Starting phenix.real_space_refine on Sat Aug 8 12:41:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kbi_62226/08_2026/9kbi_62226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kbi_62226/08_2026/9kbi_62226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kbi_62226/08_2026/9kbi_62226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kbi_62226/08_2026/9kbi_62226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kbi_62226/08_2026/9kbi_62226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kbi_62226/08_2026/9kbi_62226.map" } resolution = 3.43 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= 0.075 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: 6 Type Number sf(0) Gaussians P 63 5.49 5 Mg 8 5.21 5 S 144 5.16 5 C 17999 2.51 5 N 4748 2.21 5 O 5286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28248 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2272 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2282 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2282 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2282 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2287 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2253 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2272 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2282 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2282 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2282 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2287 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2253 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "N" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 289 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.98, per 1000 atoms: 0.25 Number of scatterers: 28248 At special positions: 0 Unit cell: (145.92, 153.6, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 63 15.00 Mg 8 11.99 O 5286 8.00 N 4748 7.00 C 17999 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6536 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 24 sheets defined 54.3% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 210 through 226 removed outlier: 3.557A pdb=" N LYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 226 " --> pdb=" O TRP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.719A pdb=" N TYR A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 269 removed outlier: 4.210A pdb=" N ILE A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 286 through 289 Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.694A pdb=" N GLY A 307 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.516A pdb=" N ALA A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 removed outlier: 3.842A pdb=" N ALA A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 431 through 438 removed outlier: 3.911A pdb=" N ARG A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 3.631A pdb=" N ALA A 469 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 470 " --> pdb=" O TRP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.990A pdb=" N TRP A 478 " --> pdb=" O HIS A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'B' and resid 210 through 227 Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.695A pdb=" N TYR B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 269 removed outlier: 3.631A pdb=" N GLN B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.673A pdb=" N LYS B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.576A pdb=" N SER B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 389 removed outlier: 3.832A pdb=" N ALA B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 400 removed outlier: 3.508A pdb=" N GLN B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 437 removed outlier: 3.568A pdb=" N GLU B 437 " --> pdb=" O LYS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 479 removed outlier: 4.169A pdb=" N TRP B 478 " --> pdb=" O HIS B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 226 removed outlier: 3.512A pdb=" N LYS C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 238 Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.563A pdb=" N TYR C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 268 removed outlier: 3.513A pdb=" N LYS C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 286 through 289 Processing helix chain 'C' and resid 290 through 299 removed outlier: 3.549A pdb=" N LEU C 297 " --> pdb=" O VAL C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 315 removed outlier: 3.843A pdb=" N ASP C 315 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 removed outlier: 3.607A pdb=" N ALA C 338 " --> pdb=" O LYS C 334 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 389 removed outlier: 3.814A pdb=" N ALA C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 399 Processing helix chain 'C' and resid 431 through 438 removed outlier: 3.870A pdb=" N GLU C 437 " --> pdb=" O LYS C 433 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.680A pdb=" N GLN C 470 " --> pdb=" O TRP C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 480 removed outlier: 3.711A pdb=" N GLU C 476 " --> pdb=" O TRP C 472 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 226 Processing helix chain 'D' and resid 230 through 238 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 248 through 269 removed outlier: 3.950A pdb=" N GLN D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE D 255 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS D 260 " --> pdb=" O GLN D 256 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 261 " --> pdb=" O SER D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 286 through 289 Processing helix chain 'D' and resid 290 through 299 Processing helix chain 'D' and resid 302 through 315 removed outlier: 3.525A pdb=" N ASP D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.572A pdb=" N VAL D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 379 No H-bonds generated for 'chain 'D' and resid 377 through 379' Processing helix chain 'D' and resid 380 through 389 removed outlier: 3.644A pdb=" N ALA D 386 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 400 Processing helix chain 'D' and resid 431 through 437 removed outlier: 3.759A pdb=" N GLU D 437 " --> pdb=" O LYS D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 469 removed outlier: 3.780A pdb=" N ALA D 469 " --> pdb=" O THR D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 480 removed outlier: 4.071A pdb=" N TRP D 478 " --> pdb=" O HIS D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 499 Processing helix chain 'E' and resid 210 through 226 Processing helix chain 'E' and resid 230 through 238 Processing helix chain 'E' and resid 238 through 247 removed outlier: 3.719A pdb=" N TYR E 242 " --> pdb=" O ASP E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 269 removed outlier: 3.601A pdb=" N PHE E 253 " --> pdb=" O HIS E 249 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 removed outlier: 3.604A pdb=" N LEU E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 289 Processing helix chain 'E' and resid 290 through 299 Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.655A pdb=" N LYS E 312 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 343 removed outlier: 3.582A pdb=" N LEU E 337 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 380 through 388 removed outlier: 3.995A pdb=" N ALA E 386 " --> pdb=" O GLU E 382 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 400 removed outlier: 3.766A pdb=" N GLN E 397 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 437 removed outlier: 3.777A pdb=" N LYS E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU E 437 " --> pdb=" O LYS E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 470 Processing helix chain 'E' and resid 472 through 480 removed outlier: 4.413A pdb=" N TRP E 478 " --> pdb=" O HIS E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 226 Processing helix chain 'F' and resid 230 through 238 Processing helix chain 'F' and resid 238 through 246 Processing helix chain 'F' and resid 248 through 268 removed outlier: 3.843A pdb=" N GLN F 254 " --> pdb=" O SER F 250 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 277 removed