Starting phenix.real_space_refine on Fri May 30 02:32:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufc_42192/05_2025/8ufc_42192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufc_42192/05_2025/8ufc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ufc_42192/05_2025/8ufc_42192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufc_42192/05_2025/8ufc_42192.map" model { file = "/net/cci-nas-00/data/ceres_data/8ufc_42192/05_2025/8ufc_42192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufc_42192/05_2025/8ufc_42192.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 19.08, per 1000 atoms: 0.57 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: 8.67 Conformation dependent library (CDL) restraints added in 4.2 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: 4.73 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: 13.08 Time building geometry restraints manager: 9.77 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: 0.03 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 73.150 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 : 1.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (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 TRP 0.032 0.004 TRP Y 89 HIS 0.011 0.002 HIS B 253 PHE 0.022 0.002 PHE G 421 TYR 0.028 0.005 TYR D 309 ARG 0.027 0.003 ARG D 110 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 8) link_NAG-ASN : angle 2.48148 ( 24) hydrogen bonds : bond 0.20200 ( 1135) hydrogen bonds : angle 8.42540 ( 2853) SS BOND : bond 0.00407 ( 84) SS BOND : angle 1.24629 ( 168) covalent geometry : bond 0.00260 (34504) covalent geometry : angle 0.65281 (46996) *********************** 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 : 3.578 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: 0.4596 time to fit residues: 502.2818 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 : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 361 optimal weight: 20.0000 chunk 324 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 335 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN B 8 GLN B 213 HIS B 230 ASN B 236 ASN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 HIS D 176 ASN D 223 GLN D 356 HIS E 80 ASN E 120 HIS E 151 ASN E 175 HIS E 213 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.182122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130867 restraints weight = 37312.188| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.43 r_work: 0.3320 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.135 34596 Z= 0.254 Angle : 0.651 12.054 47188 Z= 0.347 Chirality : 0.050 0.213 5224 Planarity : 0.005 0.055 6080 Dihedral : 5.355 88.627 4840 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.83 % Allowed : 5.26 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.13), residues: 4304 helix: 1.45 (0.24), residues: 492 sheet: 0.39 (0.13), residues: 1372 loop : 0.37 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 327 HIS 0.012 0.001 HIS K 213 PHE 0.024 0.002 PHE C 24 TYR 0.026 0.002 TYR J 309 ARG 0.007 0.001 ARG B 135 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 8) link_NAG-ASN : angle 2.12839 ( 24) hydrogen bonds : bond 0.04728 ( 1135) hydrogen bonds : angle 6.40202 ( 2853) SS BOND : bond 0.00578 ( 84) SS BOND : angle 1.96549 ( 168) covalent geometry : bond 0.00625 (34504) covalent geometry : angle 0.64013 (46996) *********************** 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 520 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 452 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 SER cc_start: 0.8549 (m) cc_final: 0.8293 (p) REVERT: A 99 GLU cc_start: 0.7639 (mp0) cc_final: 0.7088 (mp0) REVERT: A 141 SER cc_start: 0.8187 (t) cc_final: 0.7801 (p) REVERT: A 161 LYS cc_start: 0.8558 (ttpt) cc_final: 0.7855 (ttmt) REVERT: A 290 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7754 (mmt180) REVERT: B 60 VAL cc_start: 0.7620 (p) cc_final: 0.7314 (t) REVERT: D 45 GLU cc_start: 0.8563 (tp30) cc_final: 0.8351 (mm-30) REVERT: D 109 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7792 (mt-10) REVERT: D 176 ASN cc_start: 0.8404 (t0) cc_final: 0.8042 (t0) REVERT: D 282 ASP cc_start: 0.8112 (t0) cc_final: 0.7764 (t0) REVERT: D 299 ASP cc_start: 0.8169 (t0) cc_final: 0.7961 (m-30) REVERT: D 301 GLU cc_start: 0.7564 (tp30) cc_final: 0.7158 (pm20) REVERT: D 328 ASN cc_start: 0.7703 (t0) cc_final: 0.7432 (t0) REVERT: D 344 ASP cc_start: 0.8478 (p0) cc_final: 0.8247 (p0) REVERT: E 171 LEU cc_start: 0.8766 (mm) cc_final: 0.8467 (mt) REVERT: E 399 LEU cc_start: 0.7167 (mp) cc_final: 0.6929 (mp) REVERT: F 7 MET cc_start: 0.5115 (mmt) cc_final: 0.4775 (mmt) REVERT: F 78 TRP cc_start: 0.6336 (OUTLIER) cc_final: 0.5404 (p-90) REVERT: G 82 SER cc_start: 0.9048 (p) cc_final: 0.8623 (m) REVERT: G 105 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8059 (mt-10) REVERT: G 148 TYR cc_start: 0.8760 (m-80) cc_final: 0.8427 (m-80) REVERT: G 163 ILE cc_start: 0.7580 (mt) cc_final: 0.7347 (mp) REVERT: G 299 ASP cc_start: 0.7976 (t0) cc_final: 0.7258 (t0) REVERT: G 343 ASN cc_start: 0.8156 (m-40) cc_final: 0.7944 (m-40) REVERT: G 373 SER cc_start: 0.7681 (t) cc_final: 0.7177 (m) REVERT: H 129 GLU cc_start: 0.8576 (pt0) cc_final: 0.8305 (pt0) REVERT: H 166 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8780 (ptp) REVERT: H 376 MET cc_start: 0.6208 (mmp) cc_final: 0.4908 (mtp) REVERT: I 7 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5405 (mmt) REVERT: J 98 THR cc_start: 0.9005 (p) cc_final: 0.8559 (m) REVERT: J 322 LYS cc_start: 0.7709 (mttp) cc_final: 0.7244 (mtmt) REVERT: J 343 ASN cc_start: 0.8454 (m-40) cc_final: 0.7890 (m-40) REVERT: J 412 LYS cc_start: 0.7137 (mttt) cc_final: 0.6835 (mtpt) REVERT: K 102 GLN cc_start: 0.8612 (mt0) cc_final: 0.8379 (mt0) REVERT: K 339 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7354 (mp0) REVERT: Y 63 ASP cc_start: 0.4622 (t0) cc_final: 0.4417 (t0) outliers start: 68 outliers final: 43 residues processed: 494 average time/residue: 0.4375 time to fit residues: 354.0431 Evaluate side-chains 454 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 408 time to evaluate : 3.511 ------------------------------------------------------------------------------- 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 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 395 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 306 GLU 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 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 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 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 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 94 optimal weight: 6.9990 chunk 395 optimal weight: 10.0000 chunk 253 optimal weight: 0.7980 chunk 372 optimal weight: 3.9990 chunk 328 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 393 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 168 GLN B 213 HIS B 236 ASN B 253 HIS