrogen bonds : bond 0.03404 / 2.32 ( 1135) hydrogen bonds : angle 5.45436 / 3.81 ( 2853) link_NAG-ASN : bond 0.00300 / 0.16 ( 8) link_NAG-ASN : angle 2.11138 / 1.17 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11048.44 seconds wall clock time: 189 minutes 14.83 seconds (11354.83 seconds total)