outlier: 3.635A pdb=" N LEU F 276 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 289 Processing helix chain 'F' and resid 290 through 299 Processing helix chain 'F' and resid 302 through 315 Processing helix chain 'F' and resid 333 through 343 Processing helix chain 'F' and resid 377 through 379 No H-bonds generated for 'chain 'F' and resid 377 through 379' Processing helix chain 'F' and resid 380 through 390 removed outlier: 3.834A pdb=" N ALA F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 400 Processing helix chain 'F' and resid 431 through 438 removed outlier: 3.640A pdb=" N LYS F 436 " --> pdb=" O ALA F 432 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU F 437 " --> pdb=" O LYS F 433 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 453 removed outlier: 3.990A pdb=" N GLY F 453 " --> pdb=" O PRO F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 470 removed outlier: 3.533A pdb=" N VAL F 460 " --> pdb=" O THR F 456 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA F 469 " --> pdb=" O THR F 465 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN F 470 " --> pdb=" O TRP F 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 480 removed outlier: 3.789A pdb=" N TRP F 478 " --> pdb=" O HIS F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 494 removed outlier: 3.738A pdb=" N LEU F 494 " --> pdb=" O ALA F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 499 Processing helix chain 'G' and resid 210 through 226 Processing helix chain 'G' and resid 230 through 238 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.821A pdb=" N TYR G 242 " --> pdb=" O ASP G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 269 Processing helix chain 'G' and resid 272 through 277 removed outlier: 3.573A pdb=" N LEU G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 289 removed outlier: 3.563A pdb=" N ASP G 289 " --> pdb=" O CYS G 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 286 through 289' Processing helix chain 'G' and resid 290 through 299 Processing helix chain 'G' and resid 302 through 315 Processing helix chain 'G' and resid 333 through 345 removed outlier: 3.609A pdb=" N ALA G 338 " --> pdb=" O LYS G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 354 No H-bonds generated for 'chain 'G' and resid 352 through 354' Processing helix chain 'G' and resid 377 through 379 No H-bonds generated for 'chain 'G' and resid 377 through 379' Processing helix chain 'G' and resid 380 through 389 removed outlier: 3.786A pdb=" N ALA G 386 " --> pdb=" O GLU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 401 Processing helix chain 'G' and resid 431 through 438 removed outlier: 3.992A pdb=" N ARG G 438 " --> pdb=" O ALA G 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 456 through 470 Processing helix chain 'G' and resid 472 through 480 removed outlier: 3.964A pdb=" N GLU G 476 " --> pdb=" O TRP G 472 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN G 477 " --> pdb=" O ASP G 473 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TRP G 478 " --> pdb=" O HIS G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 495 through 499 Processing helix chain 'H' and resid 210 through 227 Processing helix chain 'H' and resid 230 through 238 Processing helix chain 'H' and resid 238 through 246 removed outlier: 3.602A pdb=" N TYR H 242 " --> pdb=" O ASP H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 269 removed outlier: 3.609A pdb=" N GLN H 256 " --> pdb=" O SER H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'H' and resid 290 through 299 Processing helix chain 'H' and resid 302 through 314 removed outlier: 3.619A pdb=" N LYS H 312 " --> pdb=" O GLN H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 345 removed outlier: 3.703A pdb=" N VAL H 345 " --> pdb=" O ILE H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 389 Processing helix chain 'H' and resid 393 through 400 removed outlier: 3.641A pdb=" N LYS H 398 " --> pdb=" O ARG H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 438 removed outlier: 3.561A pdb=" N GLU H 437 " --> pdb=" O LYS H 433 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG H 438 " --> pdb=" O ALA H 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 469 Processing helix chain 'H' and resid 472 through 480 removed outlier: 4.148A pdb=" N GLU H 476 " --> pdb=" O TRP H 472 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN H 477 " --> pdb=" O ASP H 473 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP H 478 " --> pdb=" O HIS H 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 226 removed outlier: 3.677A pdb=" N LYS I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 238 Processing helix chain 'I' and resid 238 through 246 removed outlier: 3.936A pdb=" N TYR I 242 " --> pdb=" O ASP I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 268 removed outlier: 3.534A pdb=" N LYS I 260 " --> pdb=" O GLN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 277 removed outlier: 3.681A pdb=" N LEU I 276 " --> pdb=" O THR I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 289 Processing helix chain 'I' and resid 290 through 299 Processing helix chain 'I' and resid 302 through 315 removed outlier: 3.561A pdb=" N LYS I 312 " --> pdb=" O GLN I 308 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP I 315 " --> pdb=" O LEU I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 343 removed outlier: 3.532A pdb=" N ILE I 341 " --> pdb=" O LEU I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 379 No H-bonds generated for 'chain 'I' and resid 377 through 379' Processing helix chain 'I' and resid 380 through 388 removed outlier: 3.988A pdb=" N ALA I 386 " --> pdb=" O GLU I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 399 Processing helix chain 'I' and resid 431 through 438 removed outlier: 3.580A pdb=" N GLU I 437 " --> pdb=" O LYS I 433 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG I 438 " --> pdb=" O ALA I 434 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 470 removed outlier: 3.501A pdb=" N ALA I 469 " --> pdb=" O THR I 465 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 480 removed outlier: 3.771A pdb=" N GLU I 476 " --> pdb=" O TRP I 472 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN I 477 " --> pdb=" O ASP I 473 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP I 478 " --> pdb=" O HIS I 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 499 Processing helix chain 'J' and resid 210 through 226 Processing helix chain 'J' and resid 230 through 238 Processing helix chain 'J' and resid 238 through 246 removed outlier: 3.725A pdb=" N TYR J 242 " --> pdb=" O ASP J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 268 removed outlier: 4.282A pdb=" N GLN J 254 " --> pdb=" O SER J 250 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE J 255 " --> pdb=" O GLY J 251 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN J 256 " --> pdb=" O SER J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 277 removed outlier: 3.882A pdb=" N LEU J 276 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 289 Processing helix chain 'J' and resid 290 through 299 Processing helix chain 'J' and resid 302 through 315 Processing helix chain 'J' and resid 333 through 345 removed outlier: 3.533A pdb=" N ALA J 338 " --> pdb=" O LYS J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 354 No H-bonds generated for 'chain 'J' and resid 352 through 354' Processing helix chain 'J' and resid 377 through 379 No H-bonds generated for 'chain 'J' and resid 377 through 379' Processing helix chain 'J' and resid 380 through 389 removed outlier: 4.006A pdb=" N ALA J 386 " --> pdb=" O GLU J 382 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 393 through 400 removed outlier: 3.672A pdb=" N ARG J 400 " --> pdb=" O ASP J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 437 removed outlier: 3.561A pdb=" N LYS J 436 " --> pdb=" O ALA J 432 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU J 437 " --> pdb=" O LYS J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 470 removed outlier: 3.817A pdb=" N VAL J 460 " --> pdb=" O THR J 456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA J 