Starting phenix.real_space_refine on Tue Aug 26 03:16:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufc_42192/08_2025/8ufc_42192.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufc_42192/08_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_42192/08_2025/8ufc_42192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufc_42192/08_2025/8ufc_42192.map" model { file = "/net/cci-nas-00/data/ceres_data/8ufc_42192/08_2025/8ufc_42192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufc_42192/08_2025/8ufc_42192.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 240 5.16 5 C 21216 2.51 5 N 5828 2.21 5 O 6332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33624 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "B" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "C" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "D" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "E" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "F" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "G" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "H" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "I" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "J" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "K" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "L" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "V" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "W" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "X" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "Y" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 589 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.44, per 1000 atoms: 0.22 Number of scatterers: 33624 At special positions: 0 Unit cell: (161.069, 171.879, 202.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 240 16.00 O 6332 8.00 N 5828 7.00 C 21216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=84, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.04 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.04 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 413 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.02 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 272 " distance=2.03 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 377 " distance=2.03 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 329 " - pdb=" SG CYS D 371 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 103 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 199 " - pdb=" SG CYS E 223 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS E 393 " - pdb=" SG CYS E 413 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.02 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 260 " - pdb=" SG CYS G 272 " distance=2.03 Simple disulfide: pdb=" SG CYS G 302 " - pdb=" SG CYS G 377 " distance=2.03 Simple disulfide: pdb=" SG CYS G 307 " - pdb=" SG CYS G 381 " distance=2.03 Simple disulfide: pdb=" SG CYS G 329 " - pdb=" SG CYS G 371 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 27 " distance=2.03 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 103 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 263 " distance=2.03 Simple disulfide: pdb=" SG CYS H 199 " - pdb=" SG CYS H 223 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 217 " distance=2.04 Simple disulfide: pdb=" SG CYS H 393 " - pdb=" SG CYS H 413 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.02 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 260 " - pdb=" SG CYS J 272 " distance=2.03 Simple disulfide: pdb=" SG CYS J 302 " - pdb=" SG CYS J 377 " distance=2.03 Simple disulfide: pdb=" SG CYS J 307 " - pdb=" SG CYS J 381 " distance=2.03 Simple disulfide: pdb=" SG CYS J 329 " - pdb=" SG CYS J 371 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 122 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 27 " distance=2.03 Simple disulfide: pdb=" SG CYS K 89 " - pdb=" SG CYS K 103 " distance=2.03 Simple disulfide: pdb=" SG CYS K 150 " - pdb=" SG CYS K 263 " distance=2.03 Simple disulfide: pdb=" SG CYS K 199 " - pdb=" SG CYS K 223 " distance=2.04 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 217 " distance=2.03 Simple disulfide: pdb=" SG CYS K 393 " - pdb=" SG CYS K 413 " distance=2.03 Simple disulfide: pdb=" SG CYS V 33 " - pdb=" SG CYS V 45 " distance=2.03 Simple disulfide: pdb=" SG CYS V 40 " - pdb=" SG CYS V 58 " distance=2.04 Simple disulfide: pdb=" SG CYS V 52 " - pdb=" SG CYS V 67 " distance=2.03 Simple disulfide: pdb=" SG CYS V 72 " - pdb=" SG CYS V 84 " distance=2.03 Simple disulfide: pdb=" SG CYS V 79 " - pdb=" SG CYS V 97 " distance=2.03 Simple disulfide: pdb=" SG CYS V 91 " - pdb=" SG CYS V 108 " distance=2.03 Simple disulfide: pdb=" SG CYS W 33 " - pdb=" SG CYS W 45 " distance=2.03 Simple disulfide: pdb=" SG CYS W 40 " - pdb=" SG CYS W 58 " distance=2.03 Simple disulfide: pdb=" SG CYS W 52 " - pdb=" SG CYS W 67 " distance=2.03 Simple disulfide: pdb=" SG CYS W 72 " - pdb=" SG CYS W 84 " distance=2.03 Simple disulfide: pdb=" SG CYS W 79 " - pdb=" SG CYS W 97 " distance=2.04 Simple disulfide: pdb=" SG CYS W 91 " - pdb=" SG CYS W 108 " distance=2.03 Simple disulfide: pdb=" SG CYS X 33 " - pdb=" SG CYS X 45 " distance=2.03 Simple disulfide: pdb=" SG CYS X 40 " - pdb=" SG CYS X 58 " distance=2.04 Simple disulfide: pdb=" SG CYS X 52 " - pdb=" SG CYS X 67 " distance=2.03 Simple disulfide: pdb=" SG CYS X 72 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 79 " - pdb=" SG CYS X 97 " distance=2.04 Simple disulfide: pdb=" SG CYS X 91 " - pdb=" SG CYS X 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 33 " - pdb=" SG CYS Y 45 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 40 " - pdb=" SG CYS Y 58 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 52 " - pdb=" SG CYS Y 67 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 72 " - pdb=" SG CYS Y 84 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 79 " - pdb=" SG CYS Y 97 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 91 " - pdb=" SG CYS Y 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 134 " " NAG B 501 " - " ASN B 315 " " NAG D 501 " - " ASN D 134 " " NAG E 501 " - " ASN E 315 " " NAG G 501 " - " ASN G 134 " " NAG H 501 " - " ASN H 315 " " NAG J 501 " - " ASN J 134 " " NAG K 501 " - " ASN K 315 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8008 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 86 sheets defined 16.1% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 239 through 248 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 404 through 441 Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 348 through 360 Processing helix chain 'B' and resid 360 through 399 Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 239 through 248 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 404 through 441 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 8 through 12 Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 348 through 360 Processing helix chain 'E' and resid 360 through 399 Proline residue: E 396 - end of helix Processing helix chain 'E' and resid 406 through 413 removed outlier: 3.685A pdb=" N ALA E 410 " --> pdb=" O PRO E 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 40 removed outlier: 3.525A pdb=" N ALA F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 removed outlier: 4.392A pdb=" N SER F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 200 through 202 No H-bonds generated for 'chain 'G' and resid 200 through 202' Processing helix chain 'G' and resid 239 through 248 Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 257 through 260 Processing helix chain 'G' and resid 284 through 288 Processing helix chain 'G' and resid 290 through 294 Processing helix chain 'G' and resid 404 through 441 Processing helix chain 'H' and resid 8 through 12 Processing helix chain 'H' and resid 219 through 221 No H-bonds generated for 'chain 'H' and resid 219 through 221' Processing helix chain 'H' and resid 348 through 360 Processing helix chain 'H' and resid 360 through 399 Proline residue: H 396 - end of helix Processing helix chain 'H' and resid 406 through 413 Processing helix chain 'I' and resid 37 through 41 removed outlier: 3.692A pdb=" N ALA I 40 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE I 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 37 through 41' Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'J' and resid 112 through 116 Processing helix chain 'J' and resid 200 through 202 No H-bonds generated for 'chain 'J' and resid 200 through 202' Processing helix chain 'J' and resid 239 through 248 removed outlier: 3.516A pdb=" N LYS J 246 " --> pdb=" O GLU J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 256 Processing helix chain 'J' and resid 257 through 260 Processing helix chain 'J' and resid 284 through 288 Processing helix chain 'J' and resid 290 through 294 Processing helix chain 'J' and resid 404 through 441 removed outlier: 3.603A pdb=" N ARG J 440 " --> pdb=" O LEU J 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 8 through 12 Processing helix chain 'K' and resid 219 through 221 No H-bonds generated for 'chain 'K' and resid 219 through 221' Processing helix chain 'K' and resid 348 through 360 Processing helix chain 'K' and resid 360 through 399 Proline residue: K 396 - end of helix Processing helix chain 'K' and resid 406 through 413 Processing helix chain 'L' and resid 35 through 40 Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 57 through 61 Processing helix chain 'V' and resid 49 through 51 No H-bonds generated for 'chain 'V' and resid 49 through 51' Processing helix chain 'V' and resid 88 through 90 No H-bonds generated for 'chain 'V' and resid 88 through 90' Processing helix chain 'V' and resid 99 through 104 removed outlier: 4.536A pdb=" N ASP V 102 " --> pdb=" O ASP V 99 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 51 No H-bonds generated for 'chain 'W' and resid 49 through 51' Processing helix chain 'W' and resid 88 through 90 No H-bonds generated for 'chain 'W' and resid 88 through 90' Processing helix chain 'W' and resid 100 through 108 Proline residue: W 105 - end of helix Processing helix chain 'X' and resid 49 through 52 removed outlier: 4.429A pdb=" N CYS X 52 " --> pdb=" O LEU X 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 49 through 52' Processing helix chain 'X' and resid 61 through 66 removed outlier: 3.568A pdb=" N LYS X 65 " --> pdb=" O GLY X 61 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN X 66 " --> pdb=" O SER X 