D 223 GLN E 275 HIS J 328 ASN K 21 ASN ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 HIS K 346 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131523 restraints weight = 37268.017| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.58 r_work: 0.3293 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34596 Z= 0.190 Angle : 0.570 8.127 47188 Z= 0.301 Chirality : 0.047 0.199 5224 Planarity : 0.004 0.063 6080 Dihedral : 5.312 87.370 4840 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.05 % Allowed : 6.85 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.13), residues: 4304 helix: 1.86 (0.24), residues: 472 sheet: 0.33 (0.14), residues: 1272 loop : 0.22 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 327 HIS 0.010 0.001 HIS K 213 PHE 0.022 0.002 PHE C 24 TYR 0.026 0.002 TYR K 197 ARG 0.009 0.000 ARG H 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 8) link_NAG-ASN : angle 2.39620 ( 24) hydrogen bonds : bond 0.04088 ( 1135) hydrogen bonds : angle 5.93722 ( 2853) SS BOND : bond 0.00345 ( 84) SS BOND : angle 1.55253 ( 168) covalent geometry : bond 0.00464 (34504) covalent geometry : angle 0.56135 (46996) *********************** 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 520 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 444 time to evaluate : 3.631 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 41 SER cc_start: 0.8586 (m) cc_final: 0.8361 (p) REVERT: A 99 GLU cc_start: 0.7562 (mp0) cc_final: 0.6817 (mp0) REVERT: A 161 LYS cc_start: 0.8605 (ttpt) cc_final: 0.7903 (ttmt) REVERT: A 290 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7974 (mtp85) REVERT: B 60 VAL cc_start: 0.7584 (p) cc_final: 0.7257 (t) REVERT: B 80 ASN cc_start: 0.7824 (m-40) cc_final: 0.7438 (t0) REVERT: D 45 GLU cc_start: 0.8635 (tp30) cc_final: 0.8394 (mm-30) REVERT: D 109 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7912 (mt-10) REVERT: D 142 TRP cc_start: 0.8402 (m100) cc_final: 0.7927 (m100) REVERT: D 146 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8397 (t0) REVERT: D 282 ASP cc_start: 0.8103 (t0) cc_final: 0.7737 (t70) REVERT: D 299 ASP cc_start: 0.8204 (t0) cc_final: 0.7936 (m-30) REVERT: D 301 GLU cc_start: 0.7534 (tp30) cc_final: 0.7071 (pm20) REVERT: D 328 ASN cc_start: 0.7777 (t0) cc_final: 0.7517 (t0) REVERT: D 344 ASP cc_start: 0.8469 (p0) cc_final: 0.8174 (p0) REVERT: E 171 LEU cc_start: 0.8714 (mm) cc_final: 0.8369 (mt) REVERT: E 399 LEU cc_start: 0.7156 (mp) cc_final: 0.6875 (mp) REVERT: F 78 TRP cc_start: 0.6450 (OUTLIER) cc_final: 0.5480 (p-90) REVERT: G 82 SER cc_start: 0.9012 (p) cc_final: 0.8649 (m) REVERT: G 105 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8147 (mt-10) REVERT: G 148 TYR cc_start: 0.8841 (m-80) cc_final: 0.8471 (m-80) REVERT: G 163 ILE cc_start: 0.7620 (mt) cc_final: 0.7405 (mp) REVERT: G 212 ASN cc_start: 0.8604 (m-40) cc_final: 0.8242 (p0) REVERT: G 299 ASP cc_start: 0.8007 (t0) cc_final: 0.7243 (t0) REVERT: G 343 ASN cc_start: 0.8140 (m-40) cc_final: 0.7886 (m-40) REVERT: G 373 SER cc_start: 0.7628 (t) cc_final: 0.7190 (m) REVERT: H 77 LYS cc_start: 0.9008 (mttt) cc_final: 0.8472 (tttm) REVERT: H 129 GLU cc_start: 0.8682 (pt0) cc_final: 0.8431 (pt0) REVERT: H 166 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8782 (ptp) REVERT: H 186 LYS cc_start: 0.6202 (tttt) cc_final: 0.5786 (ttpt) REVERT: H 196 LYS cc_start: 0.7541 (tttt) cc_final: 0.7091 (tttm) REVERT: H 376 MET cc_start: 0.6316 (mmp) cc_final: 0.5025 (mtp) REVERT: I 7 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.5424 (mmt) REVERT: I 60 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6331 (ttt) REVERT: J 98 THR cc_start: 0.9029 (p) cc_final: 0.8618 (m) REVERT: J 125 HIS cc_start: 0.7143 (m90) cc_final: 0.6914 (m90) REVERT: J 322 LYS cc_start: 0.7722 (mttp) cc_final: 0.7322 (mtmt) REVERT: J 343 ASN cc_start: 0.8600 (m-40) cc_final: 0.8050 (m-40) REVERT: J 412 LYS cc_start: 0.7180 (mttt) cc_final: 0.6897 (mtpt) REVERT: K 147 GLU cc_start: 0.8507 (tt0) cc_final: 0.8172 (tt0) REVERT: K 339 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7265 (mp0) REVERT: K 376 MET cc_start: 0.7179 (mmt) cc_final: 0.6940 (mmt) REVERT: Y 63 ASP cc_start: 0.4613 (t0) cc_final: 0.4367 (t0) outliers start: 76 outliers final: 50 residues processed: 492 average time/residue: 0.4347 time to fit residues: 350.4504 Evaluate side-chains 451 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 396 time to evaluate : 3.546 ------------------------------------------------------------------------------- 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 184 GLU Chi-restraints excluded: chain A residue 195 THR 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 B residue 296 SER 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 79 GLN 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 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 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 413 VAL 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 60 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 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 354 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 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 175 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 78 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 164 optimal weight: 0.4980 chunk 421 optimal weight: 0.0970 chunk 388 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 397 optimal weight: 9.9990 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 236 ASN D 176 ASN D 223 GLN E 140 HIS E 213 HIS H 277 HIS K 213 HIS L 80 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.182401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130701 restraints weight = 37260.539| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.60 r_work: 0.3274 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 34596 Z= 0.242 Angle : 0.611 11.443 47188 Z= 0.321 Chirality : 0.048 0.194 5224 Planarity : 0.005 0.050 6080 Dihedral : 5.515 85.696 4840 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.13 % Allowed : 8.09 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.13), residues: 4304 helix: 1.56 (0.24), residues: 504 sheet: 0.10 (0.14), residues: 1304 loop : 0.05 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 78 HIS 0.007 0.001 HIS K 213 PHE 0.024 0.002 PHE C 24 TYR 0.028 0.002 TYR J 309 ARG 0.005 0.001 ARG H 26 Details of bonding type rmsd link_NAG-ASN : bond 0.00479 ( 8) link_NAG-ASN : angle 2.85760 ( 24) hydrogen bonds : bond 0.03944 ( 1135) hydrogen bonds : angle 5.83674 ( 2853) SS BOND : bond 0.00453 ( 84) SS BOND : angle 1.87774 ( 168) covalent geometry : bond 0.00594 (34504) covalent geometry : angle 0.59876 (46996) *********************** 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 490 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 411 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 SER cc_start: 0.8627 (m) cc_final: 0.8415 (p) REVERT: A 99 GLU cc_start: 0.7633 (mp0) cc_final: 0.6914 (mp0) REVERT: A 161 LYS cc_start: 0.8601 (ttpt) cc_final: 0.7900 (ttmt) REVERT: B 60 VAL cc_start: 0.7667 (p) cc_final: 0.7335 (t) REVERT: B 80 ASN cc_start: 0.7831 (m-40) cc_final: 0.7429 (t0) REVERT: B 339 GLU cc_start: 0.7829 (mp0) cc_final: 0.7526 (mp0) REVERT: D 45 GLU cc_start: 0.8650 (tp30) cc_final: 0.8334 (mm-30) REVERT: D 109 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7907 (mt-10) REVERT: D 134 ASN cc_start: 0.8691 (t0) cc_final: 0.8482 (t0) REVERT: D 146 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8424 (t0) REVERT: D 282 ASP cc_start: 0.8089 (t0) cc_final: 0.7669 (t70) REVERT: D 299 ASP cc_start: 0.8211 (t0) cc_final: 0.7920 (m-30) REVERT: D 301 GLU cc_start: 0.7574 (tp30) cc_final: 0.7063 (pm20) REVERT: D 344 ASP cc_start: 0.8548 (p0) cc_final: 0.8138 (p0) REVERT: D 440 ARG cc_start: 0.5371 (ttm-80) cc_final: 0.4842 (mtp180) REVERT: E 171 LEU cc_start: 0.8671 (mm) cc_final: 0.8430 (mm) REVERT: E 399 LEU cc_start: 0.7146 (mp) cc_final: 0.6823 (mp) REVERT: F 7 MET cc_start: 0.5163 (mmt) cc_final: 0.4909 (mmp) REVERT: F 78 TRP cc_start: 0.6345 (OUTLIER) cc_final: 0.5396 (p-90) REVERT: G 13 ILE cc_start: 0.8875 (mm) cc_final: 0.8661 (mt) REVERT: G 82 SER cc_start: 0.9035 (p) cc_final: 0.8696 (m) REVERT: G 105 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8194 (mt-10) REVERT: G 148 TYR cc_start: 0.8824 (m-80) cc_final: 0.8440 (m-80) REVERT: G 163 ILE cc_start: 0.7616 (mt) cc_final: 0.7389 (mp) REVERT: G 212 ASN cc_start: 0.8656 (m-40) cc_final: 0.8325 (p0) REVERT: G 299 ASP cc_start: 0.7901 (t0) cc_final: 0.7192 (t0) REVERT: G 343 ASN cc_start: 0.8082 (m-40) cc_final: 0.7806 (m-40) REVERT: G 373 SER cc_start: 0.7594 (t) cc_final: 0.7194 (m) REVERT: G 421 PHE cc_start: 0.6271 (OUTLIER) cc_final: 0.5142 (t80) REVERT: H 77 LYS cc_start: 0.9042 (mttt) cc_final: 0.8757 (mtpp) REVERT: H 166 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8763 (ptp) REVERT: H 186 LYS cc_start: 0.6236 (tttt) cc_final: 0.5838 (ttpt) REVERT: H 196 LYS cc_start: 0.7556 (tttt) cc_final: 0.7169 (tttp) REVERT: I 60 MET cc_start: 0.6582 (OUTLIER) cc_final: 0.6251 (ttt) REVERT: J 98 THR cc_start: 0.9000 (p) cc_final: 0.8627 (m) REVERT: J 125 HIS cc_start: 0.7363 (m90) cc_final: 0.7123 (m90) REVERT: J 313 PHE cc_start: 0.9122 (m-80) cc_final: 0.8860 (m-80) REVERT: J 322 LYS cc_start: 0.7473 (mttp) cc_final: 0.7098 (mtmt) REVERT: J 343 ASN cc_start: 0.8591 (m-40) cc_final: 0.8018 (m-40) REVERT: J 412 LYS cc_start: 0.7160 (mttt) cc_final: 0.6875 (mtpt) REVERT: K 69 ASN cc_start: 0.8247 (t0) cc_final: 0.8018 (t0) REVERT: K 339 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7319 (mp0) REVERT: K 376 MET cc_start: 0.7215 (mmt) cc_final: 0.7007 (mmt) REVERT: L 60 MET cc_start: 0.6269 (mtm) cc_final: 0.5943 (mtm) REVERT: L 78 TRP cc_start: 0.7373 (p-90) cc_final: 0.6632 (p-90) REVERT: V 38 PHE cc_start: 0.7496 (t80) cc_final: 0.6893 (t80) REVERT: V 60 ASP cc_start: 0.7917 (t0) cc_final: 0.7402 (p0) REVERT: Y 63 ASP cc_start: 0.4781 (t0) cc_final: 0.4518 (t0) outliers start: 79 outliers final: 62 residues processed: 463 average time/residue: 0.4527 time to fit residues: 343.1596 Evaluate side-chains 460 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 393 time to evaluate : 3.605 ------------------------------------------------------------------------------- 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 184 GLU 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 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 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 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 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 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 G residue 27 VAL 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 G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL 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 19 VAL 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 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 354 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 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 175 HIS 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 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 256 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 199 optimal weight: 7.9990 chunk 192 optimal weight: 0.4980 chunk 390 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 0.0370 chunk 311 optimal weight: 0.9980 chunk 252 optimal weight: 0.0030 chunk 61 optimal weight: 20.0000 overall best weight: 1.1070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 HIS B 168 GLN B 213 HIS B 236 ASN D 176 ASN D 223 GLN E 213 HIS ** K 230 ASN ** 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 = 0.4030 r_free = 0.4030 target = 0.182799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133516 restraints weight = 37126.412| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.25 r_work: 0.3346 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34596 Z= 0.117 Angle : 0.509 7.823 47188 Z= 0.268 Chirality : 0.044 0.184 5224 Planarity : 0.004 0.043 6080 Dihedral : 5.119 84.672 4840 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.54 % Allowed : 8.98 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 4304 helix: 1.91 (0.24), residues: 504 sheet: 0.22 (0.14), residues: 1240 loop : 0.12 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 142 HIS 0.014 0.001 HIS B 213 PHE 0.016 0.001 PHE C 24 TYR 0.026 0.001 TYR K 197 ARG 0.005 0.000 ARG E 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 8) link_NAG-ASN : angle 2.16777 ( 24) hydrogen bonds : bond 0.03363 ( 1135) hydrogen bonds : angle 5.54604 ( 2853) SS BOND : bond 0.00323 ( 84) SS BOND : angle 1.23815 ( 168) covalent geometry : bond 0.00270 (34504) covalent geometry : angle 0.50250 (46996) *********************** 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 472 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 415 time to evaluate : 3.543 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 99 GLU cc_start: 0.7661 (mp0) cc_final: 0.7041 (mp0) REVERT: A 161 LYS cc_start: 0.8553 (ttpt) cc_final: 0.7890 (ttmt) REVERT: A 207 ARG cc_start: 0.8989 (mmt180) cc_final: 0.8616 (mmt180) REVERT: A 306 GLU cc_start: 0.8028 (tt0) cc_final: 0.7756 (pt0) REVERT: B 60 VAL cc_start: 0.7637 (p) cc_final: 0.7347 (t) REVERT: B 80 ASN cc_start: 0.7842 (m-40) cc_final: 0.7481 (t0) REVERT: C 104 ARG cc_start: 0.7068 (mtt-85) cc_final: 0.6389 (mtt-85) REVERT: D 45 GLU cc_start: 0.8549 (tp30) cc_final: 0.8284 (mm-30) REVERT: D 109 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7834 (mt-10) REVERT: D 159 ASP cc_start: 0.7541 (t0) cc_final: 0.7333 (t0) REVERT: D 282 ASP cc_start: 0.8097 (t0) cc_final: 0.7755 (t70) REVERT: D 299 ASP cc_start: 0.8213 (t0) cc_final: 0.7957 (m-30) REVERT: D 301 GLU cc_start: 0.7467 (tp30) cc_final: 0.7013 (pm20) REVERT: D 328 ASN cc_start: 0.7704 (t0) cc_final: 0.7437 (t0) REVERT: D 344 ASP cc_start: 0.8469 (p0) cc_final: 0.8064 (p0) REVERT: E 399 LEU cc_start: 0.7138 (mp) cc_final: 0.6830 (mp) REVERT: F 4 PHE cc_start: 0.6599 (m-80) cc_final: 0.6288 (m-80) REVERT: F 7 MET cc_start: 0.5115 (mmt) cc_final: 0.4763 (mmp) REVERT: G 82 SER cc_start: 0.9007 (p) cc_final: 0.8711 (m) REVERT: G 105 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8052 (mt-10) REVERT: G 136 THR cc_start: 0.8648 (p) cc_final: 0.8441 (m) REVERT: G 140 VAL cc_start: 0.7918 (t) cc_final: 0.7364 (m) REVERT: G 148 TYR cc_start: 0.8753 (m-80) cc_final: 0.8465 (m-80) REVERT: G 163 ILE cc_start: 0.7643 (mt) cc_final: 0.7431 (mp) REVERT: G 212 ASN cc_start: 0.8559 (m-40) cc_final: 0.8321 (p0) REVERT: G 299 ASP cc_start: 0.7925 (t0) cc_final: 0.7254 (t0) REVERT: G 343 ASN cc_start: 0.8084 (m-40) cc_final: 0.7810 (m-40) REVERT: G 373 SER cc_start: 0.7622 (t) cc_final: 0.7213 (m) REVERT: G 421 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.5048 (t80) REVERT: H 16 ILE cc_start: 0.9136 (mt) cc_final: 0.8927 (mt) REVERT: H 77 LYS cc_start: 0.8910 (mttt) cc_final: 0.8653 (mtpp) REVERT: H 166 MET cc_start: 0.9015 (ptp) cc_final: 0.8767 (ptp) REVERT: H 186 LYS cc_start: 0.6250 (tttt) cc_final: 0.5665 (ttpt) REVERT: H 196 LYS cc_start: 0.7621 (tttt) cc_final: 0.7341 (ttpp) REVERT: J 98 THR cc_start: 0.9023 (p) cc_final: 0.8633 (m) REVERT: J 343 ASN cc_start: 0.8584 (m-40) cc_final: 0.8048 (m-40) REVERT: J 412 LYS cc_start: 0.7234 (mttt) cc_final: 0.6980 (mtpt) REVERT: K 69 ASN cc_start: 0.8226 (t0) cc_final: 0.8012 (t0) REVERT: K 376 MET cc_start: 0.7302 (mmt) cc_final: 0.7084 (mmt) REVERT: L 60 MET cc_start: 0.6212 (mtm) cc_final: 0.5894 (mtm) REVERT: L 78 TRP cc_start: 0.7455 (p-90) cc_final: 0.6655 (p-90) REVERT: V 38 PHE cc_start: 0.7616 (t80) cc_final: 0.6980 (t80) REVERT: V 60 ASP cc_start: 0.7906 (t0) cc_final: 0.7444 (p0) REVERT: Y 63 ASP cc_start: 0.5021 (t0) cc_final: 0.4760 (t0) outliers start: 57 outliers final: 42 residues processed: 448 average time/residue: 0.4253 time to fit residues: 314.8306 Evaluate side-chains 441 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 398 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 184 GLU 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 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 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 136 THR Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain E residue 22 CYS 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 G residue 27 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 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 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 208 THR Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR 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 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 78 VAL 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 75 optimal weight: 0.9990 chunk 325 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 411 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 46 optimal weight: 10.0000 chunk 314 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 HIS B 168 GLN B 213 HIS B 230 ASN D 223 GLN D 369 GLN E 21 ASN E 213 HIS E 230 ASN G 176 ASN J 32 GLN ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.183770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134716 restraints weight = 37119.826| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.45 r_work: 0.3311 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34596 Z= 0.178 Angle : 0.540 8.663 47188 Z= 0.283 Chirality : 0.046 0.180 5224 Planarity : 0.004 0.045 6080 Dihedral : 5.131 82.977 4840 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.08 % Allowed : 9.28 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.13), residues: 4304 helix: 1.90 (0.24), residues: 504 sheet: 0.08 (0.14), residues: 1304 loop : 0.09 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 142 HIS 0.004 0.001 HIS J 73 PHE 0.019 0.002 PHE C 24 TYR 0.025 0.002 TYR J 309 ARG 0.006 0.000 ARG E 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 8) link_NAG-ASN : angle 2.03481 ( 24) hydrogen bonds : bond 0.03456 ( 1135) hydrogen bonds : angle 5.50340 ( 2853) SS BOND : bond 0.00321 ( 84) SS BOND : angle 1.38989 ( 168) covalent geometry : bond 0.00433 (34504) covalent geometry : angle 0.53267 (46996) *********************** 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 484 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 407 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7773 (mp0) cc_final: 0.7313 (mp0) REVERT: A 161 LYS cc_start: 0.8564 (ttpt) cc_final: 0.7935 (ttmt) REVERT: A 207 ARG cc_start: 0.8992 (mmt180) cc_final: 0.8614 (mmt180) REVERT: A 290 ARG cc_start: 0.8306 (mtp85) cc_final: 0.8078 (mmt180) REVERT: A 306 GLU cc_start: 0.8077 (tt0) cc_final: 0.7764 (pt0) REVERT: A 421 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6030 (t80) REVERT: B 60 VAL cc_start: 0.7629 (p) cc_final: 0.7333 (t) REVERT: B 80 ASN cc_start: 0.7843 (m-40) cc_final: 0.7499 (t0) REVERT: B 339 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6609 (mt-10) REVERT: C 104 ARG cc_start: 0.7150 (mtt-85) cc_final: 0.6365 (mtt-85) REVERT: D 37 ARG cc_start: 0.8762 (mtm-85) cc_final: 0.8469 (mtm110) REVERT: D 45 GLU cc_start: 0.8569 (tp30) cc_final: 0.8278 (mm-30) REVERT: D 109 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7864 (mt-10) REVERT: D 282 ASP cc_start: 0.8033 (t0) cc_final: 0.7682 (t70) REVERT: D 301 GLU cc_start: 0.7472 (tp30) cc_final: 0.7054 (pm20) REVERT: D 328 ASN cc_start: 0.7792 (t0) cc_final: 0.7510 (t0) REVERT: D 344 ASP cc_start: 0.8479 (p0) cc_final: 0.8117 (p0) REVERT: D 440 ARG cc_start: 0.5282 (mtp180) cc_final: 0.4993 (mtp180) REVERT: E 171 LEU cc_start: 0.8727 (mm) cc_final: 0.8316 (mt) REVERT: E 399 LEU cc_start: 0.7289 (mp) cc_final: 0.6984 (mp) REVERT: F 4 PHE cc_start: 0.6690 (m-80) cc_final: 0.6365 (m-80) REVERT: F 7 MET cc_start: 0.5153 (mmt) cc_final: 0.4787 (mmp) REVERT: F 78 TRP cc_start: 0.6470 (OUTLIER) cc_final: 0.5564 (p-90) REVERT: G 13 ILE cc_start: 0.8937 (mm) cc_final: 0.8716 (mt) REVERT: G 82 SER cc_start: 0.9010 (p) cc_final: 0.8721 (m) REVERT: G 105 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8095 (mt-10) REVERT: G 140 VAL cc_start: 0.7963 (t) cc_final: 0.7412 (m) REVERT: G 148 TYR cc_start: 0.8770 (m-80) cc_final: 0.8453 (m-80) REVERT: G 163 ILE cc_start: 0.7667 (mt) cc_final: 0.7458 (mp) REVERT: G 212 ASN cc_start: 0.8572 (m-40) cc_final: 0.8372 (p0) REVERT: G 299 ASP cc_start: 0.7907 (t0) cc_final: 0.7238 (t0) REVERT: G 343 ASN cc_start: 0.8091 (m-40) cc_final: 0.7830 (m-40) REVERT: G 373 SER cc_start: 0.7600 (t) cc_final: 0.7165 (m) REVERT: G 421 PHE cc_start: 0.6245 (OUTLIER) cc_final: 0.5099 (t80) REVERT: H 77 LYS cc_start: 0.8896 (mttt) cc_final: 0.8665 (mtpp) REVERT: H 166 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8737 (ptp) REVERT: H 186 LYS cc_start: 0.6377 (tttt) cc_final: 0.5767 (ttpt) REVERT: H 196 LYS cc_start: 0.7656 (tttt) cc_final: 0.7374 (ttpp) REVERT: J 98 THR cc_start: 0.9054 (p) cc_final: 0.8649 (m) REVERT: J 125 HIS cc_start: 0.7262 (m90) cc_final: 0.7061 (m90) REVERT: J 343 ASN cc_start: 0.8571 (m-40) cc_final: 0.8114 (m-40) REVERT: J 412 LYS cc_start: 0.7208 (mttt) cc_final: 0.6968 (mtpt) REVERT: K 376 MET cc_start: 0.7272 (mmt) cc_final: 0.7051 (mmt) REVERT: L 60 MET cc_start: 0.6344 (mtm) cc_final: 0.5997 (mtm) REVERT: L 78 TRP cc_start: 0.7488 (p-90) cc_final: 0.6631 (p-90) REVERT: V 38 PHE cc_start: 0.7780 (t80) cc_final: 0.7172 (t80) REVERT: V 60 ASP cc_start: 0.7900 (t0) cc_final: 0.7460 (p0) REVERT: Y 63 ASP cc_start: 0.5042 (t0) cc_final: 0.4777 (t0) outliers start: 77 outliers final: 63 residues processed: 461 average time/residue: 0.4170 time to fit residues: 316.9735 Evaluate side-chains 466 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 398 time to evaluate : 3.643 ------------------------------------------------------------------------------- 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 184 GLU 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 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 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 136 THR 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 D residue 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 133 VAL 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 27 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 H residue 166 MET 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 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 208 THR Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 354 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 175 HIS 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 V residue 78 VAL 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 230 optimal weight: 6.9990 chunk 231 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 403 optimal weight: 7.9990 chunk 364 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 372 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 291 optimal weight: 10.0000 chunk 279 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS D 223 GLN E 213 HIS W 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.184159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134019 restraints weight = 37098.249| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.55 r_work: 0.3297 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2818 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= 0.154 Angle : 0.523 7.635 47188 Z= 0.274 Chirality : 0.045 0.179 5224 Planarity : 0.004 0.045 6080 Dihedral : 5.050 81.033 4840 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.24 % Allowed : 9.36 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.13), residues: 4304 helix: 2.01 (0.24), residues: 496 sheet: 0.08 (0.14), residues: 1324 loop : 0.09 (0.13), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 142 HIS 0.012 0.001 HIS B 213 PHE 0.018 0.001 PHE C 24 TYR 0.025 0.001 TYR K 197 ARG 0.005 0.000 ARG E 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 8) link_NAG-ASN : angle 2.15180 ( 24) hydrogen bonds : bond 0.03334 ( 1135) hydrogen bonds : angle 5.43624 ( 2853) SS BOND : bond 0.00285 ( 84) SS BOND : angle 1.18139 ( 168) covalent geometry : bond 0.00371 (34504) covalent geometry : angle 0.51712 (46996) *********************** 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 487 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 404 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.7727 (mp0) cc_final: 0.7214 (mp0) REVERT: A 161 LYS cc_start: 0.8588 (ttpt) cc_final: 0.7939 (ttmt) REVERT: A 207 ARG cc_start: 0.9020 (mmt180) cc_final: 0.8659 (mmt180) REVERT: A 306 GLU cc_start: 0.8174 (tt0) cc_final: 0.7778 (pt0) REVERT: A 344 ASP cc_start: 0.8367 (p0) cc_final: 0.8156 (p0) REVERT: A 421 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.5986 (t80) REVERT: B 60 VAL cc_start: 0.7628 (p) cc_final: 0.7308 (t) REVERT: B 80 ASN cc_start: 0.7904 (m-40) cc_final: 0.7505 (t0) REVERT: B 339 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6690 (mt-10) REVERT: C 104 ARG cc_start: 0.7172 (mtt-85) cc_final: 0.6434 (mtt-85) REVERT: D 45 GLU cc_start: 0.8648 (tp30) cc_final: 0.8359 (mm-30) REVERT: D 109 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7940 (mt-10) REVERT: D 282 ASP cc_start: 0.8130 (t0) cc_final: 0.7785 (t70) REVERT: D 301 GLU cc_start: 0.7545 (tp30) cc_final: 0.7021 (pm20) REVERT: D 344 ASP cc_start: 0.8515 (p0) cc_final: 0.8114 (p0) REVERT: E 171 LEU cc_start: 0.8735 (mm) cc_final: 0.8332 (mt) REVERT: E 399 LEU cc_start: 0.7217 (mp) cc_final: 0.6895 (mp) REVERT: F 4 PHE cc_start: 0.6789 (m-80) cc_final: 0.6408 (m-80) REVERT: F 7 MET cc_start: 0.5120 (mmt) cc_final: 0.4757 (mmp) REVERT: F 78 TRP cc_start: 0.6415 (OUTLIER) cc_final: 0.5508 (p-90) REVERT: G 45 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7788 (mm-30) REVERT: G 82 SER cc_start: 0.9032 (p) cc_final: 0.8766 (m) REVERT: G 105 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8149 (mt-10) REVERT: G 148 TYR cc_start: 0.8829 (m-80) cc_final: 0.8519 (m-80) REVERT: G 163 ILE cc_start: 0.7705 (mt) cc_final: 0.7491 (mp) REVERT: G 299 ASP cc_start: 0.7983 (t0) cc_final: 0.7334 (t0) REVERT: G 343 ASN cc_start: 0.8133 (m-40) cc_final: 0.7911 (m-40) REVERT: G 373 SER cc_start: 0.7927 (t) cc_final: 0.7426 (m) REVERT: G 421 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.5007 (t80) REVERT: H 77 LYS cc_start: 0.8933 (mttt) cc_final: 0.8689 (mtpp) REVERT: H 166 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8764 (ptp) REVERT: H 186 LYS cc_start: 0.6375 (tttt) cc_final: 0.5766 (ttpt) REVERT: H 196 LYS cc_start: 0.7609 (tttt) cc_final: 0.7338 (tttp) REVERT: J 98 THR cc_start: 0.9026 (p) cc_final: 0.8634 (m) REVERT: J 125 HIS cc_start: 0.7295 (m90) cc_final: 0.7071 (m90) REVERT: J 130 GLN cc_start: 0.8690 (mt0) cc_final: 0.8383 (mt0) REVERT: J 343 ASN cc_start: 0.8583 (m-40) cc_final: 0.8131 (m-40) REVERT: J 412 LYS cc_start: 0.7239 (mttt) cc_final: 0.7014 (mtpt) REVERT: K 339 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7324 (mp0) REVERT: K 376 MET cc_start: 0.7293 (mmt) cc_final: 0.7089 (mmt) REVERT: L 60 MET cc_start: 0.6431 (mtm) cc_final: 0.5961 (mtm) REVERT: L 78 TRP cc_start: 0.7463 (p-90) cc_final: 0.6499 (p-90) REVERT: V 38 PHE cc_start: 0.7769 (t80) cc_final: 0.7164 (t80) REVERT: V 60 ASP cc_start: 0.7916 (t0) cc_final: 0.7429 (p0) REVERT: Y 63 ASP cc_start: 0.5012 (t0) cc_final: 0.4750 (t0) outliers start: 83 outliers final: 71 residues processed: 460 average time/residue: 0.4252 time to fit residues: 322.4530 Evaluate side-chains 474 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 398 time to evaluate : 3.482 ------------------------------------------------------------------------------- 