469 " --> pdb=" O THR J 465 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN J 470 " --> pdb=" O TRP J 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 472 through 480 removed outlier: 4.484A pdb=" N TRP J 478 " --> pdb=" O HIS J 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 490 through 494 removed outlier: 3.530A pdb=" N LEU J 494 " --> pdb=" O ALA J 491 " (cutoff:3.500A) Processing helix chain 'J' and resid 495 through 499 Processing helix chain 'K' and resid 210 through 226 Processing helix chain 'K' and resid 230 through 238 Processing helix chain 'K' and resid 238 through 247 Processing helix chain 'K' and resid 248 through 269 removed outlier: 3.551A pdb=" N SER K 252 " --> pdb=" O SER K 248 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE K 253 " --> pdb=" O HIS K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 276 Processing helix chain 'K' and resid 290 through 299 Processing helix chain 'K' and resid 302 through 315 Processing helix chain 'K' and resid 333 through 343 Processing helix chain 'K' and resid 352 through 354 No H-bonds generated for 'chain 'K' and resid 352 through 354' Processing helix chain 'K' and resid 380 through 388 removed outlier: 3.680A pdb=" N ALA K 386 " --> pdb=" O GLU K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 400 Processing helix chain 'K' and resid 431 through 439 removed outlier: 3.566A pdb=" N ARG K 438 " --> pdb=" O ALA K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 456 through 470 removed outlier: 3.523A pdb=" N TRP K 463 " --> pdb=" O ASP K 459 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA K 469 " --> pdb=" O THR K 465 " (cutoff:3.500A) Processing helix chain 'K' and resid 472 through 480 removed outlier: 3.620A pdb=" N GLU K 476 " --> pdb=" O TRP K 472 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN K 477 " --> pdb=" O ASP K 473 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TRP K 478 " --> pdb=" O HIS K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 495 through 499 Processing helix chain 'L' and resid 210 through 226 Processing helix chain 'L' and resid 230 through 238 Processing helix chain 'L' and resid 238 through 246 removed outlier: 3.680A pdb=" N TYR L 242 " --> pdb=" O ASP L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 268 removed outlier: 3.712A pdb=" N GLN L 254 " --> pdb=" O SER L 250 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN L 256 " --> pdb=" O SER L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 276 Processing helix chain 'L' and resid 290 through 299 removed outlier: 3.559A pdb=" N GLN L 299 " --> pdb=" O LEU L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 315 removed outlier: 3.565A pdb=" N LEU L 311 " --> pdb=" O GLY L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 333 through 343 Processing helix chain 'L' and resid 352 through 354 No H-bonds generated for 'chain 'L' and resid 352 through 354' Processing helix chain 'L' and resid 377 through 379 No H-bonds generated for 'chain 'L' and resid 377 through 379' Processing helix chain 'L' and resid 380 through 390 removed outlier: 3.763A pdb=" N ALA L 386 " --> pdb=" O GLU L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 400 Processing helix chain 'L' and resid 431 through 438 removed outlier: 3.610A pdb=" N GLU L 437 " --> pdb=" O LYS L 433 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG L 438 " --> pdb=" O ALA L 434 " (cutoff:3.500A) Processing helix chain 'L' and resid 456 through 470 removed outlier: 3.784A pdb=" N VAL L 460 " --> pdb=" O THR L 456 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA L 469 " --> pdb=" O THR L 465 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN L 470 " --> pdb=" O TRP L 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 472 through 480 removed outlier: 3.700A pdb=" N GLU L 476 " --> pdb=" O TRP L 472 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP L 478 " --> pdb=" O HIS L 474 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE L 480 " --> pdb=" O GLU L 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 350 removed outlier: 6.396A pdb=" N GLY A 349 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL A 369 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N THR A 413 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP A 371 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 423 Processing sheet with id=AA3, first strand: chain 'B' and resid 348 through 350 removed outlier: 6.395A pdb=" N VAL B 369 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N THR B 413 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP B 371 " --> pdb=" O THR B 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 421 through 423 removed outlier: 3.518A pdb=" N VAL B 421 " --> pdb=" O THR B 428 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 348 through 350 removed outlier: 6.553A pdb=" N GLY C 349 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ASP C 372 " --> pdb=" O GLY C 349 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL C 369 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR C 413 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP C 371 " --> pdb=" O THR C 413 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 422 through 423 Processing sheet with id=AA7, first strand: chain 'D' and resid 348 through 350 removed outlier: 6.529A pdb=" N GLY D 349 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP D 372 " --> pdb=" O GLY D 349 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 421 through 423 Processing sheet with id=AA9, first strand: chain 'E' and resid 348 through 350 removed outlier: 6.455A pdb=" N VAL E 369 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N THR E 413 " --> pdb=" O VAL E 369 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP E 371 " --> pdb=" O THR E 413 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 421 through 422 Processing sheet with id=AB2, first strand: chain 'F' and resid 348 through 350 removed outlier: 6.544A pdb=" N GLY F 349 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ASP F 372 " --> pdb=" O GLY F 349 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 421 through 423 Processing sheet with id=AB4, first strand: chain 'G' and resid 349 through 350 removed outlier: 6.591A pdb=" N GLY G 349 " --> pdb=" O VAL G 370 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASP G 372 " --> pdb=" O GLY G 349 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL G 369 " --> pdb=" O VAL G 411 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR G 413 " --> pdb=" O VAL G 369 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP G 371 " --> pdb=" O THR G 413 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 421 through 423 Processing sheet with id=AB6, first strand: chain 'H' and resid 348 through 350 removed outlier: 6.301A pdb=" N GLY H 349 " --> pdb=" O VAL H 370 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASP H 372 " --> pdb=" O GLY H 349 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL H 369 " --> pdb=" O VAL H 411 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR H 413 " --> pdb=" O VAL H 369 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP H 371 " --> pdb=" O THR H 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 421 through 423 Processing sheet with id=AB8, first strand: chain 'I' and resid 348 through 350 removed outlier: 6.778A pdb=" N GLY I 349 " --> pdb=" O VAL I 370 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ASP I 372 " --> pdb=" O GLY I 349 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL I 369 " --> pdb=" O VAL I 411 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR I 413 " --> pdb=" O VAL I 369 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP I 371 " --> pdb=" O THR I 413 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR I 323 " --> pdb=" O VAL I 440 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU I 442 " --> pdb=" O THR I 323 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N TRP I 325 " --> pdb=" O LEU I 442 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 421 through 423 Processing sheet with id=AC1, first strand: chain 'J' and resid 349 through 