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 61 through 66' Processing helix chain 'X' and resid 88 through 90 No H-bonds generated for 'chain 'X' and resid 88 through 90' Processing helix chain 'X' and resid 100 through 104 Processing helix chain 'Y' and resid 49 through 51 No H-bonds generated for 'chain 'Y' and resid 49 through 51' Processing helix chain 'Y' and resid 61 through 66 removed outlier: 4.685A pdb=" N ASN Y 66 " --> pdb=" O SER Y 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 88 through 90 No H-bonds generated for 'chain 'Y' and resid 88 through 90' Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.539A pdb=" N LYS A 161 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.494A pdb=" N MET A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR A 36 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLN A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE A 38 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 128 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TYR A 46 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 148 current: chain 'A' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 184 through 186 current: chain 'A' and resid 268 through 270 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 101 through 110 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 206 Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA7, first strand: chain 'A' and resid 297 through 306 removed outlier: 5.439A pdb=" N ASP A 299 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS A 322 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A 316 " --> pdb=" O THR A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA9, first strand: chain 'A' and resid 365 through 368 Processing sheet with id=AB1, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'B' and resid 17 through 19 removed outlier: 3.606A pdb=" N CYS B 27 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.653A pdb=" N GLN B 48 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B 36 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 27.786A pdb=" N ARG B 46 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 22.803A pdb=" N ASN B 69 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 16.976A pdb=" N GLN B 48 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 13.745A pdb=" N PHE B 67 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 12.167A pdb=" N SER B 50 " --> pdb=" O MET B 65 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N MET B 65 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N MET B 52 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N ALA B 63 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 54 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 72 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 82 through 84 removed outlier: 4.377A pdb=" N ASP B 107 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 146 through 153 Processing sheet with id=AB6, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AB8, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AB9, first strand: chain 'B' and resid 272 through 276 Processing sheet with id=AC1, first strand: chain 'C' and resid 32 through 33 removed outlier: 6.378A pdb=" N PHE C 4 " --> pdb=" O TYR C 15 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TYR C 15 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 6 " --> pdb=" O ASN C 13 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N TYR C 15 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 74 through 78 removed outlier: 9.607A pdb=" N ALA C 82 " --> pdb=" O PRO C 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 89 through 93 current: chain 'C' and resid 113 through 123 removed outlier: 8.225A pdb=" N ALA C 115 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N TRP C 134 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL C 117 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL C 132 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AC4, first strand: chain 'D' and resid 15 through 19 removed outlier: 6.450A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE D 38 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N THR D 128 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR D 126 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR D 42 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL D 124 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU D 44 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TYR D 122 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR D 46 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS D 120 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TYR D 137 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER D 141 " --> pdb=" O TYR D 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 140 through 148 current: chain 'D' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 184 through 186 current: chain 'D' and resid 268 through 270 Processing sheet with id=AC5, first strand: chain 'D' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 51 through 54 current: chain 'D' and resid 101 through 110 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AC7, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AC8, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AC9, first strand: chain 'D' and resid 297 through 306 removed outlier: 4.938A pdb=" N ASP D 299 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS D 322 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE D 316 " --> pdb=" O THR D 305 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 344 through 347 Processing sheet with id=AD2, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AD3, first strand: chain 'E' and resid 17 through 22 removed outlier: 4.625A pdb=" N ASN E 21 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER E 25 " --> pdb=" O ASN E 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 33 through 37 removed outlier: 3.536A pdb=" N SER E 93 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN E 102 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU E 91 " --> pdb=" O GLN E 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 52 through 56 removed outlier: 11.550A pdb=" N MET E 52 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ALA E 63 " --> pdb=" O MET E 52 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY E 54 " --> pdb=" O ASP E 61 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.516A pdb=" N THR E 108 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N HIS E 126 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR E 110 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL E 124 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLY E 112 " --> pdb=" O CYS E 122 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS E 122 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N HIS E 114 " --> pdb=" O HIS E 120 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N HIS E 120 " --> pdb=" O HIS E 114 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 146 through 153 Processing sheet with id=AD8, first strand: chain 'E' and resid 234 through 235 Processing sheet with id=AD9, first strand: chain 'E' and resid 172 through 173 Processing sheet with id=AE1, first strand: chain 'E' and resid 178 through 179 Processing sheet with id=AE2, first strand: chain 'E' and resid 272 through 276 Processing sheet with id=AE3, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.123A pdb=" N PHE F 4 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR F 15 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE F 6 " --> pdb=" O ASN F 13 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR F 15 " --> pdb=" O PRO F 26 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 66 through 67 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 66 through 67 current: chain 'F' and resid 81 through 86 removed outlier: 9.334A pdb=" N ALA F 82 " --> pdb=" O PRO F 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 89 through 93 current: chain 'F' and resid 112 through 122 removed outlier: 8.042A pdb=" N ALA F 115 " --> pdb=" O TRP F 134 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N TRP F 134 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL F 117 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL F 132 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AE6, first strand: chain 'G' and resid 15 through 19 removed outlier: 6.486A pdb=" N MET G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR G 36 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN G 130 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE G 38 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR G 128 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR G 126 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N THR G 42 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL G 124 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU G 44 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR G 122 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR G 46 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LYS G 120 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR G 137 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER G 141 " --> pdb=" O TYR G 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 140 through 148 current: chain 'G' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 184 through 186 current: chain 'G' and resid 268 through 270 Processing sheet with id=AE7, first strand: chain 'G' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 54 current: chain 'G' and resid 101 through 110 No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AE9, first strand: chain 'G' and resid 204 through 206 Processing sheet with id=AF1, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AF2, first strand: chain 'G' and resid 297 through 306 removed outlier: 4.772A pdb=" N ASP G 299 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS G 322 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE G 316 " --> pdb=" O THR G 305 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 344 through 346 Processing sheet with id=AF4, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AF5, first strand: chain 'H' and resid 17 through 22 removed outlier: 5.294A pdb=" N ASP H 18 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER H 29 " --> pdb=" O ASP H 18 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N CYS H 27 " --> pdb=" O PRO H 20 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER H 25 