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 184 GLU 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 421 PHE Chi-restraints excluded: chain A residue 432 VAL 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 323 LEU 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 136 THR 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 D residue 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 146 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 F residue 121 VAL Chi-restraints excluded: chain G residue 27 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 166 MET 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 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 208 THR Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 421 PHE 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 175 HIS 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 V residue 58 CYS Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain X residue 58 CYS 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 29 optimal weight: 0.2980 chunk 415 optimal weight: 1.9990 chunk 389 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 328 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 198 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 392 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS E 213 HIS ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.182962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132443 restraints weight = 36975.655| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.36 r_work: 0.3347 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 34596 Z= 0.104 Angle : 0.496 7.813 47188 Z= 0.259 Chirality : 0.044 0.178 5224 Planarity : 0.004 0.044 6080 Dihedral : 4.880 79.521 4840 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.78 % Allowed : 10.01 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.13), residues: 4304 helix: 2.15 (0.24), residues: 496 sheet: 0.13 (0.14), residues: 1304 loop : 0.12 (0.13), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 142 HIS 0.025 0.001 HIS B 213 PHE 0.014 0.001 PHE C 24 TYR 0.023 0.001 TYR K 197 ARG 0.010 0.000 ARG D 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 8) link_NAG-ASN : angle 2.48486 ( 24) hydrogen bonds : bond 0.03137 ( 1135) hydrogen bonds : angle 5.32006 ( 2853) SS BOND : bond 0.00217 ( 84) SS BOND : angle 1.16262 ( 168) covalent geometry : bond 0.00238 (34504) covalent geometry : angle 0.48900 (46996) *********************** 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 471 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 405 time to evaluate : 3.229 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 99 GLU cc_start: 0.7663 (mp0) cc_final: 0.7180 (mp0) REVERT: A 161 LYS cc_start: 0.8518 (ttpt) cc_final: 0.7856 (ttmt) REVERT: A 207 ARG cc_start: 0.9010 (mmt180) cc_final: 0.8672 (mmt180) REVERT: A 306 GLU cc_start: 0.7962 (tt0) cc_final: 0.7670 (pt0) REVERT: A 421 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6011 (t80) REVERT: B 60 VAL cc_start: 0.7714 (p) cc_final: 0.7443 (t) REVERT: B 80 ASN cc_start: 0.7844 (m-40) cc_final: 0.7465 (t0) REVERT: B 339 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6635 (mt-10) REVERT: C 104 ARG cc_start: 0.7138 (mtt-85) cc_final: 0.6440 (mtt-85) REVERT: D 37 ARG cc_start: 0.8767 (mtm-85) cc_final: 0.8534 (mtm110) REVERT: D 45 GLU cc_start: 0.8589 (tp30) cc_final: 0.8319 (mm-30) REVERT: D 109 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7865 (mt-10) REVERT: D 176 ASN cc_start: 0.8452 (t0) cc_final: 0.8172 (t0) REVERT: D 282 ASP cc_start: 0.8083 (t0) cc_final: 0.7723 (t70) REVERT: D 301 GLU cc_start: 0.7431 (tp30) cc_final: 0.7001 (pm20) REVERT: D 344 ASP cc_start: 0.8419 (p0) cc_final: 0.8004 (p0) REVERT: D 440 ARG cc_start: 0.5212 (ttm-80) cc_final: 0.4945 (mtp180) REVERT: E 171 LEU cc_start: 0.8679 (mm) cc_final: 0.8271 (mt) REVERT: E 339 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7653 (mm-30) REVERT: E 399 LEU cc_start: 0.7194 (mp) cc_final: 0.6900 (mp) REVERT: F 4 PHE cc_start: 0.6739 (m-80) cc_final: 0.6380 (m-80) REVERT: F 7 MET cc_start: 0.5179 (mmt) cc_final: 0.4831 (mmp) REVERT: F 78 TRP cc_start: 0.6407 (OUTLIER) cc_final: 0.5466 (p-90) REVERT: G 82 SER cc_start: 0.8986 (p) cc_final: 0.8724 (m) REVERT: G 105 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8054 (mt-10) REVERT: G 148 TYR cc_start: 0.8732 (m-80) cc_final: 0.8472 (m-80) REVERT: G 163 ILE cc_start: 0.7640 (mt) cc_final: 0.7423 (mp) REVERT: G 223 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8207 (mm-40) REVERT: G 299 ASP cc_start: 0.7932 (t0) cc_final: 0.7370 (t0) REVERT: G 343 ASN cc_start: 0.8096 (m-40) cc_final: 0.7846 (m-40) REVERT: G 373 SER cc_start: 0.7902 (t) cc_final: 0.7402 (m) REVERT: G 421 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.5019 (t80) REVERT: H 77 LYS cc_start: 0.8873 (mttt) cc_final: 0.8648 (mtpp) REVERT: H 166 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8724 (ptp) REVERT: H 186 LYS cc_start: 0.6507 (tttt) cc_final: 0.5906 (ttpt) REVERT: H 196 LYS cc_start: 0.7568 (tttt) cc_final: 0.7222 (tttm) REVERT: J 98 THR cc_start: 0.9012 (p) cc_final: 0.8593 (m) REVERT: J 132 MET cc_start: 0.8660 (ttm) cc_final: 0.8425 (tpt) REVERT: J 343 ASN cc_start: 0.8575 (m-40) cc_final: 0.8134 (m-40) REVERT: J 394 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7879 (mm-40) REVERT: J 412 LYS cc_start: 0.7267 (mttt) cc_final: 0.7041 (mtpt) REVERT: K 339 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7318 (mp0) REVERT: K 376 MET cc_start: 0.7318 (mmt) cc_final: 0.7109 (mmt) REVERT: L 60 MET cc_start: 0.6447 (mtm) cc_final: 0.6012 (mtm) REVERT: L 78 TRP cc_start: 0.7432 (p-90) cc_final: 0.6502 (p-90) REVERT: V 38 PHE cc_start: 0.7736 (t80) cc_final: 0.7157 (t80) REVERT: V 60 ASP cc_start: 0.7872 (t0) cc_final: 0.7438 (p0) REVERT: Y 63 ASP cc_start: 0.5101 (t0) cc_final: 0.4848 (t0) outliers start: 66 outliers final: 56 residues processed: 448 average time/residue: 0.4334 time to fit residues: 317.9740 Evaluate side-chains 459 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 398 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 184 GLU 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 421 PHE 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 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 168 SER 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 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 27 VAL 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 166 MET 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 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 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 386 ASP Chi-restraints excluded: chain J residue 421 PHE 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 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain X residue 58 CYS 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 311 optimal weight: 0.5980 chunk 221 