350 removed outlier: 6.687A pdb=" N GLY J 349 " --> pdb=" O VAL J 370 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP J 372 " --> pdb=" O GLY J 349 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL J 369 " --> pdb=" O VAL J 411 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N THR J 413 " --> pdb=" O VAL J 369 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP J 371 " --> pdb=" O THR J 413 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 421 through 423 Processing sheet with id=AC3, first strand: chain 'K' and resid 348 through 350 removed outlier: 6.724A pdb=" N GLY K 349 " --> pdb=" O VAL K 370 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASP K 372 " --> pdb=" O GLY K 349 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 421 through 422 Processing sheet with id=AC5, first strand: chain 'L' and resid 349 through 350 removed outlier: 6.633A pdb=" N GLY L 349 " --> pdb=" O VAL L 370 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASP L 372 " --> pdb=" O GLY L 349 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL L 369 " --> pdb=" O VAL L 411 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR L 413 " --> pdb=" O VAL L 369 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TRP L 371 " --> pdb=" O THR L 413 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 421 through 423 1179 hydrogen bonds defined for protein. 3342 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: 6.01 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4736 1.33 - 1.45: 7901 1.45 - 1.57: 16043 1.57 - 1.69: 113 1.69 - 1.82: 216 Bond restraints: 29009 Sorted by residual: bond pdb=" N3B ANP G 601 " pdb=" PG ANP G 601 " ideal model delta sigma weight residual 1.795 1.595 0.200 2.00e-02 2.50e+03 9.96e+01 bond pdb=" N3B ANP K 601 " pdb=" PG ANP K 601 " ideal model delta sigma weight residual 1.795 1.596 0.199 2.00e-02 2.50e+03 9.91e+01 bond pdb=" N3B ANP F 601 " pdb=" PG ANP F 601 " ideal model delta sigma weight residual 1.795 1.596 0.199 2.00e-02 2.50e+03 9.87e+01 bond pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 1.795 1.597 0.198 2.00e-02 2.50e+03 9.82e+01 bond pdb=" N3B ANP L 601 " pdb=" PG ANP L 601 " ideal model delta sigma weight residual 1.795 1.597 0.198 2.00e-02 2.50e+03 9.81e+01 ... (remaining 29004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 39204 2.59 - 5.18: 377 5.18 - 7.77: 65 7.77 - 10.36: 15 10.36 - 12.95: 26 Bond angle restraints: 39687 Sorted by residual: angle pdb=" N PRO J 406 " pdb=" CA PRO J 406 " pdb=" C PRO J 406 " ideal model delta sigma weight residual 112.47 99.82 12.65 2.06e+00 2.36e-01 3.77e+01 angle pdb=" N PRO K 406 " pdb=" CA PRO K 406 " pdb=" CB PRO K 406 " ideal model delta sigma weight residual 103.25 97.55 5.70 1.05e+00 9.07e-01 2.95e+01 angle pdb=" CA GLY K 407 " pdb=" C GLY K 407 " pdb=" N VAL K 408 " ideal model delta sigma weight residual 114.65 119.30 -4.65 9.20e-01 1.18e+00 2.56e+01 angle pdb=" N MET J 399 " pdb=" CA MET J 399 " pdb=" C MET J 399 " ideal model delta sigma weight residual 111.14 105.77 5.37 1.08e+00 8.57e-01 2.48e+01 angle pdb=" N MET C 399 " pdb=" CA MET C 399 " pdb=" C MET C 399 " ideal model delta sigma weight residual 113.23 107.09 6.14 1.24e+00 6.50e-01 2.46e+01 ... (remaining 39682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.11: 16529 34.11 - 68.21: 479 68.21 - 102.32: 82 102.32 - 136.42: 5 136.42 - 170.53: 7 Dihedral angle restraints: 17102 sinusoidal: 7026 harmonic: 10076 Sorted by residual: dihedral pdb=" CA ARG J 400 " pdb=" C ARG J 400 " pdb=" N GLY J 401 " pdb=" CA GLY J 401 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LEU J 454 " pdb=" C LEU J 454 " pdb=" N LEU J 455 " pdb=" CA LEU J 455 " ideal model delta harmonic sigma weight residual -180.00 -152.81 -27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA VAL A 405 " pdb=" C VAL A 405 " pdb=" N PRO A 406 " pdb=" CA PRO A 406 " ideal model delta harmonic sigma weight residual -180.00 -154.85 -25.15 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 17099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4411 0.110 - 0.220: 83 0.220 - 0.330: 17 0.330 - 0.440: 0 0.440 - 0.550: 1 Chirality restraints: 4512 Sorted by residual: chirality pdb=" P DC N 13 " pdb=" OP1 DC N 13 " pdb=" OP2 DC N 13 " pdb=" O5' DC N 13 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.55 2.00e-01 2.50e+01 7.57e+00 chirality pdb=" CG LEU J 454 " pdb=" CB LEU J 454 " pdb=" CD1 LEU J 454 " pdb=" CD2 LEU J 454 " both_signs ideal model delta sigma weight residual False -2.59 -2.92 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C3' ANP D 601 " pdb=" C2' ANP D 601 " pdb=" C4' ANP D 601 " pdb=" O3' ANP D 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 4509 not shown) Planarity restraints: 4799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS J 398 " -0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C LYS J 398 " 0.068 2.00e-02 2.50e+03 pdb=" O LYS J 398 " -0.026 2.00e-02 2.50e+03 pdb=" N MET J 399 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 395 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C VAL I 395 " 0.058 2.00e-02 2.50e+03 pdb=" O VAL I 395 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP I 396 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 405 " -0.050 5.00e-02 4.00e+02 7.70e-02 9.50e+00 pdb=" N PRO A 406 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 406 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 406 " -0.043 5.00e-02 4.00e+02 ... (remaining 4796 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 240 2.60 - 3.17: 23972 3.17 - 3.75: 42825 3.75 - 4.32: 58253 4.32 - 4.90: 95819 Nonbonded interactions: 221109 Sorted by model distance: nonbonded pdb=" O2G ANP I 601 " pdb="MG MG I 602 " model vdw 2.023 2.170 nonbonded pdb=" O3G ANP A 601 " pdb="MG MG A 602 " model vdw 2.067 2.170 nonbonded pdb=" N3B ANP G 601 " pdb="MG MG G 602 " model vdw 2.074 2.250 nonbonded pdb=" OG1 THR L 335 " pdb="MG MG L 602 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR A 335 " pdb="MG MG A 602 " model vdw 2.093 2.170 ... (remaining 221104 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 202 through 400 or resid 406 through 601)) selection = (chain 'B' and (resid 202 through 277 or resid 286 through 400 or resid 406 thro \ ugh 601)) selection = (chain 'C' and (resid 202 through 277 or resid 286 through 400 or resid 406 thro \ ugh 601)) selection = (chain 'D' and (resid 202 through 277 or resid 286 through 400 or resid 406 thro \ ugh 601)) selection = (chain 'E' and (resid 202 through 277 or resid 286 through 400 or resid 406 thro \ ugh 601)) selection = (chain 'F' and (resid 202 through 277 or resid 286 through 601)) selection = (chain 'G' and (resid 202 through 400 or resid 406 through 601)) selection = (chain 'H' and (resid 202 through 277 or resid 286 through 400 or resid 406 thro \ ugh 601)) selection = (chain 'I' and (resid 202 through 277 or resid 286 through 400 or resid 406 thro \ ugh 601)) selection = (chain 'J' and (resid 202 through 277 or resid 286 through 400 or resid 406 thro \ ugh 601)) selection = (chain 'K' and (resid 202 through 277 or resid 286 through 400 or resid 406 thro \ ugh 601)) selection = (chain 'L' and (resid 202 through 277 or resid 286 through 601)) } 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 27.440 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 : 0.006 0.200 29013 Z= 0.346 Angle : 0.734 12.949 39687 Z= 0.398 Chirality : 0.045 0.550 4512 Planarity : 0.004 0.077 4799 Dihedral : 16.646 170.527 10566 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.38 % Allowed : 1.98 % Favored : 97.64 % Rotamer: Outliers : 1.02 % Allowed : 0.53 % Favored : 98.45 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3430 helix: 0.77 (0.13), residues: 1592 sheet: 1.16 (0.27), residues: 368 loop : 0.35 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 438 TYR 0.021 0.001 TYR C 348 PHE 0.018 0.001 PHE I 486 TRP 0.026 0.001 TRP C 466 HIS 0.005 0.000 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.35 (29009) covalent geometry : angle 0.73405 / 0.40 (39687) hydrogen bonds : bond 0.24852 / 15.74 ( 1179) hydrogen bonds : angle 6.48931 / 4.69 ( 3342) Misc. bond : bond 0.00430 / 0.22 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 328 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 394 ARG cc_start: 0.8489 (ptp-110) cc_final: 0.7999 (ttp80) REVERT: G 356 GLU cc_start: 0.7766 (tp30) cc_final: 0.7510 (tp30) REVERT: G 399 MET cc_start: 0.8285 (tmm) cc_final: 0.7910 (tmm) REVERT: H 387 ILE cc_start: 0.9081 (tp) cc_final: 0.8878 (tp) REVERT: I 373 GLU cc_start: 0.7797 (pm20) cc_final: 0.7576 (pm20) REVERT: I 399 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.5224 (tpp) REVERT: L 350 MET cc_start: 0.7770 (mtp) cc_final: 0.7493 (mtm) outliers start: 31 outliers final: 14 residues processed: 352 average time/residue: 0.1905 time to fit residues: 107.3024 Evaluate side-chains 261 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 246 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain G residue 448 CYS Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain H residue 399 MET Chi-restraints excluded: chain I residue 398 LYS Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain K residue 399 MET Chi-restraints excluded: chain K residue 403 VAL Chi-restraints excluded: chain K residue 406 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 474 HIS D 217 GLN D 357 ASN D 499 GLN E 357 ASN F 226 ASN G 221 ASN G 397 GLN H 431 HIS J 226 ASN J 309 HIS K 431 HIS K 495 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.092345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073727 restraints weight = 81731.636| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.55 r_work: 0.3092 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29013 Z= 0.170 Angle : 0.581 14.174 39687 Z= 0.309 Chirality : 0.042 0.183 4512 Planarity : 0.004 0.065 4799 Dihedral : 16.404 171.542 4272 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.04 % Favored : 97.78 % Rotamer: Outliers : 1.35 % Allowed : 5.75 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.14), residues: 3430 helix: 0.84 (0.13), residues: 1676 sheet: 1.10 (0.27), residues: 368 loop : 0.36 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 394 TYR 0.024 0.001 TYR G 348 PHE 0.012 0.001 PHE J 420 TRP 0.023 0.001 TRP I 466 HIS 0.005 0.001 HIS L 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (29009) covalent geometry : angle 0.58107 / 0.31 (39687) hydrogen bonds : bond 0.06181 / 3.90 ( 1179) hydrogen bonds : angle 4.94192 / 3.56 ( 3342) Misc. bond : bond 0.01011 / 0.51 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 394 ARG cc_start: 0.8504 (ptp-110) cc_final: 0.7871 (ttp80) REVERT: D 399 MET cc_start: 0.9226 (mmm) cc_final: 0.8618 (tmm) REVERT: F 382 GLU cc_start: 0.8167 (pm20) cc_final: 0.7925 (pm20) REVERT: G 356 GLU cc_start: 0.7741 (tp30) cc_final: 0.7506 (tp30) REVERT: G 399 MET cc_start: 0.8548 (tmm) cc_final: 0.8170 (tmm) REVERT: I 327 TYR cc_start: 0.8133 (t80) cc_final: 0.7872 (t80) REVERT: I 373 GLU cc_start: 0.8165 (pm20) cc_final: 0.7869 (pm20) REVERT: I 399 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.5188 (tpp) REVERT: J 291 LYS cc_start: 0.8897 (mmpt) cc_final: 0.8325 (mttt) REVERT: L 350 MET cc_start: 0.8144 (mtp) cc_final: 0.7825 (mtm) outliers start: 41 outliers final: 30 residues processed: 287 average time/residue: 0.1900 time to fit residues: 87.3337 Evaluate side-chains 271 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain G residue 448 CYS Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 459 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain I residue 398 LYS Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain J residue 350 MET Chi-restraints excluded: chain J residue 399 MET Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain K residue 403 VAL Chi-restraints excluded: chain K residue 428 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 345 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 355 ASN B 474 HIS D 357 ASN E 357 ASN G 431 HIS ** I 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.091676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072923 restraints weight = 81087.538| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.57 r_work: 0.3068 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29013 Z= 0.170 Angle : 0.542 13.369 39687 Z= 0.285 Chirality : 0.042 0.354 4512 Planarity : 0.004 0.069 4799 Dihedral : 15.302 174.639 4262 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.30 % Favored : 97.49 % Rotamer: Outliers : 1.45 % Allowed : 7.50 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.14), residues: 3430 helix: 0.90 (0.13), residues: 1672 sheet: 1.05 (0.27), residues: 366 loop : 0.31 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 394 TYR 0.027 0.001 TYR G 348 PHE 0.010 0.001 PHE I 239 TRP 0.024 0.001 TRP I 466 HIS 0.004 0.001 HIS F 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (29009) covalent geometry : angle 0.54178 / 0.28 (39687) hydrogen bonds : bond 0.05312 / 3.37 ( 1179) hydrogen bonds : angle 4.65594 / 3.34 ( 3342) Misc. bond : bond 0.00163 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 394 ARG cc_start: 0.8522 (ptp-110) cc_final: 0.7984 (tmm160) REVERT: F 373 GLU cc_start: 0.7187 (mp0) cc_final: 0.6906 (mp0) REVERT: F 382 GLU cc_start: 0.8166 (pm20) cc_final: 0.7925 (pm20) REVERT: G 399 MET cc_start: 0.8488 (tmm) cc_final: 0.8068 (tmm) REVERT: H 439 MET cc_start: 0.8735 (ttm) cc_final: 0.8356 (mtp) REVERT: I 373 GLU cc_start: 0.8285 (pm20) cc_final: 0.7975 (pm20) REVERT: I 399 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.5531 (ttt) REVERT: J 291 LYS cc_start: 0.8884 (mmpt) cc_final: 0.8285 (mttt) REVERT: K 361 ASN cc_start: 0.8448 (m-40) cc_final: 0.7720 (p0) REVERT: L 394 ARG cc_start: 0.7723 (mtp180) cc_final: 0.7480 (mtp180) REVERT: L 452 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.6063 (ttp) outliers start: 44 outliers final: 29 residues processed: 278 average time/residue: 0.1727 time to fit residues: 77.8972 Evaluate side-chains 265 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain D residue 403 VAL Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 448 CYS Chi-restraints excluded: chain G residue 459 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain I residue 399 MET Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain K residue 403 VAL Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain L residue 452 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 189 optimal weight: 1.9990 chunk 287 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 188 optimal weight: 0.0030 chunk 2 optimal weight: 3.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 474 HIS E 357 ASN I 462 GLN J 309 HIS J 431 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.091630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072922 restraints weight = 80584.157| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.55 r_work: 0.3071 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29013 Z= 0.152 Angle : 0.528 13.636 39687 Z= 0.277 Chirality : 0.041 0.182 4512 Planarity : 0.004 0.066 4799 Dihedral : 14.623 175.075 4249 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.51 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 8.49 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3430 helix: 0.90 (0.13), residues: 1670 sheet: 1.04 (0.27), residues: 366 loop : 0.35 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 394 TYR 0.025 0.001 TYR G 348 PHE 0.009 0.001 PHE E 253 TRP 0.028 0.001 TRP I 466 HIS 0.004 0.001 HIS F 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (29009) covalent geometry : angle 0.52776 / 0.28 (39687) hydrogen bonds : bond 0.04683 / 2.97 ( 1179) hydrogen bonds : angle 4.49925 / 3.22 ( 3342) Misc. bond : bond 0.00191 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 253 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.8322 (tmm) cc_final: 0.7784 (tmm) REVERT: A 478 TRP cc_start: 0.8192 (t60) cc_final: 0.7768 (t60) REVERT: B 439 MET cc_start: 0.9053 (mtp) cc_final: 0.8847 (mtp) REVERT: B 466 TRP cc_start: 0.7900 (t60) cc_final: 0.7611 (t60) REVERT: C 348 TYR cc_start: 0.8685 (p90) cc_final: 0.8457 (p90) REVERT: C 394 ARG cc_start: 0.8525 (ptp-110) cc_final: 0.8053 (tmm160) REVERT: F 373 GLU cc_start: 