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 33 through 37 removed outlier: 8.596A pdb=" N ILE H 33 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER H 50 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 10.244A pdb=" N SER H 50 " --> pdb=" O MET H 68 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N MET H 68 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR H 64 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N LYS H 56 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N LEU H 62 " --> pdb=" O LYS H 56 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 82 through 84 removed outlier: 3.695A pdb=" N THR H 108 " --> pdb=" O HIS H 126 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N HIS H 126 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N THR H 110 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL H 124 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLY H 112 " --> pdb=" O CYS H 122 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS H 122 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS H 114 " --> pdb=" O HIS H 120 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N HIS H 120 " --> pdb=" O HIS H 114 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 146 through 153 Processing sheet with id=AF9, first strand: chain 'H' and resid 234 through 235 Processing sheet with id=AG1, first strand: chain 'H' and resid 172 through 173 Processing sheet with id=AG2, first strand: chain 'H' and resid 178 through 179 Processing sheet with id=AG3, first strand: chain 'H' and resid 272 through 276 Processing sheet with id=AG4, first strand: chain 'I' and resid 32 through 33 removed outlier: 3.703A pdb=" N GLY I 14 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N TYR I 15 " --> pdb=" O PRO I 26 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 74 through 78 removed outlier: 9.812A pdb=" N ALA I 82 " --> pdb=" O PRO I 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 89 through 93 current: chain 'I' and resid 113 through 122 removed outlier: 8.853A pdb=" N VAL I 114 " --> pdb=" O TRP I 134 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP I 134 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER I 130 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY I 120 " --> pdb=" O ALA I 128 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA I 128 " --> pdb=" O GLY I 120 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASN I 122 " --> pdb=" O ARG I 126 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ARG I 126 " --> pdb=" O ASN I 122 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.560A pdb=" N LYS J 161 " --> pdb=" O ASP J 282 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 15 through 19 removed outlier: 6.564A pdb=" N MET J 132 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR J 36 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLN J 130 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE J 38 " --> pdb=" O THR J 128 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR J 128 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR J 126 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR J 42 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL J 124 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU J 44 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR J 122 " --> pdb=" O LEU J 44 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR J 46 " --> pdb=" O LYS J 120 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS J 120 " --> pdb=" O TYR J 46 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR J 137 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N SER J 141 " --> pdb=" O TYR J 137 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 140 through 148 current: chain 'J' and resid 184 through 186 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 184 through 186 current: chain 'J' and resid 268 through 270 Processing sheet with id=AG8, first strand: chain 'J' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 51 through 54 current: chain 'J' and resid 101 through 110 No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AH1, first strand: chain 'J' and resid 204 through 206 Processing sheet with id=AH2, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AH3, first strand: chain 'J' and resid 296 through 306 removed outlier: 6.047A pdb=" N VAL J 297 " --> pdb=" O SER J 324 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER J 324 " --> pdb=" O VAL J 297 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP J 299 " --> pdb=" O LYS J 322 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS J 322 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE J 316 " --> pdb=" O THR J 305 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 344 through 346 Processing sheet with id=AH5, first strand: chain 'J' and resid 388 through 389 Processing sheet with id=AH6, first strand: chain 'K' and resid 17 through 19 removed outlier: 3.639A pdb=" N CYS K 27 " --> pdb=" O CYS K 19 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 33 through 37 removed outlier: 8.478A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N SER K 50 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N MET K 68 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N TYR K 64 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N LYS K 56 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 9.552A pdb=" N LEU K 62 " --> pdb=" O LYS K 56 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 82 through 84 removed outlier: 3.549A pdb=" N THR K 108 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS K 126 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N THR K 110 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL K 124 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLY K 112 " --> pdb=" O CYS K 122 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N CYS K 122 " --> pdb=" O GLY K 112 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N HIS K 114 " --> pdb=" O HIS K 120 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS K 120 " --> pdb=" O HIS K 114 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 146 through 153 Processing sheet with id=AI1, first strand: chain 'K' and resid 234 through 235 Processing sheet with id=AI2, first strand: chain 'K' and resid 172 through 173 Processing sheet with id=AI3, first strand: chain 'K' and resid 178 through 179 Processing sheet with id=AI4, first strand: chain 'K' and resid 272 through 276 Processing sheet with id=AI5, first strand: chain 'L' and resid 32 through 33 removed outlier: 3.743A pdb=" N GLY L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TYR L 15 " --> pdb=" O PRO L 26 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY L 54 " --> pdb=" O VAL L 23 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 74 through 78 removed outlier: 8.984A pdb=" N ALA L 82 " --> pdb=" O PRO L 93 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 89 through 93 current: chain 'L' and resid 113 through 122 removed outlier: 9.040A pdb=" N VAL L 114 " --> pdb=" O TRP L 134 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TRP L 134 " --> pdb=" O VAL L 114 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER L 130 " --> pdb=" O LEU L 118 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY L 120 " --> pdb=" O ALA L 128 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA L 128 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASN L 122 " --> pdb=" O ARG L 126 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG L 126 " --> pdb=" O ASN L 122 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 37 through 39 Processing sheet with id=AI8, first strand: chain 'V' and resid 76 through 78 Processing sheet with id=AI9, first strand: chain 'W' and resid 37 through 39 Processing sheet with id=AJ1, first strand: chain 'W' and resid 76 through 78 Processing sheet with id=AJ2, first strand: chain 'X' and resid 37 through 39 Processing sheet with id=AJ3, first strand: chain 'X' and resid 76 through 78 Processing sheet with id=AJ4, first strand: chain 'Y' and resid 37 through 39 Processing sheet with id=AJ5, first strand: chain 'Y' and resid 76 through 78 1135 hydrogen bonds defined for protein. 2853 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.53 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11000 1.35 - 1.47: 8258 1.47 - 1.59: 14962 1.59 - 1.71: 0 1.71 - 1.83: 284 Bond restraints: 34504 Sorted by residual: bond pdb=" C1 NAG K 501 " pdb=" O5 NAG K 501 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 NAG H 501 " pdb=" O5 NAG H 501 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" N ALA X 31 " pdb=" CA ALA X 31 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ALA W 31 " pdb=" CA ALA W 31 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 34499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 44207 1.28 - 2.56: 2234 2.56 - 3.84: 503 3.84 - 5.11: 49 5.11 - 6.39: 3 Bond angle restraints: 46996 Sorted by residual: angle pdb=" N ASN Y 66 " pdb=" CA ASN Y 66 " pdb=" C ASN Y 66 " ideal model delta sigma weight residual 112.90 117.67 -4.77 1.31e+00 5.83e-01 1.33e+01 angle pdb=" N LYS Y 65 " pdb=" CA LYS Y 65 " pdb=" C LYS Y 65 " ideal model delta sigma weight residual 111.07 114.69 -3.62 1.07e+00 8.73e-01 1.15e+01 angle pdb=" N VAL A 55 " pdb=" CA VAL A 55 " pdb=" C VAL A 55 " ideal model delta sigma weight residual 108.15 111.01 -2.86 9.90e-01 1.02e+00 8.35e+00 angle pdb=" N ALA H 42 " pdb=" CA ALA H 42 " pdb=" C ALA H 42 " ideal model delta sigma weight residual 109.11 113.07 -3.96 1.42e+00 4.96e-01 7.76e+00 angle pdb=" N TRP H 327 " pdb=" CA TRP H 327 " pdb=" C TRP H 327 " ideal model delta sigma weight residual 109.96 105.35 4.61 1.68e+00 3.54e-01 7.53e+00 ... (remaining 46991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 20070 17.95 - 35.91: 592 35.91 - 53.86: 159 53.86 - 71.82: 39 71.82 - 89.77: 16 Dihedral angle restraints: 20876 sinusoidal: 8368 harmonic: 12508 Sorted by residual: dihedral pdb=" CB CYS J 329 " pdb=" SG CYS J 329 " pdb=" SG CYS J 371 " pdb=" CB CYS J 371 " ideal model delta sinusoidal sigma weight residual 93.00 148.40 -55.40 1 1.00e+01 1.00e-02 4.15e+01 dihedral pdb=" CB CYS X 52 " pdb=" SG CYS X 52 " pdb=" SG CYS X 67 " pdb=" CB CYS X 67 " ideal model delta sinusoidal sigma weight residual 93.00 142.94 -49.94 1 1.00e+01 1.00e-02 3.42e+01 dihedral pdb=" CB CYS V 52 " pdb=" SG CYS V 52 " pdb=" SG CYS V 67 " pdb=" CB CYS V 67 " ideal model delta sinusoidal sigma weight residual 93.00 137.69 -44.69 