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 382 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 367 optimal weight: 6.9990 chunk 279 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 GLN B 213 HIS D 223 GLN E 213 HIS ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.183949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.132422 restraints weight = 37185.988| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.58 r_work: 0.3308 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34596 Z= 0.163 Angle : 0.526 7.310 47188 Z= 0.274 Chirality : 0.046 0.183 5224 Planarity : 0.004 0.044 6080 Dihedral : 4.942 77.424 4840 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.91 % Allowed : 10.25 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.13), residues: 4304 helix: 2.10 (0.24), residues: 496 sheet: 0.09 (0.14), residues: 1304 loop : 0.05 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 142 HIS 0.024 0.001 HIS B 213 PHE 0.018 0.001 PHE C 24 TYR 0.024 0.001 TYR J 309 ARG 0.010 0.000 ARG E 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 8) link_NAG-ASN : angle 2.54324 ( 24) hydrogen bonds : bond 0.03283 ( 1135) hydrogen bonds : angle 5.34853 ( 2853) SS BOND : bond 0.00309 ( 84) SS BOND : angle 1.17560 ( 168) covalent geometry : bond 0.00395 (34504) covalent geometry : angle 0.51908 (46996) *********************** 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 473 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 402 time to evaluate : 3.869 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: 0.7576 (tptt) cc_final: 0.6867 (ttmt) REVERT: A 79 GLN cc_start: 0.8140 (tt0) cc_final: 0.7919 (tp40) REVERT: A 99 GLU cc_start: 0.7658 (mp0) cc_final: 0.7104 (mp0) REVERT: A 161 LYS cc_start: 0.8523 (ttpt) cc_final: 0.7827 (ttmt) REVERT: A 207 ARG cc_start: 0.9043 (mmt180) cc_final: 0.8678 (mmt180) REVERT: A 306 GLU cc_start: 0.7980 (tt0) cc_final: 0.7575 (pt0) REVERT: A 421 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.5961 (t80) REVERT: B 60 VAL cc_start: 0.7679 (p) cc_final: 0.7380 (t) REVERT: B 80 ASN cc_start: 0.7837 (m-40) cc_final: 0.7413 (t0) REVERT: B 339 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.6710 (mt-10) REVERT: C 45 LYS cc_start: 0.6952 (tttt) cc_final: 0.6336 (mmtt) REVERT: C 104 ARG cc_start: 0.7249 (mtt-85) cc_final: 0.6433 (mtt-85) REVERT: D 37 ARG cc_start: 0.8774 (mtm-85) cc_final: 0.8553 (mtm110) REVERT: D 45 GLU cc_start: 0.8642 (tp30) cc_final: 0.8354 (mm-30) REVERT: D 109 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7916 (mt-10) REVERT: D 176 ASN cc_start: 0.8466 (t0) cc_final: 0.8173 (t0) REVERT: D 282 ASP cc_start: 0.8102 (t0) cc_final: 0.7741 (t70) REVERT: D 344 ASP cc_start: 0.8438 (p0) cc_final: 0.7999 (p0) REVERT: D 385 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7397 (mmtm) REVERT: D 440 ARG cc_start: 0.5256 (ttm-80) cc_final: 0.4854 (mtp180) REVERT: E 171 LEU cc_start: 0.8683 (mm) cc_final: 0.8243 (mt) REVERT: E 339 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7675 (mm-30) REVERT: E 399 LEU cc_start: 0.7223 (mp) cc_final: 0.6912 (mp) REVERT: F 4 PHE cc_start: 0.6755 (m-80) cc_final: 0.6285 (m-80) REVERT: F 7 MET cc_start: 0.5129 (mmt) cc_final: 0.4761 (mmp) REVERT: F 78 TRP cc_start: 0.6352 (OUTLIER) cc_final: 0.5462 (p-90) REVERT: G 82 SER cc_start: 0.9007 (p) cc_final: 0.8733 (m) REVERT: G 105 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8141 (mt-10) REVERT: G 148 TYR cc_start: 0.8755 (m-80) cc_final: 0.8501 (m-80) REVERT: G 163 ILE cc_start: 0.7601 (mt) cc_final: 0.7375 (mp) REVERT: G 299 ASP cc_start: 0.7937 (t0) cc_final: 0.7346 (t0) REVERT: G 343 ASN cc_start: 0.8137 (m-40) cc_final: 0.7897 (m-40) REVERT: G 373 SER cc_start: 0.7990 (t) cc_final: 0.7400 (m) REVERT: G 421 PHE cc_start: 0.6127 (OUTLIER) cc_final: 0.4989 (t80) REVERT: H 77 LYS cc_start: 0.8890 (mttt) cc_final: 0.8618 (mtpp) REVERT: H 166 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8738 (ptp) REVERT: H 186 LYS cc_start: 0.6346 (tttt) cc_final: 0.5747 (ttpt) REVERT: H 196 LYS cc_start: 0.7402 (tttt) cc_final: 0.7036 (tttm) REVERT: H 376 MET cc_start: 0.6204 (mmp) cc_final: 0.5839 (mmt) REVERT: J 98 THR cc_start: 0.8996 (p) cc_final: 0.8583 (m) REVERT: J 343 ASN cc_start: 0.8583 (m-40) cc_final: 0.8130 (m-40) REVERT: J 412 LYS cc_start: 0.7160 (mttt) cc_final: 0.6939 (mtpt) REVERT: K 339 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7246 (mp0) REVERT: K 376 MET cc_start: 0.7232 (mmt) cc_final: 0.7031 (mmt) REVERT: L 60 MET cc_start: 0.6370 (mtm) cc_final: 0.5925 (mtm) REVERT: V 38 PHE cc_start: 0.7621 (t80) cc_final: 0.7019 (t80) REVERT: V 60 ASP cc_start: 0.7895 (t0) cc_final: 0.7460 (p0) REVERT: W 89 TRP cc_start: 0.8396 (m-10) cc_final: 0.8131 (m-10) REVERT: Y 63 ASP cc_start: 0.5065 (t0) cc_final: 0.4805 (t0) outliers start: 71 outliers final: 61 residues processed: 448 average time/residue: 0.4319 time to fit residues: 319.0377 Evaluate side-chains 463 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 397 time to evaluate : 3.665 ------------------------------------------------------------------------------- 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 184 GLU 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 421 PHE 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 323 LEU 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 168 SER 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 D residue 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 27 VAL 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 166 MET 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 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 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 354 THR Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 421 PHE 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 175 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain V residue 78 VAL Chi-restraints excluded: chain X residue 58 CYS 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 3 optimal weight: 4.9990 chunk 400 optimal weight: 0.5980 chunk 131 optimal weight: 7.9990 chunk 354 optimal weight: 4.9990 chunk 365 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 331 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 258 optimal weight: 0.7980 chunk 349 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS D 219 ASN D 223 GLN E 213 HIS ** K 230 ASN ** 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 = 0.4048 r_free = 0.4048 target = 0.183969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134326 restraints weight = 36994.257| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.56 r_work: 0.3324 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2965 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= 0.137 Angle : 0.512 7.480 47188 Z= 0.267 Chirality : 0.045 0.180 5224 Planarity : 0.004 0.044 6080 Dihedral : 4.912 75.645 4840 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.91 % Allowed : 10.17 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.13), residues: 4304 helix: 2.13 (0.24), residues: 496 sheet: 0.08 (0.14), residues: 1304 loop : 0.05 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 142 HIS 0.018 0.001 HIS B 213 PHE 0.017 0.001 PHE C 24 TYR 0.023 0.001 TYR K 197 ARG 0.009 0.000 ARG E 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 8) link_NAG-ASN : angle 2.35098 ( 24) hydrogen bonds : bond 0.03199 ( 1135) hydrogen bonds : angle 5.31809 ( 2853) SS BOND : bond 0.00273 ( 84) SS BOND : angle 1.09921 ( 168) covalent geometry : bond 0.00328 (34504) covalent geometry : angle 0.50587 (46996) ********************** 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 470 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 399 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7566 (tptt) cc_final: 0.6903 (ttmt) REVERT: A 99 GLU cc_start: 0.7712 (mp0) cc_final: 0.7168 (mp0) REVERT: A 161 LYS cc_start: 0.8532 (ttpt) cc_final: 0.7868 (ttmt) REVERT: A 207 ARG cc_start: 0.9034 (mmt180) cc_final: 0.8677 (mmt180) REVERT: A 293 GLU cc_start: 0.7675 (mm-30) cc_final: 0.6853 (tm-30) REVERT: A 306 GLU cc_start: 0.8052 (tt0) cc_final: 0.7657 (pt0) REVERT: A 344 ASP cc_start: 0.8362 (p0) cc_final: 0.8160 (p0) REVERT: A 421 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.5959 (t80) REVERT: B 60 VAL cc_start: 0.7707 (p) cc_final: 0.7396 (t) REVERT: B 80 ASN cc_start: 0.7825 (m-40) cc_final: 0.7430 (t0) REVERT: B 339 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.6676 (mt-10) REVERT: C 45 LYS cc_start: 0.6914 (tttt) cc_final: 0.6307 (mmtt) REVERT: C 104 ARG cc_start: 0.7276 (mtt-85) cc_final: 0.6490 (mtt-85) REVERT: D 37 ARG cc_start: 0.8775 (mtm-85) cc_final: 0.8546 (mtm110) REVERT: D 45 GLU cc_start: 0.8641 (tp30) cc_final: 0.8355 (mm-30) REVERT: D 109 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7900 (mt-10) REVERT: D 176 ASN cc_start: 0.8469 (t0) cc_final: 0.8205 (t0) REVERT: D 282 ASP cc_start: 0.8114 (t0) cc_final: 0.7763 (t70) REVERT: D 301 GLU cc_start: 0.7536 (tp30) cc_final: 0.7094 (pm20) REVERT: D 344 ASP cc_start: 0.8448 (p0) cc_final: 0.8020 (p0) REVERT: E 171 LEU cc_start: 0.8700 (mm) cc_final: 0.8258 (mt) REVERT: E 339 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7671 (mm-30) REVERT: E 399 LEU cc_start: 0.7154 (mp) cc_final: 0.6835 (mp) REVERT: F 4 PHE cc_start: 0.6754 (m-80) cc_final: 0.6193 (m-80) REVERT: F 7 MET cc_start: 0.5123 (mmt) cc_final: 0.4761 (mmp) REVERT: F 78 TRP cc_start: 0.6390 (OUTLIER) cc_final: 0.5435 (p-90) REVERT: G 82 SER cc_start: 0.9000 (p) cc_final: 0.8737 (m) REVERT: G 105 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8124 (mt-10) REVERT: G 148 TYR cc_start: 0.8736 (m-80) cc_final: 0.8491 (m-80) REVERT: G 163 ILE cc_start: 0.7634 (mt) cc_final: 0.7400 (mp) REVERT: G 299 ASP cc_start: 0.7966 (t0) cc_final: 0.7393 (t0) REVERT: G 313 PHE cc_start: 0.8944 (m-80) cc_final: 0.8620 (m-10) REVERT: G 343 ASN cc_start: 0.8122 (m-40) cc_final: 0.7888 (m-40) REVERT: G 373 SER cc_start: 0.8134 (t) cc_final: 0.7553 (m) REVERT: G 421 PHE cc_start: 0.6121 (OUTLIER) cc_final: 0.4983 (t80) REVERT: H 77 LYS cc_start: 0.8911 (mttt) cc_final: 0.8646 (mtpp) REVERT: H 166 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8737 (ptp) REVERT: H 186 LYS cc_start: 0.6472 (tttt) cc_final: 0.5874 (ttpt) REVERT: H 196 LYS cc_start: 0.7494 (tttt) cc_final: 0.7101 (tttm) REVERT: H 376 MET cc_start: 0.6226 (mmp) cc_final: 0.5860 (mmt) REVERT: J 98 THR cc_start: 0.9010 (p) cc_final: 0.8595 (m) REVERT: J 343 ASN cc_start: 0.8591 (m-40) cc_final: 0.8148 (m-40) REVERT: J 412 LYS cc_start: 0.7214 (mttt) cc_final: 0.6972 (mtpt) REVERT: K 339 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7288 (mp0) REVERT: L 60 MET cc_start: 0.6364 (mtm) cc_final: 0.5917 (mtm) REVERT: V 38 PHE cc_start: 0.7664 (t80) cc_final: 0.7064 (t80) REVERT: V 60 ASP cc_start: 0.7882 (t0) cc_final: 0.7456 (p0) REVERT: W 89 TRP cc_start: 0.8406 (m-10) cc_final: 0.8137 (m-10) REVERT: Y 63 ASP cc_start: 0.5095 (t0) cc_final: 0.4833 (t0) outliers start: 71 outliers final: 64 residues processed: 445 average time/residue: 0.4211 time to fit residues: 308.1611 Evaluate side-chains 463 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 394 time to evaluate : 3.879 ------------------------------------------------------------------------------- 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 184 GLU 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 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 171 LEU 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 314 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 339 GLU Chi-restraints excluded: chain C residue 48 ILE 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 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 D residue 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 25 LYS Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 27 VAL 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 166 MET 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 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 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 354 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain J residue 421 PHE 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 175 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain X residue 58 CYS 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 44 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 392 optimal weight: 0.6980 chunk 398 optimal weight: 9.9990 chunk 366 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS B 236 ASN C 28 HIS D 77 GLN D 223 GLN E 144 HIS E 213 HIS F 37 GLN I 11 GLN K 80 ASN K 114 HIS ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.180009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.128471 restraints weight = 37201.784| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.56 r_work: 0.3260 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 34596 Z= 0.309 Angle : 0.642 9.111 47188 Z= 0.335 Chirality : 0.050 0.204 5224 Planarity : 0.005 0.054 6080 Dihedral : 5.413 72.073 4840 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.10 % Allowed : 10.17 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 4304 helix: 1.76 (0.24), residues: 496 sheet: -0.18 (0.14), residues: 1308 loop : -0.21 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 142 HIS 0.011 0.001 HIS B 213 PHE 0.029 0.002 PHE C 24 TYR 0.033 0.002 TYR J 309 ARG 0.012 0.001 ARG E 242 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 8) link_NAG-ASN : angle 2.33280 ( 24) hydrogen bonds : bond 0.03827 ( 1135) hydrogen bonds : angle 5.67195 ( 2853) SS BOND : bond 0.00488 ( 84) SS BOND : angle 1.46885 ( 168) covalent geometry : bond 0.00759 (34504) covalent geometry : angle 0.63544 (46996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21571.77 seconds wall clock time: 372 minutes 13.70 seconds (22333.70 seconds total)