0.7462 (mp0) cc_final: 0.7120 (mp0) REVERT: F 382 GLU cc_start: 0.8162 (pm20) cc_final: 0.7925 (pm20) REVERT: G 399 MET cc_start: 0.8436 (tmm) cc_final: 0.7922 (tmm) REVERT: H 236 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8707 (mm) REVERT: H 439 MET cc_start: 0.8725 (ttm) cc_final: 0.8403 (mtp) REVERT: I 327 TYR cc_start: 0.8116 (t80) cc_final: 0.7858 (t80) REVERT: I 373 GLU cc_start: 0.8297 (pm20) cc_final: 0.7956 (pm20) REVERT: I 399 MET cc_start: 0.6566 (mmt) cc_final: 0.5479 (ttt) REVERT: I 457 GLU cc_start: 0.8395 (mp0) cc_final: 0.8155 (mp0) REVERT: J 291 LYS cc_start: 0.8881 (mmpt) cc_final: 0.8290 (mttt) REVERT: J 485 ASP cc_start: 0.8653 (t0) cc_final: 0.8442 (t0) REVERT: K 361 ASN cc_start: 0.8447 (m-40) cc_final: 0.7737 (p0) REVERT: L 452 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.6056 (ttp) outliers start: 49 outliers final: 37 residues processed: 282 average time/residue: 0.1854 time to fit residues: 84.3449 Evaluate side-chains 279 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 240 ASN Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 448 CYS Chi-restraints excluded: chain G residue 459 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 448 CYS Chi-restraints excluded: chain I residue 462 GLN Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain K residue 403 VAL Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain L residue 452 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 262 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 282 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 273 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS E 357 ASN J 309 HIS K 397 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.091256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.072500 restraints weight = 80623.733| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 3.55 r_work: 0.3059 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29013 Z= 0.160 Angle : 0.526 13.746 39687 Z= 0.276 Chirality : 0.041 0.194 4512 Planarity : 0.004 0.067 4799 Dihedral : 14.201 176.011 4244 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.71 % Favored : 97.14 % Rotamer: Outliers : 1.98 % Allowed : 9.28 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3430 helix: 0.90 (0.13), residues: 1678 sheet: 0.99 (0.27), residues: 354 loop : 0.24 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 394 TYR 0.027 0.001 TYR G 348 PHE 0.010 0.001 PHE C 275 TRP 0.034 0.001 TRP I 466 HIS 0.004 0.001 HIS F 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (29009) covalent geometry : angle 0.52620 / 0.28 (39687) hydrogen bonds : bond 0.04543 / 2.89 ( 1179) hydrogen bonds : angle 4.41576 / 3.16 ( 3342) Misc. bond : bond 0.00192 / 0.09 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 250 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.8330 (tmm) cc_final: 0.7800 (tmm) REVERT: A 478 TRP cc_start: 0.8206 (t60) cc_final: 0.7839 (t60) REVERT: B 466 TRP cc_start: 0.7923 (t60) cc_final: 0.7625 (t60) REVERT: C 348 TYR cc_start: 0.8741 (p90) cc_final: 0.8489 (p90) REVERT: C 394 ARG cc_start: 0.8483 (ptp-110) cc_final: 0.8015 (tmm160) REVERT: E 399 MET cc_start: 0.5789 (mtt) cc_final: 0.5101 (ttm) REVERT: F 373 GLU cc_start: 0.7564 (mp0) cc_final: 0.7196 (mp0) REVERT: F 382 GLU cc_start: 0.8169 (pm20) cc_final: 0.7940 (pm20) REVERT: G 399 MET cc_start: 0.8385 (tmm) cc_final: 0.7894 (tmm) REVERT: H 236 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8773 (mm) REVERT: H 439 MET cc_start: 0.8730 (ttm) cc_final: 0.8460 (mtp) REVERT: I 300 ASN cc_start: 0.7490 (t0) cc_final: 0.7263 (t0) REVERT: I 327 TYR cc_start: 0.8118 (t80) cc_final: 0.7840 (t80) REVERT: I 373 GLU cc_start: 0.8335 (pm20) cc_final: 0.7996 (pm20) REVERT: I 399 MET cc_start: 0.6472 (mmt) cc_final: 0.5437 (ttt) REVERT: I 457 GLU cc_start: 0.8430 (mp0) cc_final: 0.8227 (mp0) REVERT: J 291 LYS cc_start: 0.8889 (mmpt) cc_final: 0.8300 (mttt) REVERT: J 485 ASP cc_start: 0.8753 (t0) cc_final: 0.8534 (t0) REVERT: K 361 ASN cc_start: 0.8439 (m-40) cc_final: 0.7726 (p0) REVERT: L 394 ARG cc_start: 0.7813 (mtp180) cc_final: 0.7539 (mtp180) REVERT: L 452 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6030 (ttp) outliers start: 60 outliers final: 46 residues processed: 290 average time/residue: 0.1716 time to fit residues: 80.6214 Evaluate side-chains 284 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 ASN Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 402 SER Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 448 CYS Chi-restraints excluded: chain G residue 459 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 448 CYS Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 339 MET Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 395 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain K residue 403 VAL Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain L residue 452 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 126 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 282 optimal weight: 8.9990 chunk 192 optimal weight: 0.3980 chunk 103 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 85 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 307 optimal weight: 9.9990 chunk 336 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 HIS B 474 HIS E 357 ASN ** I 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.091752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.072957 restraints weight = 80022.659| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.56 r_work: 0.3070 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29013 Z= 0.133 Angle : 0.509 13.705 39687 Z= 0.268 Chirality : 0.040 0.209 4512 Planarity : 0.004 0.066 4799 Dihedral : 13.913 176.765 4244 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.51 % Favored : 97.38 % Rotamer: Outliers : 1.62 % Allowed : 10.34 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3430 helix: 0.97 (0.13), residues: 1676 sheet: 1.01 (0.27), residues: 354 loop : 0.26 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 447 TYR 0.026 0.001 TYR G 348 PHE 0.009 0.001 PHE C 275 TRP 0.033 0.001 TRP I 466 HIS 0.003 0.001 HIS F 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (29009) covalent geometry : angle 0.50911 / 0.27 (39687) hydrogen bonds : bond 0.04246 / 2.69 ( 1179) hydrogen bonds : angle 4.28428 / 3.07 ( 3342) Misc. bond : bond 0.00211 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.8344 (tmm) cc_final: 0.7746 (tmm) REVERT: A 478 TRP cc_start: 0.8185 (t60) cc_final: 0.7819 (t60) REVERT: B 466 TRP cc_start: 0.7936 (t60) cc_final: 0.7630 (t60) REVERT: C 348 TYR cc_start: 0.8743 (p90) cc_final: 0.8477 (p90) REVERT: C 394 ARG cc_start: 0.8476 (ptp-110) cc_final: 0.8011 (tmm160) REVERT: C 466 TRP cc_start: 0.8313 (t60) cc_final: 0.8068 (t60) REVERT: D 295 LEU cc_start: 0.7929 (tt) cc_final: 0.7727 (mm) REVERT: D 399 MET cc_start: 0.9157 (mmm) cc_final: 0.8593 (tmm) REVERT: F 372 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7981 (t0) REVERT: F 382 GLU cc_start: 0.8238 (pm20) cc_final: 0.8013 (pm20) REVERT: G 399 MET cc_start: 0.8295 (tmm) cc_final: 0.7796 (tmm) REVERT: H 439 MET cc_start: 0.8717 (ttm) cc_final: 0.8476 (mtp) REVERT: I 327 TYR cc_start: 0.8102 (t80) cc_final: 0.7855 (t80) REVERT: I 373 GLU cc_start: 0.8291 (pm20) cc_final: 0.7963 (pm20) REVERT: I 399 MET cc_start: 0.6622 (mmt) cc_final: 0.5548 (ttt) REVERT: J 291 LYS cc_start: 0.8882 (mmpt) cc_final: 0.8295 (mttt) REVERT: J 485 ASP cc_start: 0.8768 (t0) cc_final: 0.8557 (t0) REVERT: K 276 LEU cc_start: 0.9470 (mp) cc_final: 0.9204 (mt) REVERT: K 361 ASN cc_start: 0.8469 (m-40) cc_final: 0.7769 (p0) REVERT: L 394 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7577 (mtp180) REVERT: L 452 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6098 (ttp) outliers start: 49 outliers final: 40 residues processed: 286 average time/residue: 0.1700 time to fit residues: 79.6771 Evaluate side-chains 284 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 394 ARG Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 ASN Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 372 ASP Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain G residue 448 CYS Chi-restraints excluded: chain G residue 459 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 448 CYS Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 395 VAL Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain L residue 452 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 202 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 327 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 229 optimal weight: 0.0370 chunk 207 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS D 241 GLN E 357 ASN G 474 HIS I 462 GLN J 309 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.089761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.070990 restraints weight = 80824.897| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.52 r_work: 0.3030 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29013 Z= 0.224 Angle : 0.589 14.478 39687 Z= 0.306 Chirality : 0.043 0.213 4512 Planarity : 0.004 0.064 4799 Dihedral : 13.793 176.573 4243 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.32 % Favored : 96.53 % Rotamer: Outliers : 2.18 % Allowed : 11.10 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3430 helix: 0.80 (0.13), residues: 1678 sheet: 0.72 (0.27), residues: 354 loop : 0.09 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 394 TYR 0.026 0.002 TYR G 348 PHE 0.013 0.001 PHE C 360 TRP 0.035 0.001 TRP I 466 HIS 0.005 0.001 HIS F 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (29009) covalent geometry : angle 0.58862 / 0.31 (39687) hydrogen bonds : bond 0.04871 / 3.10 ( 1179) hydrogen bonds : angle 4.50192 / 3.22 ( 3342) Misc. bond : bond 0.00240 / 0.12 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 MET cc_start: 0.8345 (tmm) cc_final: 0.8049 (tmm) REVERT: A 478 TRP cc_start: 0.8224 (t60) cc_final: 0.7789 (t60) REVERT: B 466 TRP cc_start: 0.7922 (t60) cc_final: 0.7601 (t60) REVERT: C 394 ARG cc_start: 0.8490 (ptp-110) cc_final: 0.7985 (tmm160) REVERT: C 466 TRP cc_start: 0.8343 (t60) cc_final: 0.8082 (t60) REVERT: D 399 MET cc_start: 0.9159 (mmm) cc_final: 0.8608 (tmm) REVERT: F 382 GLU cc_start: 0.8249 (pm20) cc_final: 0.8032 (pm20) REVERT: F 399 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8503 (mpp) REVERT: G 399 MET cc_start: 0.8375 (tmm) cc_final: 0.7864 (tmm) REVERT: I 327 TYR cc_start: 0.8086 (t80) cc_final: 0.7852 (t80) REVERT: I 373 GLU cc_start: 0.8445 (pm20) cc_final: 0.8067 (pm20) REVERT: I 399 MET cc_start: 0.6512 (mmt) cc_final: 0.5527 (ttt) REVERT: J 485 ASP cc_start: 0.8849 (t0) cc_final: 0.8641 (t0) REVERT: K 361 ASN cc_start: 0.8493 (m-40) cc_final: 0.7754 (p0) REVERT: L 350 MET cc_start: 0.8237 (mtp) cc_final: 0.7858 (mtp) REVERT: L 394 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7633 (mtp180) REVERT: L 452 MET cc_start: 0.6488 (OUTLIER) cc_final: 0.6085 (ttp) outliers start: 66 outliers final: 51 residues processed: 285 average time/residue: 0.1621 time to fit residues: 75.6458 Evaluate side-chains 284 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain B residue 225 GLU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 240 ASN Chi-restraints excluded: chain E residue 324 LEU Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 431 HIS Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 422 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 459 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain H residue 402 SER Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain I residue 396 ASP Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 448 CYS Chi-restraints excluded: chain I residue 486 PHE Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 339 MET Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 395 VAL Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain K residue 292 ILE Chi-restraints excluded: chain K residue 310 VAL Chi-restraints excluded: chain K residue 324 LEU Chi-restraints excluded: chain K residue 403 VAL Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain L residue 452 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 320 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 197 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 233 optimal weight: 0.9990 chunk 347 optimal weight: 50.0000 chunk 27 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 124 optimal weight: 0.0970 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS D 241 GLN E 357 ASN G 474 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.073559 restraints weight = 80067.772| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.57 r_work: 0.3082 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 29013 Z= 0.105 Angle : 0.509 13.925 39687 Z= 0.269 Chirality : 0.040 0.198 4512 Planarity : 0.004 0.067 4799 Dihedral : 13.585 178.339 4242 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.30 % Favored : 97.58 % Rotamer: Outliers : 1.55 % Allowed : 11.72 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.15), residues: 3430 helix: 1.11 (0.13), residues: 1646 sheet: 1.02 (0.27), residues: 354 loop : 0.20 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 394 TYR 0.025 0.001 TYR G 348 PHE 0.010 0.001 PHE E 253 TRP 0.040 0.001 TRP I 466 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (29009) covalent geometry : angle 0.50940 / 0.27 (39687) hydrogen bonds : bond 0.03884 / 2.46 ( 1179) hydrogen bonds : angle 4.12853 / 2.97 ( 3342) Misc. bond : bond 0.00201 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 399 MET cc_start: 0.8346 (tmm) cc_final: 0.7754 (tmm) REVERT: A 478 TRP cc_start: 0.8141 (t60) cc_final: 0.7736 (t60) REVERT: B 405 VAL cc_start: 0.4686 (OUTLIER) cc_final: 0.4246 (p) REVERT: B 466 TRP cc_start: 0.7935 (t60) cc_final: 0.7610 (t60) REVERT: C 394 ARG cc_start: 0.8501 (ptp-110) cc_final: 0.7984 (tmm160) REVERT: C 466 TRP cc_start: 0.8283 (t60) cc_final: 0.8017 (t60) REVERT: D 373 GLU cc_start: 0.8100 (mp0) cc_final: 0.7356 (mp0) REVERT: D 399 MET cc_start: 0.9139 (mmm) cc_final: 0.8574 (tmm) REVERT: F 382 GLU cc_start: 0.8214 (pm20) cc_final: 0.8004 (pm20) REVERT: F 399 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8507 (mpp) REVERT: G 399 MET cc_start: 0.8335 (tmm) cc_final: 0.7783 (tmm) REVERT: I 327 TYR cc_start: 0.8076 (t80) cc_final: 0.7866 (t80) REVERT: I 373 GLU cc_start: 0.8279 (pm20) cc_final: 0.7944 (pm20) REVERT: I 399 MET cc_start: 0.6596 (mmt) cc_final: 0.5517 (ttt) REVERT: J 472 TRP cc_start: 0.6945 (m-10) cc_final: 0.6294 (m-10) REVERT: K 276 LEU cc_start: 0.9444 (mp) cc_final: 0.9202 (mt) REVERT: K 361 ASN cc_start: 0.8521 (m-40) cc_final: 0.7810 (p0) REVERT: L 350 MET cc_start: 0.7886 (mtp) cc_final: 0.7499 (mtm) REVERT: L 394 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7702 (mtp180) REVERT: L 452 MET cc_start: 0.6365 (OUTLIER) cc_final: 0.6034 (ttp) outliers start: 47 outliers final: 33 residues processed: 294 average time/residue: 0.1662 time to fit residues: 79.3894 Evaluate side-chains 287 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 357 ASN Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 273 SER Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 459 ASP Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 448 CYS Chi-restraints excluded: chain I residue 486 PHE Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 339 MET Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain K residue 403 VAL Chi-restraints excluded: chain K residue 413 THR Chi-restraints excluded: chain L residue 452 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 144 optimal weight: 7.9990 chunk 266 optimal weight: 0.3980 chunk 233 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 142 optimal weight: 0.2980 chunk 140 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 321 optimal weight: 0.0870 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS E 357 ASN F 431 HIS G 474 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.092209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073358 restraints weight = 79947.650| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.55 r_work: 0.3078 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29013 Z= 0.122 Angle : 0.507 14.055 39687 Z= 0.268 Chirality : 0.040 0.185 4512 Planarity : 