1 1.00e+01 1.00e-02 2.78e+01 ... (remaining 20873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3269 0.035 - 0.071: 1279 0.071 - 0.106: 460 0.106 - 0.141: 197 0.141 - 0.177: 19 Chirality restraints: 5224 Sorted by residual: chirality pdb=" C1 NAG K 501 " pdb=" ND2 ASN K 315 " pdb=" C2 NAG K 501 " pdb=" O5 NAG K 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CA PRO B 286 " pdb=" N PRO B 286 " pdb=" C PRO B 286 " pdb=" CB PRO B 286 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA CYS D 371 " pdb=" N CYS D 371 " pdb=" C CYS D 371 " pdb=" CB CYS D 371 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 5221 not shown) Planarity restraints: 6088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 84 " 0.274 9.50e-02 1.11e+02 1.23e-01 1.06e+01 pdb=" NE ARG B 84 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG B 84 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 84 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 84 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 239 " -0.277 9.50e-02 1.11e+02 1.24e-01 9.72e+00 pdb=" NE ARG K 239 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG K 239 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG K 239 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG K 239 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 110 " 0.240 9.50e-02 1.11e+02 1.08e-01 9.56e+00 pdb=" NE ARG D 110 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG D 110 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG D 110 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG D 110 " -0.000 2.00e-02 2.50e+03 ... (remaining 6085 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1990 2.73 - 3.27: 32508 3.27 - 3.81: 54575 3.81 - 4.36: 67618 4.36 - 4.90: 118904 Nonbonded interactions: 275595 Sorted by model distance: nonbonded pdb=" OD2 ASP Y 63 " pdb="CA CA Y 201 " model vdw 2.186 2.510 nonbonded pdb=" OD1 ASP Y 53 " pdb="CA CA Y 201 " model vdw 2.206 2.510 nonbonded pdb=" O TRP V 89 " pdb="CA CA V 202 " model vdw 2.254 2.510 nonbonded pdb=" O TRP Y 50 " pdb="CA CA Y 201 " model vdw 2.264 2.510 nonbonded pdb=" O LYS H 398 " pdb=" NH1 ARG L 22 " model vdw 2.280 3.120 ... (remaining 275590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 29.850 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.780 ------------------------------------------------------------------------------- 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 : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.12), residues: 4304 helix: 0.73 (0.22), residues: 488 sheet: 0.62 (0.14), residues: 1320 loop : 0.51 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG D 110 TYR 0.028 0.005 TYR D 309 PHE 0.022 0.002 PHE G 421 TRP 0.032 0.004 TRP Y 89 HIS 0.011 0.002 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00260 (34504) covalent geometry : angle 0.65281 (46996) SS BOND : bond 0.00407 ( 84) SS BOND : angle 1.24629 ( 168) hydrogen bonds : bond 0.20200 ( 1135) hydrogen bonds : angle 8.42540 ( 2853) link_NAG-ASN : bond 0.00257 ( 8) link_NAG-ASN : angle 2.48148 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 687 time to evaluate : 1.219 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: 0.6574 (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: 0.1999 time to fit residues: 218.8587 Evaluate side-chains 441 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN B 8 GLN B 102 GLN B 213 HIS B 230 ASN B 236 ASN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN D 223 GLN D 356 HIS E 80 ASN E 120 HIS E 151 ASN E 175 HIS E 213 HIS 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 = 0.4030 r_free = 0.4030 target = 0.182018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.130419 restraints weight = 37386.341| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.57 r_work: 0.3280 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 34596 Z= 0.323 Angle : 0.714 12.184 47188 Z= 0.379 Chirality : 0.052 0.222 5224 Planarity : 0.005 0.059 6080 Dihedral : 5.671 88.052 4840 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.94 % Allowed : 5.50 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.12), residues: 4304 helix: 1.28 (0.24), residues: 492 sheet: 0.28 (0.13), residues: 1340 loop : 0.20 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 26 TYR 0.030 0.003 TYR J 309 PHE 0.030 0.003 PHE C 24 TRP 0.020 0.002 TRP B 327 HIS 0.012 0.002 HIS K 213 Details of bonding type rmsd covalent geometry : bond 0.00796 (34504) covalent geometry : angle 0.70362 (46996) SS BOND : bond 0.00598 ( 84) SS BOND : angle 2.02686 ( 168) hydrogen bonds : bond 0.04766 ( 1135) hydrogen bonds : angle 6.37304 ( 2853) link_NAG-ASN : bond 0.00394 ( 8) link_NAG-ASN : angle 2.22717 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 447 time to evaluate : 1.310 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: 0.8599 (m) cc_final: 0.8370 (p) REVERT: A 99 GLU cc_start: 0.7703 (mp0) cc_final: 0.7155 (mp0) REVERT: A 141 SER cc_start: 0.8177 (t) cc_final: 0.7778 (p) REVERT: A 161 LYS cc_start: 0.8603 (ttpt) cc_final: 0.7909 (ttmt) REVERT: A 290 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7869 (mtp85) REVERT: A 293 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7375 (mm-30) REVERT: A 344 ASP cc_start: 0.8470 (p0) cc_final: 0.8256 (p0) REVERT: B 60 VAL cc_start: 0.7644 (p) cc_final: 0.7311 (t) REVERT: D 45 GLU cc_start: 0.8607 (tp30) cc_final: 0.8356 (mm-30) REVERT: D 109 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7881 (mt-10) REVERT: D 134 ASN cc_start: 0.8707 (t0) cc_final: 0.8435 (t0) REVERT: D 146 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8506 (t0) REVERT: D 282 ASP cc_start: 0.8120 (t0) cc_final: 0.7785 (t0) REVERT: D 299 ASP cc_start: 0.8218 (t0) cc_final: 0.7979 (m-30) REVERT: D 301 GLU cc_start: 0.7592 (tp30) cc_final: 0.7163 (pm20) REVERT: D 344 ASP cc_start: 0.8548 (p0) cc_final: 0.8206 (p0) REVERT: F 78 TRP cc_start: 0.6171 (OUTLIER) cc_final: 0.5187 (p-90) REVERT: F 117 VAL cc_start: 0.6691 (t) cc_final: 0.6393 (m) REVERT: G 82 SER cc_start: 0.9069 (p) cc_final: 0.8673 (m) REVERT: G 148 TYR cc_start: 0.8798 (m-80) cc_final: 0.8468 (m-80) REVERT: G 163 ILE cc_start: 0.7617 (mt) cc_final: 0.7387 (mp) REVERT: G 212 ASN cc_start: 0.8637 (m-40) cc_final: 0.8267 (p0) REVERT: G 299 ASP cc_start: 0.7992 (t0) cc_final: 0.7260 (t0) REVERT: G 343 ASN cc_start: 0.8202 (m-40) cc_final: 0.7951 (m-40) REVERT: G 373 SER cc_start: 0.7712 (t) cc_final: 0.7205 (m) REVERT: H 77 LYS cc_start: 0.9012 (mttt) cc_final: 0.8731 (mtpp) REVERT: H 129 GLU cc_start: 0.8675 (pt0) cc_final: 0.8439 (pt0) REVERT: H 166 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8780 (ptp) REVERT: H 302 ASN cc_start: 0.8137 (t0) cc_final: 0.7899 (m-40) REVERT: H 358 ASN cc_start: 0.8589 (m-40) cc_final: 0.8275 (m110) REVERT: H 376 MET cc_start: 0.6196 (mmp) cc_final: 0.4872 (mtp) REVERT: I 7 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5576 (mmt) REVERT: J 98 THR cc_start: 0.9020 (p) cc_final: 0.8608 (m) REVERT: J 322 LYS cc_start: 0.7548 (mttp) cc_final: 0.7076 (mtmt) REVERT: J 343 ASN cc_start: 0.8512 (m-40) cc_final: 0.7949 (m-40) REVERT: J 412 LYS cc_start: 0.7153 (mttt) cc_final: 0.6837 (mtpt) REVERT: K 102 GLN cc_start: 0.8706 (mt0) cc_final: 0.8373 (tt0) REVERT: K 339 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7395 (mp0) REVERT: Y 63 ASP cc_start: 0.4677 (t0) cc_final: 0.4415 (t0) outliers start: 72 outliers final: 48 residues processed: 494 average time/residue: 0.1876 time to fit residues: 152.1571 Evaluate side-chains 445 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 393 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain H residue 160 GLN Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 146 ASP Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain K residue 21 ASN Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 370 THR Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 84 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 270 optimal weight: 0.6980 chunk 411 optimal weight: 0.3980 chunk 89 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 360 optimal weight: 5.9990 chunk 304 optimal weight: 0.9980 chunk 276 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 102 GLN B 168 GLN B 213 HIS B 253 HIS C 79 HIS D 176 ASN D 223 GLN H 344 ASN K 73 GLN ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.184395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.134703 restraints weight = 37274.068| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.29 r_work: 0.3358 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34596 Z= 0.112 Angle : 0.526 9.153 47188 Z= 0.279 Chirality : 0.045 0.200 5224 Planarity : 0.004 0.059 6080 Dihedral : 5.223 87.532 4840 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.38 % Allowed : 7.34 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.13), residues: 4304 helix: 1.99 (0.24), residues: 472 sheet: 0.27 (0.14), residues: 1340 loop : 0.28 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 119 TYR 0.024 0.001 TYR K 197 PHE 0.015 0.001 PHE G 421 TRP 0.013 0.001 TRP B 327 HIS 0.009 0.001 HIS K 213 Details of bonding type rmsd covalent geometry : bond 0.00251 (34504) covalent geometry : angle 0.51513 (46996) SS BOND : bond 0.00440 ( 84) SS BOND : angle 1.64015 ( 168) hydrogen bonds : bond 0.03815 ( 1135) hydrogen bonds : angle 5.86041 ( 2853) link_NAG-ASN : bond 0.00378 ( 8) link_NAG-ASN : angle 2.37018 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 450 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8043 (mm-30) REVERT: A 99 GLU cc_start: 0.7570 (mp0) cc_final: 0.7082 (mp0) REVERT: A 161 LYS cc_start: 0.8560 (ttpt) cc_final: 0.7901 (ttmt) REVERT: A 207 ARG cc_start: 0.8931 (mmt180) cc_final: 0.8541 (mmt180) REVERT: A 290 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7904 (mmt180) REVERT: B 60 VAL cc_start: 0.7584 (p) cc_final: 0.7271 (t) REVERT: B 80 ASN cc_start: 0.7834 (m-40) cc_final: 0.7461 (t0) REVERT: C 134 TRP cc_start: 0.6436 (m-90) cc_final: 0.6011 (m-90) REVERT: D 109 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7877 (mt-10) REVERT: D 142 TRP cc_start: 0.8415 (m100) cc_final: 0.7969 (m100) REVERT: D 176 ASN cc_start: 0.8481 (t0) cc_final: 0.8178 (t0) REVERT: D 282 ASP cc_start: 0.8118 (t0) cc_final: 0.7759 (t70) REVERT: D 299 ASP cc_start: 0.8186 (t0) cc_final: 0.7970 (m-30) REVERT: D 301 GLU cc_start: 0.7510 (tp30) cc_final: 0.7139 (pm20) REVERT: D 328 ASN cc_start: 0.7638 (t0) cc_final: 0.7387 (t0) REVERT: D 344 ASP cc_start: 0.8401 (p0) cc_final: 0.8122 (p0) REVERT: E 399 LEU cc_start: 0.7029 (mp) cc_final: 0.6776 (mp) REVERT: F 7 MET cc_start: 0.5193 (mmt) cc_final: 0.4833 (mmp) REVERT: F 78 TRP cc_start: 0.6467 (OUTLIER) cc_final: 0.5550 (p-90) REVERT: G 82 SER cc_start: 0.9022 (p) cc_final: 0.8644 (m) REVERT: G 105 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8012 (mt-10) REVERT: G 148 TYR cc_start: 0.8789 (m-80) cc_final: 0.8408 (m-80) REVERT: G 163 ILE cc_start: 0.7632 (mt) cc_final: 0.7418 (mp) REVERT: G 212 ASN cc_start: 0.8542 (m-40) cc_final: 0.8242 (p0) REVERT: G 299 ASP cc_start: 0.7963 (t0) cc_final: 0.7249 (t0) REVERT: G 343 ASN cc_start: 0.8100 (m-40) cc_final: 0.7818 (m-40) REVERT: G 373 SER cc_start: 0.7687 (t) cc_final: 0.7298 (m) REVERT: G 394 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8242 (mm-40) REVERT: H 77 LYS cc_start: 0.8991 (mttt) cc_final: 0.8620 (tttm) REVERT: H 129 GLU cc_start: 0.8607 (pt0) cc_final: 0.8326 (pt0) REVERT: H 166 MET cc_start: 0.9000 (ptp) cc_final: 0.8753 (ptp) REVERT: H 186 LYS cc_start: 0.6206 (tttt) cc_final: 0.5593 (ttpt) REVERT: H 196 LYS cc_start: 0.7602 (tttt) cc_final: 0.7204 (ttpp) REVERT: H 310 ARG cc_start: 0.8497 (ptp-110) cc_final: 0.8087 (ptp90) REVERT: H 376 MET cc_start: 0.6310 (mmp) cc_final: 0.5022 (mtp) REVERT: I 60 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.6203 (ttt) REVERT: J 98 THR cc_start: 0.9017 (p) cc_final: 0.8596 (m) REVERT: J 322 LYS cc_start: 0.7643 (mttp) cc_final: 0.7245 (mtmt) REVERT: J 343 ASN cc_start: 0.8564 (m-40) cc_final: 0.8042 (m-40) REVERT: J 412 LYS cc_start: 0.7202 (mttt) cc_final: 0.6932 (mtpt) REVERT: K 147 GLU cc_start: 0.8426 (tt0) cc_final: 0.8149 (tt0) REVERT: K 339 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7390 (mp0) REVERT: K 376 MET cc_start: 0.7222 (mmt) cc_final: 0.6972 (mmt) REVERT: Y 63 ASP cc_start: 0.4600 (t0) cc_final: 0.4339 (t0) outliers start: 51 outliers final: 28 residues processed: 478 average time/residue: 0.1832 time to fit residues: 143.3747 Evaluate side-chains 437 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 407 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 60 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 319 VAL 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 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 K residue 22 CYS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 234 optimal weight: 10.0000 chunk 142 optimal weight: 20.0000 chunk 413 optimal weight: 0.9980 chunk 314 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 394 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 298 optimal weight: 0.0030 chunk 395 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 204 optimal weight: 4.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- 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 D 223 GLN E 140 HIS E 213 HIS E 275 HIS H 277 HIS J 328 ASN K 73 GLN ** K 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 213 HIS L 80 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.182221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.129926 restraints weight = 37068.514| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.59 r_work: 0.3283 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 34596 Z= 0.246 Angle : 0.611 11.030 47188 Z= 0.321 Chirality : 0.048 0.196 5224 Planarity : 0.005 0.053 6080 Dihedral : 5.459 85.722 4840 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.89 % Allowed : 8.50 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.13), residues: 4304 helix: 1.62 (0.24), residues: 504 sheet: 0.11 (0.14), residues: 1296 loop : 0.07 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 26 TYR 0.029 0.002 TYR J 309 PHE 0.024 0.002 PHE C 24 TRP 0.020 0.001 TRP L 78 HIS 0.007 0.001 HIS K 213 Details of bonding type rmsd covalent geometry : bond 0.00604 (34504) covalent geometry : angle 0.60092 (46996) SS BOND : bond 0.00521 ( 84) SS BOND : angle 1.72624 ( 168) hydrogen bonds : bond 0.03941 ( 1135) hydrogen bonds : angle 5.81991 ( 2853) link_NAG-ASN : bond 0.00396 ( 8) link_NAG-ASN : angle 2.63132 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 410 time to evaluate : 0.826 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 45 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8173 (mm-30) REVERT: A 99 GLU cc_start: 0.7644 (mp0) cc_final: 0.6935 (mp0) REVERT: A 161 LYS cc_start: 0.8576 (ttpt) cc_final: 0.7883 (ttmt) REVERT: A 207 ARG cc_start: 0.9000 (mmt180) cc_final: 0.8598 (mmt180) REVERT: A 344 ASP cc_start: 0.8421 (p0) cc_final: 0.8140 (p0) REVERT: B 60 VAL cc_start: 0.7682 (p) cc_final: 0.7362 (t) REVERT: B 80 ASN cc_start: 0.7817 (m-40) cc_final: 0.7456 (t0) REVERT: D 45 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8322 (mm-30) REVERT: D 109 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7867 (mt-10) REVERT: D 134 ASN cc_start: 0.8666 (t0) cc_final: 0.8447 (t0) REVERT: D 146 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8545 (t0) REVERT: D 282 ASP cc_start: 0.8054 (t0) cc_final: 0.7682 (t70) REVERT: D 299 ASP cc_start: 0.8182 (t0) cc_final: 0.7919 (m-30) REVERT: D 301 GLU cc_start: 0.7562 (tp30) cc_final: 0.7083 (pm20) REVERT: D 344 ASP cc_start: 0.8502 (p0) cc_final: 0.8103 (p0) REVERT: E 399 LEU cc_start: 0.7192 (mp) cc_final: 0.6944 (mp) REVERT: F 7 MET cc_start: 0.5129 (mmt) cc_final: 0.4745 (mmp) REVERT: F 78 TRP cc_start: 0.6369 (OUTLIER) cc_final: 0.5501 (p-90) REVERT: F 117 VAL cc_start: 0.6781 (t) cc_final: 0.6479 (m) REVERT: G 82 SER cc_start: 0.9027 (p) cc_final: 0.8677 (m) REVERT: G 105 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8162 (mt-10) REVERT: G 125 HIS cc_start: 0.8118 (m90) cc_final: 0.7900 (m90) REVERT: G 148 TYR cc_start: 0.8813 (m-80) cc_final: 0.8422 (m-80) REVERT: G 163 ILE cc_start: 0.7616 (mt) cc_final: 0.7395 (mp) REVERT: G 212 ASN cc_start: 0.8639 (m-40) cc_final: 0.8318 (p0) REVERT: G 299 ASP cc_start: 0.7883 (t0) cc_final: 0.7176 (t0) REVERT: G 343 ASN cc_start: 0.8093 (m-40) cc_final: 0.7810 (m-40) REVERT: G 373 SER cc_start: 0.7540 (t) cc_final: 0.7062 (m) REVERT: G 421 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.5170 (t80) REVERT: H 65 MET cc_start: 0.8600 (ttp) cc_final: 0.8319 (ttp) REVERT: H 77 LYS cc_start: 0.9026 (mttt) cc_final: 0.8744 (mtpp) REVERT: H 166 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8810 (ptp) REVERT: H 186 LYS cc_start: 0.6283 (tttt) cc_final: 0.5876 (ttpt) REVERT: H 196 LYS cc_start: 0.7596 (tttt) cc_final: 0.7163 (ttpp) REVERT: I 60 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6347 (ttt) REVERT: J 98 THR cc_start: 0.9010 (p) cc_final: 0.8630 (m) REVERT: J 125 HIS cc_start: 0.7343 (m90) cc_final: 0.7104 (m90) REVERT: J 322 LYS cc_start: 0.7545 (mttp) cc_final: 0.7172 (mtmt) REVERT: J 343 ASN cc_start: 0.8572 (m-40) cc_final: 0.8016 (m-40) REVERT: J 412 LYS cc_start: 0.7194 (mttt) cc_final: 0.6911 (mtpt) REVERT: K 69 ASN cc_start: 0.8258 (t0) cc_final: 0.8028 (t0) REVERT: K 339 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7295 (mp0) REVERT: K 376 MET cc_start: 0.7219 (mmt) cc_final: 0.6973 (mmt) REVERT: L 78 TRP cc_start: 0.7394 (p-90) cc_final: 0.6769 (p-90) REVERT: V 38 PHE cc_start: 0.7559 (t80) cc_final: 0.6988 (t80) REVERT: V 60 ASP cc_start: 0.7921 (t0) cc_final: 0.7450 (p0) REVERT: Y 63 ASP cc_start: 0.5132 (t0) cc_final: 0.4883 (t0) outliers start: 70 outliers final: 58 residues processed: 454 average time/residue: 0.1788 time to fit residues: 133.8712 Evaluate side-chains 457 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 394 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 67 TYR 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 261 SER Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 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 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 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 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 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 175 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 247 THR 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 91 optimal weight: 20.0000 chunk 361 optimal weight: 10.0000 chunk 399 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 321 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 422 optimal weight: 6.9990 chunk 386 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 409 optimal weight: 0.0270 chunk 46 optimal weight: 0.8980 overall best weight: 1.7242 ------------------------------------------------------------------------------- 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 D 176 ASN D 223 GLN E 213 HIS J 32 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136103 restraints weight = 37163.668| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.26 r_work: 0.3323 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34596 Z= 0.145 Angle : 0.524 7.933 47188 Z= 0.275 Chirality : 0.045 0.180 5224 Planarity : 0.004 0.048 6080 Dihedral : 5.191 84.504 4840 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.91 % Allowed : 8.93 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.13), residues: 4304 helix: 1.86 (0.24), residues: 504 sheet: 0.11 (0.14), residues: 1296 loop : 0.12 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 242 TYR 0.026 0.001 TYR K 197 PHE 0.018 0.001 PHE C 24 TRP 0.015 0.001 TRP D 142 HIS 0.013 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00348 (34504) covalent geometry : angle 0.51698 (46996) SS BOND : bond 0.00277 ( 84) SS BOND : angle 1.26120 ( 168) hydrogen bonds : bond 0.03453 ( 1135) hydrogen bonds : angle 5.58091 ( 2853) link_NAG-ASN : bond 0.00315 ( 8) link_NAG-ASN : angle 2.13671 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 403 time to evaluate : 1.073 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 45 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8147 (mm-30) REVERT: A 99 GLU cc_start: 0.7701 (mp0) cc_final: 0.7065 (mp0) REVERT: A 161 LYS cc_start: 0.8547 (ttpt) cc_final: 0.7902 (ttmt) REVERT: A 207 ARG cc_start: 0.8996 (mmt180) cc_final: 0.8617 (mmt180) REVERT: A 344 ASP cc_start: 0.8362 (p0) cc_final: 0.8090 (p0) REVERT: B 60 VAL cc_start: 0.7657 (p) cc_final: 0.7333 (t) REVERT: B 80 ASN cc_start: 0.7873 (m-40) cc_final: 0.7486 (t0) REVERT: C 104 ARG cc_start: 0.7075 (mtt-85) cc_final: 0.6395 (mtt-85) REVERT: D 45 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8341 (mm-30) REVERT: D 109 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7888 (mt-10) REVERT: D 142 TRP cc_start: 0.8433 (m100) cc_final: 0.7957 (m100) REVERT: D 282 ASP cc_start: 0.8107 (t0) cc_final: 0.7755 (t70) REVERT: D 299 ASP cc_start: 0.8227 (t0) cc_final: 0.7953 (m-30) REVERT: D 301 GLU cc_start: 0.7492 (tp30) cc_final: 0.7010 (pm20) REVERT: D 344 ASP cc_start: 0.8504 (p0) cc_final: 0.8095 (p0) REVERT: E 399 LEU cc_start: 0.7138 (mp) cc_final: 0.6841 (mp) REVERT: F 7 MET cc_start: 0.5118 (mmt) cc_final: 0.4742 (mmp) REVERT: F 78 TRP cc_start: 0.6463 (OUTLIER) cc_final: 0.5488 (p-90) REVERT: G 82 SER cc_start: 0.9028 (p) cc_final: 0.8721 (m) REVERT: G 105 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8093 (mt-10) REVERT: G 148 TYR cc_start: 0.8771 (m-80) cc_final: 0.8498 (m-80) REVERT: G 163 ILE cc_start: 0.7641 (mt) cc_final: 0.7427 (mp) REVERT: G 212 ASN cc_start: 0.8593 (m-40) cc_final: 0.8343 (p0) REVERT: G 299 ASP cc_start: 0.7917 (t0) cc_final: 0.7237 (t0) REVERT: G 343 ASN cc_start: 0.8074 (m-40) cc_final: 0.7784 (m-40) REVERT: G 373 SER cc_start: 0.7567 (t) cc_final: 0.7125 (m) REVERT: G 394 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8233 (mm-40) REVERT: G 421 PHE cc_start: 0.6219 (OUTLIER) cc_final: 0.5084 (t80) REVERT: H 77 LYS cc_start: 0.8942 (mttt) cc_final: 0.8652 (mtpp) REVERT: H 166 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8789 (ptp) REVERT: H 186 LYS cc_start: 0.6235 (tttt) cc_final: 0.5653 (ttpt) REVERT: H 196 LYS cc_start: 0.7611 (tttt) cc_final: 0.7305 (ttpp) REVERT: J 98 THR cc_start: 0.9043 (p) cc_final: 0.8632 (m) REVERT: J 343 ASN cc_start: 0.8593 (m-40) cc_final: 0.8055 (m-40) REVERT: J 412 LYS cc_start: 0.7255 (mttt) cc_final: 0.6996 (mtpt) REVERT: K 69 ASN cc_start: 0.8201 (t0) cc_final: 0.7990 (t0) REVERT: K 339 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7323 (mp0) REVERT: K 376 MET cc_start: 0.7281 (mmt) cc_final: 0.7059 (mmt) REVERT: L 7 MET cc_start: 0.5123 (OUTLIER) cc_final: 0.4425 (mmt) REVERT: L 60 MET cc_start: 0.6264 (mtm) cc_final: 0.5955 (mtm) REVERT: L 78 TRP cc_start: 0.7450 (p-90) cc_final: 0.6715 (p-90) REVERT: V 38 PHE cc_start: 0.7611 (t80) cc_final: 0.6947 (t80) REVERT: V 60 ASP cc_start: 0.7912 (t0) cc_final: 0.7409 (p0) REVERT: Y 63 ASP cc_start: 0.5396 (t0) cc_final: 0.5188 (t0) outliers start: 71 outliers final: 54 residues processed: 451 average time/residue: 0.1805 time to fit residues: 134.8615 Evaluate side-chains 452 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 394 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 291 ILE 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 C residue 60 MET 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 261 SER Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 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 218 THR Chi-restraints excluded: chain H residue 246 ASP Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 135 ILE Chi-restraints excluded: chain J residue 211 SER Chi-restraints excluded: chain J residue 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER 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 315 ASN Chi-restraints excluded: chain L residue 7 MET 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 Y residue 58 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 271 optimal weight: 0.4980 chunk 256 optimal weight: 8.9990 chunk 253 optimal weight: 2.9990 chunk 390 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 chunk 317 optimal weight: 0.0020 chunk 333 optimal weight: 10.0000 chunk 313 optimal weight: 3.9990 overall best weight: 1.8994 ------------------------------------------------------------------------------- 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 D 223 GLN E 21 ASN E 213 HIS E 230 ASN W 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.184095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.134689 restraints weight = 36959.649| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.32 r_work: 0.3319 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2731 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= 0.156 Angle : 0.526 8.268 47188 Z= 0.276 Chirality : 0.045 0.179 5224 Planarity : 0.004 0.048 6080 Dihedral : 5.103 83.070 4840 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.29 % Allowed : 9.09 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.13), residues: 4304 helix: 1.92 (0.24), residues: 504 sheet: 0.08 (0.14), residues: 1296 loop : 0.10 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 242 TYR 0.025 0.001 TYR K 197 PHE 0.018 0.001 PHE C 24 TRP 0.014 0.001 TRP B 327 HIS 0.005 0.001 HIS E 95 Details of bonding type rmsd covalent geometry : bond 0.00375 (34504) covalent geometry : angle 0.51839 (46996) SS BOND : bond 0.00333 ( 84) SS BOND : angle 1.44767 ( 168) hydrogen bonds : bond 0.03386 ( 1135) hydrogen bonds : angle 5.49714 ( 2853) link_NAG-ASN : bond 0.00300 ( 8) link_NAG-ASN : angle 2.03276 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 397 time to evaluate : 1.007 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: 0.7776 (mp0) cc_final: 0.7313 (mp0) REVERT: A 161 LYS cc_start: 0.8546 (ttpt) cc_final: 0.7917 (ttmt) REVERT: A 207 ARG cc_start: 0.8998 (mmt180) cc_final: 0.8716 (mmt180) REVERT: A 344 ASP cc_start: 0.8349 (p0) cc_final: 0.8056 (p0) REVERT: A 421 PHE cc_start: 0.7129 (OUTLIER) cc_final: 0.6004 (t80) REVERT: B 60 VAL cc_start: 0.7642 (p) cc_final: 0.7325 (t) REVERT: B 80 ASN cc_start: 0.7885 (m-40) cc_final: 0.7497 (t0) REVERT: C 104 ARG cc_start: 0.7119 (mtt-85) cc_final: 0.6352 (mtt-85) REVERT: D 45 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8338 (mm-30) REVERT: D 109 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7869 (mt-10) REVERT: D 142 TRP cc_start: 0.8445 (m100) cc_final: 0.7939 (m100) REVERT: D 282 ASP cc_start: 0.8084 (t0) cc_final: 0.7728 (t70) REVERT: D 301 GLU cc_start: 0.7474 (tp30) cc_final: 0.7031 (pm20) REVERT: D 344 ASP cc_start: 0.8498 (p0) cc_final: 0.8090 (p0) REVERT: D 385 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7451 (mmtm) REVERT: E 399 LEU cc_start: 0.7213 (mp) cc_final: 0.6921 (mp) REVERT: F 4 PHE cc_start: 0.6653 (m-80) cc_final: 0.6299 (m-80) REVERT: F 7 MET cc_start: 0.5192 (mmt) cc_final: 0.4815 (mmp) REVERT: F 78 TRP cc_start: 0.6451 (OUTLIER) cc_final: 0.5544 (p-90) REVERT: G 45 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7787 (mm-30) REVERT: G 82 SER cc_start: 0.9011 (p) cc_final: 0.8722 (m) REVERT: G 105 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8084 (mt-10) REVERT: G 148 TYR cc_start: 0.8758 (m-80) cc_final: 0.8454 (m-80) REVERT: G 163 ILE cc_start: 0.7656 (mt) cc_final: 0.7433 (mp) REVERT: G 299 ASP cc_start: 0.7942 (t0) cc_final: 0.7295 (t0) REVERT: G 343 ASN cc_start: 0.8107 (m-40) cc_final: 0.7846 (m-40) REVERT: G 373 SER cc_start: 0.7605 (t) cc_final: 0.7173 (m) REVERT: G 421 PHE cc_start: 0.6085 (OUTLIER) cc_final: 0.4951 (t80) REVERT: H 77 LYS cc_start: 0.8919 (mttt) cc_final: 0.8669 (mtpp) REVERT: H 166 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8783 (ptp) REVERT: H 186 LYS cc_start: 0.6353 (tttt) cc_final: 0.5747 (ttpt) REVERT: H 196 LYS cc_start: 0.7616 (tttt) cc_final: 0.7337 (tttp) REVERT: J 98 THR cc_start: 0.9014 (p) cc_final: 0.8623 (m) REVERT: J 343 ASN cc_start: 0.8572 (m-40) cc_final: 0.8136 (m-40) REVERT: J 412 LYS cc_start: 0.7170 (mttt) cc_final: 0.6930 (mtpt) REVERT: K 339 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7363 (mp0) REVERT: K 376 MET cc_start: 0.7285 (mmt) cc_final: 0.7066 (mmt) REVERT: L 7 MET cc_start: 0.5172 (OUTLIER) cc_final: 0.4535 (mmt) REVERT: L 60 MET cc_start: 0.6305 (mtm) cc_final: 0.5959 (mtm) REVERT: L 78 TRP cc_start: 0.7454 (p-90) cc_final: 0.6778 (p-90) REVERT: V 38 PHE cc_start: 0.7724 (t80) cc_final: 0.7109 (t80) REVERT: V 60 ASP cc_start: 0.7916 (t0) cc_final: 0.7445 (p0) REVERT: Y 63 ASP cc_start: 0.5391 (t0) cc_final: 0.5179 (t0) outliers start: 85 outliers final: 73 residues processed: 455 average time/residue: 0.1746 time to fit residues: 132.7284 Evaluate side-chains 465 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 387 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 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 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 395 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 396 THR Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 168 SER Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 331 ILE Chi-restraints excluded: chain G residue 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 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 221 LYS Chi-restraints excluded: chain J residue 235 THR Chi-restraints excluded: chain J residue 318 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain K residue 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 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 7 MET 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 W residue 39 GLN Chi-restraints excluded: chain X residue 58 CYS Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 266 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 249 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 415 optimal weight: 7.