0.004 0.067 4799 Dihedral : 13.495 178.445 4241 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.62 % Favored : 97.26 % Rotamer: Outliers : 1.29 % Allowed : 12.29 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 3430 helix: 1.10 (0.13), residues: 1650 sheet: 1.04 (0.27), residues: 354 loop : 0.22 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 447 TYR 0.028 0.001 TYR A 327 PHE 0.020 0.001 PHE E 358 TRP 0.039 0.001 TRP I 466 HIS 0.003 0.001 HIS F 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (29009) covalent geometry : angle 0.50711 / 0.27 (39687) hydrogen bonds : bond 0.03814 / 2.42 ( 1179) hydrogen bonds : angle 4.08473 / 2.94 ( 3342) Misc. bond : bond 0.00210 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 1.248 Fit side-chains revert: symmetry clash REVERT: A 399 MET cc_start: 0.8337 (tmm) cc_final: 0.7715 (tmm) REVERT: A 478 TRP cc_start: 0.8154 (t60) cc_final: 0.7806 (t60) REVERT: B 405 VAL cc_start: 0.4683 (OUTLIER) cc_final: 0.4246 (p) REVERT: B 466 TRP cc_start: 0.7956 (t60) cc_final: 0.7628 (t60) REVERT: C 394 ARG cc_start: 0.8514 (ptp-110) cc_final: 0.7954 (tmm160) REVERT: C 466 TRP cc_start: 0.8319 (t60) cc_final: 0.8065 (t60) REVERT: D 373 GLU cc_start: 0.8118 (mp0) cc_final: 0.7373 (mp0) REVERT: D 399 MET cc_start: 0.9161 (mmm) cc_final: 0.8587 (tmm) REVERT: E 219 MET cc_start: 0.8310 (tmm) cc_final: 0.7877 (ttt) REVERT: F 373 GLU cc_start: 0.7423 (mp0) cc_final: 0.7116 (mp0) REVERT: F 382 GLU cc_start: 0.8212 (pm20) cc_final: 0.8005 (pm20) REVERT: F 399 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8452 (mpp) REVERT: G 399 MET cc_start: 0.8365 (tmm) cc_final: 0.7791 (tmm) REVERT: I 373 GLU cc_start: 0.8285 (pm20) cc_final: 0.8024 (pm20) REVERT: I 399 MET cc_start: 0.6601 (mmt) cc_final: 0.5558 (ttt) REVERT: K 276 LEU cc_start: 0.9429 (mp) cc_final: 0.9187 (mt) REVERT: K 361 ASN cc_start: 0.8531 (m-40) cc_final: 0.7813 (p0) REVERT: L 350 MET cc_start: 0.7872 (mtp) cc_final: 0.7380 (mtp) REVERT: L 394 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7703 (mtp180) REVERT: L 452 MET cc_start: 0.6530 (OUTLIER) cc_final: 0.6176 (ttp) outliers start: 39 outliers final: 31 residues processed: 273 average time/residue: 0.1723 time to fit residues: 76.6083 Evaluate side-chains 281 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 247 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 273 SER Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 459 ASP Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 486 PHE Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 339 MET Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain K residue 403 VAL Chi-restraints excluded: chain L residue 427 THR Chi-restraints excluded: chain L residue 452 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 285 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 272 optimal weight: 0.0870 chunk 44 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 overall best weight: 1.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS D 499 GLN E 357 ASN G 397 GLN G 474 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.092703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.073856 restraints weight = 79317.227| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.56 r_work: 0.3087 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 29013 Z= 0.108 Angle : 0.500 14.001 39687 Z= 0.264 Chirality : 0.039 0.287 4512 Planarity : 0.004 0.065 4799 Dihedral : 13.422 179.018 4241 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.57 % Favored : 97.32 % Rotamer: Outliers : 1.32 % Allowed : 12.32 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.15), residues: 3430 helix: 1.14 (0.13), residues: 1654 sheet: 1.13 (0.28), residues: 352 loop : 0.28 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 447 TYR 0.027 0.001 TYR A 327 PHE 0.009 0.001 PHE E 253 TRP 0.043 0.001 TRP I 466 HIS 0.003 0.001 HIS F 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (29009) covalent geometry : angle 0.49954 / 0.26 (39687) hydrogen bonds : bond 0.03631 / 2.30 ( 1179) hydrogen bonds : angle 3.99629 / 2.88 ( 3342) Misc. bond : bond 0.00207 / 0.10 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6860 Ramachandran restraints generated. 3430 Oldfield, 0 Emsley, 3430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 399 MET cc_start: 0.8320 (tmm) cc_final: 0.7718 (tmm) REVERT: A 478 TRP cc_start: 0.8147 (t60) cc_final: 0.7805 (t60) REVERT: B 405 VAL cc_start: 0.4409 (OUTLIER) cc_final: 0.4053 (p) REVERT: B 466 TRP cc_start: 0.7924 (t60) cc_final: 0.7590 (t60) REVERT: C 394 ARG cc_start: 0.8494 (ptp-110) cc_final: 0.7930 (tmm160) REVERT: C 466 TRP cc_start: 0.8343 (t60) cc_final: 0.8093 (t60) REVERT: D 373 GLU cc_start: 0.8114 (mp0) cc_final: 0.7380 (mp0) REVERT: D 382 GLU cc_start: 0.8817 (pp20) cc_final: 0.8339 (tp30) REVERT: D 399 MET cc_start: 0.9147 (mmm) cc_final: 0.8611 (tmm) REVERT: F 382 GLU cc_start: 0.8262 (pm20) cc_final: 0.8045 (pm20) REVERT: F 399 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8444 (mpp) REVERT: G 399 MET cc_start: 0.8296 (tmm) cc_final: 0.7729 (tmm) REVERT: H 399 MET cc_start: 0.7750 (mmm) cc_final: 0.6564 (tmm) REVERT: I 373 GLU cc_start: 0.8266 (pm20) cc_final: 0.7960 (pm20) REVERT: I 399 MET cc_start: 0.6621 (mmt) cc_final: 0.5583 (ttt) REVERT: K 361 ASN cc_start: 0.8546 (m-40) cc_final: 0.7844 (p0) REVERT: L 350 MET cc_start: 0.7889 (mtp) cc_final: 0.7337 (mtp) REVERT: L 452 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.5940 (ttp) outliers start: 40 outliers final: 33 residues processed: 276 average time/residue: 0.1811 time to fit residues: 81.4734 Evaluate side-chains 282 residues out of total 3040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 452 MET Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 459 ASP Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 399 MET Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain G residue 261 LEU Chi-restraints excluded: chain G residue 273 SER Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 459 ASP Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 339 MET Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain I residue 278 HIS Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 486 PHE Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 339 MET Chi-restraints excluded: chain J residue 356 GLU Chi-restraints excluded: chain J residue 454 LEU Chi-restraints excluded: chain J residue 460 VAL Chi-restraints excluded: chain K residue 403 VAL Chi-restraints excluded: chain L residue 427 THR Chi-restraints excluded: chain L residue 452 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 233 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 chunk 284 optimal weight: 0.2980 chunk 298 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 255 optimal weight: 0.3980 chunk 299 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 125 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 HIS D 499 GLN E 357 ASN G 474 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.093974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.075150 restraints weight = 79496.999| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 3.59 r_work: 0.3115 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 29013 Z= 0.097 Angle : 0.488 13.751 39687 Z= 0.259 Chirality : 0.039 0.163 4512 Planarity : 0.004 0.065 4799 Dihedral : 13.309 179.321 4241 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.55 % Rotamer: Outliers : 1.19 % Allowed : 12.71 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.15), residues: 3430 helix: 1.22 (0.13), residues: 1658 sheet: 1.30 (0.28), residues: 352 loop : 0.34 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 447 TYR 0.026 0.001 TYR A 327 PHE 0.009 0.001 PHE E 253 TRP 0.042 0.001 TRP I 466 HIS 0.002 0.000 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (29009) covalent geometry : angle 0.48827 / 0.26 (39687) hydrogen bonds : bond 0.03239 / 2.05 ( 1179) hydrogen bonds : angle 3.87268 / 2.80 ( 3342) Misc. bond : bond 0.00197 / 0.10 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5334.21 seconds wall clock time: 92 minutes 52.20 seconds (5572.20 seconds total)