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 ASN D 223 GLN E 21 ASN E 144 HIS E 213 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.181735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131624 restraints weight = 37297.238| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.31 r_work: 0.3329 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34596 Z= 0.135 Angle : 0.509 7.445 47188 Z= 0.266 Chirality : 0.045 0.179 5224 Planarity : 0.004 0.047 6080 Dihedral : 4.995 81.678 4840 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.05 % Allowed : 9.55 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.13), residues: 4304 helix: 2.04 (0.24), residues: 496 sheet: 0.11 (0.14), residues: 1316 loop : 0.12 (0.13), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 242 TYR 0.024 0.001 TYR K 197 PHE 0.017 0.001 PHE C 24 TRP 0.013 0.001 TRP B 327 HIS 0.004 0.001 HIS E 95 Details of bonding type rmsd covalent geometry : bond 0.00322 (34504) covalent geometry : angle 0.50242 (46996) SS BOND : bond 0.00280 ( 84) SS BOND : angle 1.22763 ( 168) hydrogen bonds : bond 0.03272 ( 1135) hydrogen bonds : angle 5.41742 ( 2853) link_NAG-ASN : bond 0.00267 ( 8) link_NAG-ASN : angle 2.22451 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 405 time to evaluate : 1.137 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 99 GLU cc_start: 0.7713 (mp0) cc_final: 0.7250 (mp0) REVERT: A 161 LYS cc_start: 0.8541 (ttpt) cc_final: 0.7912 (ttmt) REVERT: A 207 ARG cc_start: 0.9000 (mmt180) cc_final: 0.8647 (mmt180) REVERT: A 344 ASP cc_start: 0.8330 (p0) cc_final: 0.8044 (p0) REVERT: A 421 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6041 (t80) REVERT: B 60 VAL cc_start: 0.7640 (p) cc_final: 0.7332 (t) REVERT: B 80 ASN cc_start: 0.7884 (m-40) cc_final: 0.7522 (t0) REVERT: C 104 ARG cc_start: 0.7161 (mtt-85) cc_final: 0.6413 (mtt-85) REVERT: D 45 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8337 (mm-30) REVERT: D 109 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7888 (mt-10) REVERT: D 282 ASP cc_start: 0.8096 (t0) cc_final: 0.7747 (t70) REVERT: D 301 GLU cc_start: 0.7481 (tp30) cc_final: 0.7052 (pm20) REVERT: D 344 ASP cc_start: 0.8497 (p0) cc_final: 0.8107 (p0) REVERT: D 385 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7469 (mmtm) REVERT: E 399 LEU cc_start: 0.7281 (mp) cc_final: 0.6986 (mp) REVERT: F 4 PHE cc_start: 0.6773 (m-80) cc_final: 0.6439 (m-80) REVERT: F 7 MET cc_start: 0.5223 (mmt) cc_final: 0.4838 (mmp) REVERT: G 45 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7808 (mm-30) REVERT: G 82 SER cc_start: 0.9010 (p) cc_final: 0.8736 (m) REVERT: G 105 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8077 (mt-10) REVERT: G 148 TYR cc_start: 0.8758 (m-80) cc_final: 0.8450 (m-80) REVERT: G 163 ILE cc_start: 0.7704 (mt) cc_final: 0.7493 (mp) REVERT: G 299 ASP cc_start: 0.7956 (t0) cc_final: 0.7317 (t0) REVERT: G 343 ASN cc_start: 0.8109 (m-40) cc_final: 0.7857 (m-40) REVERT: G 373 SER cc_start: 0.7955 (t) cc_final: 0.7473 (m) REVERT: G 421 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.4990 (t80) REVERT: H 77 LYS cc_start: 0.8883 (mttt) cc_final: 0.8668 (mtpp) REVERT: H 166 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8794 (ptp) REVERT: H 186 LYS cc_start: 0.6384 (tttt) cc_final: 0.5778 (ttpt) REVERT: H 196 LYS cc_start: 0.7641 (tttt) cc_final: 0.7359 (ttpp) REVERT: J 98 THR cc_start: 0.9029 (p) cc_final: 0.8622 (m) REVERT: J 130 GLN cc_start: 0.8654 (mt0) cc_final: 0.8344 (mt0) REVERT: J 343 ASN cc_start: 0.8581 (m-40) cc_final: 0.8159 (m-40) REVERT: J 412 LYS cc_start: 0.7298 (mttt) cc_final: 0.7081 (mtpt) REVERT: K 339 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7356 (mp0) REVERT: K 376 MET cc_start: 0.7358 (mmt) cc_final: 0.7149 (mmt) REVERT: L 7 MET cc_start: 0.5320 (OUTLIER) cc_final: 0.4693 (mmt) REVERT: L 78 TRP cc_start: 0.7494 (p-90) cc_final: 0.6838 (p-90) REVERT: V 38 PHE cc_start: 0.7809 (t80) cc_final: 0.7219 (t80) REVERT: V 60 ASP cc_start: 0.7912 (t0) cc_final: 0.7486 (p0) REVERT: Y 63 ASP cc_start: 0.5475 (t0) cc_final: 0.5266 (t0) outliers start: 76 outliers final: 68 residues processed: 453 average time/residue: 0.1785 time to fit residues: 133.7092 Evaluate side-chains 470 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 398 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 208 THR Chi-restraints excluded: chain A residue 214 LEU 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 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 314 VAL 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 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 261 SER 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 31 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 115 SER 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 331 ILE 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 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 359 THR Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 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 7 MET 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 406 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 chunk 314 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 405 optimal weight: 0.0010 chunk 21 optimal weight: 5.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- 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 B 236 ASN D 77 GLN D 223 GLN E 21 ASN E 213 HIS F 37 GLN G 176 ASN I 11 GLN W 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.181045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.128924 restraints weight = 37195.115| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.55 r_work: 0.3271 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 34596 Z= 0.245 Angle : 0.594 8.669 47188 Z= 0.310 Chirality : 0.048 0.195 5224 Planarity : 0.005 0.048 6080 Dihedral : 5.308 78.400 4840 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.64 % Allowed : 9.39 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.13), residues: 4304 helix: 1.82 (0.24), residues: 496 sheet: -0.10 (0.14), residues: 1316 loop : -0.10 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 242 TYR 0.030 0.002 TYR J 309 PHE 0.024 0.002 PHE C 24 TRP 0.023 0.001 TRP D 142 HIS 0.008 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00601 (34504) covalent geometry : angle 0.58708 (46996) SS BOND : bond 0.00409 ( 84) SS BOND : angle 1.36984 ( 168) hydrogen bonds : bond 0.03658 ( 1135) hydrogen bonds : angle 5.59251 ( 2853) link_NAG-ASN : bond 0.00345 ( 8) link_NAG-ASN : angle 2.40948 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 401 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8173 (mm-30) REVERT: A 61 LYS cc_start: 0.7591 (tptt) cc_final: 0.6879 (ttmt) REVERT: A 99 GLU cc_start: 0.7685 (mp0) cc_final: 0.6865 (mp0) REVERT: A 161 LYS cc_start: 0.8561 (ttpt) cc_final: 0.7867 (ttmt) REVERT: A 207 ARG cc_start: 0.9025 (mmt180) cc_final: 0.8704 (mmt180) REVERT: A 421 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.5971 (t80) REVERT: B 60 VAL cc_start: 0.7560 (p) cc_final: 0.7212 (t) REVERT: B 80 ASN cc_start: 0.7892 (m-40) cc_final: 0.7445 (t0) REVERT: B 296 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8799 (t) REVERT: C 104 ARG cc_start: 0.7246 (mtt-85) cc_final: 0.6417 (mtt-85) REVERT: D 282 ASP cc_start: 0.8081 (t0) cc_final: 0.7735 (t70) REVERT: D 344 ASP cc_start: 0.8475 (p0) cc_final: 0.8027 (p0) REVERT: D 385 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7444 (mmtm) REVERT: E 399 LEU cc_start: 0.7266 (mp) cc_final: 0.6933 (mp) REVERT: F 4 PHE cc_start: 0.6846 (m-80) cc_final: 0.6254 (m-80) REVERT: F 78 TRP cc_start: 0.6509 (OUTLIER) cc_final: 0.5605 (p-90) REVERT: F 114 VAL cc_start: 0.4830 (m) cc_final: 0.4178 (p) REVERT: G 82 SER cc_start: 0.9024 (p) cc_final: 0.8742 (m) REVERT: G 105 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8200 (mt-10) REVERT: G 148 TYR cc_start: 0.8779 (m-80) cc_final: 0.8474 (m-80) REVERT: G 163 ILE cc_start: 0.7662 (mt) cc_final: 0.7435 (mp) REVERT: G 299 ASP cc_start: 0.7912 (t0) cc_final: 0.7248 (t0) REVERT: G 313 PHE cc_start: 0.8986 (m-80) cc_final: 0.8706 (m-10) REVERT: G 343 ASN cc_start: 0.8096 (m-40) cc_final: 0.7829 (m-40) REVERT: G 373 SER cc_start: 0.7964 (t) cc_final: 0.7424 (m) REVERT: G 421 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5078 (t80) REVERT: H 77 LYS cc_start: 0.8951 (mttt) cc_final: 0.8650 (mtpp) REVERT: H 166 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8801 (ptp) REVERT: H 186 LYS cc_start: 0.6247 (tttt) cc_final: 0.5662 (ttpt) REVERT: H 196 LYS cc_start: 0.7330 (tttt) cc_final: 0.7021 (tttp) REVERT: J 98 THR cc_start: 0.9002 (p) cc_final: 0.8569 (m) REVERT: J 343 ASN cc_start: 0.8606 (m-40) cc_final: 0.8124 (m-40) REVERT: J 412 LYS cc_start: 0.7172 (mttt) cc_final: 0.6910 (mtpt) REVERT: K 284 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8779 (mt) REVERT: K 339 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7260 (mp0) REVERT: K 376 MET cc_start: 0.7236 (mmt) cc_final: 0.7027 (mmt) REVERT: L 7 MET cc_start: 0.5119 (OUTLIER) cc_final: 0.4558 (mmt) REVERT: L 60 MET cc_start: 0.6347 (mtm) cc_final: 0.6104 (mtm) REVERT: V 38 PHE cc_start: 0.7807 (t80) cc_final: 0.7304 (t80) REVERT: V 60 ASP cc_start: 0.7935 (t0) cc_final: 0.7477 (p0) outliers start: 98 outliers final: 78 residues processed: 469 average time/residue: 0.1877 time to fit residues: 145.6575 Evaluate side-chains 463 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 378 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 THR 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 323 LEU Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain 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 210 THR 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 31 ILE Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 331 ILE Chi-restraints excluded: chain G residue 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 18 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 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 318 THR Chi-restraints excluded: chain J residue 359 THR Chi-restraints excluded: chain J residue 386 ASP Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 66 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 175 HIS Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 7 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain X residue 42 ASN Chi-restraints excluded: chain X residue 58 CYS Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 238 optimal weight: 3.9990 chunk 125 optimal weight: 0.0570 chunk 115 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 0.4980 chunk 203 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 287 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 344 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS D 176 ASN D 369 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 = 0.4031 r_free = 0.4031 target = 0.182637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133665 restraints weight = 36894.973| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.21 r_work: 0.3345 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34596 Z= 0.098 Angle : 0.499 7.807 47188 Z= 0.262 Chirality : 0.044 0.180 5224 Planarity : 0.004 0.046 6080 Dihedral : 4.944 76.632 4840 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.65 % Allowed : 10.41 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.13), residues: 4304 helix: 2.09 (0.24), residues: 496 sheet: 0.05 (0.14), residues: 1308 loop : 0.05 (0.13), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 242 TYR 0.024 0.001 TYR K 197 PHE 0.014 0.001 PHE C 24 TRP 0.024 0.001 TRP D 142 HIS 0.039 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00216 (34504) covalent geometry : angle 0.49291 (46996) SS BOND : bond 0.00246 ( 84) SS BOND : angle 1.03588 ( 168) hydrogen bonds : bond 0.03114 ( 1135) hydrogen bonds : angle 5.36058 ( 2853) link_NAG-ASN : bond 0.00241 ( 8) link_NAG-ASN : angle 2.56374 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 389 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7722 (tptt) cc_final: 0.7038 (ttmt) REVERT: A 99 GLU cc_start: 0.7666 (mp0) cc_final: 0.7204 (mp0) REVERT: A 161 LYS cc_start: 0.8518 (ttpt) cc_final: 0.7877 (ttmt) REVERT: A 207 ARG cc_start: 0.9003 (mmt180) cc_final: 0.8701 (mmt180) REVERT: A 344 ASP cc_start: 0.8339 (p0) cc_final: 0.8092 (p0) REVERT: A 421 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.5996 (t80) REVERT: B 60 VAL cc_start: 0.7627 (p) cc_final: 0.7303 (t) REVERT: B 80 ASN cc_start: 0.7861 (m-40) cc_final: 0.7478 (t0) REVERT: C 45 LYS cc_start: 0.6993 (tttt) cc_final: 0.6391 (mmtt) REVERT: C 104 ARG cc_start: 0.7219 (mtt-85) cc_final: 0.6484 (mtt-85) REVERT: D 282 ASP cc_start: 0.8087 (t0) cc_final: 0.7731 (t70) REVERT: D 301 GLU cc_start: 0.7591 (tp30) cc_final: 0.7215 (pm20) REVERT: D 344 ASP cc_start: 0.8413 (p0) cc_final: 0.8114 (p0) REVERT: D 385 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7484 (mmtm) REVERT: E 399 LEU cc_start: 0.7256 (mp) cc_final: 0.6932 (mp) REVERT: F 4 PHE cc_start: 0.6784 (m-80) cc_final: 0.6209 (m-80) REVERT: F 7 MET cc_start: 0.5155 (mmt) cc_final: 0.4906 (mmp) REVERT: F 78 TRP cc_start: 0.6469 (OUTLIER) cc_final: 0.5491 (p-90) REVERT: G 82 SER cc_start: 0.8994 (p) cc_final: 0.8750 (m) REVERT: G 105 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8063 (mt-10) REVERT: G 148 TYR cc_start: 0.8704 (m-80) cc_final: 0.8501 (m-80) REVERT: G 163 ILE cc_start: 0.7701 (mt) cc_final: 0.7474 (mp) REVERT: G 299 ASP cc_start: 0.7973 (t0) cc_final: 0.7437 (t0) REVERT: G 313 PHE cc_start: 0.8990 (m-80) cc_final: 0.8667 (m-10) REVERT: G 343 ASN cc_start: 0.8127 (m-40) cc_final: 0.7892 (m-40) REVERT: G 373 SER cc_start: 0.8201 (t) cc_final: 0.7646 (m) REVERT: G 421 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.4945 (t80) REVERT: H 68 MET cc_start: 0.9103 (mmt) cc_final: 0.8631 (mmt) REVERT: H 77 LYS cc_start: 0.8915 (mttt) cc_final: 0.8669 (mtpp) REVERT: H 166 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8733 (ptp) REVERT: H 186 LYS cc_start: 0.6459 (tttt) cc_final: 0.5851 (ttpt) REVERT: H 196 LYS cc_start: 0.7559 (tttt) cc_final: 0.7164 (tttm) REVERT: H 376 MET cc_start: 0.6240 (mmp) cc_final: 0.5868 (mmt) REVERT: J 98 THR cc_start: 0.9013 (p) cc_final: 0.8616 (m) REVERT: J 132 MET cc_start: 0.8663 (ttm) cc_final: 0.8436 (tpt) REVERT: J 343 ASN cc_start: 0.8572 (m-40) cc_final: 0.8144 (m-40) REVERT: J 412 LYS cc_start: 0.7267 (mttt) cc_final: 0.7027 (mtpt) REVERT: K 339 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7325 (mp0) REVERT: K 376 MET cc_start: 0.7330 (mmt) cc_final: 0.7119 (mmt) REVERT: L 7 MET cc_start: 0.5246 (OUTLIER) cc_final: 0.4646 (mmt) REVERT: L 60 MET cc_start: 0.6345 (mtm) cc_final: 0.6077 (mtm) REVERT: V 38 PHE cc_start: 0.7773 (t80) cc_final: 0.7175 (t80) REVERT: V 60 ASP cc_start: 0.7888 (t0) cc_final: 0.7503 (p0) REVERT: W 89 TRP cc_start: 0.8433 (m-10) cc_final: 0.8188 (m-10) outliers start: 61 outliers final: 45 residues processed: 426 average time/residue: 0.1872 time to fit residues: 131.9785 Evaluate side-chains 443 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 393 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 421 PHE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 329 CYS 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 178 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 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 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 22 CYS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 315 ASN Chi-restraints excluded: chain L residue 7 MET 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 79 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 351 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 W 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.184468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.134966 restraints weight = 37498.216| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.27 r_work: 0.3365 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34596 Z= 0.166 Angle : 0.530 7.533 47188 Z= 0.276 Chirality : 0.046 0.184 5224 Planarity : 0.004 0.046 6080 Dihedral : 4.974 74.482 4840 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.54 % Allowed : 10.79 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.13), residues: 4304 helix: 2.06 (0.24), residues: 496 sheet: 0.02 (0.14), residues: 1308 loop : -0.01 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 242 TYR 0.024 0.002 TYR J 309 PHE 0.018 0.001 PHE C 24 TRP 0.022 0.001 TRP D 142 HIS 0.024 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00405 (34504) covalent geometry : angle 0.52396 (46996) SS BOND : bond 0.00317 ( 84) SS BOND : angle 1.17723 ( 168) hydrogen bonds : bond 0.03275 ( 1135) hydrogen bonds : angle 5.37876 ( 2853) link_NAG-ASN : bond 0.00239 ( 8) link_NAG-ASN : angle 2.26631 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8608 Ramachandran restraints generated. 4304 Oldfield, 0 Emsley, 4304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 390 time to evaluate : 0.933 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: 0.7744 (tptt) cc_final: 0.7030 (ttmt) REVERT: A 96 CYS cc_start: 0.7487 (m) cc_final: 0.7088 (m) REVERT: A 99 GLU cc_start: 0.7688 (mp0) cc_final: 0.7258 (mp0) REVERT: A 161 LYS cc_start: 0.8538 (ttpt) cc_final: 0.7899 (ttmt) REVERT: A 207 ARG cc_start: 0.9022 (mmt180) cc_final: 0.8690 (mmt180) REVERT: A 344 ASP cc_start: 0.8349 (p0) cc_final: 0.8143 (p0) REVERT: A 421 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.5982 (t80) REVERT: B 60 VAL cc_start: 0.7559 (p) cc_final: 0.7230 (t) REVERT: B 80 ASN cc_start: 0.7852 (m-40) cc_final: 0.7444 (t0) REVERT: C 104 ARG cc_start: 0.7264 (mtt-85) cc_final: 0.6470 (mtt-85) REVERT: D 282 ASP cc_start: 0.8095 (t0) cc_final: 0.7757 (t70) REVERT: D 301 GLU cc_start: 0.7591 (tp30) cc_final: 0.7186 (pm20) REVERT: D 344 ASP cc_start: 0.8417 (p0) cc_final: 0.8118 (p0) REVERT: D 385 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7481 (mmtm) REVERT: E 399 LEU cc_start: 0.7257 (mp) cc_final: 0.6912 (mp) REVERT: F 4 PHE cc_start: 0.6751 (m-80) cc_final: 0.6180 (m-80) REVERT: F 7 MET cc_start: 0.5093 (mmt) cc_final: 0.4805 (mmp) REVERT: F 78 TRP cc_start: 0.6418 (OUTLIER) cc_final: 0.5495 (p-90) REVERT: G 82 SER cc_start: 0.8974 (p) cc_final: 0.8727 (m) REVERT: G 105 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8104 (mt-10) REVERT: G 148 TYR cc_start: 0.8719 (m-80) cc_final: 0.8496 (m-80) REVERT: G 163 ILE cc_start: 0.7662 (mt) cc_final: 0.7426 (mp) REVERT: G 299 ASP cc_start: 0.7866 (t0) cc_final: 0.7305 (t0) REVERT: G 313 PHE cc_start: 0.8988 (m-80) cc_final: 0.8690 (m-10) REVERT: G 343 ASN cc_start: 0.8137 (m-40) cc_final: 0.7919 (m-40) REVERT: G 373 SER cc_start: 0.8186 (t) cc_final: 0.7624 (m) REVERT: G 421 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.4952 (t80) REVERT: H 68 MET cc_start: 0.9112 (mmt) cc_final: 0.8671 (mmt) REVERT: H 77 LYS cc_start: 0.8929 (mttt) cc_final: 0.8673 (mtpp) REVERT: H 166 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8740 (ptp) REVERT: H 186 LYS cc_start: 0.6396 (tttt) cc_final: 0.5793 (ttpt) REVERT: H 196 LYS cc_start: 0.7554 (tttt) cc_final: 0.7162 (tttm) REVERT: H 376 MET cc_start: 0.6274 (mmp) cc_final: 0.5894 (mmt) REVERT: J 98 THR cc_start: 0.9027 (p) cc_final: 0.8639 (m) REVERT: J 322 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7651 (mtpp) REVERT: J 343 ASN cc_start: 0.8548 (m-40) cc_final: 0.8090 (m-40) REVERT: J 412 LYS cc_start: 0.7253 (mttt) cc_final: 0.7043 (mtpt) REVERT: K 339 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7315 (mp0) REVERT: K 376 MET cc_start: 0.7326 (mmt) cc_final: 0.7107 (mmt) REVERT: L 7 MET cc_start: 0.5102 (OUTLIER) cc_final: 0.4554 (mmt) REVERT: L 60 MET cc_start: 0.6311 (mtm) cc_final: 0.6040 (mtm) REVERT: V 38 PHE cc_start: 0.7814 (t80) cc_final: 0.7275 (t80) REVERT: V 60 ASP cc_start: 0.7874 (t0) cc_final: 0.7503 (p0) outliers start: 57 outliers final: 51 residues processed: 427 average time/residue: 0.1873 time to fit residues: 131.8423 Evaluate side-chains 438 residues out of total 3708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 382 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 199 CYS Chi-restraints excluded: chain B residue 213 HIS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 329 CYS 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 146 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 385 LEU Chi-restraints excluded: chain F residue 78 TRP Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 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 121 VAL Chi-restraints excluded: chain J residue 4 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 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 7 MET Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain V residue 58 CYS Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain X residue 58 CYS Chi-restraints excluded: chain Y residue 58 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 252 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 295 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 372 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 223 GLN E 213 HIS J 130 GLN K 114 HIS W 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.183322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134789 restraints weight = 37018.177| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.50 r_work: 0.3318 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 34596 Z= 0.193 Angle : 0.660 59.199 47188 Z= 0.367 Chirality : 0.050 1.101 5224 Planarity : 0.005 0.164 6080 Dihedral : 4.978 74.455 4840 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.70 % Allowed : 10.87 % Favored : 87.43 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.13), residues: 4304 helix: 2.05 (0.24), residues: 496 sheet: 0.02 (0.14), residues: 1308 loop : -0.01 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 242 TYR 0.025 0.002 TYR J 309 PHE 0.018 0.001 PHE C 24 TRP 0.020 0.001 TRP D 142 HIS 0.206 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00440 (34504) covalent geometry : angle 0.64433 (46996) SS BOND : bond 0.00439 ( 84) SS BOND : angle 2.34570 ( 168) hydrogen bonds : bond 0.03296 ( 1135) hydrogen bonds : angle 5.38163 ( 2853) link_NAG-ASN : bond 0.00246 ( 8) link_NAG-ASN : angle 2.25481 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10086.59 seconds wall clock time: 172 minutes 35.32 seconds (10355.32 seconds total)